1

Welcome

2

Presented by Varsha Gayatonde

SupervisorProf J P Shahi

Co-SupervisorProf K Srivastava

3

Flow of presentation History of Agriculture

Crop domestication

Centers of domestication

Domestication genes in crops

Super-domestication

Polyploidy

Genome sequencing

NGS

GWAS

Finding adoptive genes

Re-wild the plants

Genome editing

Gene sharing

Conclusion

4

bull Story of agriculture dates back to almost 10000 BC It wasinitiated by people who depended on diets composed of wildplants and animals

bull By 4000 BC ancient peoples had completed thedomestication of all major crop species upon which humansurvival is dependent including rice wheat and maize

bull Recent research has begun to reveal the genes responsible forthis agricultural revolution boosts ldquoGene tinkeringrdquo

History of Agriculture

5

Domestication

Human influence change in genetics of plant population

leads to ldquoAdaptive syndrome of domesticationrdquo

bull May be deliberate or not

(ldquounconsciousrdquo or ldquoincidentalrdquo)

bull Due to change in selective environment and control

over reproduction (eg harvesting grains with

sickle sowing saved seeds)

6

Domesticated- refers more generally to plants that are

morphologically and genetically distinct from their wild ancestors

as a result of artificial selection or are no longer known to occur

outside of cultivation

Semi-domesticated- as a crop that is under cultivation and

subjected to conscious artificial selection pressures

Undomesticated refers to uncultivated plants that continue to be

wild-harvested with no conscious artificial selection pressures

and no discernible morphological and frasl or genetic differentiations

that could be used to distinguish them as a domesticate (eg

Brazil nut)

Nivara

Rufipogon

Glaberrima

7

Domesticated Rice

8

Wild wheat

9

Domesticated Wheat

10

Maize

11

Domesticated maize

12

Barley Domestication

Prognt H spontanium

13

14

Domesticated Pearl MilletPennisetum glaucum

better seed recovery and yield but less able to survive in natural conditions compared to wild progenitor

bull more apical dominance (less

branching)

bull compact growth habit

bull flowering at same time (rather

than spread over long period)

bull larger spikes

bull non-shattering spikelets

bull loss of bristles amp glumes around

grains

bull larger seeds

bull non-dormant seeds

bull germinate at same time

15

Ppolystachian

Oats domestication

Wild- A sterilis Modern

sativa

16

Domestication of Sorghum

S helepense

S bicolor17

JR Harlan 1976 Sci American

Divergent

selection for

different

purposes

httpenwikipediaorgwikiImageBrassica_oleracea0jpg

httpwwwcehacukimagesclip_image002_001jpg

Brassica oleracea cabbage

broccoli cauliflower kale

romanesco collards kohrabi

brussels sprouts18

Solanum pimpinellifolium

Solanum lycopersicum19

Domestication of carrot

Queen Annes Lace

Daucus carota

20

Domestication of peanut

A villosulicarpa Hoehne andA Stenosperma (Brazil)

AABB

21

Domestication of Chilli

22

StrawberryBanana

Musa acuminata Musa balbisiana (2n=3x=33) AB genomeFRAGARIA X ANANASSA

Wood berries (F vesca) and Musky strawberries (F moschata)23

Wild SoybeanGlycin soja2n=40

Cultivated soybeanGlycin max 2n=40

24

Increased in domesticate

seed germination

determinate growth

longer pods

bigger (heavier) seeds

earliness

harvest index (seed yieldbiomass)

Decreased in domesticate

seed dispersal

seed dormancy

twining

number of nodes

length of internode

number of pods

photoperiod sensitivity

Common Bean Phaseolus vulgarishttpwwwplantsciencesucdavisedugeptspb143pb143htm

copy Paul Gepts

25

Wild pigeon peaCajanus cajanifolius

Cultivated pigeon pea

26

27

28

WHY OTHERS ARE NOT DOMESTICATED

bull 350000 plants

bull 4629 mammals

bull 9200 birds

bull 10000000 insects

bull 500000 fungi

bull But only 200 plants

bull 15 mammals 5 birds and

bull 2 insects are domesticated

bull Spread of these few species

bull Little change since early

agriculture

bull Repeated domestication of these

species (sometimes)

bull Lack of new species even with

attempts with species known to be

valuable Some groups are good

candidates with no domestication

eg ferns sub-Saharan mammals

29

WHY OTHERS HAVE TO BE DOMESTICATED

New uses and demands ndash biofuels animal feed

medicinalneutraceutical waterclimate food changes

Knowledge why species arenrsquot suitable for domestication or

were not useful

Better understanding of genetics and selection

Sustainability of production

Reliability of production

To meet the food demand in an alternative way

WHY OTHERS HAVE TO BE DOMESTICATED

30

Reallocate biomass for human use

More efficient metabolism and photosynthesis increase

leaf surface decrease root system increase leaf

longevity

Grains more fertile florets larger inflorescence OR

number of ears different ways to get more seed

Larger seeds (automatic vs deliberate selection)

Oil plants increased oil content or more seed

Fiber plants long strong fibers

Domestication syndrome

31

Centers of Domestication

Fuller 2011

32

Centers of Domestication in India

Fuller 2011

33

Indian centers of domestication South India (Deccan centre) Vigna radiate Vigna mungo

Macrotyloma uniflorum (Horse gram) Sataria verticillata S plumila

wheat (macaroni) and two rowed barleybrachiaria ramosa

Orissa (Mahanadi river) Pegion pea Horsegram mung small millets

like Echinichloa Paspalum and Sataria

The Middle Ganges (Harappan civilization) Oryza nivara O rufipogon

and wild sativa Sateria pumia Cannabis sativa even the diffusion of

japonica rice

Saurashtra (Harappan civilization) Eleucine coracana Sateria italica

Paicum spp Brachypodia pearl millet and sorghum Dollicos lablab

The Himalayan foothills of the Punjab region Was a centre of

diversity for Japonica type rice and many temperate fruits and

vegetables

34

DOMESTICATION RELATED TRAITS CONTROLLED BY ONLY FEW GENES

Trait Crops

Plant architecturegrowth habit Ricemaizemilletsbeantomato

Flowering timephotoperiod sensitivity Ricemaizesorghumbeantomato

Fruit size Tomato egg plant

Grain size Ricemaizesorghumbean

Seed dispersal Brassica rice

Inflorescence modification Brassica

Dormancy Bean

35

Genes Crop Moleular and phenotypic function Causative change

Genes identified as controlling domestication traits

tb1 Maize Transcriptional regulator (TCP) plant and

inflorescence structure

regulatory change

tga1 Maize Transcriptional regulator (SBP) seed casing amino acid change

qSH1 Rice Transcriptional regulator (homeodomain)

abscission layer formation shattering

regulatory change

Rc Rice Transcriptional regulator (bHLH) seed color disrupted coding

sequence

sh4 Rice Transcriptional regulator (Myb3) abscission

layer formation shattering

regulatoryamino

acid change

fw22 Tomato Cell signaling fruit weight regulatory change

Q Wheat Transcriptional regulator (AP2) inflorescence

structure

regulatoryamino

acid change

Vrs1 Barley Inflorescence structure Premature stop Amino acid change

Genes of interest in crop domestication and improvement

36

Genes Crop Moleular and phenotypic function Causative change

c1

r1

Maize Transcriptional regulator (MYB) kernel color and

Transcriptional regulator (bHLH) kernel color

regulatory change

sh2 Maize pyrophosphorylase supersweet sweet corn transposon

insertion

su1 Maize isoamylase sweet corn gene amino acid change

brix9-2-5 Tomato Invertase fruit soluble solid content amino acid change

ovate Tomato Unknown fruit shap early stop codon

R Pea Starch branching enzyme seed sugar content transposon

insertion

ehd1 Rice B-type response regulator flowering time amino acid change

hd1 Rice Transcriptional regulator (zinc finger) flowering

time

disrupted coding

sequence

waxy Rice Starch synthase sticky grains intron splicing

defect

rht Wheat Transcriptional regulator (SH2) plant height early stop codon

vrn1 Wheat Transcriptional regulator (MADS) vernalization regulatory change

vrn2 Wheat Transcriptional regulator (ZCCT) vernalization amino acid change

Genes Identified as Controlling Varietal Differences

37

Process of domestication over the yearshellip

Rachel S Meyer 2012

38

Genetic bottleneck

Cultivated crops undergone with narrowing of diversity problem

But this is not the case in weeds

Weeds are the major threats from the beginning of domestication till

today

Problem arose due to

1 Crop mimicry

2 Genetic assimilation

3 Genetic evolution

39

Super- Domestication Vaughn et al (2007) first used the term super-domestication

The processes that lead to a domesticate with dramatically

increased yield that could not be selected in natural environments

from naturally occurring variation without recourse to new

technologies

Super-domesticates can be constructed with knowledge led

approaches based on current needs using the range of new

technologies now available

Plants exploited for continuous selection introduction hybridization

etc which boosted the process of domestication but now the plant

genetic engineering approach is exploiting plants towards synthetic

biology

40

How to use diversitybull Cross two varieties

bull Genome manipulations

Cell fusion hybrids

bull Chromosome manipulation Backcross a new species

bull Generate recombinants Chromosome recombinations

bull Use a new species wild germplasm

Transgenic approach Modern mutagenesis synthetic gene

construction by utilizing green florescent protein genome editing

NGS GWAS sequencing etchelliphelliphelliphelliphellip

41

Reduce genetic bottlenecks through polyplodization

More vigour

SC

Buffering capacity

Heterotic advantage

Enhaced vegetative

charachers

Enhanced oil

Meiotic stability

42

Approach 1 Use one tetraploid and one diploid as parents (4X ndash 2X) followed by the

chromosome doubling of triploid hybrids (Chrom doubling)

a) Cross between B juncea (AjAjBjBj ) and B oleracea (CoCo) to produce hexaploids

(AjAjBjBjCoCo)

(b) Cross between B napus (AnAnCnCn) and B nigra (BniBni) to produce hexaploids

(AnAnBniBniCnCn)

(c) Cross between B carinata (BcaBcaCcaCca) and B rapa (ArAr) to produce hexaploids

(ArArBcaBcaCcaCca)

Approach 2 Use three tetraploids as parents

(a) Cross between B napus (AnAnCnCn) and B carinata (BcaBcaCcaCca) to produce unbalanced

allotetraploids (AnBcaCnCca ndash unreduced gametes gametes with the somatic chromosome

number and cross with B juncea (AjAjBjBj) to obtain allohexaploids (AnAjBcaBjCnCca

(b) Cross between B napus (AnAnCnCn) and B juncea (AjAjBjBj) to produce unbalanced

allotetraploids (AnAjBjCn ndash unreduced gametes) and cross with B carinata (BcaBcaCcaCca) to

obtain allohexaploids (AnAjBcaBjCnCca)

(c) Cross between B carinata (BcaBcaCcaCca) and B juncea (AjAjBjBj) to produce unbalanced

allotetraploids (AjBcaBjCca - ndash unreduced gametes) and cross with B napus (AnAnCnCn) to obtain

allohexaploids (AnAjBcaBjCnCca)

Approach 3 Use three diploids as parents (2X ndash 2X ndash 2X) Cross between B rapa (ArAr) B

nigra (BniBni) and B oleracea (CoCo) sequentially to obtain hexaploid hybrids (ArArBniBniCoCo)

43

Continuehellip

Guijun Yan 2012

44

Applications of Genomic

tools in Super-Domestication

45

Genome Sequencing

Potential methods of sequencing

1 Clone by clone approach

2 Whole genome shotgun approach

3 Combination of the two methods

Till today no of cultivated plants completely sequenced -85

2016- Arachis duranensis

2015- Solanum cumersonii (Wild potato)

(Ref- NCBI)

46

GWAS

It is a study design in which many markers spread across a genome

are genotyped and test a statistical association with a phenotype are

performed locally along the genome

It is also an examination of many common genetic variants in different

individuals to see if any variant is associated with a trait

Used in successfully studying maize sorghum and barley

Method is efficient for large scale low cost genotyping (even with the

minimum number of SNPs)

Cannot be utilized generally because it needs large population size

GWAS identify rare alleles more precisely

If small population we can opt NAM

47

GWAS and whole genome prediction

Xuehui Huang and Bin Han 2014

48

Five high throuput genotyping methods

Xuehui Huang and Bin Han 2014

49

Role of NGS in domestication Capture of novel genes from wild species will be made easier by

understanding the molecular events associated with crop domestication

Re-sequencing of domesticated species can identify low diversity regions

resulting from selection during domestication

To identify gene-specific sequences to aid the cloning of homologues of key

domestication genes from wild relatives

Candidate genes from wild and domesticated plant populations can define

diversity of target genes in wild populations and lead to the discovery of key

genes for important traits by association analysis

NGS of amplicons of large numbers of candidate genes from wild and

domesticated plant populations can define diversity of target genes in

wild populations and lead to the discovery of key genes for important

traits by association analysis

50

NGS

supports the rapid domestication of new plant species and the efficient

identification and capture of novel genetic variation from related species

Allows whole-genome analysis to determine the genetic basis of

phenotypic differences

NGS allows rapid expansion of genomic analysis to investigation of non-

model species

Made rice study easy by related grass

cost-effective method for plant identification

useful strategy to analysis the chloroplast genome sequence from whole-

genome shot-gun sequencing

facilitates managing this diversity and any changes in crop performance

over time due to genetic drift

Patterns of gene expression have been evaluated in hybrids using NGS

51

Two Approaches to Finding Adaptive Genes

Ross-Ibarra et al2007

52

Techniques to re-wild the plants (transgene free)

1 Introgression

breeding

2 Specific

insertion of lost genes

3 Precision

mutagenesis

Palmgren et al2014

53

Process of rewilding

Palmgren et al2014

54

Synthetic biology projects(i) Modifying cereals including wheat to fix atmospheric nitrogen

(ii) Redesigning metabolic pathways to increase the yield of

secondary metabolites or to generate compounds with enhanced

properties

(iii) Transferring the C4 photosynthesis pathway to rice

(iv) Modifying the glycosylation pathway in plants to accommodate

production of therapeutic proteins

(v) Introducing synthetic signal transduction systems that respond to

external cues

55

Synthetic biology projects

Nicholas J Baltes et al 2015

56

Refactoring the N fixation gene cluster from Klebsiella

Karsten Temme et al 2012

2

Presented by Varsha Gayatonde

SupervisorProf J P Shahi

Co-SupervisorProf K Srivastava

3

Flow of presentation History of Agriculture

Crop domestication

Centers of domestication

Domestication genes in crops

Super-domestication

Polyploidy

Genome sequencing

NGS

GWAS

Finding adoptive genes

Re-wild the plants

Genome editing

Gene sharing

Conclusion

4

bull Story of agriculture dates back to almost 10000 BC It wasinitiated by people who depended on diets composed of wildplants and animals

bull By 4000 BC ancient peoples had completed thedomestication of all major crop species upon which humansurvival is dependent including rice wheat and maize

bull Recent research has begun to reveal the genes responsible forthis agricultural revolution boosts ldquoGene tinkeringrdquo

History of Agriculture

5

Domestication

Human influence change in genetics of plant population

leads to ldquoAdaptive syndrome of domesticationrdquo

bull May be deliberate or not

(ldquounconsciousrdquo or ldquoincidentalrdquo)

bull Due to change in selective environment and control

over reproduction (eg harvesting grains with

sickle sowing saved seeds)

6

Domesticated- refers more generally to plants that are

morphologically and genetically distinct from their wild ancestors

as a result of artificial selection or are no longer known to occur

outside of cultivation

Semi-domesticated- as a crop that is under cultivation and

subjected to conscious artificial selection pressures

Undomesticated refers to uncultivated plants that continue to be

wild-harvested with no conscious artificial selection pressures

and no discernible morphological and frasl or genetic differentiations

that could be used to distinguish them as a domesticate (eg

Brazil nut)

Nivara

Rufipogon

Glaberrima

7

Domesticated Rice

8

Wild wheat

9

Domesticated Wheat

10

Maize

11

Domesticated maize

12

Barley Domestication

Prognt H spontanium

13

14

Domesticated Pearl MilletPennisetum glaucum

better seed recovery and yield but less able to survive in natural conditions compared to wild progenitor

bull more apical dominance (less

branching)

bull compact growth habit

bull flowering at same time (rather

than spread over long period)

bull larger spikes

bull non-shattering spikelets

bull loss of bristles amp glumes around

grains

bull larger seeds

bull non-dormant seeds

bull germinate at same time

15

Ppolystachian

Oats domestication

Wild- A sterilis Modern

sativa

16

Domestication of Sorghum

S helepense

S bicolor17

JR Harlan 1976 Sci American

Divergent

selection for

different

purposes

httpenwikipediaorgwikiImageBrassica_oleracea0jpg

httpwwwcehacukimagesclip_image002_001jpg

Brassica oleracea cabbage

broccoli cauliflower kale

romanesco collards kohrabi

brussels sprouts18

Solanum pimpinellifolium

Solanum lycopersicum19

Domestication of carrot

Queen Annes Lace

Daucus carota

20

Domestication of peanut

A villosulicarpa Hoehne andA Stenosperma (Brazil)

AABB

21

Domestication of Chilli

22

StrawberryBanana

Musa acuminata Musa balbisiana (2n=3x=33) AB genomeFRAGARIA X ANANASSA

Wood berries (F vesca) and Musky strawberries (F moschata)23

Wild SoybeanGlycin soja2n=40

Cultivated soybeanGlycin max 2n=40

24

Increased in domesticate

seed germination

determinate growth

longer pods

bigger (heavier) seeds

earliness

harvest index (seed yieldbiomass)

Decreased in domesticate

seed dispersal

seed dormancy

twining

number of nodes

length of internode

number of pods

photoperiod sensitivity

Common Bean Phaseolus vulgarishttpwwwplantsciencesucdavisedugeptspb143pb143htm

copy Paul Gepts

25

Wild pigeon peaCajanus cajanifolius

Cultivated pigeon pea

26

27

28

WHY OTHERS ARE NOT DOMESTICATED

bull 350000 plants

bull 4629 mammals

bull 9200 birds

bull 10000000 insects

bull 500000 fungi

bull But only 200 plants

bull 15 mammals 5 birds and

bull 2 insects are domesticated

bull Spread of these few species

bull Little change since early

agriculture

bull Repeated domestication of these

species (sometimes)

bull Lack of new species even with

attempts with species known to be

valuable Some groups are good

candidates with no domestication

eg ferns sub-Saharan mammals

29

WHY OTHERS HAVE TO BE DOMESTICATED

New uses and demands ndash biofuels animal feed

medicinalneutraceutical waterclimate food changes

Knowledge why species arenrsquot suitable for domestication or

were not useful

Better understanding of genetics and selection

Sustainability of production

Reliability of production

To meet the food demand in an alternative way

WHY OTHERS HAVE TO BE DOMESTICATED

30

Reallocate biomass for human use

More efficient metabolism and photosynthesis increase

leaf surface decrease root system increase leaf

longevity

Grains more fertile florets larger inflorescence OR

number of ears different ways to get more seed

Larger seeds (automatic vs deliberate selection)

Oil plants increased oil content or more seed

Fiber plants long strong fibers

Domestication syndrome

31

Centers of Domestication

Fuller 2011

32

Centers of Domestication in India

Fuller 2011

33

Indian centers of domestication South India (Deccan centre) Vigna radiate Vigna mungo

Macrotyloma uniflorum (Horse gram) Sataria verticillata S plumila

wheat (macaroni) and two rowed barleybrachiaria ramosa

Orissa (Mahanadi river) Pegion pea Horsegram mung small millets

like Echinichloa Paspalum and Sataria

The Middle Ganges (Harappan civilization) Oryza nivara O rufipogon

and wild sativa Sateria pumia Cannabis sativa even the diffusion of

japonica rice

Saurashtra (Harappan civilization) Eleucine coracana Sateria italica

Paicum spp Brachypodia pearl millet and sorghum Dollicos lablab

The Himalayan foothills of the Punjab region Was a centre of

diversity for Japonica type rice and many temperate fruits and

vegetables

34

DOMESTICATION RELATED TRAITS CONTROLLED BY ONLY FEW GENES

Trait Crops

Plant architecturegrowth habit Ricemaizemilletsbeantomato

Flowering timephotoperiod sensitivity Ricemaizesorghumbeantomato

Fruit size Tomato egg plant

Grain size Ricemaizesorghumbean

Seed dispersal Brassica rice

Inflorescence modification Brassica

Dormancy Bean

35

Genes Crop Moleular and phenotypic function Causative change

Genes identified as controlling domestication traits

tb1 Maize Transcriptional regulator (TCP) plant and

inflorescence structure

regulatory change

tga1 Maize Transcriptional regulator (SBP) seed casing amino acid change

qSH1 Rice Transcriptional regulator (homeodomain)

abscission layer formation shattering

regulatory change

Rc Rice Transcriptional regulator (bHLH) seed color disrupted coding

sequence

sh4 Rice Transcriptional regulator (Myb3) abscission

layer formation shattering

regulatoryamino

acid change

fw22 Tomato Cell signaling fruit weight regulatory change

Q Wheat Transcriptional regulator (AP2) inflorescence

structure

regulatoryamino

acid change

Vrs1 Barley Inflorescence structure Premature stop Amino acid change

Genes of interest in crop domestication and improvement

36

Genes Crop Moleular and phenotypic function Causative change

c1

r1

Maize Transcriptional regulator (MYB) kernel color and

Transcriptional regulator (bHLH) kernel color

regulatory change

sh2 Maize pyrophosphorylase supersweet sweet corn transposon

insertion

su1 Maize isoamylase sweet corn gene amino acid change

brix9-2-5 Tomato Invertase fruit soluble solid content amino acid change

ovate Tomato Unknown fruit shap early stop codon

R Pea Starch branching enzyme seed sugar content transposon

insertion

ehd1 Rice B-type response regulator flowering time amino acid change

hd1 Rice Transcriptional regulator (zinc finger) flowering

time

disrupted coding

sequence

waxy Rice Starch synthase sticky grains intron splicing

defect

rht Wheat Transcriptional regulator (SH2) plant height early stop codon

vrn1 Wheat Transcriptional regulator (MADS) vernalization regulatory change

vrn2 Wheat Transcriptional regulator (ZCCT) vernalization amino acid change

Genes Identified as Controlling Varietal Differences

37

Process of domestication over the yearshellip

Rachel S Meyer 2012

38

Genetic bottleneck

Cultivated crops undergone with narrowing of diversity problem

But this is not the case in weeds

Weeds are the major threats from the beginning of domestication till

today

Problem arose due to

1 Crop mimicry

2 Genetic assimilation

3 Genetic evolution

39

Super- Domestication Vaughn et al (2007) first used the term super-domestication

The processes that lead to a domesticate with dramatically

increased yield that could not be selected in natural environments

from naturally occurring variation without recourse to new

technologies

Super-domesticates can be constructed with knowledge led

approaches based on current needs using the range of new

technologies now available

Plants exploited for continuous selection introduction hybridization

etc which boosted the process of domestication but now the plant

genetic engineering approach is exploiting plants towards synthetic

biology

40

How to use diversitybull Cross two varieties

bull Genome manipulations

Cell fusion hybrids

bull Chromosome manipulation Backcross a new species

bull Generate recombinants Chromosome recombinations

bull Use a new species wild germplasm

Transgenic approach Modern mutagenesis synthetic gene

construction by utilizing green florescent protein genome editing

NGS GWAS sequencing etchelliphelliphelliphelliphellip

41

Reduce genetic bottlenecks through polyplodization

More vigour

SC

Buffering capacity

Heterotic advantage

Enhaced vegetative

charachers

Enhanced oil

Meiotic stability

42

Approach 1 Use one tetraploid and one diploid as parents (4X ndash 2X) followed by the

chromosome doubling of triploid hybrids (Chrom doubling)

a) Cross between B juncea (AjAjBjBj ) and B oleracea (CoCo) to produce hexaploids

(AjAjBjBjCoCo)

(b) Cross between B napus (AnAnCnCn) and B nigra (BniBni) to produce hexaploids

(AnAnBniBniCnCn)

(c) Cross between B carinata (BcaBcaCcaCca) and B rapa (ArAr) to produce hexaploids

(ArArBcaBcaCcaCca)

Approach 2 Use three tetraploids as parents

(a) Cross between B napus (AnAnCnCn) and B carinata (BcaBcaCcaCca) to produce unbalanced

allotetraploids (AnBcaCnCca ndash unreduced gametes gametes with the somatic chromosome

number and cross with B juncea (AjAjBjBj) to obtain allohexaploids (AnAjBcaBjCnCca

(b) Cross between B napus (AnAnCnCn) and B juncea (AjAjBjBj) to produce unbalanced

allotetraploids (AnAjBjCn ndash unreduced gametes) and cross with B carinata (BcaBcaCcaCca) to

obtain allohexaploids (AnAjBcaBjCnCca)

(c) Cross between B carinata (BcaBcaCcaCca) and B juncea (AjAjBjBj) to produce unbalanced

allotetraploids (AjBcaBjCca - ndash unreduced gametes) and cross with B napus (AnAnCnCn) to obtain

allohexaploids (AnAjBcaBjCnCca)

Approach 3 Use three diploids as parents (2X ndash 2X ndash 2X) Cross between B rapa (ArAr) B

nigra (BniBni) and B oleracea (CoCo) sequentially to obtain hexaploid hybrids (ArArBniBniCoCo)

43

Continuehellip

Guijun Yan 2012

44

Applications of Genomic

tools in Super-Domestication

45

Genome Sequencing

Potential methods of sequencing

1 Clone by clone approach

2 Whole genome shotgun approach

3 Combination of the two methods

Till today no of cultivated plants completely sequenced -85

2016- Arachis duranensis

2015- Solanum cumersonii (Wild potato)

(Ref- NCBI)

46

GWAS

It is a study design in which many markers spread across a genome

are genotyped and test a statistical association with a phenotype are

performed locally along the genome

It is also an examination of many common genetic variants in different

individuals to see if any variant is associated with a trait

Used in successfully studying maize sorghum and barley

Method is efficient for large scale low cost genotyping (even with the

minimum number of SNPs)

Cannot be utilized generally because it needs large population size

GWAS identify rare alleles more precisely

If small population we can opt NAM

47

GWAS and whole genome prediction

Xuehui Huang and Bin Han 2014

48

Five high throuput genotyping methods

Xuehui Huang and Bin Han 2014

49

Role of NGS in domestication Capture of novel genes from wild species will be made easier by

understanding the molecular events associated with crop domestication

Re-sequencing of domesticated species can identify low diversity regions

resulting from selection during domestication

To identify gene-specific sequences to aid the cloning of homologues of key

domestication genes from wild relatives

Candidate genes from wild and domesticated plant populations can define

diversity of target genes in wild populations and lead to the discovery of key

genes for important traits by association analysis

NGS of amplicons of large numbers of candidate genes from wild and

domesticated plant populations can define diversity of target genes in

wild populations and lead to the discovery of key genes for important

traits by association analysis

50

NGS

supports the rapid domestication of new plant species and the efficient

identification and capture of novel genetic variation from related species

Allows whole-genome analysis to determine the genetic basis of

phenotypic differences

NGS allows rapid expansion of genomic analysis to investigation of non-

model species

Made rice study easy by related grass

cost-effective method for plant identification

useful strategy to analysis the chloroplast genome sequence from whole-

genome shot-gun sequencing

facilitates managing this diversity and any changes in crop performance

over time due to genetic drift

Patterns of gene expression have been evaluated in hybrids using NGS

51

Two Approaches to Finding Adaptive Genes

Ross-Ibarra et al2007

52

Techniques to re-wild the plants (transgene free)

1 Introgression

breeding

2 Specific

insertion of lost genes

3 Precision

mutagenesis

Palmgren et al2014

53

Process of rewilding

Palmgren et al2014

54

Synthetic biology projects(i) Modifying cereals including wheat to fix atmospheric nitrogen

(ii) Redesigning metabolic pathways to increase the yield of

secondary metabolites or to generate compounds with enhanced

properties

(iii) Transferring the C4 photosynthesis pathway to rice

(iv) Modifying the glycosylation pathway in plants to accommodate

production of therapeutic proteins

(v) Introducing synthetic signal transduction systems that respond to

external cues

55

Synthetic biology projects

Nicholas J Baltes et al 2015

56

Refactoring the N fixation gene cluster from Klebsiella

Karsten Temme et al 2012

3

Flow of presentation History of Agriculture

Crop domestication

Centers of domestication

Domestication genes in crops

Super-domestication

Polyploidy

Genome sequencing

NGS

GWAS

Finding adoptive genes

Re-wild the plants

Genome editing

Gene sharing

Conclusion

4

bull Story of agriculture dates back to almost 10000 BC It wasinitiated by people who depended on diets composed of wildplants and animals

bull By 4000 BC ancient peoples had completed thedomestication of all major crop species upon which humansurvival is dependent including rice wheat and maize

bull Recent research has begun to reveal the genes responsible forthis agricultural revolution boosts ldquoGene tinkeringrdquo

History of Agriculture

5

Domestication

Human influence change in genetics of plant population

leads to ldquoAdaptive syndrome of domesticationrdquo

bull May be deliberate or not

(ldquounconsciousrdquo or ldquoincidentalrdquo)

bull Due to change in selective environment and control

over reproduction (eg harvesting grains with

sickle sowing saved seeds)

6

Domesticated- refers more generally to plants that are

morphologically and genetically distinct from their wild ancestors

as a result of artificial selection or are no longer known to occur

outside of cultivation

Semi-domesticated- as a crop that is under cultivation and

subjected to conscious artificial selection pressures

Undomesticated refers to uncultivated plants that continue to be

wild-harvested with no conscious artificial selection pressures

and no discernible morphological and frasl or genetic differentiations

that could be used to distinguish them as a domesticate (eg

Brazil nut)

Nivara

Rufipogon

Glaberrima

7

Domesticated Rice

8

Wild wheat

9

Domesticated Wheat

10

Maize

11

Domesticated maize

12

Barley Domestication

Prognt H spontanium

13

14

Domesticated Pearl MilletPennisetum glaucum

better seed recovery and yield but less able to survive in natural conditions compared to wild progenitor

bull more apical dominance (less

branching)

bull compact growth habit

bull flowering at same time (rather

than spread over long period)

bull larger spikes

bull non-shattering spikelets

bull loss of bristles amp glumes around

grains

bull larger seeds

bull non-dormant seeds

bull germinate at same time

15

Ppolystachian

Oats domestication

Wild- A sterilis Modern

sativa

16

Domestication of Sorghum

S helepense

S bicolor17

JR Harlan 1976 Sci American

Divergent

selection for

different

purposes

httpenwikipediaorgwikiImageBrassica_oleracea0jpg

httpwwwcehacukimagesclip_image002_001jpg

Brassica oleracea cabbage

broccoli cauliflower kale

romanesco collards kohrabi

brussels sprouts18

Solanum pimpinellifolium

Solanum lycopersicum19

Domestication of carrot

Queen Annes Lace

Daucus carota

20

Domestication of peanut

A villosulicarpa Hoehne andA Stenosperma (Brazil)

AABB

21

Domestication of Chilli

22

StrawberryBanana

Musa acuminata Musa balbisiana (2n=3x=33) AB genomeFRAGARIA X ANANASSA

Wood berries (F vesca) and Musky strawberries (F moschata)23

Wild SoybeanGlycin soja2n=40

Cultivated soybeanGlycin max 2n=40

24

Increased in domesticate

seed germination

determinate growth

longer pods

bigger (heavier) seeds

earliness

harvest index (seed yieldbiomass)

Decreased in domesticate

seed dispersal

seed dormancy

twining

number of nodes

length of internode

number of pods

photoperiod sensitivity

Common Bean Phaseolus vulgarishttpwwwplantsciencesucdavisedugeptspb143pb143htm

copy Paul Gepts

25

Wild pigeon peaCajanus cajanifolius

Cultivated pigeon pea

26

27

28

WHY OTHERS ARE NOT DOMESTICATED

bull 350000 plants

bull 4629 mammals

bull 9200 birds

bull 10000000 insects

bull 500000 fungi

bull But only 200 plants

bull 15 mammals 5 birds and

bull 2 insects are domesticated

bull Spread of these few species

bull Little change since early

agriculture

bull Repeated domestication of these

species (sometimes)

bull Lack of new species even with

attempts with species known to be

valuable Some groups are good

candidates with no domestication

eg ferns sub-Saharan mammals

29

WHY OTHERS HAVE TO BE DOMESTICATED

New uses and demands ndash biofuels animal feed

medicinalneutraceutical waterclimate food changes

Knowledge why species arenrsquot suitable for domestication or

were not useful

Better understanding of genetics and selection

Sustainability of production

Reliability of production

To meet the food demand in an alternative way

WHY OTHERS HAVE TO BE DOMESTICATED

30

Reallocate biomass for human use

More efficient metabolism and photosynthesis increase

leaf surface decrease root system increase leaf

longevity

Grains more fertile florets larger inflorescence OR

number of ears different ways to get more seed

Larger seeds (automatic vs deliberate selection)

Oil plants increased oil content or more seed

Fiber plants long strong fibers

Domestication syndrome

31

Centers of Domestication

Fuller 2011

32

Centers of Domestication in India

Fuller 2011

33

Indian centers of domestication South India (Deccan centre) Vigna radiate Vigna mungo

Macrotyloma uniflorum (Horse gram) Sataria verticillata S plumila

wheat (macaroni) and two rowed barleybrachiaria ramosa

Orissa (Mahanadi river) Pegion pea Horsegram mung small millets

like Echinichloa Paspalum and Sataria

The Middle Ganges (Harappan civilization) Oryza nivara O rufipogon

and wild sativa Sateria pumia Cannabis sativa even the diffusion of

japonica rice

Saurashtra (Harappan civilization) Eleucine coracana Sateria italica

Paicum spp Brachypodia pearl millet and sorghum Dollicos lablab

The Himalayan foothills of the Punjab region Was a centre of

diversity for Japonica type rice and many temperate fruits and

vegetables

34

DOMESTICATION RELATED TRAITS CONTROLLED BY ONLY FEW GENES

Trait Crops

Plant architecturegrowth habit Ricemaizemilletsbeantomato

Flowering timephotoperiod sensitivity Ricemaizesorghumbeantomato

Fruit size Tomato egg plant

Grain size Ricemaizesorghumbean

Seed dispersal Brassica rice

Inflorescence modification Brassica

Dormancy Bean

35

Genes Crop Moleular and phenotypic function Causative change

Genes identified as controlling domestication traits

tb1 Maize Transcriptional regulator (TCP) plant and

inflorescence structure

regulatory change

tga1 Maize Transcriptional regulator (SBP) seed casing amino acid change

qSH1 Rice Transcriptional regulator (homeodomain)

abscission layer formation shattering

regulatory change

Rc Rice Transcriptional regulator (bHLH) seed color disrupted coding

sequence

sh4 Rice Transcriptional regulator (Myb3) abscission

layer formation shattering

regulatoryamino

acid change

fw22 Tomato Cell signaling fruit weight regulatory change

Q Wheat Transcriptional regulator (AP2) inflorescence

structure

regulatoryamino

acid change

Vrs1 Barley Inflorescence structure Premature stop Amino acid change

Genes of interest in crop domestication and improvement

36

Genes Crop Moleular and phenotypic function Causative change

c1

r1

Maize Transcriptional regulator (MYB) kernel color and

Transcriptional regulator (bHLH) kernel color

regulatory change

sh2 Maize pyrophosphorylase supersweet sweet corn transposon

insertion

su1 Maize isoamylase sweet corn gene amino acid change

brix9-2-5 Tomato Invertase fruit soluble solid content amino acid change

ovate Tomato Unknown fruit shap early stop codon

R Pea Starch branching enzyme seed sugar content transposon

insertion

ehd1 Rice B-type response regulator flowering time amino acid change

hd1 Rice Transcriptional regulator (zinc finger) flowering

time

disrupted coding

sequence

waxy Rice Starch synthase sticky grains intron splicing

defect

rht Wheat Transcriptional regulator (SH2) plant height early stop codon

vrn1 Wheat Transcriptional regulator (MADS) vernalization regulatory change

vrn2 Wheat Transcriptional regulator (ZCCT) vernalization amino acid change

Genes Identified as Controlling Varietal Differences

37

Process of domestication over the yearshellip

Rachel S Meyer 2012

38

Genetic bottleneck

Cultivated crops undergone with narrowing of diversity problem

But this is not the case in weeds

Weeds are the major threats from the beginning of domestication till

today

Problem arose due to

1 Crop mimicry

2 Genetic assimilation

3 Genetic evolution

39

Super- Domestication Vaughn et al (2007) first used the term super-domestication

The processes that lead to a domesticate with dramatically

increased yield that could not be selected in natural environments

from naturally occurring variation without recourse to new

technologies

Super-domesticates can be constructed with knowledge led

approaches based on current needs using the range of new

technologies now available

Plants exploited for continuous selection introduction hybridization

etc which boosted the process of domestication but now the plant

genetic engineering approach is exploiting plants towards synthetic

biology

40

How to use diversitybull Cross two varieties

bull Genome manipulations

Cell fusion hybrids

bull Chromosome manipulation Backcross a new species

bull Generate recombinants Chromosome recombinations

bull Use a new species wild germplasm

Transgenic approach Modern mutagenesis synthetic gene

construction by utilizing green florescent protein genome editing

NGS GWAS sequencing etchelliphelliphelliphelliphellip

41

Reduce genetic bottlenecks through polyplodization

More vigour

SC

Buffering capacity

Heterotic advantage

Enhaced vegetative

charachers

Enhanced oil

Meiotic stability

42

Approach 1 Use one tetraploid and one diploid as parents (4X ndash 2X) followed by the

chromosome doubling of triploid hybrids (Chrom doubling)

a) Cross between B juncea (AjAjBjBj ) and B oleracea (CoCo) to produce hexaploids

(AjAjBjBjCoCo)

(b) Cross between B napus (AnAnCnCn) and B nigra (BniBni) to produce hexaploids

(AnAnBniBniCnCn)

(c) Cross between B carinata (BcaBcaCcaCca) and B rapa (ArAr) to produce hexaploids

(ArArBcaBcaCcaCca)

Approach 2 Use three tetraploids as parents

(a) Cross between B napus (AnAnCnCn) and B carinata (BcaBcaCcaCca) to produce unbalanced

allotetraploids (AnBcaCnCca ndash unreduced gametes gametes with the somatic chromosome

number and cross with B juncea (AjAjBjBj) to obtain allohexaploids (AnAjBcaBjCnCca

(b) Cross between B napus (AnAnCnCn) and B juncea (AjAjBjBj) to produce unbalanced

allotetraploids (AnAjBjCn ndash unreduced gametes) and cross with B carinata (BcaBcaCcaCca) to

obtain allohexaploids (AnAjBcaBjCnCca)

(c) Cross between B carinata (BcaBcaCcaCca) and B juncea (AjAjBjBj) to produce unbalanced

allotetraploids (AjBcaBjCca - ndash unreduced gametes) and cross with B napus (AnAnCnCn) to obtain

allohexaploids (AnAjBcaBjCnCca)

Approach 3 Use three diploids as parents (2X ndash 2X ndash 2X) Cross between B rapa (ArAr) B

nigra (BniBni) and B oleracea (CoCo) sequentially to obtain hexaploid hybrids (ArArBniBniCoCo)

43

Continuehellip

Guijun Yan 2012

44

Applications of Genomic

tools in Super-Domestication

45

Genome Sequencing

Potential methods of sequencing

1 Clone by clone approach

2 Whole genome shotgun approach

3 Combination of the two methods

Till today no of cultivated plants completely sequenced -85

2016- Arachis duranensis

2015- Solanum cumersonii (Wild potato)

(Ref- NCBI)

46

GWAS

It is a study design in which many markers spread across a genome

are genotyped and test a statistical association with a phenotype are

performed locally along the genome

It is also an examination of many common genetic variants in different

individuals to see if any variant is associated with a trait

Used in successfully studying maize sorghum and barley

Method is efficient for large scale low cost genotyping (even with the

minimum number of SNPs)

Cannot be utilized generally because it needs large population size

GWAS identify rare alleles more precisely

If small population we can opt NAM

47

GWAS and whole genome prediction

Xuehui Huang and Bin Han 2014

48

Five high throuput genotyping methods

Xuehui Huang and Bin Han 2014

49

Role of NGS in domestication Capture of novel genes from wild species will be made easier by

understanding the molecular events associated with crop domestication

Re-sequencing of domesticated species can identify low diversity regions

resulting from selection during domestication

To identify gene-specific sequences to aid the cloning of homologues of key

domestication genes from wild relatives

Candidate genes from wild and domesticated plant populations can define

diversity of target genes in wild populations and lead to the discovery of key

genes for important traits by association analysis

NGS of amplicons of large numbers of candidate genes from wild and

domesticated plant populations can define diversity of target genes in

wild populations and lead to the discovery of key genes for important

traits by association analysis

50

NGS

supports the rapid domestication of new plant species and the efficient

identification and capture of novel genetic variation from related species

Allows whole-genome analysis to determine the genetic basis of

phenotypic differences

NGS allows rapid expansion of genomic analysis to investigation of non-

model species

Made rice study easy by related grass

cost-effective method for plant identification

useful strategy to analysis the chloroplast genome sequence from whole-

genome shot-gun sequencing

facilitates managing this diversity and any changes in crop performance

over time due to genetic drift

Patterns of gene expression have been evaluated in hybrids using NGS

51

Two Approaches to Finding Adaptive Genes

Ross-Ibarra et al2007

52

Techniques to re-wild the plants (transgene free)

1 Introgression

breeding

2 Specific

insertion of lost genes

3 Precision

mutagenesis

Palmgren et al2014

53

Process of rewilding

Palmgren et al2014

54

Synthetic biology projects(i) Modifying cereals including wheat to fix atmospheric nitrogen

(ii) Redesigning metabolic pathways to increase the yield of

secondary metabolites or to generate compounds with enhanced

properties

(iii) Transferring the C4 photosynthesis pathway to rice

(iv) Modifying the glycosylation pathway in plants to accommodate

production of therapeutic proteins

(v) Introducing synthetic signal transduction systems that respond to

external cues

55

Synthetic biology projects

Nicholas J Baltes et al 2015

56

Refactoring the N fixation gene cluster from Klebsiella

Karsten Temme et al 2012

4

bull Story of agriculture dates back to almost 10000 BC It wasinitiated by people who depended on diets composed of wildplants and animals

bull By 4000 BC ancient peoples had completed thedomestication of all major crop species upon which humansurvival is dependent including rice wheat and maize

bull Recent research has begun to reveal the genes responsible forthis agricultural revolution boosts ldquoGene tinkeringrdquo

History of Agriculture

5

Domestication

Human influence change in genetics of plant population

leads to ldquoAdaptive syndrome of domesticationrdquo

bull May be deliberate or not

(ldquounconsciousrdquo or ldquoincidentalrdquo)

bull Due to change in selective environment and control

over reproduction (eg harvesting grains with

sickle sowing saved seeds)

6

Domesticated- refers more generally to plants that are

morphologically and genetically distinct from their wild ancestors

as a result of artificial selection or are no longer known to occur

outside of cultivation

Semi-domesticated- as a crop that is under cultivation and

subjected to conscious artificial selection pressures

Undomesticated refers to uncultivated plants that continue to be

wild-harvested with no conscious artificial selection pressures

and no discernible morphological and frasl or genetic differentiations

that could be used to distinguish them as a domesticate (eg

Brazil nut)

Nivara

Rufipogon

Glaberrima

7

Domesticated Rice

8

Wild wheat

9

Domesticated Wheat

10

Maize

11

Domesticated maize

12

Barley Domestication

Prognt H spontanium

13

14

Domesticated Pearl MilletPennisetum glaucum

better seed recovery and yield but less able to survive in natural conditions compared to wild progenitor

bull more apical dominance (less

branching)

bull compact growth habit

bull flowering at same time (rather

than spread over long period)

bull larger spikes

bull non-shattering spikelets

bull loss of bristles amp glumes around

grains

bull larger seeds

bull non-dormant seeds

bull germinate at same time

15

Ppolystachian

Oats domestication

Wild- A sterilis Modern

sativa

16

Domestication of Sorghum

S helepense

S bicolor17

JR Harlan 1976 Sci American

Divergent

selection for

different

purposes

httpenwikipediaorgwikiImageBrassica_oleracea0jpg

httpwwwcehacukimagesclip_image002_001jpg

Brassica oleracea cabbage

broccoli cauliflower kale

romanesco collards kohrabi

brussels sprouts18

Solanum pimpinellifolium

Solanum lycopersicum19

Domestication of carrot

Queen Annes Lace

Daucus carota

20

Domestication of peanut

A villosulicarpa Hoehne andA Stenosperma (Brazil)

AABB

21

Domestication of Chilli

22

StrawberryBanana

Musa acuminata Musa balbisiana (2n=3x=33) AB genomeFRAGARIA X ANANASSA

Wood berries (F vesca) and Musky strawberries (F moschata)23

Wild SoybeanGlycin soja2n=40

Cultivated soybeanGlycin max 2n=40

24

Increased in domesticate

seed germination

determinate growth

longer pods

bigger (heavier) seeds

earliness

harvest index (seed yieldbiomass)

Decreased in domesticate

seed dispersal

seed dormancy

twining

number of nodes

length of internode

number of pods

photoperiod sensitivity

Common Bean Phaseolus vulgarishttpwwwplantsciencesucdavisedugeptspb143pb143htm

copy Paul Gepts

25

Wild pigeon peaCajanus cajanifolius

Cultivated pigeon pea

26

27

28

WHY OTHERS ARE NOT DOMESTICATED

bull 350000 plants

bull 4629 mammals

bull 9200 birds

bull 10000000 insects

bull 500000 fungi

bull But only 200 plants

bull 15 mammals 5 birds and

bull 2 insects are domesticated

bull Spread of these few species

bull Little change since early

agriculture

bull Repeated domestication of these

species (sometimes)

bull Lack of new species even with

attempts with species known to be

valuable Some groups are good

candidates with no domestication

eg ferns sub-Saharan mammals

29

WHY OTHERS HAVE TO BE DOMESTICATED

New uses and demands ndash biofuels animal feed

medicinalneutraceutical waterclimate food changes

Knowledge why species arenrsquot suitable for domestication or

were not useful

Better understanding of genetics and selection

Sustainability of production

Reliability of production

To meet the food demand in an alternative way

WHY OTHERS HAVE TO BE DOMESTICATED

30

Reallocate biomass for human use

More efficient metabolism and photosynthesis increase

leaf surface decrease root system increase leaf

longevity

Grains more fertile florets larger inflorescence OR

number of ears different ways to get more seed

Larger seeds (automatic vs deliberate selection)

Oil plants increased oil content or more seed

Fiber plants long strong fibers

Domestication syndrome

31

Centers of Domestication

Fuller 2011

32

Centers of Domestication in India

Fuller 2011

33

Indian centers of domestication South India (Deccan centre) Vigna radiate Vigna mungo

Macrotyloma uniflorum (Horse gram) Sataria verticillata S plumila

wheat (macaroni) and two rowed barleybrachiaria ramosa

Orissa (Mahanadi river) Pegion pea Horsegram mung small millets

like Echinichloa Paspalum and Sataria

The Middle Ganges (Harappan civilization) Oryza nivara O rufipogon

and wild sativa Sateria pumia Cannabis sativa even the diffusion of

japonica rice

Saurashtra (Harappan civilization) Eleucine coracana Sateria italica

Paicum spp Brachypodia pearl millet and sorghum Dollicos lablab

The Himalayan foothills of the Punjab region Was a centre of

diversity for Japonica type rice and many temperate fruits and

vegetables

34

DOMESTICATION RELATED TRAITS CONTROLLED BY ONLY FEW GENES

Trait Crops

Plant architecturegrowth habit Ricemaizemilletsbeantomato

Flowering timephotoperiod sensitivity Ricemaizesorghumbeantomato

Fruit size Tomato egg plant

Grain size Ricemaizesorghumbean

Seed dispersal Brassica rice

Inflorescence modification Brassica

Dormancy Bean

35

Genes Crop Moleular and phenotypic function Causative change

Genes identified as controlling domestication traits

tb1 Maize Transcriptional regulator (TCP) plant and

inflorescence structure

regulatory change

tga1 Maize Transcriptional regulator (SBP) seed casing amino acid change

qSH1 Rice Transcriptional regulator (homeodomain)

abscission layer formation shattering

regulatory change

Rc Rice Transcriptional regulator (bHLH) seed color disrupted coding

sequence

sh4 Rice Transcriptional regulator (Myb3) abscission

layer formation shattering

regulatoryamino

acid change

fw22 Tomato Cell signaling fruit weight regulatory change

Q Wheat Transcriptional regulator (AP2) inflorescence

structure

regulatoryamino

acid change

Vrs1 Barley Inflorescence structure Premature stop Amino acid change

Genes of interest in crop domestication and improvement

36

Genes Crop Moleular and phenotypic function Causative change

c1

r1

Maize Transcriptional regulator (MYB) kernel color and

Transcriptional regulator (bHLH) kernel color

regulatory change

sh2 Maize pyrophosphorylase supersweet sweet corn transposon

insertion

su1 Maize isoamylase sweet corn gene amino acid change

brix9-2-5 Tomato Invertase fruit soluble solid content amino acid change

ovate Tomato Unknown fruit shap early stop codon

R Pea Starch branching enzyme seed sugar content transposon

insertion

ehd1 Rice B-type response regulator flowering time amino acid change

hd1 Rice Transcriptional regulator (zinc finger) flowering

time

disrupted coding

sequence

waxy Rice Starch synthase sticky grains intron splicing

defect

rht Wheat Transcriptional regulator (SH2) plant height early stop codon

vrn1 Wheat Transcriptional regulator (MADS) vernalization regulatory change

vrn2 Wheat Transcriptional regulator (ZCCT) vernalization amino acid change

Genes Identified as Controlling Varietal Differences

37

Process of domestication over the yearshellip

Rachel S Meyer 2012

38

Genetic bottleneck

Cultivated crops undergone with narrowing of diversity problem

But this is not the case in weeds

Weeds are the major threats from the beginning of domestication till

today

Problem arose due to

1 Crop mimicry

2 Genetic assimilation

3 Genetic evolution

39

Super- Domestication Vaughn et al (2007) first used the term super-domestication

The processes that lead to a domesticate with dramatically

increased yield that could not be selected in natural environments

from naturally occurring variation without recourse to new

technologies

Super-domesticates can be constructed with knowledge led

approaches based on current needs using the range of new

technologies now available

Plants exploited for continuous selection introduction hybridization

etc which boosted the process of domestication but now the plant

genetic engineering approach is exploiting plants towards synthetic

biology

40

How to use diversitybull Cross two varieties

bull Genome manipulations

Cell fusion hybrids

bull Chromosome manipulation Backcross a new species

bull Generate recombinants Chromosome recombinations

bull Use a new species wild germplasm

Transgenic approach Modern mutagenesis synthetic gene

construction by utilizing green florescent protein genome editing

NGS GWAS sequencing etchelliphelliphelliphelliphellip

41

Reduce genetic bottlenecks through polyplodization

More vigour

SC

Buffering capacity

Heterotic advantage

Enhaced vegetative

charachers

Enhanced oil

Meiotic stability

42

Approach 1 Use one tetraploid and one diploid as parents (4X ndash 2X) followed by the

chromosome doubling of triploid hybrids (Chrom doubling)

a) Cross between B juncea (AjAjBjBj ) and B oleracea (CoCo) to produce hexaploids

(AjAjBjBjCoCo)

(b) Cross between B napus (AnAnCnCn) and B nigra (BniBni) to produce hexaploids

(AnAnBniBniCnCn)

(c) Cross between B carinata (BcaBcaCcaCca) and B rapa (ArAr) to produce hexaploids

(ArArBcaBcaCcaCca)

Approach 2 Use three tetraploids as parents

(a) Cross between B napus (AnAnCnCn) and B carinata (BcaBcaCcaCca) to produce unbalanced

allotetraploids (AnBcaCnCca ndash unreduced gametes gametes with the somatic chromosome

number and cross with B juncea (AjAjBjBj) to obtain allohexaploids (AnAjBcaBjCnCca

(b) Cross between B napus (AnAnCnCn) and B juncea (AjAjBjBj) to produce unbalanced

allotetraploids (AnAjBjCn ndash unreduced gametes) and cross with B carinata (BcaBcaCcaCca) to

obtain allohexaploids (AnAjBcaBjCnCca)

(c) Cross between B carinata (BcaBcaCcaCca) and B juncea (AjAjBjBj) to produce unbalanced

allotetraploids (AjBcaBjCca - ndash unreduced gametes) and cross with B napus (AnAnCnCn) to obtain

allohexaploids (AnAjBcaBjCnCca)

Approach 3 Use three diploids as parents (2X ndash 2X ndash 2X) Cross between B rapa (ArAr) B

nigra (BniBni) and B oleracea (CoCo) sequentially to obtain hexaploid hybrids (ArArBniBniCoCo)

43

Continuehellip

Guijun Yan 2012

44

Applications of Genomic

tools in Super-Domestication

45

Genome Sequencing

Potential methods of sequencing

1 Clone by clone approach

2 Whole genome shotgun approach

3 Combination of the two methods

Till today no of cultivated plants completely sequenced -85

2016- Arachis duranensis

2015- Solanum cumersonii (Wild potato)

(Ref- NCBI)

46

GWAS

It is a study design in which many markers spread across a genome

are genotyped and test a statistical association with a phenotype are

performed locally along the genome

It is also an examination of many common genetic variants in different

individuals to see if any variant is associated with a trait

Used in successfully studying maize sorghum and barley

Method is efficient for large scale low cost genotyping (even with the

minimum number of SNPs)

Cannot be utilized generally because it needs large population size

GWAS identify rare alleles more precisely

If small population we can opt NAM

47

GWAS and whole genome prediction

Xuehui Huang and Bin Han 2014

48

Five high throuput genotyping methods

Xuehui Huang and Bin Han 2014

49

Role of NGS in domestication Capture of novel genes from wild species will be made easier by

understanding the molecular events associated with crop domestication

Re-sequencing of domesticated species can identify low diversity regions

resulting from selection during domestication

To identify gene-specific sequences to aid the cloning of homologues of key

domestication genes from wild relatives

Candidate genes from wild and domesticated plant populations can define

diversity of target genes in wild populations and lead to the discovery of key

genes for important traits by association analysis

NGS of amplicons of large numbers of candidate genes from wild and

domesticated plant populations can define diversity of target genes in

wild populations and lead to the discovery of key genes for important

traits by association analysis

50

NGS

supports the rapid domestication of new plant species and the efficient

identification and capture of novel genetic variation from related species

Allows whole-genome analysis to determine the genetic basis of

phenotypic differences

NGS allows rapid expansion of genomic analysis to investigation of non-

model species

Made rice study easy by related grass

cost-effective method for plant identification

useful strategy to analysis the chloroplast genome sequence from whole-

genome shot-gun sequencing

facilitates managing this diversity and any changes in crop performance

over time due to genetic drift

Patterns of gene expression have been evaluated in hybrids using NGS

51

Two Approaches to Finding Adaptive Genes

Ross-Ibarra et al2007

52

Techniques to re-wild the plants (transgene free)

1 Introgression

breeding

2 Specific

insertion of lost genes

3 Precision

mutagenesis

Palmgren et al2014

53

Process of rewilding

Palmgren et al2014

54

Synthetic biology projects(i) Modifying cereals including wheat to fix atmospheric nitrogen

(ii) Redesigning metabolic pathways to increase the yield of

secondary metabolites or to generate compounds with enhanced

properties

(iii) Transferring the C4 photosynthesis pathway to rice

(iv) Modifying the glycosylation pathway in plants to accommodate

production of therapeutic proteins

(v) Introducing synthetic signal transduction systems that respond to

external cues

55

Synthetic biology projects

Nicholas J Baltes et al 2015

56

Refactoring the N fixation gene cluster from Klebsiella

Karsten Temme et al 2012

5

Domestication

Human influence change in genetics of plant population

leads to ldquoAdaptive syndrome of domesticationrdquo

bull May be deliberate or not

(ldquounconsciousrdquo or ldquoincidentalrdquo)

bull Due to change in selective environment and control

over reproduction (eg harvesting grains with

sickle sowing saved seeds)

6

Domesticated- refers more generally to plants that are

morphologically and genetically distinct from their wild ancestors

as a result of artificial selection or are no longer known to occur

outside of cultivation

Semi-domesticated- as a crop that is under cultivation and

subjected to conscious artificial selection pressures

Undomesticated refers to uncultivated plants that continue to be

wild-harvested with no conscious artificial selection pressures

and no discernible morphological and frasl or genetic differentiations

that could be used to distinguish them as a domesticate (eg

Brazil nut)

Nivara

Rufipogon

Glaberrima

7

Domesticated Rice

8

Wild wheat

9

Domesticated Wheat

10

Maize

11

Domesticated maize

12

Barley Domestication

Prognt H spontanium

13

14

Domesticated Pearl MilletPennisetum glaucum

better seed recovery and yield but less able to survive in natural conditions compared to wild progenitor

bull more apical dominance (less

branching)

bull compact growth habit

bull flowering at same time (rather

than spread over long period)

bull larger spikes

bull non-shattering spikelets

bull loss of bristles amp glumes around

grains

bull larger seeds

bull non-dormant seeds

bull germinate at same time

15

Ppolystachian

Oats domestication

Wild- A sterilis Modern

sativa

16

Domestication of Sorghum

S helepense

S bicolor17

JR Harlan 1976 Sci American

Divergent

selection for

different

purposes

httpenwikipediaorgwikiImageBrassica_oleracea0jpg

httpwwwcehacukimagesclip_image002_001jpg

Brassica oleracea cabbage

broccoli cauliflower kale

romanesco collards kohrabi

brussels sprouts18

Solanum pimpinellifolium

Solanum lycopersicum19

Domestication of carrot

Queen Annes Lace

Daucus carota

20

Domestication of peanut

A villosulicarpa Hoehne andA Stenosperma (Brazil)

AABB

21

Domestication of Chilli

22

StrawberryBanana

Musa acuminata Musa balbisiana (2n=3x=33) AB genomeFRAGARIA X ANANASSA

Wood berries (F vesca) and Musky strawberries (F moschata)23

Wild SoybeanGlycin soja2n=40

Cultivated soybeanGlycin max 2n=40

24

Increased in domesticate

seed germination

determinate growth

longer pods

bigger (heavier) seeds

earliness

harvest index (seed yieldbiomass)

Decreased in domesticate

seed dispersal

seed dormancy

twining

number of nodes

length of internode

number of pods

photoperiod sensitivity

Common Bean Phaseolus vulgarishttpwwwplantsciencesucdavisedugeptspb143pb143htm

copy Paul Gepts

25

Wild pigeon peaCajanus cajanifolius

Cultivated pigeon pea

26

27

28

WHY OTHERS ARE NOT DOMESTICATED

bull 350000 plants

bull 4629 mammals

bull 9200 birds

bull 10000000 insects

bull 500000 fungi

bull But only 200 plants

bull 15 mammals 5 birds and

bull 2 insects are domesticated

bull Spread of these few species

bull Little change since early

agriculture

bull Repeated domestication of these

species (sometimes)

bull Lack of new species even with

attempts with species known to be

valuable Some groups are good

candidates with no domestication

eg ferns sub-Saharan mammals

29

WHY OTHERS HAVE TO BE DOMESTICATED

New uses and demands ndash biofuels animal feed

medicinalneutraceutical waterclimate food changes

Knowledge why species arenrsquot suitable for domestication or

were not useful

Better understanding of genetics and selection

Sustainability of production

Reliability of production

To meet the food demand in an alternative way

WHY OTHERS HAVE TO BE DOMESTICATED

30

Reallocate biomass for human use

More efficient metabolism and photosynthesis increase

leaf surface decrease root system increase leaf

longevity

Grains more fertile florets larger inflorescence OR

number of ears different ways to get more seed

Larger seeds (automatic vs deliberate selection)

Oil plants increased oil content or more seed

Fiber plants long strong fibers

Domestication syndrome

31

Centers of Domestication

Fuller 2011

32

Centers of Domestication in India

Fuller 2011

33

Indian centers of domestication South India (Deccan centre) Vigna radiate Vigna mungo

Macrotyloma uniflorum (Horse gram) Sataria verticillata S plumila

wheat (macaroni) and two rowed barleybrachiaria ramosa

Orissa (Mahanadi river) Pegion pea Horsegram mung small millets

like Echinichloa Paspalum and Sataria

The Middle Ganges (Harappan civilization) Oryza nivara O rufipogon

and wild sativa Sateria pumia Cannabis sativa even the diffusion of

japonica rice

Saurashtra (Harappan civilization) Eleucine coracana Sateria italica

Paicum spp Brachypodia pearl millet and sorghum Dollicos lablab

The Himalayan foothills of the Punjab region Was a centre of

diversity for Japonica type rice and many temperate fruits and

vegetables

34

DOMESTICATION RELATED TRAITS CONTROLLED BY ONLY FEW GENES

Trait Crops

Plant architecturegrowth habit Ricemaizemilletsbeantomato

Flowering timephotoperiod sensitivity Ricemaizesorghumbeantomato

Fruit size Tomato egg plant

Grain size Ricemaizesorghumbean

Seed dispersal Brassica rice

Inflorescence modification Brassica

Dormancy Bean

35

Genes Crop Moleular and phenotypic function Causative change

Genes identified as controlling domestication traits

tb1 Maize Transcriptional regulator (TCP) plant and

inflorescence structure

regulatory change

tga1 Maize Transcriptional regulator (SBP) seed casing amino acid change

qSH1 Rice Transcriptional regulator (homeodomain)

abscission layer formation shattering

regulatory change

Rc Rice Transcriptional regulator (bHLH) seed color disrupted coding

sequence

sh4 Rice Transcriptional regulator (Myb3) abscission

layer formation shattering

regulatoryamino

acid change

fw22 Tomato Cell signaling fruit weight regulatory change

Q Wheat Transcriptional regulator (AP2) inflorescence

structure

regulatoryamino

acid change

Vrs1 Barley Inflorescence structure Premature stop Amino acid change

Genes of interest in crop domestication and improvement

36

Genes Crop Moleular and phenotypic function Causative change

c1

r1

Maize Transcriptional regulator (MYB) kernel color and

Transcriptional regulator (bHLH) kernel color

regulatory change

sh2 Maize pyrophosphorylase supersweet sweet corn transposon

insertion

su1 Maize isoamylase sweet corn gene amino acid change

brix9-2-5 Tomato Invertase fruit soluble solid content amino acid change

ovate Tomato Unknown fruit shap early stop codon

R Pea Starch branching enzyme seed sugar content transposon

insertion

ehd1 Rice B-type response regulator flowering time amino acid change

hd1 Rice Transcriptional regulator (zinc finger) flowering

time

disrupted coding

sequence

waxy Rice Starch synthase sticky grains intron splicing

defect

rht Wheat Transcriptional regulator (SH2) plant height early stop codon

vrn1 Wheat Transcriptional regulator (MADS) vernalization regulatory change

vrn2 Wheat Transcriptional regulator (ZCCT) vernalization amino acid change

Genes Identified as Controlling Varietal Differences

37

Process of domestication over the yearshellip

Rachel S Meyer 2012

38

Genetic bottleneck

Cultivated crops undergone with narrowing of diversity problem

But this is not the case in weeds

Weeds are the major threats from the beginning of domestication till

today

Problem arose due to

1 Crop mimicry

2 Genetic assimilation

3 Genetic evolution

39

Super- Domestication Vaughn et al (2007) first used the term super-domestication

The processes that lead to a domesticate with dramatically

increased yield that could not be selected in natural environments

from naturally occurring variation without recourse to new

technologies

Super-domesticates can be constructed with knowledge led

approaches based on current needs using the range of new

technologies now available

Plants exploited for continuous selection introduction hybridization

etc which boosted the process of domestication but now the plant

genetic engineering approach is exploiting plants towards synthetic

biology

40

How to use diversitybull Cross two varieties

bull Genome manipulations

Cell fusion hybrids

bull Chromosome manipulation Backcross a new species

bull Generate recombinants Chromosome recombinations

bull Use a new species wild germplasm

Transgenic approach Modern mutagenesis synthetic gene

construction by utilizing green florescent protein genome editing

NGS GWAS sequencing etchelliphelliphelliphelliphellip

41

Reduce genetic bottlenecks through polyplodization

More vigour

SC

Buffering capacity

Heterotic advantage

Enhaced vegetative

charachers

Enhanced oil

Meiotic stability

42

Approach 1 Use one tetraploid and one diploid as parents (4X ndash 2X) followed by the

chromosome doubling of triploid hybrids (Chrom doubling)

a) Cross between B juncea (AjAjBjBj ) and B oleracea (CoCo) to produce hexaploids

(AjAjBjBjCoCo)

(b) Cross between B napus (AnAnCnCn) and B nigra (BniBni) to produce hexaploids

(AnAnBniBniCnCn)

(c) Cross between B carinata (BcaBcaCcaCca) and B rapa (ArAr) to produce hexaploids

(ArArBcaBcaCcaCca)

Approach 2 Use three tetraploids as parents

(a) Cross between B napus (AnAnCnCn) and B carinata (BcaBcaCcaCca) to produce unbalanced

allotetraploids (AnBcaCnCca ndash unreduced gametes gametes with the somatic chromosome

number and cross with B juncea (AjAjBjBj) to obtain allohexaploids (AnAjBcaBjCnCca

(b) Cross between B napus (AnAnCnCn) and B juncea (AjAjBjBj) to produce unbalanced

allotetraploids (AnAjBjCn ndash unreduced gametes) and cross with B carinata (BcaBcaCcaCca) to

obtain allohexaploids (AnAjBcaBjCnCca)

(c) Cross between B carinata (BcaBcaCcaCca) and B juncea (AjAjBjBj) to produce unbalanced

allotetraploids (AjBcaBjCca - ndash unreduced gametes) and cross with B napus (AnAnCnCn) to obtain

allohexaploids (AnAjBcaBjCnCca)

Approach 3 Use three diploids as parents (2X ndash 2X ndash 2X) Cross between B rapa (ArAr) B

nigra (BniBni) and B oleracea (CoCo) sequentially to obtain hexaploid hybrids (ArArBniBniCoCo)

43

Continuehellip

Guijun Yan 2012

44

Applications of Genomic

tools in Super-Domestication

45

Genome Sequencing

Potential methods of sequencing

1 Clone by clone approach

2 Whole genome shotgun approach

3 Combination of the two methods

Till today no of cultivated plants completely sequenced -85

2016- Arachis duranensis

2015- Solanum cumersonii (Wild potato)

(Ref- NCBI)

46

GWAS

It is a study design in which many markers spread across a genome

are genotyped and test a statistical association with a phenotype are

performed locally along the genome

It is also an examination of many common genetic variants in different

individuals to see if any variant is associated with a trait

Used in successfully studying maize sorghum and barley

Method is efficient for large scale low cost genotyping (even with the

minimum number of SNPs)

Cannot be utilized generally because it needs large population size

GWAS identify rare alleles more precisely

If small population we can opt NAM

47

GWAS and whole genome prediction

Xuehui Huang and Bin Han 2014

48

Five high throuput genotyping methods

Xuehui Huang and Bin Han 2014

49

Role of NGS in domestication Capture of novel genes from wild species will be made easier by

understanding the molecular events associated with crop domestication

Re-sequencing of domesticated species can identify low diversity regions

resulting from selection during domestication

To identify gene-specific sequences to aid the cloning of homologues of key

domestication genes from wild relatives

Candidate genes from wild and domesticated plant populations can define

diversity of target genes in wild populations and lead to the discovery of key

genes for important traits by association analysis

NGS of amplicons of large numbers of candidate genes from wild and

domesticated plant populations can define diversity of target genes in

wild populations and lead to the discovery of key genes for important

traits by association analysis

50

NGS

supports the rapid domestication of new plant species and the efficient

identification and capture of novel genetic variation from related species

Allows whole-genome analysis to determine the genetic basis of

phenotypic differences

NGS allows rapid expansion of genomic analysis to investigation of non-

model species

Made rice study easy by related grass

cost-effective method for plant identification

useful strategy to analysis the chloroplast genome sequence from whole-

genome shot-gun sequencing

facilitates managing this diversity and any changes in crop performance

over time due to genetic drift

Patterns of gene expression have been evaluated in hybrids using NGS

51

Two Approaches to Finding Adaptive Genes

Ross-Ibarra et al2007

52

Techniques to re-wild the plants (transgene free)

1 Introgression

breeding

2 Specific

insertion of lost genes

3 Precision

mutagenesis

Palmgren et al2014

53

Process of rewilding

Palmgren et al2014

54

Synthetic biology projects(i) Modifying cereals including wheat to fix atmospheric nitrogen

(ii) Redesigning metabolic pathways to increase the yield of

secondary metabolites or to generate compounds with enhanced

properties

(iii) Transferring the C4 photosynthesis pathway to rice

(iv) Modifying the glycosylation pathway in plants to accommodate

production of therapeutic proteins

(v) Introducing synthetic signal transduction systems that respond to

external cues

55

Synthetic biology projects

Nicholas J Baltes et al 2015

56

Refactoring the N fixation gene cluster from Klebsiella

Karsten Temme et al 2012

6

Domesticated- refers more generally to plants that are

morphologically and genetically distinct from their wild ancestors

as a result of artificial selection or are no longer known to occur

outside of cultivation

Semi-domesticated- as a crop that is under cultivation and

subjected to conscious artificial selection pressures

Undomesticated refers to uncultivated plants that continue to be

wild-harvested with no conscious artificial selection pressures

and no discernible morphological and frasl or genetic differentiations

that could be used to distinguish them as a domesticate (eg

Brazil nut)

Nivara

Rufipogon

Glaberrima

7

Domesticated Rice

8

Wild wheat

9

Domesticated Wheat

10

Maize

11

Domesticated maize

12

Barley Domestication

Prognt H spontanium

13

14

Domesticated Pearl MilletPennisetum glaucum

better seed recovery and yield but less able to survive in natural conditions compared to wild progenitor

bull more apical dominance (less

branching)

bull compact growth habit

bull flowering at same time (rather

than spread over long period)

bull larger spikes

bull non-shattering spikelets

bull loss of bristles amp glumes around

grains

bull larger seeds

bull non-dormant seeds

bull germinate at same time

15

Ppolystachian

Oats domestication

Wild- A sterilis Modern

sativa

16

Domestication of Sorghum

S helepense

S bicolor17

JR Harlan 1976 Sci American

Divergent

selection for

different

purposes

httpenwikipediaorgwikiImageBrassica_oleracea0jpg

httpwwwcehacukimagesclip_image002_001jpg

Brassica oleracea cabbage

broccoli cauliflower kale

romanesco collards kohrabi

brussels sprouts18

Solanum pimpinellifolium

Solanum lycopersicum19

Domestication of carrot

Queen Annes Lace

Daucus carota

20

Domestication of peanut

A villosulicarpa Hoehne andA Stenosperma (Brazil)

AABB

21

Domestication of Chilli

22

StrawberryBanana

Musa acuminata Musa balbisiana (2n=3x=33) AB genomeFRAGARIA X ANANASSA

Wood berries (F vesca) and Musky strawberries (F moschata)23

Wild SoybeanGlycin soja2n=40

Cultivated soybeanGlycin max 2n=40

24

Increased in domesticate

seed germination

determinate growth

longer pods

bigger (heavier) seeds

earliness

harvest index (seed yieldbiomass)

Decreased in domesticate

seed dispersal

seed dormancy

twining

number of nodes

length of internode

number of pods

photoperiod sensitivity

Common Bean Phaseolus vulgarishttpwwwplantsciencesucdavisedugeptspb143pb143htm

copy Paul Gepts

25

Wild pigeon peaCajanus cajanifolius

Cultivated pigeon pea

26

27

28

WHY OTHERS ARE NOT DOMESTICATED

bull 350000 plants

bull 4629 mammals

bull 9200 birds

bull 10000000 insects

bull 500000 fungi

bull But only 200 plants

bull 15 mammals 5 birds and

bull 2 insects are domesticated

bull Spread of these few species

bull Little change since early

agriculture

bull Repeated domestication of these

species (sometimes)

bull Lack of new species even with

attempts with species known to be

valuable Some groups are good

candidates with no domestication

eg ferns sub-Saharan mammals

29

WHY OTHERS HAVE TO BE DOMESTICATED

New uses and demands ndash biofuels animal feed

medicinalneutraceutical waterclimate food changes

Knowledge why species arenrsquot suitable for domestication or

were not useful

Better understanding of genetics and selection

Sustainability of production

Reliability of production

To meet the food demand in an alternative way

WHY OTHERS HAVE TO BE DOMESTICATED

30

Reallocate biomass for human use

More efficient metabolism and photosynthesis increase

leaf surface decrease root system increase leaf

longevity

Grains more fertile florets larger inflorescence OR

number of ears different ways to get more seed

Larger seeds (automatic vs deliberate selection)

Oil plants increased oil content or more seed

Fiber plants long strong fibers

Domestication syndrome

31

Centers of Domestication

Fuller 2011

32

Centers of Domestication in India

Fuller 2011

33

Indian centers of domestication South India (Deccan centre) Vigna radiate Vigna mungo

Macrotyloma uniflorum (Horse gram) Sataria verticillata S plumila

wheat (macaroni) and two rowed barleybrachiaria ramosa

Orissa (Mahanadi river) Pegion pea Horsegram mung small millets

like Echinichloa Paspalum and Sataria

The Middle Ganges (Harappan civilization) Oryza nivara O rufipogon

and wild sativa Sateria pumia Cannabis sativa even the diffusion of

japonica rice

Saurashtra (Harappan civilization) Eleucine coracana Sateria italica

Paicum spp Brachypodia pearl millet and sorghum Dollicos lablab

The Himalayan foothills of the Punjab region Was a centre of

diversity for Japonica type rice and many temperate fruits and

vegetables

34

DOMESTICATION RELATED TRAITS CONTROLLED BY ONLY FEW GENES

Trait Crops

Plant architecturegrowth habit Ricemaizemilletsbeantomato

Flowering timephotoperiod sensitivity Ricemaizesorghumbeantomato

Fruit size Tomato egg plant

Grain size Ricemaizesorghumbean

Seed dispersal Brassica rice

Inflorescence modification Brassica

Dormancy Bean

35

Genes Crop Moleular and phenotypic function Causative change

Genes identified as controlling domestication traits

tb1 Maize Transcriptional regulator (TCP) plant and

inflorescence structure

regulatory change

tga1 Maize Transcriptional regulator (SBP) seed casing amino acid change

qSH1 Rice Transcriptional regulator (homeodomain)

abscission layer formation shattering

regulatory change

Rc Rice Transcriptional regulator (bHLH) seed color disrupted coding

sequence

sh4 Rice Transcriptional regulator (Myb3) abscission

layer formation shattering

regulatoryamino

acid change

fw22 Tomato Cell signaling fruit weight regulatory change

Q Wheat Transcriptional regulator (AP2) inflorescence

structure

regulatoryamino

acid change

Vrs1 Barley Inflorescence structure Premature stop Amino acid change

Genes of interest in crop domestication and improvement

36

Genes Crop Moleular and phenotypic function Causative change

c1

r1

Maize Transcriptional regulator (MYB) kernel color and

Transcriptional regulator (bHLH) kernel color

regulatory change

sh2 Maize pyrophosphorylase supersweet sweet corn transposon

insertion

su1 Maize isoamylase sweet corn gene amino acid change

brix9-2-5 Tomato Invertase fruit soluble solid content amino acid change

ovate Tomato Unknown fruit shap early stop codon

R Pea Starch branching enzyme seed sugar content transposon

insertion

ehd1 Rice B-type response regulator flowering time amino acid change

hd1 Rice Transcriptional regulator (zinc finger) flowering

time

disrupted coding

sequence

waxy Rice Starch synthase sticky grains intron splicing

defect

rht Wheat Transcriptional regulator (SH2) plant height early stop codon

vrn1 Wheat Transcriptional regulator (MADS) vernalization regulatory change

vrn2 Wheat Transcriptional regulator (ZCCT) vernalization amino acid change

Genes Identified as Controlling Varietal Differences

37

Process of domestication over the yearshellip

Rachel S Meyer 2012

38

Genetic bottleneck

Cultivated crops undergone with narrowing of diversity problem

But this is not the case in weeds

Weeds are the major threats from the beginning of domestication till

today

Problem arose due to

1 Crop mimicry

2 Genetic assimilation

3 Genetic evolution

39

Super- Domestication Vaughn et al (2007) first used the term super-domestication

The processes that lead to a domesticate with dramatically

increased yield that could not be selected in natural environments

from naturally occurring variation without recourse to new

technologies

Super-domesticates can be constructed with knowledge led

approaches based on current needs using the range of new

technologies now available

Plants exploited for continuous selection introduction hybridization

etc which boosted the process of domestication but now the plant

genetic engineering approach is exploiting plants towards synthetic

biology

40

How to use diversitybull Cross two varieties

bull Genome manipulations

Cell fusion hybrids

bull Chromosome manipulation Backcross a new species

bull Generate recombinants Chromosome recombinations

bull Use a new species wild germplasm

Transgenic approach Modern mutagenesis synthetic gene

construction by utilizing green florescent protein genome editing

NGS GWAS sequencing etchelliphelliphelliphelliphellip

41

Reduce genetic bottlenecks through polyplodization

More vigour

SC

Buffering capacity

Heterotic advantage

Enhaced vegetative

charachers

Enhanced oil

Meiotic stability

42

Approach 1 Use one tetraploid and one diploid as parents (4X ndash 2X) followed by the

chromosome doubling of triploid hybrids (Chrom doubling)

a) Cross between B juncea (AjAjBjBj ) and B oleracea (CoCo) to produce hexaploids

(AjAjBjBjCoCo)

(b) Cross between B napus (AnAnCnCn) and B nigra (BniBni) to produce hexaploids

(AnAnBniBniCnCn)

(c) Cross between B carinata (BcaBcaCcaCca) and B rapa (ArAr) to produce hexaploids

(ArArBcaBcaCcaCca)

Approach 2 Use three tetraploids as parents

(a) Cross between B napus (AnAnCnCn) and B carinata (BcaBcaCcaCca) to produce unbalanced

allotetraploids (AnBcaCnCca ndash unreduced gametes gametes with the somatic chromosome

number and cross with B juncea (AjAjBjBj) to obtain allohexaploids (AnAjBcaBjCnCca

(b) Cross between B napus (AnAnCnCn) and B juncea (AjAjBjBj) to produce unbalanced

allotetraploids (AnAjBjCn ndash unreduced gametes) and cross with B carinata (BcaBcaCcaCca) to

obtain allohexaploids (AnAjBcaBjCnCca)

(c) Cross between B carinata (BcaBcaCcaCca) and B juncea (AjAjBjBj) to produce unbalanced

allotetraploids (AjBcaBjCca - ndash unreduced gametes) and cross with B napus (AnAnCnCn) to obtain

allohexaploids (AnAjBcaBjCnCca)

Approach 3 Use three diploids as parents (2X ndash 2X ndash 2X) Cross between B rapa (ArAr) B

nigra (BniBni) and B oleracea (CoCo) sequentially to obtain hexaploid hybrids (ArArBniBniCoCo)

43

Continuehellip

Guijun Yan 2012

44

Applications of Genomic

tools in Super-Domestication

45

Genome Sequencing

Potential methods of sequencing

1 Clone by clone approach

2 Whole genome shotgun approach

3 Combination of the two methods

Till today no of cultivated plants completely sequenced -85

2016- Arachis duranensis

2015- Solanum cumersonii (Wild potato)

(Ref- NCBI)

46

GWAS

It is a study design in which many markers spread across a genome

are genotyped and test a statistical association with a phenotype are

performed locally along the genome

It is also an examination of many common genetic variants in different

individuals to see if any variant is associated with a trait

Used in successfully studying maize sorghum and barley

Method is efficient for large scale low cost genotyping (even with the

minimum number of SNPs)

Cannot be utilized generally because it needs large population size

GWAS identify rare alleles more precisely

If small population we can opt NAM

47

GWAS and whole genome prediction

Xuehui Huang and Bin Han 2014

48

Five high throuput genotyping methods

Xuehui Huang and Bin Han 2014

49

Role of NGS in domestication Capture of novel genes from wild species will be made easier by

understanding the molecular events associated with crop domestication

Re-sequencing of domesticated species can identify low diversity regions

resulting from selection during domestication

To identify gene-specific sequences to aid the cloning of homologues of key

domestication genes from wild relatives

Candidate genes from wild and domesticated plant populations can define

diversity of target genes in wild populations and lead to the discovery of key

genes for important traits by association analysis

NGS of amplicons of large numbers of candidate genes from wild and

domesticated plant populations can define diversity of target genes in

wild populations and lead to the discovery of key genes for important

traits by association analysis

50

NGS

supports the rapid domestication of new plant species and the efficient

identification and capture of novel genetic variation from related species

Allows whole-genome analysis to determine the genetic basis of

phenotypic differences

NGS allows rapid expansion of genomic analysis to investigation of non-

model species

Made rice study easy by related grass

cost-effective method for plant identification

useful strategy to analysis the chloroplast genome sequence from whole-

genome shot-gun sequencing

facilitates managing this diversity and any changes in crop performance

over time due to genetic drift

Patterns of gene expression have been evaluated in hybrids using NGS

51

Two Approaches to Finding Adaptive Genes

Ross-Ibarra et al2007

52

Techniques to re-wild the plants (transgene free)

1 Introgression

breeding

2 Specific

insertion of lost genes

3 Precision

mutagenesis

Palmgren et al2014

53

Process of rewilding

Palmgren et al2014

54

Synthetic biology projects(i) Modifying cereals including wheat to fix atmospheric nitrogen

(ii) Redesigning metabolic pathways to increase the yield of

secondary metabolites or to generate compounds with enhanced

properties

(iii) Transferring the C4 photosynthesis pathway to rice

(iv) Modifying the glycosylation pathway in plants to accommodate

production of therapeutic proteins

(v) Introducing synthetic signal transduction systems that respond to

external cues

55

Synthetic biology projects

Nicholas J Baltes et al 2015

56

Refactoring the N fixation gene cluster from Klebsiella

Karsten Temme et al 2012

Nivara

Rufipogon

Glaberrima

7

Domesticated Rice

8

Wild wheat

9

Domesticated Wheat

10

Maize

11

Domesticated maize

12

Barley Domestication

Prognt H spontanium

13

14

Domesticated Pearl MilletPennisetum glaucum

better seed recovery and yield but less able to survive in natural conditions compared to wild progenitor

bull more apical dominance (less

branching)

bull compact growth habit

bull flowering at same time (rather

than spread over long period)

bull larger spikes

bull non-shattering spikelets

bull loss of bristles amp glumes around

grains

bull larger seeds

bull non-dormant seeds

bull germinate at same time

15

Ppolystachian

Oats domestication

Wild- A sterilis Modern

sativa

16

Domestication of Sorghum

S helepense

S bicolor17

JR Harlan 1976 Sci American

Divergent

selection for

different

purposes

httpenwikipediaorgwikiImageBrassica_oleracea0jpg

httpwwwcehacukimagesclip_image002_001jpg

Brassica oleracea cabbage

broccoli cauliflower kale

romanesco collards kohrabi

brussels sprouts18

Solanum pimpinellifolium

Solanum lycopersicum19

Domestication of carrot

Queen Annes Lace

Daucus carota

20

Domestication of peanut

A villosulicarpa Hoehne andA Stenosperma (Brazil)

AABB

21

Domestication of Chilli

22

StrawberryBanana

Musa acuminata Musa balbisiana (2n=3x=33) AB genomeFRAGARIA X ANANASSA

Wood berries (F vesca) and Musky strawberries (F moschata)23

Wild SoybeanGlycin soja2n=40

Cultivated soybeanGlycin max 2n=40

24

Increased in domesticate

seed germination

determinate growth

longer pods

bigger (heavier) seeds

earliness

harvest index (seed yieldbiomass)

Decreased in domesticate

seed dispersal

seed dormancy

twining

number of nodes

length of internode

number of pods

photoperiod sensitivity

Common Bean Phaseolus vulgarishttpwwwplantsciencesucdavisedugeptspb143pb143htm

copy Paul Gepts

25

Wild pigeon peaCajanus cajanifolius

Cultivated pigeon pea

26

27

28

WHY OTHERS ARE NOT DOMESTICATED

bull 350000 plants

bull 4629 mammals

bull 9200 birds

bull 10000000 insects

bull 500000 fungi

bull But only 200 plants

bull 15 mammals 5 birds and

bull 2 insects are domesticated

bull Spread of these few species

bull Little change since early

agriculture

bull Repeated domestication of these

species (sometimes)

bull Lack of new species even with

attempts with species known to be

valuable Some groups are good

candidates with no domestication

eg ferns sub-Saharan mammals

29

WHY OTHERS HAVE TO BE DOMESTICATED

New uses and demands ndash biofuels animal feed

medicinalneutraceutical waterclimate food changes

Knowledge why species arenrsquot suitable for domestication or

were not useful

Better understanding of genetics and selection

Sustainability of production

Reliability of production

To meet the food demand in an alternative way

WHY OTHERS HAVE TO BE DOMESTICATED

30

Reallocate biomass for human use

More efficient metabolism and photosynthesis increase

leaf surface decrease root system increase leaf

longevity

Grains more fertile florets larger inflorescence OR

number of ears different ways to get more seed

Larger seeds (automatic vs deliberate selection)

Oil plants increased oil content or more seed

Fiber plants long strong fibers

Domestication syndrome

31

Centers of Domestication

Fuller 2011

32

Centers of Domestication in India

Fuller 2011

33

Indian centers of domestication South India (Deccan centre) Vigna radiate Vigna mungo

Macrotyloma uniflorum (Horse gram) Sataria verticillata S plumila

wheat (macaroni) and two rowed barleybrachiaria ramosa

Orissa (Mahanadi river) Pegion pea Horsegram mung small millets

like Echinichloa Paspalum and Sataria

The Middle Ganges (Harappan civilization) Oryza nivara O rufipogon

and wild sativa Sateria pumia Cannabis sativa even the diffusion of

japonica rice

Saurashtra (Harappan civilization) Eleucine coracana Sateria italica

Paicum spp Brachypodia pearl millet and sorghum Dollicos lablab

The Himalayan foothills of the Punjab region Was a centre of

diversity for Japonica type rice and many temperate fruits and

vegetables

34

DOMESTICATION RELATED TRAITS CONTROLLED BY ONLY FEW GENES

Trait Crops

Plant architecturegrowth habit Ricemaizemilletsbeantomato

Flowering timephotoperiod sensitivity Ricemaizesorghumbeantomato

Fruit size Tomato egg plant

Grain size Ricemaizesorghumbean

Seed dispersal Brassica rice

Inflorescence modification Brassica

Dormancy Bean

35

Genes Crop Moleular and phenotypic function Causative change

Genes identified as controlling domestication traits

tb1 Maize Transcriptional regulator (TCP) plant and

inflorescence structure

regulatory change

tga1 Maize Transcriptional regulator (SBP) seed casing amino acid change

qSH1 Rice Transcriptional regulator (homeodomain)

abscission layer formation shattering

regulatory change

Rc Rice Transcriptional regulator (bHLH) seed color disrupted coding

sequence

sh4 Rice Transcriptional regulator (Myb3) abscission

layer formation shattering

regulatoryamino

acid change

fw22 Tomato Cell signaling fruit weight regulatory change

Q Wheat Transcriptional regulator (AP2) inflorescence

structure

regulatoryamino

acid change

Vrs1 Barley Inflorescence structure Premature stop Amino acid change

Genes of interest in crop domestication and improvement

36

Genes Crop Moleular and phenotypic function Causative change

c1

r1

Maize Transcriptional regulator (MYB) kernel color and

Transcriptional regulator (bHLH) kernel color

regulatory change

sh2 Maize pyrophosphorylase supersweet sweet corn transposon

insertion

su1 Maize isoamylase sweet corn gene amino acid change

brix9-2-5 Tomato Invertase fruit soluble solid content amino acid change

ovate Tomato Unknown fruit shap early stop codon

R Pea Starch branching enzyme seed sugar content transposon

insertion

ehd1 Rice B-type response regulator flowering time amino acid change

hd1 Rice Transcriptional regulator (zinc finger) flowering

time

disrupted coding

sequence

waxy Rice Starch synthase sticky grains intron splicing

defect

rht Wheat Transcriptional regulator (SH2) plant height early stop codon

vrn1 Wheat Transcriptional regulator (MADS) vernalization regulatory change

vrn2 Wheat Transcriptional regulator (ZCCT) vernalization amino acid change

Genes Identified as Controlling Varietal Differences

37

Process of domestication over the yearshellip

Rachel S Meyer 2012

38

Genetic bottleneck

Cultivated crops undergone with narrowing of diversity problem

But this is not the case in weeds

Weeds are the major threats from the beginning of domestication till

today

Problem arose due to

1 Crop mimicry

2 Genetic assimilation

3 Genetic evolution

39

Super- Domestication Vaughn et al (2007) first used the term super-domestication

The processes that lead to a domesticate with dramatically

increased yield that could not be selected in natural environments

from naturally occurring variation without recourse to new

technologies

Super-domesticates can be constructed with knowledge led

approaches based on current needs using the range of new

technologies now available

Plants exploited for continuous selection introduction hybridization

etc which boosted the process of domestication but now the plant

genetic engineering approach is exploiting plants towards synthetic

biology

40

How to use diversitybull Cross two varieties

bull Genome manipulations

Cell fusion hybrids

bull Chromosome manipulation Backcross a new species

bull Generate recombinants Chromosome recombinations

bull Use a new species wild germplasm

Transgenic approach Modern mutagenesis synthetic gene

construction by utilizing green florescent protein genome editing

NGS GWAS sequencing etchelliphelliphelliphelliphellip

41

Reduce genetic bottlenecks through polyplodization

More vigour

SC

Buffering capacity

Heterotic advantage

Enhaced vegetative

charachers

Enhanced oil

Meiotic stability

42

Approach 1 Use one tetraploid and one diploid as parents (4X ndash 2X) followed by the

chromosome doubling of triploid hybrids (Chrom doubling)

a) Cross between B juncea (AjAjBjBj ) and B oleracea (CoCo) to produce hexaploids

(AjAjBjBjCoCo)

(b) Cross between B napus (AnAnCnCn) and B nigra (BniBni) to produce hexaploids

(AnAnBniBniCnCn)

(c) Cross between B carinata (BcaBcaCcaCca) and B rapa (ArAr) to produce hexaploids

(ArArBcaBcaCcaCca)

Approach 2 Use three tetraploids as parents

(a) Cross between B napus (AnAnCnCn) and B carinata (BcaBcaCcaCca) to produce unbalanced

allotetraploids (AnBcaCnCca ndash unreduced gametes gametes with the somatic chromosome

number and cross with B juncea (AjAjBjBj) to obtain allohexaploids (AnAjBcaBjCnCca

(b) Cross between B napus (AnAnCnCn) and B juncea (AjAjBjBj) to produce unbalanced

allotetraploids (AnAjBjCn ndash unreduced gametes) and cross with B carinata (BcaBcaCcaCca) to

obtain allohexaploids (AnAjBcaBjCnCca)

(c) Cross between B carinata (BcaBcaCcaCca) and B juncea (AjAjBjBj) to produce unbalanced

allotetraploids (AjBcaBjCca - ndash unreduced gametes) and cross with B napus (AnAnCnCn) to obtain

allohexaploids (AnAjBcaBjCnCca)

Approach 3 Use three diploids as parents (2X ndash 2X ndash 2X) Cross between B rapa (ArAr) B

nigra (BniBni) and B oleracea (CoCo) sequentially to obtain hexaploid hybrids (ArArBniBniCoCo)

43

Continuehellip

Guijun Yan 2012

44

Applications of Genomic

tools in Super-Domestication

45

Genome Sequencing

Potential methods of sequencing

1 Clone by clone approach

2 Whole genome shotgun approach

3 Combination of the two methods

Till today no of cultivated plants completely sequenced -85

2016- Arachis duranensis

2015- Solanum cumersonii (Wild potato)

(Ref- NCBI)

46

GWAS

It is a study design in which many markers spread across a genome

are genotyped and test a statistical association with a phenotype are

performed locally along the genome

It is also an examination of many common genetic variants in different

individuals to see if any variant is associated with a trait

Used in successfully studying maize sorghum and barley

Method is efficient for large scale low cost genotyping (even with the

minimum number of SNPs)

Cannot be utilized generally because it needs large population size

GWAS identify rare alleles more precisely

If small population we can opt NAM

47

GWAS and whole genome prediction

Xuehui Huang and Bin Han 2014

48

Five high throuput genotyping methods

Xuehui Huang and Bin Han 2014

49

Role of NGS in domestication Capture of novel genes from wild species will be made easier by

understanding the molecular events associated with crop domestication

Re-sequencing of domesticated species can identify low diversity regions

resulting from selection during domestication

To identify gene-specific sequences to aid the cloning of homologues of key

domestication genes from wild relatives

Candidate genes from wild and domesticated plant populations can define

diversity of target genes in wild populations and lead to the discovery of key

genes for important traits by association analysis

NGS of amplicons of large numbers of candidate genes from wild and

domesticated plant populations can define diversity of target genes in

wild populations and lead to the discovery of key genes for important

traits by association analysis

50

NGS

supports the rapid domestication of new plant species and the efficient

identification and capture of novel genetic variation from related species

Allows whole-genome analysis to determine the genetic basis of

phenotypic differences

NGS allows rapid expansion of genomic analysis to investigation of non-

model species

Made rice study easy by related grass

cost-effective method for plant identification

useful strategy to analysis the chloroplast genome sequence from whole-

genome shot-gun sequencing

facilitates managing this diversity and any changes in crop performance

over time due to genetic drift

Patterns of gene expression have been evaluated in hybrids using NGS

51

Two Approaches to Finding Adaptive Genes

Ross-Ibarra et al2007

52

Techniques to re-wild the plants (transgene free)

1 Introgression

breeding

2 Specific

insertion of lost genes

3 Precision

mutagenesis

Palmgren et al2014

53

Process of rewilding

Palmgren et al2014

54

Synthetic biology projects(i) Modifying cereals including wheat to fix atmospheric nitrogen

(ii) Redesigning metabolic pathways to increase the yield of

secondary metabolites or to generate compounds with enhanced

properties

(iii) Transferring the C4 photosynthesis pathway to rice

(iv) Modifying the glycosylation pathway in plants to accommodate

production of therapeutic proteins

(v) Introducing synthetic signal transduction systems that respond to

external cues

55

Synthetic biology projects

Nicholas J Baltes et al 2015

56

Refactoring the N fixation gene cluster from Klebsiella

Karsten Temme et al 2012

Domesticated Rice

8

Wild wheat

9

Domesticated Wheat

10

Maize

11

Domesticated maize

12

Barley Domestication

Prognt H spontanium

13

14

Domesticated Pearl MilletPennisetum glaucum

better seed recovery and yield but less able to survive in natural conditions compared to wild progenitor

bull more apical dominance (less

branching)

bull compact growth habit

bull flowering at same time (rather

than spread over long period)

bull larger spikes

bull non-shattering spikelets

bull loss of bristles amp glumes around

grains

bull larger seeds

bull non-dormant seeds

bull germinate at same time

15

Ppolystachian

Oats domestication

Wild- A sterilis Modern

sativa

16

Domestication of Sorghum

S helepense

S bicolor17

JR Harlan 1976 Sci American

Divergent

selection for

different

purposes

httpenwikipediaorgwikiImageBrassica_oleracea0jpg

httpwwwcehacukimagesclip_image002_001jpg

Brassica oleracea cabbage

broccoli cauliflower kale

romanesco collards kohrabi

brussels sprouts18

Solanum pimpinellifolium

Solanum lycopersicum19

Domestication of carrot

Queen Annes Lace

Daucus carota

20

Domestication of peanut

A villosulicarpa Hoehne andA Stenosperma (Brazil)

AABB

21

Domestication of Chilli

22

StrawberryBanana

Musa acuminata Musa balbisiana (2n=3x=33) AB genomeFRAGARIA X ANANASSA

Wood berries (F vesca) and Musky strawberries (F moschata)23

Wild SoybeanGlycin soja2n=40

Cultivated soybeanGlycin max 2n=40

24

Increased in domesticate

seed germination

determinate growth

longer pods

bigger (heavier) seeds

earliness

harvest index (seed yieldbiomass)

Decreased in domesticate

seed dispersal

seed dormancy

twining

number of nodes

length of internode

number of pods

photoperiod sensitivity

Common Bean Phaseolus vulgarishttpwwwplantsciencesucdavisedugeptspb143pb143htm

copy Paul Gepts

25

Wild pigeon peaCajanus cajanifolius

Cultivated pigeon pea

26

27

28

WHY OTHERS ARE NOT DOMESTICATED

bull 350000 plants

bull 4629 mammals

bull 9200 birds

bull 10000000 insects

bull 500000 fungi

bull But only 200 plants

bull 15 mammals 5 birds and

bull 2 insects are domesticated

bull Spread of these few species

bull Little change since early

agriculture

bull Repeated domestication of these

species (sometimes)

bull Lack of new species even with

attempts with species known to be

valuable Some groups are good

candidates with no domestication

eg ferns sub-Saharan mammals

29

WHY OTHERS HAVE TO BE DOMESTICATED

New uses and demands ndash biofuels animal feed

medicinalneutraceutical waterclimate food changes

Knowledge why species arenrsquot suitable for domestication or

were not useful

Better understanding of genetics and selection

Sustainability of production

Reliability of production

To meet the food demand in an alternative way

WHY OTHERS HAVE TO BE DOMESTICATED

30

Reallocate biomass for human use

More efficient metabolism and photosynthesis increase

leaf surface decrease root system increase leaf

longevity

Grains more fertile florets larger inflorescence OR

number of ears different ways to get more seed

Larger seeds (automatic vs deliberate selection)

Oil plants increased oil content or more seed

Fiber plants long strong fibers

Domestication syndrome

31

Centers of Domestication

Fuller 2011

32

Centers of Domestication in India

Fuller 2011

33

Indian centers of domestication South India (Deccan centre) Vigna radiate Vigna mungo

Macrotyloma uniflorum (Horse gram) Sataria verticillata S plumila

wheat (macaroni) and two rowed barleybrachiaria ramosa

Orissa (Mahanadi river) Pegion pea Horsegram mung small millets

like Echinichloa Paspalum and Sataria

The Middle Ganges (Harappan civilization) Oryza nivara O rufipogon

and wild sativa Sateria pumia Cannabis sativa even the diffusion of

japonica rice

Saurashtra (Harappan civilization) Eleucine coracana Sateria italica

Paicum spp Brachypodia pearl millet and sorghum Dollicos lablab

The Himalayan foothills of the Punjab region Was a centre of

diversity for Japonica type rice and many temperate fruits and

vegetables

34

DOMESTICATION RELATED TRAITS CONTROLLED BY ONLY FEW GENES

Trait Crops

Plant architecturegrowth habit Ricemaizemilletsbeantomato

Flowering timephotoperiod sensitivity Ricemaizesorghumbeantomato

Fruit size Tomato egg plant

Grain size Ricemaizesorghumbean

Seed dispersal Brassica rice

Inflorescence modification Brassica

Dormancy Bean

35

Genes Crop Moleular and phenotypic function Causative change

Genes identified as controlling domestication traits

tb1 Maize Transcriptional regulator (TCP) plant and

inflorescence structure

regulatory change

tga1 Maize Transcriptional regulator (SBP) seed casing amino acid change

qSH1 Rice Transcriptional regulator (homeodomain)

abscission layer formation shattering

regulatory change

Rc Rice Transcriptional regulator (bHLH) seed color disrupted coding

sequence

sh4 Rice Transcriptional regulator (Myb3) abscission

layer formation shattering

regulatoryamino

acid change

fw22 Tomato Cell signaling fruit weight regulatory change

Q Wheat Transcriptional regulator (AP2) inflorescence

structure

regulatoryamino

acid change

Vrs1 Barley Inflorescence structure Premature stop Amino acid change

Genes of interest in crop domestication and improvement

36

Genes Crop Moleular and phenotypic function Causative change

c1

r1

Maize Transcriptional regulator (MYB) kernel color and

Transcriptional regulator (bHLH) kernel color

regulatory change

sh2 Maize pyrophosphorylase supersweet sweet corn transposon

insertion

su1 Maize isoamylase sweet corn gene amino acid change

brix9-2-5 Tomato Invertase fruit soluble solid content amino acid change

ovate Tomato Unknown fruit shap early stop codon

R Pea Starch branching enzyme seed sugar content transposon

insertion

ehd1 Rice B-type response regulator flowering time amino acid change

hd1 Rice Transcriptional regulator (zinc finger) flowering

time

disrupted coding

sequence

waxy Rice Starch synthase sticky grains intron splicing

defect

rht Wheat Transcriptional regulator (SH2) plant height early stop codon

vrn1 Wheat Transcriptional regulator (MADS) vernalization regulatory change

vrn2 Wheat Transcriptional regulator (ZCCT) vernalization amino acid change

Genes Identified as Controlling Varietal Differences

37

Process of domestication over the yearshellip

Rachel S Meyer 2012

38

Genetic bottleneck

Cultivated crops undergone with narrowing of diversity problem

But this is not the case in weeds

Weeds are the major threats from the beginning of domestication till

today

Problem arose due to

1 Crop mimicry

2 Genetic assimilation

3 Genetic evolution

39

Super- Domestication Vaughn et al (2007) first used the term super-domestication

The processes that lead to a domesticate with dramatically

increased yield that could not be selected in natural environments

from naturally occurring variation without recourse to new

technologies

Super-domesticates can be constructed with knowledge led

approaches based on current needs using the range of new

technologies now available

Plants exploited for continuous selection introduction hybridization

etc which boosted the process of domestication but now the plant

genetic engineering approach is exploiting plants towards synthetic

biology

40

How to use diversitybull Cross two varieties

bull Genome manipulations

Cell fusion hybrids

bull Chromosome manipulation Backcross a new species

bull Generate recombinants Chromosome recombinations

bull Use a new species wild germplasm

Transgenic approach Modern mutagenesis synthetic gene

construction by utilizing green florescent protein genome editing

NGS GWAS sequencing etchelliphelliphelliphelliphellip

41

Reduce genetic bottlenecks through polyplodization

More vigour

SC

Buffering capacity

Heterotic advantage

Enhaced vegetative

charachers

Enhanced oil

Meiotic stability

42

Approach 1 Use one tetraploid and one diploid as parents (4X ndash 2X) followed by the

chromosome doubling of triploid hybrids (Chrom doubling)

a) Cross between B juncea (AjAjBjBj ) and B oleracea (CoCo) to produce hexaploids

(AjAjBjBjCoCo)

(b) Cross between B napus (AnAnCnCn) and B nigra (BniBni) to produce hexaploids

(AnAnBniBniCnCn)

(c) Cross between B carinata (BcaBcaCcaCca) and B rapa (ArAr) to produce hexaploids

(ArArBcaBcaCcaCca)

Approach 2 Use three tetraploids as parents

(a) Cross between B napus (AnAnCnCn) and B carinata (BcaBcaCcaCca) to produce unbalanced

allotetraploids (AnBcaCnCca ndash unreduced gametes gametes with the somatic chromosome

number and cross with B juncea (AjAjBjBj) to obtain allohexaploids (AnAjBcaBjCnCca

(b) Cross between B napus (AnAnCnCn) and B juncea (AjAjBjBj) to produce unbalanced

allotetraploids (AnAjBjCn ndash unreduced gametes) and cross with B carinata (BcaBcaCcaCca) to

obtain allohexaploids (AnAjBcaBjCnCca)

(c) Cross between B carinata (BcaBcaCcaCca) and B juncea (AjAjBjBj) to produce unbalanced

allotetraploids (AjBcaBjCca - ndash unreduced gametes) and cross with B napus (AnAnCnCn) to obtain

allohexaploids (AnAjBcaBjCnCca)

Approach 3 Use three diploids as parents (2X ndash 2X ndash 2X) Cross between B rapa (ArAr) B

nigra (BniBni) and B oleracea (CoCo) sequentially to obtain hexaploid hybrids (ArArBniBniCoCo)

43

Continuehellip

Guijun Yan 2012

44

Applications of Genomic

tools in Super-Domestication

45

Genome Sequencing

Potential methods of sequencing

1 Clone by clone approach

2 Whole genome shotgun approach

3 Combination of the two methods

Till today no of cultivated plants completely sequenced -85

2016- Arachis duranensis

2015- Solanum cumersonii (Wild potato)

(Ref- NCBI)

46

GWAS

It is a study design in which many markers spread across a genome

are genotyped and test a statistical association with a phenotype are

performed locally along the genome

It is also an examination of many common genetic variants in different

individuals to see if any variant is associated with a trait

Used in successfully studying maize sorghum and barley

Method is efficient for large scale low cost genotyping (even with the

minimum number of SNPs)

Cannot be utilized generally because it needs large population size

GWAS identify rare alleles more precisely

If small population we can opt NAM

47

GWAS and whole genome prediction

Xuehui Huang and Bin Han 2014

48

Five high throuput genotyping methods

Xuehui Huang and Bin Han 2014

49

Role of NGS in domestication Capture of novel genes from wild species will be made easier by

understanding the molecular events associated with crop domestication

Re-sequencing of domesticated species can identify low diversity regions

resulting from selection during domestication

To identify gene-specific sequences to aid the cloning of homologues of key

domestication genes from wild relatives

Candidate genes from wild and domesticated plant populations can define

diversity of target genes in wild populations and lead to the discovery of key

genes for important traits by association analysis

NGS of amplicons of large numbers of candidate genes from wild and

domesticated plant populations can define diversity of target genes in

wild populations and lead to the discovery of key genes for important

traits by association analysis

50

NGS

supports the rapid domestication of new plant species and the efficient

identification and capture of novel genetic variation from related species

Allows whole-genome analysis to determine the genetic basis of

phenotypic differences

NGS allows rapid expansion of genomic analysis to investigation of non-

model species

Made rice study easy by related grass

cost-effective method for plant identification

useful strategy to analysis the chloroplast genome sequence from whole-

genome shot-gun sequencing

facilitates managing this diversity and any changes in crop performance

over time due to genetic drift

Patterns of gene expression have been evaluated in hybrids using NGS

51

Two Approaches to Finding Adaptive Genes

Ross-Ibarra et al2007

52

Techniques to re-wild the plants (transgene free)

1 Introgression

breeding

2 Specific

insertion of lost genes

3 Precision

mutagenesis

Palmgren et al2014

53

Process of rewilding

Palmgren et al2014

54

Synthetic biology projects(i) Modifying cereals including wheat to fix atmospheric nitrogen

(ii) Redesigning metabolic pathways to increase the yield of

secondary metabolites or to generate compounds with enhanced

properties

(iii) Transferring the C4 photosynthesis pathway to rice

(iv) Modifying the glycosylation pathway in plants to accommodate

production of therapeutic proteins

(v) Introducing synthetic signal transduction systems that respond to

external cues

55

Synthetic biology projects

Nicholas J Baltes et al 2015

56

Refactoring the N fixation gene cluster from Klebsiella

Karsten Temme et al 2012

Wild wheat

9

Domesticated Wheat

10

Maize

11

Domesticated maize

12

Barley Domestication

Prognt H spontanium

13

14

Domesticated Pearl MilletPennisetum glaucum

better seed recovery and yield but less able to survive in natural conditions compared to wild progenitor

bull more apical dominance (less

branching)

bull compact growth habit

bull flowering at same time (rather

than spread over long period)

bull larger spikes

bull non-shattering spikelets

bull loss of bristles amp glumes around

grains

bull larger seeds

bull non-dormant seeds

bull germinate at same time

15

Ppolystachian

Oats domestication

Wild- A sterilis Modern

sativa

16

Domestication of Sorghum

S helepense

S bicolor17

JR Harlan 1976 Sci American

Divergent

selection for

different

purposes

httpenwikipediaorgwikiImageBrassica_oleracea0jpg

httpwwwcehacukimagesclip_image002_001jpg

Brassica oleracea cabbage

broccoli cauliflower kale

romanesco collards kohrabi

brussels sprouts18

Solanum pimpinellifolium

Solanum lycopersicum19

Domestication of carrot

Queen Annes Lace

Daucus carota

20

Domestication of peanut

A villosulicarpa Hoehne andA Stenosperma (Brazil)

AABB

21

Domestication of Chilli

22

StrawberryBanana

Musa acuminata Musa balbisiana (2n=3x=33) AB genomeFRAGARIA X ANANASSA

Wood berries (F vesca) and Musky strawberries (F moschata)23

Wild SoybeanGlycin soja2n=40

Cultivated soybeanGlycin max 2n=40

24

Increased in domesticate

seed germination

determinate growth

longer pods

bigger (heavier) seeds

earliness

harvest index (seed yieldbiomass)

Decreased in domesticate

seed dispersal

seed dormancy

twining

number of nodes

length of internode

number of pods

photoperiod sensitivity

Common Bean Phaseolus vulgarishttpwwwplantsciencesucdavisedugeptspb143pb143htm

copy Paul Gepts

25

Wild pigeon peaCajanus cajanifolius

Cultivated pigeon pea

26

27

28

WHY OTHERS ARE NOT DOMESTICATED

bull 350000 plants

bull 4629 mammals

bull 9200 birds

bull 10000000 insects

bull 500000 fungi

bull But only 200 plants

bull 15 mammals 5 birds and

bull 2 insects are domesticated

bull Spread of these few species

bull Little change since early

agriculture

bull Repeated domestication of these

species (sometimes)

bull Lack of new species even with

attempts with species known to be

valuable Some groups are good

candidates with no domestication

eg ferns sub-Saharan mammals

29

WHY OTHERS HAVE TO BE DOMESTICATED

New uses and demands ndash biofuels animal feed

medicinalneutraceutical waterclimate food changes

Knowledge why species arenrsquot suitable for domestication or

were not useful

Better understanding of genetics and selection

Sustainability of production

Reliability of production

To meet the food demand in an alternative way

WHY OTHERS HAVE TO BE DOMESTICATED

30

Reallocate biomass for human use

More efficient metabolism and photosynthesis increase

leaf surface decrease root system increase leaf

longevity

Grains more fertile florets larger inflorescence OR

number of ears different ways to get more seed

Larger seeds (automatic vs deliberate selection)

Oil plants increased oil content or more seed

Fiber plants long strong fibers

Domestication syndrome

31

Centers of Domestication

Fuller 2011

32

Centers of Domestication in India

Fuller 2011

33

Indian centers of domestication South India (Deccan centre) Vigna radiate Vigna mungo

Macrotyloma uniflorum (Horse gram) Sataria verticillata S plumila

wheat (macaroni) and two rowed barleybrachiaria ramosa

Orissa (Mahanadi river) Pegion pea Horsegram mung small millets

like Echinichloa Paspalum and Sataria

The Middle Ganges (Harappan civilization) Oryza nivara O rufipogon

and wild sativa Sateria pumia Cannabis sativa even the diffusion of

japonica rice

Saurashtra (Harappan civilization) Eleucine coracana Sateria italica

Paicum spp Brachypodia pearl millet and sorghum Dollicos lablab

The Himalayan foothills of the Punjab region Was a centre of

diversity for Japonica type rice and many temperate fruits and

vegetables

34

DOMESTICATION RELATED TRAITS CONTROLLED BY ONLY FEW GENES

Trait Crops

Plant architecturegrowth habit Ricemaizemilletsbeantomato

Flowering timephotoperiod sensitivity Ricemaizesorghumbeantomato

Fruit size Tomato egg plant

Grain size Ricemaizesorghumbean

Seed dispersal Brassica rice

Inflorescence modification Brassica

Dormancy Bean

35

Genes Crop Moleular and phenotypic function Causative change

Genes identified as controlling domestication traits

tb1 Maize Transcriptional regulator (TCP) plant and

inflorescence structure

regulatory change

tga1 Maize Transcriptional regulator (SBP) seed casing amino acid change

qSH1 Rice Transcriptional regulator (homeodomain)

abscission layer formation shattering

regulatory change

Rc Rice Transcriptional regulator (bHLH) seed color disrupted coding

sequence

sh4 Rice Transcriptional regulator (Myb3) abscission

layer formation shattering

regulatoryamino

acid change

fw22 Tomato Cell signaling fruit weight regulatory change

Q Wheat Transcriptional regulator (AP2) inflorescence

structure

regulatoryamino

acid change

Vrs1 Barley Inflorescence structure Premature stop Amino acid change

Genes of interest in crop domestication and improvement

36

Genes Crop Moleular and phenotypic function Causative change

c1

r1

Maize Transcriptional regulator (MYB) kernel color and

Transcriptional regulator (bHLH) kernel color

regulatory change

sh2 Maize pyrophosphorylase supersweet sweet corn transposon

insertion

su1 Maize isoamylase sweet corn gene amino acid change

brix9-2-5 Tomato Invertase fruit soluble solid content amino acid change

ovate Tomato Unknown fruit shap early stop codon

R Pea Starch branching enzyme seed sugar content transposon

insertion

ehd1 Rice B-type response regulator flowering time amino acid change

hd1 Rice Transcriptional regulator (zinc finger) flowering

time

disrupted coding

sequence

waxy Rice Starch synthase sticky grains intron splicing

defect

rht Wheat Transcriptional regulator (SH2) plant height early stop codon

vrn1 Wheat Transcriptional regulator (MADS) vernalization regulatory change

vrn2 Wheat Transcriptional regulator (ZCCT) vernalization amino acid change

Genes Identified as Controlling Varietal Differences

37

Process of domestication over the yearshellip

Rachel S Meyer 2012

38

Genetic bottleneck

Cultivated crops undergone with narrowing of diversity problem

But this is not the case in weeds

Weeds are the major threats from the beginning of domestication till

today

Problem arose due to

1 Crop mimicry

2 Genetic assimilation

3 Genetic evolution

39

Super- Domestication Vaughn et al (2007) first used the term super-domestication

The processes that lead to a domesticate with dramatically

increased yield that could not be selected in natural environments

from naturally occurring variation without recourse to new

technologies

Super-domesticates can be constructed with knowledge led

approaches based on current needs using the range of new

technologies now available

Plants exploited for continuous selection introduction hybridization

etc which boosted the process of domestication but now the plant

genetic engineering approach is exploiting plants towards synthetic

biology

40

How to use diversitybull Cross two varieties

bull Genome manipulations

Cell fusion hybrids

bull Chromosome manipulation Backcross a new species

bull Generate recombinants Chromosome recombinations

bull Use a new species wild germplasm

Transgenic approach Modern mutagenesis synthetic gene

construction by utilizing green florescent protein genome editing

NGS GWAS sequencing etchelliphelliphelliphelliphellip

41

Reduce genetic bottlenecks through polyplodization

More vigour

SC

Buffering capacity

Heterotic advantage

Enhaced vegetative

charachers

Enhanced oil

Meiotic stability

42

Approach 1 Use one tetraploid and one diploid as parents (4X ndash 2X) followed by the

chromosome doubling of triploid hybrids (Chrom doubling)

a) Cross between B juncea (AjAjBjBj ) and B oleracea (CoCo) to produce hexaploids

(AjAjBjBjCoCo)

(b) Cross between B napus (AnAnCnCn) and B nigra (BniBni) to produce hexaploids

(AnAnBniBniCnCn)

(c) Cross between B carinata (BcaBcaCcaCca) and B rapa (ArAr) to produce hexaploids

(ArArBcaBcaCcaCca)

Approach 2 Use three tetraploids as parents

(a) Cross between B napus (AnAnCnCn) and B carinata (BcaBcaCcaCca) to produce unbalanced

allotetraploids (AnBcaCnCca ndash unreduced gametes gametes with the somatic chromosome

number and cross with B juncea (AjAjBjBj) to obtain allohexaploids (AnAjBcaBjCnCca

(b) Cross between B napus (AnAnCnCn) and B juncea (AjAjBjBj) to produce unbalanced

allotetraploids (AnAjBjCn ndash unreduced gametes) and cross with B carinata (BcaBcaCcaCca) to

obtain allohexaploids (AnAjBcaBjCnCca)

(c) Cross between B carinata (BcaBcaCcaCca) and B juncea (AjAjBjBj) to produce unbalanced

allotetraploids (AjBcaBjCca - ndash unreduced gametes) and cross with B napus (AnAnCnCn) to obtain

allohexaploids (AnAjBcaBjCnCca)

Approach 3 Use three diploids as parents (2X ndash 2X ndash 2X) Cross between B rapa (ArAr) B

nigra (BniBni) and B oleracea (CoCo) sequentially to obtain hexaploid hybrids (ArArBniBniCoCo)

43

Continuehellip

Guijun Yan 2012

44

Applications of Genomic

tools in Super-Domestication

45

Genome Sequencing

Potential methods of sequencing

1 Clone by clone approach

2 Whole genome shotgun approach

3 Combination of the two methods

Till today no of cultivated plants completely sequenced -85

2016- Arachis duranensis

2015- Solanum cumersonii (Wild potato)

(Ref- NCBI)

46

GWAS

It is a study design in which many markers spread across a genome

are genotyped and test a statistical association with a phenotype are

performed locally along the genome

It is also an examination of many common genetic variants in different

individuals to see if any variant is associated with a trait

Used in successfully studying maize sorghum and barley

Method is efficient for large scale low cost genotyping (even with the

minimum number of SNPs)

Cannot be utilized generally because it needs large population size

GWAS identify rare alleles more precisely

If small population we can opt NAM

47

GWAS and whole genome prediction

Xuehui Huang and Bin Han 2014

48

Five high throuput genotyping methods

Xuehui Huang and Bin Han 2014

49

Role of NGS in domestication Capture of novel genes from wild species will be made easier by

understanding the molecular events associated with crop domestication

Re-sequencing of domesticated species can identify low diversity regions

resulting from selection during domestication

To identify gene-specific sequences to aid the cloning of homologues of key

domestication genes from wild relatives

Candidate genes from wild and domesticated plant populations can define

diversity of target genes in wild populations and lead to the discovery of key

genes for important traits by association analysis

NGS of amplicons of large numbers of candidate genes from wild and

domesticated plant populations can define diversity of target genes in

wild populations and lead to the discovery of key genes for important

traits by association analysis

50

NGS

supports the rapid domestication of new plant species and the efficient

identification and capture of novel genetic variation from related species

Allows whole-genome analysis to determine the genetic basis of

phenotypic differences

NGS allows rapid expansion of genomic analysis to investigation of non-

model species

Made rice study easy by related grass

cost-effective method for plant identification

useful strategy to analysis the chloroplast genome sequence from whole-

genome shot-gun sequencing

facilitates managing this diversity and any changes in crop performance

over time due to genetic drift

Patterns of gene expression have been evaluated in hybrids using NGS

51

Two Approaches to Finding Adaptive Genes

Ross-Ibarra et al2007

52

Techniques to re-wild the plants (transgene free)

1 Introgression

breeding

2 Specific

insertion of lost genes

3 Precision

mutagenesis

Palmgren et al2014

53

Process of rewilding

Palmgren et al2014

54

Synthetic biology projects(i) Modifying cereals including wheat to fix atmospheric nitrogen

(ii) Redesigning metabolic pathways to increase the yield of

secondary metabolites or to generate compounds with enhanced

properties

(iii) Transferring the C4 photosynthesis pathway to rice

(iv) Modifying the glycosylation pathway in plants to accommodate

production of therapeutic proteins

(v) Introducing synthetic signal transduction systems that respond to

external cues

55

Synthetic biology projects

Nicholas J Baltes et al 2015

56

Refactoring the N fixation gene cluster from Klebsiella

Karsten Temme et al 2012

Domesticated Wheat

10

Maize

11

Domesticated maize

12

Barley Domestication

Prognt H spontanium

13

14

Domesticated Pearl MilletPennisetum glaucum

better seed recovery and yield but less able to survive in natural conditions compared to wild progenitor

bull more apical dominance (less

branching)

bull compact growth habit

bull flowering at same time (rather

than spread over long period)

bull larger spikes

bull non-shattering spikelets

bull loss of bristles amp glumes around

grains

bull larger seeds

bull non-dormant seeds

bull germinate at same time

15

Ppolystachian

Oats domestication

Wild- A sterilis Modern

sativa

16

Domestication of Sorghum

S helepense

S bicolor17

JR Harlan 1976 Sci American

Divergent

selection for

different

purposes

httpenwikipediaorgwikiImageBrassica_oleracea0jpg

httpwwwcehacukimagesclip_image002_001jpg

Brassica oleracea cabbage

broccoli cauliflower kale

romanesco collards kohrabi

brussels sprouts18

Solanum pimpinellifolium

Solanum lycopersicum19

Domestication of carrot

Queen Annes Lace

Daucus carota

20

Domestication of peanut

A villosulicarpa Hoehne andA Stenosperma (Brazil)

AABB

21

Domestication of Chilli

22

StrawberryBanana

Musa acuminata Musa balbisiana (2n=3x=33) AB genomeFRAGARIA X ANANASSA

Wood berries (F vesca) and Musky strawberries (F moschata)23

Wild SoybeanGlycin soja2n=40

Cultivated soybeanGlycin max 2n=40

24

Increased in domesticate

seed germination

determinate growth

longer pods

bigger (heavier) seeds

earliness

harvest index (seed yieldbiomass)

Decreased in domesticate

seed dispersal

seed dormancy

twining

number of nodes

length of internode

number of pods

photoperiod sensitivity

Common Bean Phaseolus vulgarishttpwwwplantsciencesucdavisedugeptspb143pb143htm

copy Paul Gepts

25

Wild pigeon peaCajanus cajanifolius

Cultivated pigeon pea

26

27

28

WHY OTHERS ARE NOT DOMESTICATED

bull 350000 plants

bull 4629 mammals

bull 9200 birds

bull 10000000 insects

bull 500000 fungi

bull But only 200 plants

bull 15 mammals 5 birds and

bull 2 insects are domesticated

bull Spread of these few species

bull Little change since early

agriculture

bull Repeated domestication of these

species (sometimes)

bull Lack of new species even with

attempts with species known to be

valuable Some groups are good

candidates with no domestication

eg ferns sub-Saharan mammals

29

WHY OTHERS HAVE TO BE DOMESTICATED

New uses and demands ndash biofuels animal feed

medicinalneutraceutical waterclimate food changes

Knowledge why species arenrsquot suitable for domestication or

were not useful

Better understanding of genetics and selection

Sustainability of production

Reliability of production

To meet the food demand in an alternative way

WHY OTHERS HAVE TO BE DOMESTICATED

30

Reallocate biomass for human use

More efficient metabolism and photosynthesis increase

leaf surface decrease root system increase leaf

longevity

Grains more fertile florets larger inflorescence OR

number of ears different ways to get more seed

Larger seeds (automatic vs deliberate selection)

Oil plants increased oil content or more seed

Fiber plants long strong fibers

Domestication syndrome

31

Centers of Domestication

Fuller 2011

32

Centers of Domestication in India

Fuller 2011

33

Indian centers of domestication South India (Deccan centre) Vigna radiate Vigna mungo

Macrotyloma uniflorum (Horse gram) Sataria verticillata S plumila

wheat (macaroni) and two rowed barleybrachiaria ramosa

Orissa (Mahanadi river) Pegion pea Horsegram mung small millets

like Echinichloa Paspalum and Sataria

The Middle Ganges (Harappan civilization) Oryza nivara O rufipogon

and wild sativa Sateria pumia Cannabis sativa even the diffusion of

japonica rice

Saurashtra (Harappan civilization) Eleucine coracana Sateria italica

Paicum spp Brachypodia pearl millet and sorghum Dollicos lablab

The Himalayan foothills of the Punjab region Was a centre of

diversity for Japonica type rice and many temperate fruits and

vegetables

34

DOMESTICATION RELATED TRAITS CONTROLLED BY ONLY FEW GENES

Trait Crops

Plant architecturegrowth habit Ricemaizemilletsbeantomato

Flowering timephotoperiod sensitivity Ricemaizesorghumbeantomato

Fruit size Tomato egg plant

Grain size Ricemaizesorghumbean

Seed dispersal Brassica rice

Inflorescence modification Brassica

Dormancy Bean

35

Genes Crop Moleular and phenotypic function Causative change

Genes identified as controlling domestication traits

tb1 Maize Transcriptional regulator (TCP) plant and

inflorescence structure

regulatory change

tga1 Maize Transcriptional regulator (SBP) seed casing amino acid change

qSH1 Rice Transcriptional regulator (homeodomain)

abscission layer formation shattering

regulatory change

Rc Rice Transcriptional regulator (bHLH) seed color disrupted coding

sequence

sh4 Rice Transcriptional regulator (Myb3) abscission

layer formation shattering

regulatoryamino

acid change

fw22 Tomato Cell signaling fruit weight regulatory change

Q Wheat Transcriptional regulator (AP2) inflorescence

structure

regulatoryamino

acid change

Vrs1 Barley Inflorescence structure Premature stop Amino acid change

Genes of interest in crop domestication and improvement

36

Genes Crop Moleular and phenotypic function Causative change

c1

r1

Maize Transcriptional regulator (MYB) kernel color and

Transcriptional regulator (bHLH) kernel color

regulatory change

sh2 Maize pyrophosphorylase supersweet sweet corn transposon

insertion

su1 Maize isoamylase sweet corn gene amino acid change

brix9-2-5 Tomato Invertase fruit soluble solid content amino acid change

ovate Tomato Unknown fruit shap early stop codon

R Pea Starch branching enzyme seed sugar content transposon

insertion

ehd1 Rice B-type response regulator flowering time amino acid change

hd1 Rice Transcriptional regulator (zinc finger) flowering

time

disrupted coding

sequence

waxy Rice Starch synthase sticky grains intron splicing

defect

rht Wheat Transcriptional regulator (SH2) plant height early stop codon

vrn1 Wheat Transcriptional regulator (MADS) vernalization regulatory change

vrn2 Wheat Transcriptional regulator (ZCCT) vernalization amino acid change

Genes Identified as Controlling Varietal Differences

37

Process of domestication over the yearshellip

Rachel S Meyer 2012

38

Genetic bottleneck

Cultivated crops undergone with narrowing of diversity problem

But this is not the case in weeds

Weeds are the major threats from the beginning of domestication till

today

Problem arose due to

1 Crop mimicry

2 Genetic assimilation

3 Genetic evolution

39

Super- Domestication Vaughn et al (2007) first used the term super-domestication

The processes that lead to a domesticate with dramatically

increased yield that could not be selected in natural environments

from naturally occurring variation without recourse to new

technologies

Super-domesticates can be constructed with knowledge led

approaches based on current needs using the range of new

technologies now available

Plants exploited for continuous selection introduction hybridization

etc which boosted the process of domestication but now the plant

genetic engineering approach is exploiting plants towards synthetic

biology

40

How to use diversitybull Cross two varieties

bull Genome manipulations

Cell fusion hybrids

bull Chromosome manipulation Backcross a new species

bull Generate recombinants Chromosome recombinations

bull Use a new species wild germplasm

Transgenic approach Modern mutagenesis synthetic gene

construction by utilizing green florescent protein genome editing

NGS GWAS sequencing etchelliphelliphelliphelliphellip

41

Reduce genetic bottlenecks through polyplodization

More vigour

SC

Buffering capacity

Heterotic advantage

Enhaced vegetative

charachers

Enhanced oil

Meiotic stability

42

Approach 1 Use one tetraploid and one diploid as parents (4X ndash 2X) followed by the

chromosome doubling of triploid hybrids (Chrom doubling)

a) Cross between B juncea (AjAjBjBj ) and B oleracea (CoCo) to produce hexaploids

(AjAjBjBjCoCo)

(b) Cross between B napus (AnAnCnCn) and B nigra (BniBni) to produce hexaploids

(AnAnBniBniCnCn)

(c) Cross between B carinata (BcaBcaCcaCca) and B rapa (ArAr) to produce hexaploids

(ArArBcaBcaCcaCca)

Approach 2 Use three tetraploids as parents

(a) Cross between B napus (AnAnCnCn) and B carinata (BcaBcaCcaCca) to produce unbalanced

allotetraploids (AnBcaCnCca ndash unreduced gametes gametes with the somatic chromosome

number and cross with B juncea (AjAjBjBj) to obtain allohexaploids (AnAjBcaBjCnCca

(b) Cross between B napus (AnAnCnCn) and B juncea (AjAjBjBj) to produce unbalanced

allotetraploids (AnAjBjCn ndash unreduced gametes) and cross with B carinata (BcaBcaCcaCca) to

obtain allohexaploids (AnAjBcaBjCnCca)

(c) Cross between B carinata (BcaBcaCcaCca) and B juncea (AjAjBjBj) to produce unbalanced

allotetraploids (AjBcaBjCca - ndash unreduced gametes) and cross with B napus (AnAnCnCn) to obtain

allohexaploids (AnAjBcaBjCnCca)

Approach 3 Use three diploids as parents (2X ndash 2X ndash 2X) Cross between B rapa (ArAr) B

nigra (BniBni) and B oleracea (CoCo) sequentially to obtain hexaploid hybrids (ArArBniBniCoCo)

43

Continuehellip

Guijun Yan 2012

44

Applications of Genomic

tools in Super-Domestication

45

Genome Sequencing

Potential methods of sequencing

1 Clone by clone approach

2 Whole genome shotgun approach

3 Combination of the two methods

Till today no of cultivated plants completely sequenced -85

2016- Arachis duranensis

2015- Solanum cumersonii (Wild potato)

(Ref- NCBI)

46

GWAS

It is a study design in which many markers spread across a genome

are genotyped and test a statistical association with a phenotype are

performed locally along the genome

It is also an examination of many common genetic variants in different

individuals to see if any variant is associated with a trait

Used in successfully studying maize sorghum and barley

Method is efficient for large scale low cost genotyping (even with the

minimum number of SNPs)

Cannot be utilized generally because it needs large population size

GWAS identify rare alleles more precisely

If small population we can opt NAM

47

GWAS and whole genome prediction

Xuehui Huang and Bin Han 2014

48

Five high throuput genotyping methods

Xuehui Huang and Bin Han 2014

49

Role of NGS in domestication Capture of novel genes from wild species will be made easier by

understanding the molecular events associated with crop domestication

Re-sequencing of domesticated species can identify low diversity regions

resulting from selection during domestication

To identify gene-specific sequences to aid the cloning of homologues of key

domestication genes from wild relatives

Candidate genes from wild and domesticated plant populations can define

diversity of target genes in wild populations and lead to the discovery of key

genes for important traits by association analysis

NGS of amplicons of large numbers of candidate genes from wild and

domesticated plant populations can define diversity of target genes in

wild populations and lead to the discovery of key genes for important

traits by association analysis

50

NGS

supports the rapid domestication of new plant species and the efficient

identification and capture of novel genetic variation from related species

Allows whole-genome analysis to determine the genetic basis of

phenotypic differences

NGS allows rapid expansion of genomic analysis to investigation of non-

model species

Made rice study easy by related grass

cost-effective method for plant identification

useful strategy to analysis the chloroplast genome sequence from whole-

genome shot-gun sequencing

facilitates managing this diversity and any changes in crop performance

over time due to genetic drift

Patterns of gene expression have been evaluated in hybrids using NGS

51

Two Approaches to Finding Adaptive Genes

Ross-Ibarra et al2007

52

Techniques to re-wild the plants (transgene free)

1 Introgression

breeding

2 Specific

insertion of lost genes

3 Precision

mutagenesis

Palmgren et al2014

53

Process of rewilding

Palmgren et al2014

54

Synthetic biology projects(i) Modifying cereals including wheat to fix atmospheric nitrogen

(ii) Redesigning metabolic pathways to increase the yield of

secondary metabolites or to generate compounds with enhanced

properties

(iii) Transferring the C4 photosynthesis pathway to rice

(iv) Modifying the glycosylation pathway in plants to accommodate

production of therapeutic proteins

(v) Introducing synthetic signal transduction systems that respond to

external cues

55

Synthetic biology projects

Nicholas J Baltes et al 2015

56

Refactoring the N fixation gene cluster from Klebsiella

Karsten Temme et al 2012

Maize

11

Domesticated maize

12

Barley Domestication

Prognt H spontanium

13

14

Domesticated Pearl MilletPennisetum glaucum

better seed recovery and yield but less able to survive in natural conditions compared to wild progenitor

bull more apical dominance (less

branching)

bull compact growth habit

bull flowering at same time (rather

than spread over long period)

bull larger spikes

bull non-shattering spikelets

bull loss of bristles amp glumes around

grains

bull larger seeds

bull non-dormant seeds

bull germinate at same time

15

Ppolystachian

Oats domestication

Wild- A sterilis Modern

sativa

16

Domestication of Sorghum

S helepense

S bicolor17

JR Harlan 1976 Sci American

Divergent

selection for

different

purposes

httpenwikipediaorgwikiImageBrassica_oleracea0jpg

httpwwwcehacukimagesclip_image002_001jpg

Brassica oleracea cabbage

broccoli cauliflower kale

romanesco collards kohrabi

brussels sprouts18

Solanum pimpinellifolium

Solanum lycopersicum19

Domestication of carrot

Queen Annes Lace

Daucus carota

20

Domestication of peanut

A villosulicarpa Hoehne andA Stenosperma (Brazil)

AABB

21

Domestication of Chilli

22

StrawberryBanana

Musa acuminata Musa balbisiana (2n=3x=33) AB genomeFRAGARIA X ANANASSA

Wood berries (F vesca) and Musky strawberries (F moschata)23

Wild SoybeanGlycin soja2n=40

Cultivated soybeanGlycin max 2n=40

24

Increased in domesticate

seed germination

determinate growth

longer pods

bigger (heavier) seeds

earliness

harvest index (seed yieldbiomass)

Decreased in domesticate

seed dispersal

seed dormancy

twining

number of nodes

length of internode

number of pods

photoperiod sensitivity

Common Bean Phaseolus vulgarishttpwwwplantsciencesucdavisedugeptspb143pb143htm

copy Paul Gepts

25

Wild pigeon peaCajanus cajanifolius

Cultivated pigeon pea

26

27

28

WHY OTHERS ARE NOT DOMESTICATED

bull 350000 plants

bull 4629 mammals

bull 9200 birds

bull 10000000 insects

bull 500000 fungi

bull But only 200 plants

bull 15 mammals 5 birds and

bull 2 insects are domesticated

bull Spread of these few species

bull Little change since early

agriculture

bull Repeated domestication of these

species (sometimes)

bull Lack of new species even with

attempts with species known to be

valuable Some groups are good

candidates with no domestication

eg ferns sub-Saharan mammals

29

WHY OTHERS HAVE TO BE DOMESTICATED

New uses and demands ndash biofuels animal feed

medicinalneutraceutical waterclimate food changes

Knowledge why species arenrsquot suitable for domestication or

were not useful

Better understanding of genetics and selection

Sustainability of production

Reliability of production

To meet the food demand in an alternative way

WHY OTHERS HAVE TO BE DOMESTICATED

30

Reallocate biomass for human use

More efficient metabolism and photosynthesis increase

leaf surface decrease root system increase leaf

longevity

Grains more fertile florets larger inflorescence OR

number of ears different ways to get more seed

Larger seeds (automatic vs deliberate selection)

Oil plants increased oil content or more seed

Fiber plants long strong fibers

Domestication syndrome

31

Centers of Domestication

Fuller 2011

32

Centers of Domestication in India

Fuller 2011

33

Indian centers of domestication South India (Deccan centre) Vigna radiate Vigna mungo

Macrotyloma uniflorum (Horse gram) Sataria verticillata S plumila

wheat (macaroni) and two rowed barleybrachiaria ramosa

Orissa (Mahanadi river) Pegion pea Horsegram mung small millets

like Echinichloa Paspalum and Sataria

The Middle Ganges (Harappan civilization) Oryza nivara O rufipogon

and wild sativa Sateria pumia Cannabis sativa even the diffusion of

japonica rice

Saurashtra (Harappan civilization) Eleucine coracana Sateria italica

Paicum spp Brachypodia pearl millet and sorghum Dollicos lablab

The Himalayan foothills of the Punjab region Was a centre of

diversity for Japonica type rice and many temperate fruits and

vegetables

34

DOMESTICATION RELATED TRAITS CONTROLLED BY ONLY FEW GENES

Trait Crops

Plant architecturegrowth habit Ricemaizemilletsbeantomato

Flowering timephotoperiod sensitivity Ricemaizesorghumbeantomato

Fruit size Tomato egg plant

Grain size Ricemaizesorghumbean

Seed dispersal Brassica rice

Inflorescence modification Brassica

Dormancy Bean

35

Genes Crop Moleular and phenotypic function Causative change

Genes identified as controlling domestication traits

tb1 Maize Transcriptional regulator (TCP) plant and

inflorescence structure

regulatory change

tga1 Maize Transcriptional regulator (SBP) seed casing amino acid change

qSH1 Rice Transcriptional regulator (homeodomain)

abscission layer formation shattering

regulatory change

Rc Rice Transcriptional regulator (bHLH) seed color disrupted coding

sequence

sh4 Rice Transcriptional regulator (Myb3) abscission

layer formation shattering

regulatoryamino

acid change

fw22 Tomato Cell signaling fruit weight regulatory change

Q Wheat Transcriptional regulator (AP2) inflorescence

structure

regulatoryamino

acid change

Vrs1 Barley Inflorescence structure Premature stop Amino acid change

Genes of interest in crop domestication and improvement

36

Genes Crop Moleular and phenotypic function Causative change

c1

r1

Maize Transcriptional regulator (MYB) kernel color and

Transcriptional regulator (bHLH) kernel color

regulatory change

sh2 Maize pyrophosphorylase supersweet sweet corn transposon

insertion

su1 Maize isoamylase sweet corn gene amino acid change

brix9-2-5 Tomato Invertase fruit soluble solid content amino acid change

ovate Tomato Unknown fruit shap early stop codon

R Pea Starch branching enzyme seed sugar content transposon

insertion

ehd1 Rice B-type response regulator flowering time amino acid change

hd1 Rice Transcriptional regulator (zinc finger) flowering

time

disrupted coding

sequence

waxy Rice Starch synthase sticky grains intron splicing

defect

rht Wheat Transcriptional regulator (SH2) plant height early stop codon

vrn1 Wheat Transcriptional regulator (MADS) vernalization regulatory change

vrn2 Wheat Transcriptional regulator (ZCCT) vernalization amino acid change

Genes Identified as Controlling Varietal Differences

37

Process of domestication over the yearshellip

Rachel S Meyer 2012

38

Genetic bottleneck

Cultivated crops undergone with narrowing of diversity problem

But this is not the case in weeds

Weeds are the major threats from the beginning of domestication till

today

Problem arose due to

1 Crop mimicry

2 Genetic assimilation

3 Genetic evolution

39

Super- Domestication Vaughn et al (2007) first used the term super-domestication

The processes that lead to a domesticate with dramatically

increased yield that could not be selected in natural environments

from naturally occurring variation without recourse to new

technologies

Super-domesticates can be constructed with knowledge led

approaches based on current needs using the range of new

technologies now available

Plants exploited for continuous selection introduction hybridization

etc which boosted the process of domestication but now the plant

genetic engineering approach is exploiting plants towards synthetic

biology

40

How to use diversitybull Cross two varieties

bull Genome manipulations

Cell fusion hybrids

bull Chromosome manipulation Backcross a new species

bull Generate recombinants Chromosome recombinations

bull Use a new species wild germplasm

Transgenic approach Modern mutagenesis synthetic gene

construction by utilizing green florescent protein genome editing

NGS GWAS sequencing etchelliphelliphelliphelliphellip

41

Reduce genetic bottlenecks through polyplodization

More vigour

SC

Buffering capacity

Heterotic advantage

Enhaced vegetative

charachers

Enhanced oil

Meiotic stability

42

Approach 1 Use one tetraploid and one diploid as parents (4X ndash 2X) followed by the

chromosome doubling of triploid hybrids (Chrom doubling)

a) Cross between B juncea (AjAjBjBj ) and B oleracea (CoCo) to produce hexaploids

(AjAjBjBjCoCo)

(b) Cross between B napus (AnAnCnCn) and B nigra (BniBni) to produce hexaploids

(AnAnBniBniCnCn)

(c) Cross between B carinata (BcaBcaCcaCca) and B rapa (ArAr) to produce hexaploids

(ArArBcaBcaCcaCca)

Approach 2 Use three tetraploids as parents

(a) Cross between B napus (AnAnCnCn) and B carinata (BcaBcaCcaCca) to produce unbalanced

allotetraploids (AnBcaCnCca ndash unreduced gametes gametes with the somatic chromosome

number and cross with B juncea (AjAjBjBj) to obtain allohexaploids (AnAjBcaBjCnCca

(b) Cross between B napus (AnAnCnCn) and B juncea (AjAjBjBj) to produce unbalanced

allotetraploids (AnAjBjCn ndash unreduced gametes) and cross with B carinata (BcaBcaCcaCca) to

obtain allohexaploids (AnAjBcaBjCnCca)

(c) Cross between B carinata (BcaBcaCcaCca) and B juncea (AjAjBjBj) to produce unbalanced

allotetraploids (AjBcaBjCca - ndash unreduced gametes) and cross with B napus (AnAnCnCn) to obtain

allohexaploids (AnAjBcaBjCnCca)

Approach 3 Use three diploids as parents (2X ndash 2X ndash 2X) Cross between B rapa (ArAr) B

nigra (BniBni) and B oleracea (CoCo) sequentially to obtain hexaploid hybrids (ArArBniBniCoCo)

43

Continuehellip

Guijun Yan 2012

44

Applications of Genomic

tools in Super-Domestication

45

Genome Sequencing

Potential methods of sequencing

1 Clone by clone approach

2 Whole genome shotgun approach

3 Combination of the two methods

Till today no of cultivated plants completely sequenced -85

2016- Arachis duranensis

2015- Solanum cumersonii (Wild potato)

(Ref- NCBI)

46

GWAS

It is a study design in which many markers spread across a genome

are genotyped and test a statistical association with a phenotype are

performed locally along the genome

It is also an examination of many common genetic variants in different

individuals to see if any variant is associated with a trait

Used in successfully studying maize sorghum and barley

Method is efficient for large scale low cost genotyping (even with the

minimum number of SNPs)

Cannot be utilized generally because it needs large population size

GWAS identify rare alleles more precisely

If small population we can opt NAM

47

GWAS and whole genome prediction

Xuehui Huang and Bin Han 2014

48

Five high throuput genotyping methods

Xuehui Huang and Bin Han 2014

49

Role of NGS in domestication Capture of novel genes from wild species will be made easier by

understanding the molecular events associated with crop domestication

Re-sequencing of domesticated species can identify low diversity regions

resulting from selection during domestication

To identify gene-specific sequences to aid the cloning of homologues of key

domestication genes from wild relatives

Candidate genes from wild and domesticated plant populations can define

diversity of target genes in wild populations and lead to the discovery of key

genes for important traits by association analysis

NGS of amplicons of large numbers of candidate genes from wild and

domesticated plant populations can define diversity of target genes in

wild populations and lead to the discovery of key genes for important

traits by association analysis

50

NGS

supports the rapid domestication of new plant species and the efficient

identification and capture of novel genetic variation from related species

Allows whole-genome analysis to determine the genetic basis of

phenotypic differences

NGS allows rapid expansion of genomic analysis to investigation of non-

model species

Made rice study easy by related grass

cost-effective method for plant identification

useful strategy to analysis the chloroplast genome sequence from whole-

genome shot-gun sequencing

facilitates managing this diversity and any changes in crop performance

over time due to genetic drift

Patterns of gene expression have been evaluated in hybrids using NGS

51

Two Approaches to Finding Adaptive Genes

Ross-Ibarra et al2007

52

Techniques to re-wild the plants (transgene free)

1 Introgression

breeding

2 Specific

insertion of lost genes

3 Precision

mutagenesis

Palmgren et al2014

53

Process of rewilding

Palmgren et al2014

54

Synthetic biology projects(i) Modifying cereals including wheat to fix atmospheric nitrogen

(ii) Redesigning metabolic pathways to increase the yield of

secondary metabolites or to generate compounds with enhanced

properties

(iii) Transferring the C4 photosynthesis pathway to rice

(iv) Modifying the glycosylation pathway in plants to accommodate

production of therapeutic proteins

(v) Introducing synthetic signal transduction systems that respond to

external cues

55

Synthetic biology projects

Nicholas J Baltes et al 2015

56

Refactoring the N fixation gene cluster from Klebsiella

Karsten Temme et al 2012

Domesticated maize

12

Barley Domestication

Prognt H spontanium

13

14

Domesticated Pearl MilletPennisetum glaucum

better seed recovery and yield but less able to survive in natural conditions compared to wild progenitor

bull more apical dominance (less

branching)

bull compact growth habit

bull flowering at same time (rather

than spread over long period)

bull larger spikes

bull non-shattering spikelets

bull loss of bristles amp glumes around

grains

bull larger seeds

bull non-dormant seeds

bull germinate at same time

15

Ppolystachian

Oats domestication

Wild- A sterilis Modern

sativa

16

Domestication of Sorghum

S helepense

S bicolor17

JR Harlan 1976 Sci American

Divergent

selection for

different

purposes

httpenwikipediaorgwikiImageBrassica_oleracea0jpg

httpwwwcehacukimagesclip_image002_001jpg

Brassica oleracea cabbage

broccoli cauliflower kale

romanesco collards kohrabi

brussels sprouts18

Solanum pimpinellifolium

Solanum lycopersicum19

Domestication of carrot

Queen Annes Lace

Daucus carota

20

Domestication of peanut

A villosulicarpa Hoehne andA Stenosperma (Brazil)

AABB

21

Domestication of Chilli

22

StrawberryBanana

Musa acuminata Musa balbisiana (2n=3x=33) AB genomeFRAGARIA X ANANASSA

Wood berries (F vesca) and Musky strawberries (F moschata)23

Wild SoybeanGlycin soja2n=40

Cultivated soybeanGlycin max 2n=40

24

Increased in domesticate

seed germination

determinate growth

longer pods

bigger (heavier) seeds

earliness

harvest index (seed yieldbiomass)

Decreased in domesticate

seed dispersal

seed dormancy

twining

number of nodes

length of internode

number of pods

photoperiod sensitivity

Common Bean Phaseolus vulgarishttpwwwplantsciencesucdavisedugeptspb143pb143htm

copy Paul Gepts

25

Wild pigeon peaCajanus cajanifolius

Cultivated pigeon pea

26

27

28

WHY OTHERS ARE NOT DOMESTICATED

bull 350000 plants

bull 4629 mammals

bull 9200 birds

bull 10000000 insects

bull 500000 fungi

bull But only 200 plants

bull 15 mammals 5 birds and

bull 2 insects are domesticated

bull Spread of these few species

bull Little change since early

agriculture

bull Repeated domestication of these

species (sometimes)

bull Lack of new species even with

attempts with species known to be

valuable Some groups are good

candidates with no domestication

eg ferns sub-Saharan mammals

29

WHY OTHERS HAVE TO BE DOMESTICATED

New uses and demands ndash biofuels animal feed

medicinalneutraceutical waterclimate food changes

Knowledge why species arenrsquot suitable for domestication or

were not useful

Better understanding of genetics and selection

Sustainability of production

Reliability of production

To meet the food demand in an alternative way

WHY OTHERS HAVE TO BE DOMESTICATED

30

Reallocate biomass for human use

More efficient metabolism and photosynthesis increase

leaf surface decrease root system increase leaf

longevity

Grains more fertile florets larger inflorescence OR

number of ears different ways to get more seed

Larger seeds (automatic vs deliberate selection)

Oil plants increased oil content or more seed

Fiber plants long strong fibers

Domestication syndrome

31

Centers of Domestication

Fuller 2011

32

Centers of Domestication in India

Fuller 2011

33

Indian centers of domestication South India (Deccan centre) Vigna radiate Vigna mungo

Macrotyloma uniflorum (Horse gram) Sataria verticillata S plumila

wheat (macaroni) and two rowed barleybrachiaria ramosa

Orissa (Mahanadi river) Pegion pea Horsegram mung small millets

like Echinichloa Paspalum and Sataria

The Middle Ganges (Harappan civilization) Oryza nivara O rufipogon

and wild sativa Sateria pumia Cannabis sativa even the diffusion of

japonica rice

Saurashtra (Harappan civilization) Eleucine coracana Sateria italica

Paicum spp Brachypodia pearl millet and sorghum Dollicos lablab

The Himalayan foothills of the Punjab region Was a centre of

diversity for Japonica type rice and many temperate fruits and

vegetables

34

DOMESTICATION RELATED TRAITS CONTROLLED BY ONLY FEW GENES

Trait Crops

Plant architecturegrowth habit Ricemaizemilletsbeantomato

Flowering timephotoperiod sensitivity Ricemaizesorghumbeantomato

Fruit size Tomato egg plant

Grain size Ricemaizesorghumbean

Seed dispersal Brassica rice

Inflorescence modification Brassica

Dormancy Bean

35

Genes Crop Moleular and phenotypic function Causative change

Genes identified as controlling domestication traits

tb1 Maize Transcriptional regulator (TCP) plant and

inflorescence structure

regulatory change

tga1 Maize Transcriptional regulator (SBP) seed casing amino acid change

qSH1 Rice Transcriptional regulator (homeodomain)

abscission layer formation shattering

regulatory change

Rc Rice Transcriptional regulator (bHLH) seed color disrupted coding

sequence

sh4 Rice Transcriptional regulator (Myb3) abscission

layer formation shattering

regulatoryamino

acid change

fw22 Tomato Cell signaling fruit weight regulatory change

Q Wheat Transcriptional regulator (AP2) inflorescence

structure

regulatoryamino

acid change

Vrs1 Barley Inflorescence structure Premature stop Amino acid change

Genes of interest in crop domestication and improvement

36

Genes Crop Moleular and phenotypic function Causative change

c1

r1

Maize Transcriptional regulator (MYB) kernel color and

Transcriptional regulator (bHLH) kernel color

regulatory change

sh2 Maize pyrophosphorylase supersweet sweet corn transposon

insertion

su1 Maize isoamylase sweet corn gene amino acid change

brix9-2-5 Tomato Invertase fruit soluble solid content amino acid change

ovate Tomato Unknown fruit shap early stop codon

R Pea Starch branching enzyme seed sugar content transposon

insertion

ehd1 Rice B-type response regulator flowering time amino acid change

hd1 Rice Transcriptional regulator (zinc finger) flowering

time

disrupted coding

sequence

waxy Rice Starch synthase sticky grains intron splicing

defect

rht Wheat Transcriptional regulator (SH2) plant height early stop codon

vrn1 Wheat Transcriptional regulator (MADS) vernalization regulatory change

vrn2 Wheat Transcriptional regulator (ZCCT) vernalization amino acid change

Genes Identified as Controlling Varietal Differences

37

Process of domestication over the yearshellip

Rachel S Meyer 2012

38

Genetic bottleneck

Cultivated crops undergone with narrowing of diversity problem

But this is not the case in weeds

Weeds are the major threats from the beginning of domestication till

today

Problem arose due to

1 Crop mimicry

2 Genetic assimilation

3 Genetic evolution

39

Super- Domestication Vaughn et al (2007) first used the term super-domestication

The processes that lead to a domesticate with dramatically

increased yield that could not be selected in natural environments

from naturally occurring variation without recourse to new

technologies

Super-domesticates can be constructed with knowledge led

approaches based on current needs using the range of new

technologies now available

Plants exploited for continuous selection introduction hybridization

etc which boosted the process of domestication but now the plant

genetic engineering approach is exploiting plants towards synthetic

biology

40

How to use diversitybull Cross two varieties

bull Genome manipulations

Cell fusion hybrids

bull Chromosome manipulation Backcross a new species

bull Generate recombinants Chromosome recombinations

bull Use a new species wild germplasm

Transgenic approach Modern mutagenesis synthetic gene

construction by utilizing green florescent protein genome editing

NGS GWAS sequencing etchelliphelliphelliphelliphellip

41

Reduce genetic bottlenecks through polyplodization

More vigour

SC

Buffering capacity

Heterotic advantage

Enhaced vegetative

charachers

Enhanced oil

Meiotic stability

42

Approach 1 Use one tetraploid and one diploid as parents (4X ndash 2X) followed by the

chromosome doubling of triploid hybrids (Chrom doubling)

a) Cross between B juncea (AjAjBjBj ) and B oleracea (CoCo) to produce hexaploids

(AjAjBjBjCoCo)

(b) Cross between B napus (AnAnCnCn) and B nigra (BniBni) to produce hexaploids

(AnAnBniBniCnCn)

(c) Cross between B carinata (BcaBcaCcaCca) and B rapa (ArAr) to produce hexaploids

(ArArBcaBcaCcaCca)

Approach 2 Use three tetraploids as parents

(a) Cross between B napus (AnAnCnCn) and B carinata (BcaBcaCcaCca) to produce unbalanced

allotetraploids (AnBcaCnCca ndash unreduced gametes gametes with the somatic chromosome

number and cross with B juncea (AjAjBjBj) to obtain allohexaploids (AnAjBcaBjCnCca

(b) Cross between B napus (AnAnCnCn) and B juncea (AjAjBjBj) to produce unbalanced

allotetraploids (AnAjBjCn ndash unreduced gametes) and cross with B carinata (BcaBcaCcaCca) to

obtain allohexaploids (AnAjBcaBjCnCca)

(c) Cross between B carinata (BcaBcaCcaCca) and B juncea (AjAjBjBj) to produce unbalanced

allotetraploids (AjBcaBjCca - ndash unreduced gametes) and cross with B napus (AnAnCnCn) to obtain

allohexaploids (AnAjBcaBjCnCca)

Approach 3 Use three diploids as parents (2X ndash 2X ndash 2X) Cross between B rapa (ArAr) B

nigra (BniBni) and B oleracea (CoCo) sequentially to obtain hexaploid hybrids (ArArBniBniCoCo)

43

Continuehellip

Guijun Yan 2012

44

Applications of Genomic

tools in Super-Domestication

45

Genome Sequencing

Potential methods of sequencing

1 Clone by clone approach

2 Whole genome shotgun approach

3 Combination of the two methods

Till today no of cultivated plants completely sequenced -85

2016- Arachis duranensis

2015- Solanum cumersonii (Wild potato)

(Ref- NCBI)

46

GWAS

It is a study design in which many markers spread across a genome

are genotyped and test a statistical association with a phenotype are

performed locally along the genome

It is also an examination of many common genetic variants in different

individuals to see if any variant is associated with a trait

Used in successfully studying maize sorghum and barley

Method is efficient for large scale low cost genotyping (even with the

minimum number of SNPs)

Cannot be utilized generally because it needs large population size

GWAS identify rare alleles more precisely

If small population we can opt NAM

47

GWAS and whole genome prediction

Xuehui Huang and Bin Han 2014

48

Five high throuput genotyping methods

Xuehui Huang and Bin Han 2014

49

Role of NGS in domestication Capture of novel genes from wild species will be made easier by

understanding the molecular events associated with crop domestication

Re-sequencing of domesticated species can identify low diversity regions

resulting from selection during domestication

To identify gene-specific sequences to aid the cloning of homologues of key

domestication genes from wild relatives

Candidate genes from wild and domesticated plant populations can define

diversity of target genes in wild populations and lead to the discovery of key

genes for important traits by association analysis

NGS of amplicons of large numbers of candidate genes from wild and

domesticated plant populations can define diversity of target genes in

wild populations and lead to the discovery of key genes for important

traits by association analysis

50

NGS

supports the rapid domestication of new plant species and the efficient

identification and capture of novel genetic variation from related species

Allows whole-genome analysis to determine the genetic basis of

phenotypic differences

NGS allows rapid expansion of genomic analysis to investigation of non-

model species

Made rice study easy by related grass

cost-effective method for plant identification

useful strategy to analysis the chloroplast genome sequence from whole-

genome shot-gun sequencing

facilitates managing this diversity and any changes in crop performance

over time due to genetic drift

Patterns of gene expression have been evaluated in hybrids using NGS

51

Two Approaches to Finding Adaptive Genes

Ross-Ibarra et al2007

52

Techniques to re-wild the plants (transgene free)

1 Introgression

breeding

2 Specific

insertion of lost genes

3 Precision

mutagenesis

Palmgren et al2014

53

Process of rewilding

Palmgren et al2014

54

Synthetic biology projects(i) Modifying cereals including wheat to fix atmospheric nitrogen

(ii) Redesigning metabolic pathways to increase the yield of

secondary metabolites or to generate compounds with enhanced

properties

(iii) Transferring the C4 photosynthesis pathway to rice

(iv) Modifying the glycosylation pathway in plants to accommodate

production of therapeutic proteins

(v) Introducing synthetic signal transduction systems that respond to

external cues

55

Synthetic biology projects

Nicholas J Baltes et al 2015

56

Refactoring the N fixation gene cluster from Klebsiella

Karsten Temme et al 2012

Barley Domestication

Prognt H spontanium

13

14

Domesticated Pearl MilletPennisetum glaucum

better seed recovery and yield but less able to survive in natural conditions compared to wild progenitor

bull more apical dominance (less

branching)

bull compact growth habit

bull flowering at same time (rather

than spread over long period)

bull larger spikes

bull non-shattering spikelets

bull loss of bristles amp glumes around

grains

bull larger seeds

bull non-dormant seeds

bull germinate at same time

15

Ppolystachian

Oats domestication

Wild- A sterilis Modern

sativa

16

Domestication of Sorghum

S helepense

S bicolor17

JR Harlan 1976 Sci American

Divergent

selection for

different

purposes

httpenwikipediaorgwikiImageBrassica_oleracea0jpg

httpwwwcehacukimagesclip_image002_001jpg

Brassica oleracea cabbage

broccoli cauliflower kale

romanesco collards kohrabi

brussels sprouts18

Solanum pimpinellifolium

Solanum lycopersicum19

Domestication of carrot

Queen Annes Lace

Daucus carota

20

Domestication of peanut

A villosulicarpa Hoehne andA Stenosperma (Brazil)

AABB

21

Domestication of Chilli

22

StrawberryBanana

Musa acuminata Musa balbisiana (2n=3x=33) AB genomeFRAGARIA X ANANASSA

Wood berries (F vesca) and Musky strawberries (F moschata)23

Wild SoybeanGlycin soja2n=40

Cultivated soybeanGlycin max 2n=40

24

Increased in domesticate

seed germination

determinate growth

longer pods

bigger (heavier) seeds

earliness

harvest index (seed yieldbiomass)

Decreased in domesticate

seed dispersal

seed dormancy

twining

number of nodes

length of internode

number of pods

photoperiod sensitivity

Common Bean Phaseolus vulgarishttpwwwplantsciencesucdavisedugeptspb143pb143htm

copy Paul Gepts

25

Wild pigeon peaCajanus cajanifolius

Cultivated pigeon pea

26

27

28

WHY OTHERS ARE NOT DOMESTICATED

bull 350000 plants

bull 4629 mammals

bull 9200 birds

bull 10000000 insects

bull 500000 fungi

bull But only 200 plants

bull 15 mammals 5 birds and

bull 2 insects are domesticated

bull Spread of these few species

bull Little change since early

agriculture

bull Repeated domestication of these

species (sometimes)

bull Lack of new species even with

attempts with species known to be

valuable Some groups are good

candidates with no domestication

eg ferns sub-Saharan mammals

29

WHY OTHERS HAVE TO BE DOMESTICATED

New uses and demands ndash biofuels animal feed

medicinalneutraceutical waterclimate food changes

Knowledge why species arenrsquot suitable for domestication or

were not useful

Better understanding of genetics and selection

Sustainability of production

Reliability of production

To meet the food demand in an alternative way

WHY OTHERS HAVE TO BE DOMESTICATED

30

Reallocate biomass for human use

More efficient metabolism and photosynthesis increase

leaf surface decrease root system increase leaf

longevity

Grains more fertile florets larger inflorescence OR

number of ears different ways to get more seed

Larger seeds (automatic vs deliberate selection)

Oil plants increased oil content or more seed

Fiber plants long strong fibers

Domestication syndrome

31

Centers of Domestication

Fuller 2011

32

Centers of Domestication in India

Fuller 2011

33

Indian centers of domestication South India (Deccan centre) Vigna radiate Vigna mungo

Macrotyloma uniflorum (Horse gram) Sataria verticillata S plumila

wheat (macaroni) and two rowed barleybrachiaria ramosa

Orissa (Mahanadi river) Pegion pea Horsegram mung small millets

like Echinichloa Paspalum and Sataria

The Middle Ganges (Harappan civilization) Oryza nivara O rufipogon

and wild sativa Sateria pumia Cannabis sativa even the diffusion of

japonica rice

Saurashtra (Harappan civilization) Eleucine coracana Sateria italica

Paicum spp Brachypodia pearl millet and sorghum Dollicos lablab

The Himalayan foothills of the Punjab region Was a centre of

diversity for Japonica type rice and many temperate fruits and

vegetables

34

DOMESTICATION RELATED TRAITS CONTROLLED BY ONLY FEW GENES

Trait Crops

Plant architecturegrowth habit Ricemaizemilletsbeantomato

Flowering timephotoperiod sensitivity Ricemaizesorghumbeantomato

Fruit size Tomato egg plant

Grain size Ricemaizesorghumbean

Seed dispersal Brassica rice

Inflorescence modification Brassica

Dormancy Bean

35

Genes Crop Moleular and phenotypic function Causative change

Genes identified as controlling domestication traits

tb1 Maize Transcriptional regulator (TCP) plant and

inflorescence structure

regulatory change

tga1 Maize Transcriptional regulator (SBP) seed casing amino acid change

qSH1 Rice Transcriptional regulator (homeodomain)

abscission layer formation shattering

regulatory change

Rc Rice Transcriptional regulator (bHLH) seed color disrupted coding

sequence

sh4 Rice Transcriptional regulator (Myb3) abscission

layer formation shattering

regulatoryamino

acid change

fw22 Tomato Cell signaling fruit weight regulatory change

Q Wheat Transcriptional regulator (AP2) inflorescence

structure

regulatoryamino

acid change

Vrs1 Barley Inflorescence structure Premature stop Amino acid change

Genes of interest in crop domestication and improvement

36

Genes Crop Moleular and phenotypic function Causative change

c1

r1

Maize Transcriptional regulator (MYB) kernel color and

Transcriptional regulator (bHLH) kernel color

regulatory change

sh2 Maize pyrophosphorylase supersweet sweet corn transposon

insertion

su1 Maize isoamylase sweet corn gene amino acid change

brix9-2-5 Tomato Invertase fruit soluble solid content amino acid change

ovate Tomato Unknown fruit shap early stop codon

R Pea Starch branching enzyme seed sugar content transposon

insertion

ehd1 Rice B-type response regulator flowering time amino acid change

hd1 Rice Transcriptional regulator (zinc finger) flowering

time

disrupted coding

sequence

waxy Rice Starch synthase sticky grains intron splicing

defect

rht Wheat Transcriptional regulator (SH2) plant height early stop codon

vrn1 Wheat Transcriptional regulator (MADS) vernalization regulatory change

vrn2 Wheat Transcriptional regulator (ZCCT) vernalization amino acid change

Genes Identified as Controlling Varietal Differences

37

Process of domestication over the yearshellip

Rachel S Meyer 2012

38

Genetic bottleneck

Cultivated crops undergone with narrowing of diversity problem

But this is not the case in weeds

Weeds are the major threats from the beginning of domestication till

today

Problem arose due to

1 Crop mimicry

2 Genetic assimilation

3 Genetic evolution

39

Super- Domestication Vaughn et al (2007) first used the term super-domestication

The processes that lead to a domesticate with dramatically

increased yield that could not be selected in natural environments

from naturally occurring variation without recourse to new

technologies

Super-domesticates can be constructed with knowledge led

approaches based on current needs using the range of new

technologies now available

Plants exploited for continuous selection introduction hybridization

etc which boosted the process of domestication but now the plant

genetic engineering approach is exploiting plants towards synthetic

biology

40

How to use diversitybull Cross two varieties

bull Genome manipulations

Cell fusion hybrids

bull Chromosome manipulation Backcross a new species

bull Generate recombinants Chromosome recombinations

bull Use a new species wild germplasm

Transgenic approach Modern mutagenesis synthetic gene

construction by utilizing green florescent protein genome editing

NGS GWAS sequencing etchelliphelliphelliphelliphellip

41

Reduce genetic bottlenecks through polyplodization

More vigour

SC

Buffering capacity

Heterotic advantage

Enhaced vegetative

charachers

Enhanced oil

Meiotic stability

42

Approach 1 Use one tetraploid and one diploid as parents (4X ndash 2X) followed by the

chromosome doubling of triploid hybrids (Chrom doubling)

a) Cross between B juncea (AjAjBjBj ) and B oleracea (CoCo) to produce hexaploids

(AjAjBjBjCoCo)

(b) Cross between B napus (AnAnCnCn) and B nigra (BniBni) to produce hexaploids

(AnAnBniBniCnCn)

(c) Cross between B carinata (BcaBcaCcaCca) and B rapa (ArAr) to produce hexaploids

(ArArBcaBcaCcaCca)

Approach 2 Use three tetraploids as parents

(a) Cross between B napus (AnAnCnCn) and B carinata (BcaBcaCcaCca) to produce unbalanced

allotetraploids (AnBcaCnCca ndash unreduced gametes gametes with the somatic chromosome

number and cross with B juncea (AjAjBjBj) to obtain allohexaploids (AnAjBcaBjCnCca

(b) Cross between B napus (AnAnCnCn) and B juncea (AjAjBjBj) to produce unbalanced

allotetraploids (AnAjBjCn ndash unreduced gametes) and cross with B carinata (BcaBcaCcaCca) to

obtain allohexaploids (AnAjBcaBjCnCca)

(c) Cross between B carinata (BcaBcaCcaCca) and B juncea (AjAjBjBj) to produce unbalanced

allotetraploids (AjBcaBjCca - ndash unreduced gametes) and cross with B napus (AnAnCnCn) to obtain

allohexaploids (AnAjBcaBjCnCca)

Approach 3 Use three diploids as parents (2X ndash 2X ndash 2X) Cross between B rapa (ArAr) B

nigra (BniBni) and B oleracea (CoCo) sequentially to obtain hexaploid hybrids (ArArBniBniCoCo)

43

Continuehellip

Guijun Yan 2012

44

Applications of Genomic

tools in Super-Domestication

45

Genome Sequencing

Potential methods of sequencing

1 Clone by clone approach

2 Whole genome shotgun approach

3 Combination of the two methods

Till today no of cultivated plants completely sequenced -85

2016- Arachis duranensis

2015- Solanum cumersonii (Wild potato)

(Ref- NCBI)

46

GWAS

It is a study design in which many markers spread across a genome

are genotyped and test a statistical association with a phenotype are

performed locally along the genome

It is also an examination of many common genetic variants in different

individuals to see if any variant is associated with a trait

Used in successfully studying maize sorghum and barley

Method is efficient for large scale low cost genotyping (even with the

minimum number of SNPs)

Cannot be utilized generally because it needs large population size

GWAS identify rare alleles more precisely

If small population we can opt NAM

47

GWAS and whole genome prediction

Xuehui Huang and Bin Han 2014

48

Five high throuput genotyping methods

Xuehui Huang and Bin Han 2014

49

Role of NGS in domestication Capture of novel genes from wild species will be made easier by

understanding the molecular events associated with crop domestication

Re-sequencing of domesticated species can identify low diversity regions

resulting from selection during domestication

To identify gene-specific sequences to aid the cloning of homologues of key

domestication genes from wild relatives

Candidate genes from wild and domesticated plant populations can define

diversity of target genes in wild populations and lead to the discovery of key

genes for important traits by association analysis

NGS of amplicons of large numbers of candidate genes from wild and

domesticated plant populations can define diversity of target genes in

wild populations and lead to the discovery of key genes for important

traits by association analysis

50

NGS

supports the rapid domestication of new plant species and the efficient

identification and capture of novel genetic variation from related species

Allows whole-genome analysis to determine the genetic basis of

phenotypic differences

NGS allows rapid expansion of genomic analysis to investigation of non-

model species

Made rice study easy by related grass

cost-effective method for plant identification

useful strategy to analysis the chloroplast genome sequence from whole-

genome shot-gun sequencing

facilitates managing this diversity and any changes in crop performance

over time due to genetic drift

Patterns of gene expression have been evaluated in hybrids using NGS

51

Two Approaches to Finding Adaptive Genes

Ross-Ibarra et al2007

52

Techniques to re-wild the plants (transgene free)

1 Introgression

breeding

2 Specific

insertion of lost genes

3 Precision

mutagenesis

Palmgren et al2014

53

Process of rewilding

Palmgren et al2014

54

Synthetic biology projects(i) Modifying cereals including wheat to fix atmospheric nitrogen

(ii) Redesigning metabolic pathways to increase the yield of

secondary metabolites or to generate compounds with enhanced

properties

(iii) Transferring the C4 photosynthesis pathway to rice

(iv) Modifying the glycosylation pathway in plants to accommodate

production of therapeutic proteins

(v) Introducing synthetic signal transduction systems that respond to

external cues

55

Synthetic biology projects

Nicholas J Baltes et al 2015

56

Refactoring the N fixation gene cluster from Klebsiella

Karsten Temme et al 2012

14

Domesticated Pearl MilletPennisetum glaucum

better seed recovery and yield but less able to survive in natural conditions compared to wild progenitor

bull more apical dominance (less

branching)

bull compact growth habit

bull flowering at same time (rather

than spread over long period)

bull larger spikes

bull non-shattering spikelets

bull loss of bristles amp glumes around

grains

bull larger seeds

bull non-dormant seeds

bull germinate at same time

15

Ppolystachian

Oats domestication

Wild- A sterilis Modern

sativa

16

Domestication of Sorghum

S helepense

S bicolor17

JR Harlan 1976 Sci American

Divergent

selection for

different

purposes

httpenwikipediaorgwikiImageBrassica_oleracea0jpg

httpwwwcehacukimagesclip_image002_001jpg

Brassica oleracea cabbage

broccoli cauliflower kale

romanesco collards kohrabi

brussels sprouts18

Solanum pimpinellifolium

Solanum lycopersicum19

Domestication of carrot

Queen Annes Lace

Daucus carota

20

Domestication of peanut

A villosulicarpa Hoehne andA Stenosperma (Brazil)

AABB

21

Domestication of Chilli

22

StrawberryBanana

Musa acuminata Musa balbisiana (2n=3x=33) AB genomeFRAGARIA X ANANASSA

Wood berries (F vesca) and Musky strawberries (F moschata)23

Wild SoybeanGlycin soja2n=40

Cultivated soybeanGlycin max 2n=40

24

Increased in domesticate

seed germination

determinate growth

longer pods

bigger (heavier) seeds

earliness

harvest index (seed yieldbiomass)

Decreased in domesticate

seed dispersal

seed dormancy

twining

number of nodes

length of internode

number of pods

photoperiod sensitivity

Common Bean Phaseolus vulgarishttpwwwplantsciencesucdavisedugeptspb143pb143htm

copy Paul Gepts

25

Wild pigeon peaCajanus cajanifolius

Cultivated pigeon pea

26

27

28

WHY OTHERS ARE NOT DOMESTICATED

bull 350000 plants

bull 4629 mammals

bull 9200 birds

bull 10000000 insects

bull 500000 fungi

bull But only 200 plants

bull 15 mammals 5 birds and

bull 2 insects are domesticated

bull Spread of these few species

bull Little change since early

agriculture

bull Repeated domestication of these

species (sometimes)

bull Lack of new species even with

attempts with species known to be

valuable Some groups are good

candidates with no domestication

eg ferns sub-Saharan mammals

29

WHY OTHERS HAVE TO BE DOMESTICATED

New uses and demands ndash biofuels animal feed

medicinalneutraceutical waterclimate food changes

Knowledge why species arenrsquot suitable for domestication or

were not useful

Better understanding of genetics and selection

Sustainability of production

Reliability of production

To meet the food demand in an alternative way

WHY OTHERS HAVE TO BE DOMESTICATED

30

Reallocate biomass for human use

More efficient metabolism and photosynthesis increase

leaf surface decrease root system increase leaf

longevity

Grains more fertile florets larger inflorescence OR

number of ears different ways to get more seed

Larger seeds (automatic vs deliberate selection)

Oil plants increased oil content or more seed

Fiber plants long strong fibers

Domestication syndrome

31

Centers of Domestication

Fuller 2011

32

Centers of Domestication in India

Fuller 2011

33

Indian centers of domestication South India (Deccan centre) Vigna radiate Vigna mungo

Macrotyloma uniflorum (Horse gram) Sataria verticillata S plumila

wheat (macaroni) and two rowed barleybrachiaria ramosa

Orissa (Mahanadi river) Pegion pea Horsegram mung small millets

like Echinichloa Paspalum and Sataria

The Middle Ganges (Harappan civilization) Oryza nivara O rufipogon

and wild sativa Sateria pumia Cannabis sativa even the diffusion of

japonica rice

Saurashtra (Harappan civilization) Eleucine coracana Sateria italica

Paicum spp Brachypodia pearl millet and sorghum Dollicos lablab

The Himalayan foothills of the Punjab region Was a centre of

diversity for Japonica type rice and many temperate fruits and

vegetables

34

DOMESTICATION RELATED TRAITS CONTROLLED BY ONLY FEW GENES

Trait Crops

Plant architecturegrowth habit Ricemaizemilletsbeantomato

Flowering timephotoperiod sensitivity Ricemaizesorghumbeantomato

Fruit size Tomato egg plant

Grain size Ricemaizesorghumbean

Seed dispersal Brassica rice

Inflorescence modification Brassica

Dormancy Bean

35

Genes Crop Moleular and phenotypic function Causative change

Genes identified as controlling domestication traits

tb1 Maize Transcriptional regulator (TCP) plant and

inflorescence structure

regulatory change

tga1 Maize Transcriptional regulator (SBP) seed casing amino acid change

qSH1 Rice Transcriptional regulator (homeodomain)

abscission layer formation shattering

regulatory change

Rc Rice Transcriptional regulator (bHLH) seed color disrupted coding

sequence

sh4 Rice Transcriptional regulator (Myb3) abscission

layer formation shattering

regulatoryamino

acid change

fw22 Tomato Cell signaling fruit weight regulatory change

Q Wheat Transcriptional regulator (AP2) inflorescence

structure

regulatoryamino

acid change

Vrs1 Barley Inflorescence structure Premature stop Amino acid change

Genes of interest in crop domestication and improvement

36

Genes Crop Moleular and phenotypic function Causative change

c1

r1

Maize Transcriptional regulator (MYB) kernel color and

Transcriptional regulator (bHLH) kernel color

regulatory change

sh2 Maize pyrophosphorylase supersweet sweet corn transposon

insertion

su1 Maize isoamylase sweet corn gene amino acid change

brix9-2-5 Tomato Invertase fruit soluble solid content amino acid change

ovate Tomato Unknown fruit shap early stop codon

R Pea Starch branching enzyme seed sugar content transposon

insertion

ehd1 Rice B-type response regulator flowering time amino acid change

hd1 Rice Transcriptional regulator (zinc finger) flowering

time

disrupted coding

sequence

waxy Rice Starch synthase sticky grains intron splicing

defect

rht Wheat Transcriptional regulator (SH2) plant height early stop codon

vrn1 Wheat Transcriptional regulator (MADS) vernalization regulatory change

vrn2 Wheat Transcriptional regulator (ZCCT) vernalization amino acid change

Genes Identified as Controlling Varietal Differences

37

Process of domestication over the yearshellip

Rachel S Meyer 2012

38

Genetic bottleneck

Cultivated crops undergone with narrowing of diversity problem

But this is not the case in weeds

Weeds are the major threats from the beginning of domestication till

today

Problem arose due to

1 Crop mimicry

2 Genetic assimilation

3 Genetic evolution

39

Super- Domestication Vaughn et al (2007) first used the term super-domestication

The processes that lead to a domesticate with dramatically

increased yield that could not be selected in natural environments

from naturally occurring variation without recourse to new

technologies

Super-domesticates can be constructed with knowledge led

approaches based on current needs using the range of new

technologies now available

Plants exploited for continuous selection introduction hybridization

etc which boosted the process of domestication but now the plant

genetic engineering approach is exploiting plants towards synthetic

biology

40

How to use diversitybull Cross two varieties

bull Genome manipulations

Cell fusion hybrids

bull Chromosome manipulation Backcross a new species

bull Generate recombinants Chromosome recombinations

bull Use a new species wild germplasm

Transgenic approach Modern mutagenesis synthetic gene

construction by utilizing green florescent protein genome editing

NGS GWAS sequencing etchelliphelliphelliphelliphellip

41

Reduce genetic bottlenecks through polyplodization

More vigour

SC

Buffering capacity

Heterotic advantage

Enhaced vegetative

charachers

Enhanced oil

Meiotic stability

42

Approach 1 Use one tetraploid and one diploid as parents (4X ndash 2X) followed by the

chromosome doubling of triploid hybrids (Chrom doubling)

a) Cross between B juncea (AjAjBjBj ) and B oleracea (CoCo) to produce hexaploids

(AjAjBjBjCoCo)

(b) Cross between B napus (AnAnCnCn) and B nigra (BniBni) to produce hexaploids

(AnAnBniBniCnCn)

(c) Cross between B carinata (BcaBcaCcaCca) and B rapa (ArAr) to produce hexaploids

(ArArBcaBcaCcaCca)

Approach 2 Use three tetraploids as parents

(a) Cross between B napus (AnAnCnCn) and B carinata (BcaBcaCcaCca) to produce unbalanced

allotetraploids (AnBcaCnCca ndash unreduced gametes gametes with the somatic chromosome

number and cross with B juncea (AjAjBjBj) to obtain allohexaploids (AnAjBcaBjCnCca

(b) Cross between B napus (AnAnCnCn) and B juncea (AjAjBjBj) to produce unbalanced

allotetraploids (AnAjBjCn ndash unreduced gametes) and cross with B carinata (BcaBcaCcaCca) to

obtain allohexaploids (AnAjBcaBjCnCca)

(c) Cross between B carinata (BcaBcaCcaCca) and B juncea (AjAjBjBj) to produce unbalanced

allotetraploids (AjBcaBjCca - ndash unreduced gametes) and cross with B napus (AnAnCnCn) to obtain

allohexaploids (AnAjBcaBjCnCca)

Approach 3 Use three diploids as parents (2X ndash 2X ndash 2X) Cross between B rapa (ArAr) B

nigra (BniBni) and B oleracea (CoCo) sequentially to obtain hexaploid hybrids (ArArBniBniCoCo)

43

Continuehellip

Guijun Yan 2012

44

Applications of Genomic

tools in Super-Domestication

45

Genome Sequencing

Potential methods of sequencing

1 Clone by clone approach

2 Whole genome shotgun approach

3 Combination of the two methods

Till today no of cultivated plants completely sequenced -85

2016- Arachis duranensis

2015- Solanum cumersonii (Wild potato)

(Ref- NCBI)

46

GWAS

It is a study design in which many markers spread across a genome

are genotyped and test a statistical association with a phenotype are

performed locally along the genome

It is also an examination of many common genetic variants in different

individuals to see if any variant is associated with a trait

Used in successfully studying maize sorghum and barley

Method is efficient for large scale low cost genotyping (even with the

minimum number of SNPs)

Cannot be utilized generally because it needs large population size

GWAS identify rare alleles more precisely

If small population we can opt NAM

47

GWAS and whole genome prediction

Xuehui Huang and Bin Han 2014

48

Five high throuput genotyping methods

Xuehui Huang and Bin Han 2014

49

Role of NGS in domestication Capture of novel genes from wild species will be made easier by

understanding the molecular events associated with crop domestication

Re-sequencing of domesticated species can identify low diversity regions

resulting from selection during domestication

To identify gene-specific sequences to aid the cloning of homologues of key

domestication genes from wild relatives

Candidate genes from wild and domesticated plant populations can define

diversity of target genes in wild populations and lead to the discovery of key

genes for important traits by association analysis

NGS of amplicons of large numbers of candidate genes from wild and

domesticated plant populations can define diversity of target genes in

wild populations and lead to the discovery of key genes for important

traits by association analysis

50

NGS

supports the rapid domestication of new plant species and the efficient

identification and capture of novel genetic variation from related species

Allows whole-genome analysis to determine the genetic basis of

phenotypic differences

NGS allows rapid expansion of genomic analysis to investigation of non-

model species

Made rice study easy by related grass

cost-effective method for plant identification

useful strategy to analysis the chloroplast genome sequence from whole-

genome shot-gun sequencing

facilitates managing this diversity and any changes in crop performance

over time due to genetic drift

Patterns of gene expression have been evaluated in hybrids using NGS

51

Two Approaches to Finding Adaptive Genes

Ross-Ibarra et al2007

52

Techniques to re-wild the plants (transgene free)

1 Introgression

breeding

2 Specific

insertion of lost genes

3 Precision

mutagenesis

Palmgren et al2014

53

Process of rewilding

Palmgren et al2014

54

Synthetic biology projects(i) Modifying cereals including wheat to fix atmospheric nitrogen

(ii) Redesigning metabolic pathways to increase the yield of

secondary metabolites or to generate compounds with enhanced

properties

(iii) Transferring the C4 photosynthesis pathway to rice

(iv) Modifying the glycosylation pathway in plants to accommodate

production of therapeutic proteins

(v) Introducing synthetic signal transduction systems that respond to

external cues

55

Synthetic biology projects

Nicholas J Baltes et al 2015

56

Refactoring the N fixation gene cluster from Klebsiella

Karsten Temme et al 2012

Domesticated Pearl MilletPennisetum glaucum

better seed recovery and yield but less able to survive in natural conditions compared to wild progenitor

bull more apical dominance (less

branching)

bull compact growth habit

bull flowering at same time (rather

than spread over long period)

bull larger spikes

bull non-shattering spikelets

bull loss of bristles amp glumes around

grains

bull larger seeds

bull non-dormant seeds

bull germinate at same time

15

Ppolystachian

Oats domestication

Wild- A sterilis Modern

sativa

16

Domestication of Sorghum

S helepense

S bicolor17

JR Harlan 1976 Sci American

Divergent

selection for

different

purposes

httpenwikipediaorgwikiImageBrassica_oleracea0jpg

httpwwwcehacukimagesclip_image002_001jpg

Brassica oleracea cabbage

broccoli cauliflower kale

romanesco collards kohrabi

brussels sprouts18

Solanum pimpinellifolium

Solanum lycopersicum19

Domestication of carrot

Queen Annes Lace

Daucus carota

20

Domestication of peanut

A villosulicarpa Hoehne andA Stenosperma (Brazil)

AABB

21

Domestication of Chilli

22

StrawberryBanana

Musa acuminata Musa balbisiana (2n=3x=33) AB genomeFRAGARIA X ANANASSA

Wood berries (F vesca) and Musky strawberries (F moschata)23

Wild SoybeanGlycin soja2n=40

Cultivated soybeanGlycin max 2n=40

24

Increased in domesticate

seed germination

determinate growth

longer pods

bigger (heavier) seeds

earliness

harvest index (seed yieldbiomass)

Decreased in domesticate

seed dispersal

seed dormancy

twining

number of nodes

length of internode

number of pods

photoperiod sensitivity

Common Bean Phaseolus vulgarishttpwwwplantsciencesucdavisedugeptspb143pb143htm

copy Paul Gepts

25

Wild pigeon peaCajanus cajanifolius

Cultivated pigeon pea

26

27

28

WHY OTHERS ARE NOT DOMESTICATED

bull 350000 plants

bull 4629 mammals

bull 9200 birds

bull 10000000 insects

bull 500000 fungi

bull But only 200 plants

bull 15 mammals 5 birds and

bull 2 insects are domesticated

bull Spread of these few species

bull Little change since early

agriculture

bull Repeated domestication of these

species (sometimes)

bull Lack of new species even with

attempts with species known to be

valuable Some groups are good

candidates with no domestication

eg ferns sub-Saharan mammals

29

WHY OTHERS HAVE TO BE DOMESTICATED

New uses and demands ndash biofuels animal feed

medicinalneutraceutical waterclimate food changes

Knowledge why species arenrsquot suitable for domestication or

were not useful

Better understanding of genetics and selection

Sustainability of production

Reliability of production

To meet the food demand in an alternative way

WHY OTHERS HAVE TO BE DOMESTICATED

30

Reallocate biomass for human use

More efficient metabolism and photosynthesis increase

leaf surface decrease root system increase leaf

longevity

Grains more fertile florets larger inflorescence OR

number of ears different ways to get more seed

Larger seeds (automatic vs deliberate selection)

Oil plants increased oil content or more seed

Fiber plants long strong fibers

Domestication syndrome

31

Centers of Domestication

Fuller 2011

32

Centers of Domestication in India

Fuller 2011

33

Indian centers of domestication South India (Deccan centre) Vigna radiate Vigna mungo

Macrotyloma uniflorum (Horse gram) Sataria verticillata S plumila

wheat (macaroni) and two rowed barleybrachiaria ramosa

Orissa (Mahanadi river) Pegion pea Horsegram mung small millets

like Echinichloa Paspalum and Sataria

The Middle Ganges (Harappan civilization) Oryza nivara O rufipogon

and wild sativa Sateria pumia Cannabis sativa even the diffusion of

japonica rice

Saurashtra (Harappan civilization) Eleucine coracana Sateria italica

Paicum spp Brachypodia pearl millet and sorghum Dollicos lablab

The Himalayan foothills of the Punjab region Was a centre of

diversity for Japonica type rice and many temperate fruits and

vegetables

34

DOMESTICATION RELATED TRAITS CONTROLLED BY ONLY FEW GENES

Trait Crops

Plant architecturegrowth habit Ricemaizemilletsbeantomato

Flowering timephotoperiod sensitivity Ricemaizesorghumbeantomato

Fruit size Tomato egg plant

Grain size Ricemaizesorghumbean

Seed dispersal Brassica rice

Inflorescence modification Brassica

Dormancy Bean

35

Genes Crop Moleular and phenotypic function Causative change

Genes identified as controlling domestication traits

tb1 Maize Transcriptional regulator (TCP) plant and

inflorescence structure

regulatory change

tga1 Maize Transcriptional regulator (SBP) seed casing amino acid change

qSH1 Rice Transcriptional regulator (homeodomain)

abscission layer formation shattering

regulatory change

Rc Rice Transcriptional regulator (bHLH) seed color disrupted coding

sequence

sh4 Rice Transcriptional regulator (Myb3) abscission

layer formation shattering

regulatoryamino

acid change

fw22 Tomato Cell signaling fruit weight regulatory change

Q Wheat Transcriptional regulator (AP2) inflorescence

structure

regulatoryamino

acid change

Vrs1 Barley Inflorescence structure Premature stop Amino acid change

Genes of interest in crop domestication and improvement

36

Genes Crop Moleular and phenotypic function Causative change

c1

r1

Maize Transcriptional regulator (MYB) kernel color and

Transcriptional regulator (bHLH) kernel color

regulatory change

sh2 Maize pyrophosphorylase supersweet sweet corn transposon

insertion

su1 Maize isoamylase sweet corn gene amino acid change

brix9-2-5 Tomato Invertase fruit soluble solid content amino acid change

ovate Tomato Unknown fruit shap early stop codon

R Pea Starch branching enzyme seed sugar content transposon

insertion

ehd1 Rice B-type response regulator flowering time amino acid change

hd1 Rice Transcriptional regulator (zinc finger) flowering

time

disrupted coding

sequence

waxy Rice Starch synthase sticky grains intron splicing

defect

rht Wheat Transcriptional regulator (SH2) plant height early stop codon

vrn1 Wheat Transcriptional regulator (MADS) vernalization regulatory change

vrn2 Wheat Transcriptional regulator (ZCCT) vernalization amino acid change

Genes Identified as Controlling Varietal Differences

37

Process of domestication over the yearshellip

Rachel S Meyer 2012

38

Genetic bottleneck

Cultivated crops undergone with narrowing of diversity problem

But this is not the case in weeds

Weeds are the major threats from the beginning of domestication till

today

Problem arose due to

1 Crop mimicry

2 Genetic assimilation

3 Genetic evolution

39

Super- Domestication Vaughn et al (2007) first used the term super-domestication

The processes that lead to a domesticate with dramatically

increased yield that could not be selected in natural environments

from naturally occurring variation without recourse to new

technologies

Super-domesticates can be constructed with knowledge led

approaches based on current needs using the range of new

technologies now available

Plants exploited for continuous selection introduction hybridization

etc which boosted the process of domestication but now the plant

genetic engineering approach is exploiting plants towards synthetic

biology

40

How to use diversitybull Cross two varieties

bull Genome manipulations

Cell fusion hybrids

bull Chromosome manipulation Backcross a new species

bull Generate recombinants Chromosome recombinations

bull Use a new species wild germplasm

Transgenic approach Modern mutagenesis synthetic gene

construction by utilizing green florescent protein genome editing

NGS GWAS sequencing etchelliphelliphelliphelliphellip

41

Reduce genetic bottlenecks through polyplodization

More vigour

SC

Buffering capacity

Heterotic advantage

Enhaced vegetative

charachers

Enhanced oil

Meiotic stability

42

Approach 1 Use one tetraploid and one diploid as parents (4X ndash 2X) followed by the

chromosome doubling of triploid hybrids (Chrom doubling)

a) Cross between B juncea (AjAjBjBj ) and B oleracea (CoCo) to produce hexaploids

(AjAjBjBjCoCo)

(b) Cross between B napus (AnAnCnCn) and B nigra (BniBni) to produce hexaploids

(AnAnBniBniCnCn)

(c) Cross between B carinata (BcaBcaCcaCca) and B rapa (ArAr) to produce hexaploids

(ArArBcaBcaCcaCca)

Approach 2 Use three tetraploids as parents

(a) Cross between B napus (AnAnCnCn) and B carinata (BcaBcaCcaCca) to produce unbalanced

allotetraploids (AnBcaCnCca ndash unreduced gametes gametes with the somatic chromosome

number and cross with B juncea (AjAjBjBj) to obtain allohexaploids (AnAjBcaBjCnCca

(b) Cross between B napus (AnAnCnCn) and B juncea (AjAjBjBj) to produce unbalanced

allotetraploids (AnAjBjCn ndash unreduced gametes) and cross with B carinata (BcaBcaCcaCca) to

obtain allohexaploids (AnAjBcaBjCnCca)

(c) Cross between B carinata (BcaBcaCcaCca) and B juncea (AjAjBjBj) to produce unbalanced

allotetraploids (AjBcaBjCca - ndash unreduced gametes) and cross with B napus (AnAnCnCn) to obtain

allohexaploids (AnAjBcaBjCnCca)

Approach 3 Use three diploids as parents (2X ndash 2X ndash 2X) Cross between B rapa (ArAr) B

nigra (BniBni) and B oleracea (CoCo) sequentially to obtain hexaploid hybrids (ArArBniBniCoCo)

43

Continuehellip

Guijun Yan 2012

44

Applications of Genomic

tools in Super-Domestication

45

Genome Sequencing

Potential methods of sequencing

1 Clone by clone approach

2 Whole genome shotgun approach

3 Combination of the two methods

Till today no of cultivated plants completely sequenced -85

2016- Arachis duranensis

2015- Solanum cumersonii (Wild potato)

(Ref- NCBI)

46

GWAS

It is a study design in which many markers spread across a genome

are genotyped and test a statistical association with a phenotype are

performed locally along the genome

It is also an examination of many common genetic variants in different

individuals to see if any variant is associated with a trait

Used in successfully studying maize sorghum and barley

Method is efficient for large scale low cost genotyping (even with the

minimum number of SNPs)

Cannot be utilized generally because it needs large population size

GWAS identify rare alleles more precisely

If small population we can opt NAM

47

GWAS and whole genome prediction

Xuehui Huang and Bin Han 2014

48

Five high throuput genotyping methods

Xuehui Huang and Bin Han 2014

49

Role of NGS in domestication Capture of novel genes from wild species will be made easier by

understanding the molecular events associated with crop domestication

Re-sequencing of domesticated species can identify low diversity regions

resulting from selection during domestication

To identify gene-specific sequences to aid the cloning of homologues of key

domestication genes from wild relatives

Candidate genes from wild and domesticated plant populations can define

diversity of target genes in wild populations and lead to the discovery of key

genes for important traits by association analysis

NGS of amplicons of large numbers of candidate genes from wild and

domesticated plant populations can define diversity of target genes in

wild populations and lead to the discovery of key genes for important

traits by association analysis

50

NGS

supports the rapid domestication of new plant species and the efficient

identification and capture of novel genetic variation from related species

Allows whole-genome analysis to determine the genetic basis of

phenotypic differences

NGS allows rapid expansion of genomic analysis to investigation of non-

model species

Made rice study easy by related grass

cost-effective method for plant identification

useful strategy to analysis the chloroplast genome sequence from whole-

genome shot-gun sequencing

facilitates managing this diversity and any changes in crop performance

over time due to genetic drift

Patterns of gene expression have been evaluated in hybrids using NGS

51

Two Approaches to Finding Adaptive Genes

Ross-Ibarra et al2007

52

Techniques to re-wild the plants (transgene free)

1 Introgression

breeding

2 Specific

insertion of lost genes

3 Precision

mutagenesis

Palmgren et al2014

53

Process of rewilding

Palmgren et al2014

54

Synthetic biology projects(i) Modifying cereals including wheat to fix atmospheric nitrogen

(ii) Redesigning metabolic pathways to increase the yield of

secondary metabolites or to generate compounds with enhanced

properties

(iii) Transferring the C4 photosynthesis pathway to rice

(iv) Modifying the glycosylation pathway in plants to accommodate

production of therapeutic proteins

(v) Introducing synthetic signal transduction systems that respond to

external cues

55

Synthetic biology projects

Nicholas J Baltes et al 2015

56

Refactoring the N fixation gene cluster from Klebsiella

Karsten Temme et al 2012

Oats domestication

Wild- A sterilis Modern

sativa

16

Domestication of Sorghum

S helepense

S bicolor17

JR Harlan 1976 Sci American

Divergent

selection for

different

purposes

httpenwikipediaorgwikiImageBrassica_oleracea0jpg

httpwwwcehacukimagesclip_image002_001jpg

Brassica oleracea cabbage

broccoli cauliflower kale

romanesco collards kohrabi

brussels sprouts18

Solanum pimpinellifolium

Solanum lycopersicum19

Domestication of carrot

Queen Annes Lace

Daucus carota

20

Domestication of peanut

A villosulicarpa Hoehne andA Stenosperma (Brazil)

AABB

21

Domestication of Chilli

22

StrawberryBanana

Musa acuminata Musa balbisiana (2n=3x=33) AB genomeFRAGARIA X ANANASSA

Wood berries (F vesca) and Musky strawberries (F moschata)23

Wild SoybeanGlycin soja2n=40

Cultivated soybeanGlycin max 2n=40

24

Increased in domesticate

seed germination

determinate growth

longer pods

bigger (heavier) seeds

earliness

harvest index (seed yieldbiomass)

Decreased in domesticate

seed dispersal

seed dormancy

twining

number of nodes

length of internode

number of pods

photoperiod sensitivity

Common Bean Phaseolus vulgarishttpwwwplantsciencesucdavisedugeptspb143pb143htm

copy Paul Gepts

25

Wild pigeon peaCajanus cajanifolius

Cultivated pigeon pea

26

27

28

WHY OTHERS ARE NOT DOMESTICATED

bull 350000 plants

bull 4629 mammals

bull 9200 birds

bull 10000000 insects

bull 500000 fungi

bull But only 200 plants

bull 15 mammals 5 birds and

bull 2 insects are domesticated

bull Spread of these few species

bull Little change since early

agriculture

bull Repeated domestication of these

species (sometimes)

bull Lack of new species even with

attempts with species known to be

valuable Some groups are good

candidates with no domestication

eg ferns sub-Saharan mammals

29

WHY OTHERS HAVE TO BE DOMESTICATED

New uses and demands ndash biofuels animal feed

medicinalneutraceutical waterclimate food changes

Knowledge why species arenrsquot suitable for domestication or

were not useful

Better understanding of genetics and selection

Sustainability of production

Reliability of production

To meet the food demand in an alternative way

WHY OTHERS HAVE TO BE DOMESTICATED

30

Reallocate biomass for human use

More efficient metabolism and photosynthesis increase

leaf surface decrease root system increase leaf

longevity

Grains more fertile florets larger inflorescence OR

number of ears different ways to get more seed

Larger seeds (automatic vs deliberate selection)

Oil plants increased oil content or more seed

Fiber plants long strong fibers

Domestication syndrome

31

Centers of Domestication

Fuller 2011

32

Centers of Domestication in India

Fuller 2011

33

Indian centers of domestication South India (Deccan centre) Vigna radiate Vigna mungo

Macrotyloma uniflorum (Horse gram) Sataria verticillata S plumila

wheat (macaroni) and two rowed barleybrachiaria ramosa

Orissa (Mahanadi river) Pegion pea Horsegram mung small millets

like Echinichloa Paspalum and Sataria

The Middle Ganges (Harappan civilization) Oryza nivara O rufipogon

and wild sativa Sateria pumia Cannabis sativa even the diffusion of

japonica rice

Saurashtra (Harappan civilization) Eleucine coracana Sateria italica

Paicum spp Brachypodia pearl millet and sorghum Dollicos lablab

The Himalayan foothills of the Punjab region Was a centre of

diversity for Japonica type rice and many temperate fruits and

vegetables

34

DOMESTICATION RELATED TRAITS CONTROLLED BY ONLY FEW GENES

Trait Crops

Plant architecturegrowth habit Ricemaizemilletsbeantomato

Flowering timephotoperiod sensitivity Ricemaizesorghumbeantomato

Fruit size Tomato egg plant

Grain size Ricemaizesorghumbean

Seed dispersal Brassica rice

Inflorescence modification Brassica

Dormancy Bean

35

Genes Crop Moleular and phenotypic function Causative change

Genes identified as controlling domestication traits

tb1 Maize Transcriptional regulator (TCP) plant and

inflorescence structure

regulatory change

tga1 Maize Transcriptional regulator (SBP) seed casing amino acid change

qSH1 Rice Transcriptional regulator (homeodomain)

abscission layer formation shattering

regulatory change

Rc Rice Transcriptional regulator (bHLH) seed color disrupted coding

sequence

sh4 Rice Transcriptional regulator (Myb3) abscission

layer formation shattering

regulatoryamino

acid change

fw22 Tomato Cell signaling fruit weight regulatory change

Q Wheat Transcriptional regulator (AP2) inflorescence

structure

regulatoryamino

acid change

Vrs1 Barley Inflorescence structure Premature stop Amino acid change

Genes of interest in crop domestication and improvement

36

Genes Crop Moleular and phenotypic function Causative change

c1

r1

Maize Transcriptional regulator (MYB) kernel color and

Transcriptional regulator (bHLH) kernel color

regulatory change

sh2 Maize pyrophosphorylase supersweet sweet corn transposon

insertion

su1 Maize isoamylase sweet corn gene amino acid change

brix9-2-5 Tomato Invertase fruit soluble solid content amino acid change

ovate Tomato Unknown fruit shap early stop codon

R Pea Starch branching enzyme seed sugar content transposon

insertion

ehd1 Rice B-type response regulator flowering time amino acid change

hd1 Rice Transcriptional regulator (zinc finger) flowering

time

disrupted coding

sequence

waxy Rice Starch synthase sticky grains intron splicing

defect

rht Wheat Transcriptional regulator (SH2) plant height early stop codon

vrn1 Wheat Transcriptional regulator (MADS) vernalization regulatory change

vrn2 Wheat Transcriptional regulator (ZCCT) vernalization amino acid change

Genes Identified as Controlling Varietal Differences

37

Process of domestication over the yearshellip

Rachel S Meyer 2012

38

Genetic bottleneck

Cultivated crops undergone with narrowing of diversity problem

But this is not the case in weeds

Weeds are the major threats from the beginning of domestication till

today

Problem arose due to

1 Crop mimicry

2 Genetic assimilation

3 Genetic evolution

39

Super- Domestication Vaughn et al (2007) first used the term super-domestication

The processes that lead to a domesticate with dramatically

increased yield that could not be selected in natural environments

from naturally occurring variation without recourse to new

technologies

Super-domesticates can be constructed with knowledge led

approaches based on current needs using the range of new

technologies now available

Plants exploited for continuous selection introduction hybridization

etc which boosted the process of domestication but now the plant

genetic engineering approach is exploiting plants towards synthetic

biology

40

How to use diversitybull Cross two varieties

bull Genome manipulations

Cell fusion hybrids

bull Chromosome manipulation Backcross a new species

bull Generate recombinants Chromosome recombinations

bull Use a new species wild germplasm

Transgenic approach Modern mutagenesis synthetic gene

construction by utilizing green florescent protein genome editing

NGS GWAS sequencing etchelliphelliphelliphelliphellip

41

Reduce genetic bottlenecks through polyplodization

More vigour

SC

Buffering capacity

Heterotic advantage

Enhaced vegetative

charachers

Enhanced oil

Meiotic stability

42

Approach 1 Use one tetraploid and one diploid as parents (4X ndash 2X) followed by the

chromosome doubling of triploid hybrids (Chrom doubling)

a) Cross between B juncea (AjAjBjBj ) and B oleracea (CoCo) to produce hexaploids

(AjAjBjBjCoCo)

(b) Cross between B napus (AnAnCnCn) and B nigra (BniBni) to produce hexaploids

(AnAnBniBniCnCn)

(c) Cross between B carinata (BcaBcaCcaCca) and B rapa (ArAr) to produce hexaploids

(ArArBcaBcaCcaCca)

Approach 2 Use three tetraploids as parents

(a) Cross between B napus (AnAnCnCn) and B carinata (BcaBcaCcaCca) to produce unbalanced

allotetraploids (AnBcaCnCca ndash unreduced gametes gametes with the somatic chromosome

number and cross with B juncea (AjAjBjBj) to obtain allohexaploids (AnAjBcaBjCnCca

(b) Cross between B napus (AnAnCnCn) and B juncea (AjAjBjBj) to produce unbalanced

allotetraploids (AnAjBjCn ndash unreduced gametes) and cross with B carinata (BcaBcaCcaCca) to

obtain allohexaploids (AnAjBcaBjCnCca)

(c) Cross between B carinata (BcaBcaCcaCca) and B juncea (AjAjBjBj) to produce unbalanced

allotetraploids (AjBcaBjCca - ndash unreduced gametes) and cross with B napus (AnAnCnCn) to obtain

allohexaploids (AnAjBcaBjCnCca)

Approach 3 Use three diploids as parents (2X ndash 2X ndash 2X) Cross between B rapa (ArAr) B

nigra (BniBni) and B oleracea (CoCo) sequentially to obtain hexaploid hybrids (ArArBniBniCoCo)

43

Continuehellip

Guijun Yan 2012

44

Applications of Genomic

tools in Super-Domestication

45

Genome Sequencing

Potential methods of sequencing

1 Clone by clone approach

2 Whole genome shotgun approach

3 Combination of the two methods

Till today no of cultivated plants completely sequenced -85

2016- Arachis duranensis

2015- Solanum cumersonii (Wild potato)

(Ref- NCBI)

46

GWAS

It is a study design in which many markers spread across a genome

are genotyped and test a statistical association with a phenotype are

performed locally along the genome

It is also an examination of many common genetic variants in different

individuals to see if any variant is associated with a trait

Used in successfully studying maize sorghum and barley

Method is efficient for large scale low cost genotyping (even with the

minimum number of SNPs)

Cannot be utilized generally because it needs large population size

GWAS identify rare alleles more precisely

If small population we can opt NAM

47

GWAS and whole genome prediction

Xuehui Huang and Bin Han 2014

48

Five high throuput genotyping methods

Xuehui Huang and Bin Han 2014

49

Role of NGS in domestication Capture of novel genes from wild species will be made easier by

understanding the molecular events associated with crop domestication

Re-sequencing of domesticated species can identify low diversity regions

resulting from selection during domestication

To identify gene-specific sequences to aid the cloning of homologues of key

domestication genes from wild relatives

Candidate genes from wild and domesticated plant populations can define

diversity of target genes in wild populations and lead to the discovery of key

genes for important traits by association analysis

NGS of amplicons of large numbers of candidate genes from wild and

domesticated plant populations can define diversity of target genes in

wild populations and lead to the discovery of key genes for important

traits by association analysis

50

NGS

supports the rapid domestication of new plant species and the efficient

identification and capture of novel genetic variation from related species

Allows whole-genome analysis to determine the genetic basis of

phenotypic differences

NGS allows rapid expansion of genomic analysis to investigation of non-

model species

Made rice study easy by related grass

cost-effective method for plant identification

useful strategy to analysis the chloroplast genome sequence from whole-

genome shot-gun sequencing

facilitates managing this diversity and any changes in crop performance

over time due to genetic drift

Patterns of gene expression have been evaluated in hybrids using NGS

51

Two Approaches to Finding Adaptive Genes

Ross-Ibarra et al2007

52

Techniques to re-wild the plants (transgene free)

1 Introgression

breeding

2 Specific

insertion of lost genes

3 Precision

mutagenesis

Palmgren et al2014

53

Process of rewilding

Palmgren et al2014

54

Synthetic biology projects(i) Modifying cereals including wheat to fix atmospheric nitrogen

(ii) Redesigning metabolic pathways to increase the yield of

secondary metabolites or to generate compounds with enhanced

properties

(iii) Transferring the C4 photosynthesis pathway to rice

(iv) Modifying the glycosylation pathway in plants to accommodate

production of therapeutic proteins

(v) Introducing synthetic signal transduction systems that respond to

external cues

55

Synthetic biology projects

Nicholas J Baltes et al 2015

56

Refactoring the N fixation gene cluster from Klebsiella

Karsten Temme et al 2012

Domestication of Sorghum

S helepense

S bicolor17

JR Harlan 1976 Sci American

Divergent

selection for

different

purposes

httpenwikipediaorgwikiImageBrassica_oleracea0jpg

httpwwwcehacukimagesclip_image002_001jpg

Brassica oleracea cabbage

broccoli cauliflower kale

romanesco collards kohrabi

brussels sprouts18

Solanum pimpinellifolium

Solanum lycopersicum19

Domestication of carrot

Queen Annes Lace

Daucus carota

20

Domestication of peanut

A villosulicarpa Hoehne andA Stenosperma (Brazil)

AABB

21

Domestication of Chilli

22

StrawberryBanana

Musa acuminata Musa balbisiana (2n=3x=33) AB genomeFRAGARIA X ANANASSA

Wood berries (F vesca) and Musky strawberries (F moschata)23

Wild SoybeanGlycin soja2n=40

Cultivated soybeanGlycin max 2n=40

24

Increased in domesticate

seed germination

determinate growth

longer pods

bigger (heavier) seeds

earliness

harvest index (seed yieldbiomass)

Decreased in domesticate

seed dispersal

seed dormancy

twining

number of nodes

length of internode

number of pods

photoperiod sensitivity

Common Bean Phaseolus vulgarishttpwwwplantsciencesucdavisedugeptspb143pb143htm

copy Paul Gepts

25

Wild pigeon peaCajanus cajanifolius

Cultivated pigeon pea

26

27

28

WHY OTHERS ARE NOT DOMESTICATED

bull 350000 plants

bull 4629 mammals

bull 9200 birds

bull 10000000 insects

bull 500000 fungi

bull But only 200 plants

bull 15 mammals 5 birds and

bull 2 insects are domesticated

bull Spread of these few species

bull Little change since early

agriculture

bull Repeated domestication of these

species (sometimes)

bull Lack of new species even with

attempts with species known to be

valuable Some groups are good

candidates with no domestication

eg ferns sub-Saharan mammals

29

WHY OTHERS HAVE TO BE DOMESTICATED

New uses and demands ndash biofuels animal feed

medicinalneutraceutical waterclimate food changes

Knowledge why species arenrsquot suitable for domestication or

were not useful

Better understanding of genetics and selection

Sustainability of production

Reliability of production

To meet the food demand in an alternative way

WHY OTHERS HAVE TO BE DOMESTICATED

30

Reallocate biomass for human use

More efficient metabolism and photosynthesis increase

leaf surface decrease root system increase leaf

longevity

Grains more fertile florets larger inflorescence OR

number of ears different ways to get more seed

Larger seeds (automatic vs deliberate selection)

Oil plants increased oil content or more seed

Fiber plants long strong fibers

Domestication syndrome

31

Centers of Domestication

Fuller 2011

32

Centers of Domestication in India

Fuller 2011

33

Indian centers of domestication South India (Deccan centre) Vigna radiate Vigna mungo

Macrotyloma uniflorum (Horse gram) Sataria verticillata S plumila

wheat (macaroni) and two rowed barleybrachiaria ramosa

Orissa (Mahanadi river) Pegion pea Horsegram mung small millets

like Echinichloa Paspalum and Sataria

The Middle Ganges (Harappan civilization) Oryza nivara O rufipogon

and wild sativa Sateria pumia Cannabis sativa even the diffusion of

japonica rice

Saurashtra (Harappan civilization) Eleucine coracana Sateria italica

Paicum spp Brachypodia pearl millet and sorghum Dollicos lablab

The Himalayan foothills of the Punjab region Was a centre of

diversity for Japonica type rice and many temperate fruits and

vegetables

34

DOMESTICATION RELATED TRAITS CONTROLLED BY ONLY FEW GENES

Trait Crops

Plant architecturegrowth habit Ricemaizemilletsbeantomato

Flowering timephotoperiod sensitivity Ricemaizesorghumbeantomato

Fruit size Tomato egg plant

Grain size Ricemaizesorghumbean

Seed dispersal Brassica rice

Inflorescence modification Brassica

Dormancy Bean

35

Genes Crop Moleular and phenotypic function Causative change

Genes identified as controlling domestication traits

tb1 Maize Transcriptional regulator (TCP) plant and

inflorescence structure

regulatory change

tga1 Maize Transcriptional regulator (SBP) seed casing amino acid change

qSH1 Rice Transcriptional regulator (homeodomain)

abscission layer formation shattering

regulatory change

Rc Rice Transcriptional regulator (bHLH) seed color disrupted coding

sequence

sh4 Rice Transcriptional regulator (Myb3) abscission

layer formation shattering

regulatoryamino

acid change

fw22 Tomato Cell signaling fruit weight regulatory change

Q Wheat Transcriptional regulator (AP2) inflorescence

structure

regulatoryamino

acid change

Vrs1 Barley Inflorescence structure Premature stop Amino acid change

Genes of interest in crop domestication and improvement

36

Genes Crop Moleular and phenotypic function Causative change

c1

r1

Maize Transcriptional regulator (MYB) kernel color and

Transcriptional regulator (bHLH) kernel color

regulatory change

sh2 Maize pyrophosphorylase supersweet sweet corn transposon

insertion

su1 Maize isoamylase sweet corn gene amino acid change

brix9-2-5 Tomato Invertase fruit soluble solid content amino acid change

ovate Tomato Unknown fruit shap early stop codon

R Pea Starch branching enzyme seed sugar content transposon

insertion

ehd1 Rice B-type response regulator flowering time amino acid change

hd1 Rice Transcriptional regulator (zinc finger) flowering

time

disrupted coding

sequence

waxy Rice Starch synthase sticky grains intron splicing

defect

rht Wheat Transcriptional regulator (SH2) plant height early stop codon

vrn1 Wheat Transcriptional regulator (MADS) vernalization regulatory change

vrn2 Wheat Transcriptional regulator (ZCCT) vernalization amino acid change

Genes Identified as Controlling Varietal Differences

37

Process of domestication over the yearshellip

Rachel S Meyer 2012

38

Genetic bottleneck

Cultivated crops undergone with narrowing of diversity problem

But this is not the case in weeds

Weeds are the major threats from the beginning of domestication till

today

Problem arose due to

1 Crop mimicry

2 Genetic assimilation

3 Genetic evolution

39

Super- Domestication Vaughn et al (2007) first used the term super-domestication

The processes that lead to a domesticate with dramatically

increased yield that could not be selected in natural environments

from naturally occurring variation without recourse to new

technologies

Super-domesticates can be constructed with knowledge led

approaches based on current needs using the range of new

technologies now available

Plants exploited for continuous selection introduction hybridization

etc which boosted the process of domestication but now the plant

genetic engineering approach is exploiting plants towards synthetic

biology

40

How to use diversitybull Cross two varieties

bull Genome manipulations

Cell fusion hybrids

bull Chromosome manipulation Backcross a new species

bull Generate recombinants Chromosome recombinations

bull Use a new species wild germplasm

Transgenic approach Modern mutagenesis synthetic gene

construction by utilizing green florescent protein genome editing

NGS GWAS sequencing etchelliphelliphelliphelliphellip

41

Reduce genetic bottlenecks through polyplodization

More vigour

SC

Buffering capacity

Heterotic advantage

Enhaced vegetative

charachers

Enhanced oil

Meiotic stability

42

Approach 1 Use one tetraploid and one diploid as parents (4X ndash 2X) followed by the

chromosome doubling of triploid hybrids (Chrom doubling)

a) Cross between B juncea (AjAjBjBj ) and B oleracea (CoCo) to produce hexaploids

(AjAjBjBjCoCo)

(b) Cross between B napus (AnAnCnCn) and B nigra (BniBni) to produce hexaploids

(AnAnBniBniCnCn)

(c) Cross between B carinata (BcaBcaCcaCca) and B rapa (ArAr) to produce hexaploids

(ArArBcaBcaCcaCca)

Approach 2 Use three tetraploids as parents

(a) Cross between B napus (AnAnCnCn) and B carinata (BcaBcaCcaCca) to produce unbalanced

allotetraploids (AnBcaCnCca ndash unreduced gametes gametes with the somatic chromosome

number and cross with B juncea (AjAjBjBj) to obtain allohexaploids (AnAjBcaBjCnCca

(b) Cross between B napus (AnAnCnCn) and B juncea (AjAjBjBj) to produce unbalanced

allotetraploids (AnAjBjCn ndash unreduced gametes) and cross with B carinata (BcaBcaCcaCca) to

obtain allohexaploids (AnAjBcaBjCnCca)

(c) Cross between B carinata (BcaBcaCcaCca) and B juncea (AjAjBjBj) to produce unbalanced

allotetraploids (AjBcaBjCca - ndash unreduced gametes) and cross with B napus (AnAnCnCn) to obtain

allohexaploids (AnAjBcaBjCnCca)

Approach 3 Use three diploids as parents (2X ndash 2X ndash 2X) Cross between B rapa (ArAr) B

nigra (BniBni) and B oleracea (CoCo) sequentially to obtain hexaploid hybrids (ArArBniBniCoCo)

43

Continuehellip

Guijun Yan 2012

44

Applications of Genomic

tools in Super-Domestication

45

Genome Sequencing

Potential methods of sequencing

1 Clone by clone approach

2 Whole genome shotgun approach

3 Combination of the two methods

Till today no of cultivated plants completely sequenced -85

2016- Arachis duranensis

2015- Solanum cumersonii (Wild potato)

(Ref- NCBI)

46

GWAS

It is a study design in which many markers spread across a genome

are genotyped and test a statistical association with a phenotype are

performed locally along the genome

It is also an examination of many common genetic variants in different

individuals to see if any variant is associated with a trait

Used in successfully studying maize sorghum and barley

Method is efficient for large scale low cost genotyping (even with the

minimum number of SNPs)

Cannot be utilized generally because it needs large population size

GWAS identify rare alleles more precisely

If small population we can opt NAM

47

GWAS and whole genome prediction

Xuehui Huang and Bin Han 2014

48

Five high throuput genotyping methods

Xuehui Huang and Bin Han 2014

49

Role of NGS in domestication Capture of novel genes from wild species will be made easier by

understanding the molecular events associated with crop domestication

Re-sequencing of domesticated species can identify low diversity regions

resulting from selection during domestication

To identify gene-specific sequences to aid the cloning of homologues of key

domestication genes from wild relatives

Candidate genes from wild and domesticated plant populations can define

diversity of target genes in wild populations and lead to the discovery of key

genes for important traits by association analysis

NGS of amplicons of large numbers of candidate genes from wild and

domesticated plant populations can define diversity of target genes in

wild populations and lead to the discovery of key genes for important

traits by association analysis

50

NGS

supports the rapid domestication of new plant species and the efficient

identification and capture of novel genetic variation from related species

Allows whole-genome analysis to determine the genetic basis of

phenotypic differences

NGS allows rapid expansion of genomic analysis to investigation of non-

model species

Made rice study easy by related grass

cost-effective method for plant identification

useful strategy to analysis the chloroplast genome sequence from whole-

genome shot-gun sequencing

facilitates managing this diversity and any changes in crop performance

over time due to genetic drift

Patterns of gene expression have been evaluated in hybrids using NGS

51

Two Approaches to Finding Adaptive Genes

Ross-Ibarra et al2007

52

Techniques to re-wild the plants (transgene free)

1 Introgression

breeding

2 Specific

insertion of lost genes

3 Precision

mutagenesis

Palmgren et al2014

53

Process of rewilding

Palmgren et al2014

54

Synthetic biology projects(i) Modifying cereals including wheat to fix atmospheric nitrogen

(ii) Redesigning metabolic pathways to increase the yield of

secondary metabolites or to generate compounds with enhanced

properties

(iii) Transferring the C4 photosynthesis pathway to rice

(iv) Modifying the glycosylation pathway in plants to accommodate

production of therapeutic proteins

(v) Introducing synthetic signal transduction systems that respond to

external cues

55

Synthetic biology projects

Nicholas J Baltes et al 2015

56

Refactoring the N fixation gene cluster from Klebsiella

Karsten Temme et al 2012

JR Harlan 1976 Sci American

Divergent

selection for

different

purposes

httpenwikipediaorgwikiImageBrassica_oleracea0jpg

httpwwwcehacukimagesclip_image002_001jpg

Brassica oleracea cabbage

broccoli cauliflower kale

romanesco collards kohrabi

brussels sprouts18

Solanum pimpinellifolium

Solanum lycopersicum19

Domestication of carrot

Queen Annes Lace

Daucus carota

20

Domestication of peanut

A villosulicarpa Hoehne andA Stenosperma (Brazil)

AABB

21

Domestication of Chilli

22

StrawberryBanana

Musa acuminata Musa balbisiana (2n=3x=33) AB genomeFRAGARIA X ANANASSA

Wood berries (F vesca) and Musky strawberries (F moschata)23

Wild SoybeanGlycin soja2n=40

Cultivated soybeanGlycin max 2n=40

24

Increased in domesticate

seed germination

determinate growth

longer pods

bigger (heavier) seeds

earliness

harvest index (seed yieldbiomass)

Decreased in domesticate

seed dispersal

seed dormancy

twining

number of nodes

length of internode

number of pods

photoperiod sensitivity

Common Bean Phaseolus vulgarishttpwwwplantsciencesucdavisedugeptspb143pb143htm

copy Paul Gepts

25

Wild pigeon peaCajanus cajanifolius

Cultivated pigeon pea

26

27

28

WHY OTHERS ARE NOT DOMESTICATED

bull 350000 plants

bull 4629 mammals

bull 9200 birds

bull 10000000 insects

bull 500000 fungi

bull But only 200 plants

bull 15 mammals 5 birds and

bull 2 insects are domesticated

bull Spread of these few species

bull Little change since early

agriculture

bull Repeated domestication of these

species (sometimes)

bull Lack of new species even with

attempts with species known to be

valuable Some groups are good

candidates with no domestication

eg ferns sub-Saharan mammals

29

WHY OTHERS HAVE TO BE DOMESTICATED

New uses and demands ndash biofuels animal feed

medicinalneutraceutical waterclimate food changes

Knowledge why species arenrsquot suitable for domestication or

were not useful

Better understanding of genetics and selection

Sustainability of production

Reliability of production

To meet the food demand in an alternative way

WHY OTHERS HAVE TO BE DOMESTICATED

30

Reallocate biomass for human use

More efficient metabolism and photosynthesis increase

leaf surface decrease root system increase leaf

longevity

Grains more fertile florets larger inflorescence OR

number of ears different ways to get more seed

Larger seeds (automatic vs deliberate selection)

Oil plants increased oil content or more seed

Fiber plants long strong fibers

Domestication syndrome

31

Centers of Domestication

Fuller 2011

32

Centers of Domestication in India

Fuller 2011

33

Indian centers of domestication South India (Deccan centre) Vigna radiate Vigna mungo

Macrotyloma uniflorum (Horse gram) Sataria verticillata S plumila

wheat (macaroni) and two rowed barleybrachiaria ramosa

Orissa (Mahanadi river) Pegion pea Horsegram mung small millets

like Echinichloa Paspalum and Sataria

The Middle Ganges (Harappan civilization) Oryza nivara O rufipogon

and wild sativa Sateria pumia Cannabis sativa even the diffusion of

japonica rice

Saurashtra (Harappan civilization) Eleucine coracana Sateria italica

Paicum spp Brachypodia pearl millet and sorghum Dollicos lablab

The Himalayan foothills of the Punjab region Was a centre of

diversity for Japonica type rice and many temperate fruits and

vegetables

34

DOMESTICATION RELATED TRAITS CONTROLLED BY ONLY FEW GENES

Trait Crops

Plant architecturegrowth habit Ricemaizemilletsbeantomato

Flowering timephotoperiod sensitivity Ricemaizesorghumbeantomato

Fruit size Tomato egg plant

Grain size Ricemaizesorghumbean

Seed dispersal Brassica rice

Inflorescence modification Brassica

Dormancy Bean

35

Genes Crop Moleular and phenotypic function Causative change

Genes identified as controlling domestication traits

tb1 Maize Transcriptional regulator (TCP) plant and

inflorescence structure

regulatory change

tga1 Maize Transcriptional regulator (SBP) seed casing amino acid change

qSH1 Rice Transcriptional regulator (homeodomain)

abscission layer formation shattering

regulatory change

Rc Rice Transcriptional regulator (bHLH) seed color disrupted coding

sequence

sh4 Rice Transcriptional regulator (Myb3) abscission

layer formation shattering

regulatoryamino

acid change

fw22 Tomato Cell signaling fruit weight regulatory change

Q Wheat Transcriptional regulator (AP2) inflorescence

structure

regulatoryamino

acid change

Vrs1 Barley Inflorescence structure Premature stop Amino acid change

Genes of interest in crop domestication and improvement

36

Genes Crop Moleular and phenotypic function Causative change

c1

r1

Maize Transcriptional regulator (MYB) kernel color and

Transcriptional regulator (bHLH) kernel color

regulatory change

sh2 Maize pyrophosphorylase supersweet sweet corn transposon

insertion

su1 Maize isoamylase sweet corn gene amino acid change

brix9-2-5 Tomato Invertase fruit soluble solid content amino acid change

ovate Tomato Unknown fruit shap early stop codon

R Pea Starch branching enzyme seed sugar content transposon

insertion

ehd1 Rice B-type response regulator flowering time amino acid change

hd1 Rice Transcriptional regulator (zinc finger) flowering

time

disrupted coding

sequence

waxy Rice Starch synthase sticky grains intron splicing

defect

rht Wheat Transcriptional regulator (SH2) plant height early stop codon

vrn1 Wheat Transcriptional regulator (MADS) vernalization regulatory change

vrn2 Wheat Transcriptional regulator (ZCCT) vernalization amino acid change

Genes Identified as Controlling Varietal Differences

37

Process of domestication over the yearshellip

Rachel S Meyer 2012

38

Genetic bottleneck

Cultivated crops undergone with narrowing of diversity problem

But this is not the case in weeds

Weeds are the major threats from the beginning of domestication till

today

Problem arose due to

1 Crop mimicry

2 Genetic assimilation

3 Genetic evolution

39

Super- Domestication Vaughn et al (2007) first used the term super-domestication

The processes that lead to a domesticate with dramatically

increased yield that could not be selected in natural environments

from naturally occurring variation without recourse to new

technologies

Super-domesticates can be constructed with knowledge led

approaches based on current needs using the range of new

technologies now available

Plants exploited for continuous selection introduction hybridization

etc which boosted the process of domestication but now the plant

genetic engineering approach is exploiting plants towards synthetic

biology

40

How to use diversitybull Cross two varieties

bull Genome manipulations

Cell fusion hybrids

bull Chromosome manipulation Backcross a new species

bull Generate recombinants Chromosome recombinations

bull Use a new species wild germplasm

Transgenic approach Modern mutagenesis synthetic gene

construction by utilizing green florescent protein genome editing

NGS GWAS sequencing etchelliphelliphelliphelliphellip

41

Reduce genetic bottlenecks through polyplodization

More vigour

SC

Buffering capacity

Heterotic advantage

Enhaced vegetative

charachers

Enhanced oil

Meiotic stability

42

Approach 1 Use one tetraploid and one diploid as parents (4X ndash 2X) followed by the

chromosome doubling of triploid hybrids (Chrom doubling)

a) Cross between B juncea (AjAjBjBj ) and B oleracea (CoCo) to produce hexaploids

(AjAjBjBjCoCo)

(b) Cross between B napus (AnAnCnCn) and B nigra (BniBni) to produce hexaploids

(AnAnBniBniCnCn)

(c) Cross between B carinata (BcaBcaCcaCca) and B rapa (ArAr) to produce hexaploids

(ArArBcaBcaCcaCca)

Approach 2 Use three tetraploids as parents

(a) Cross between B napus (AnAnCnCn) and B carinata (BcaBcaCcaCca) to produce unbalanced

allotetraploids (AnBcaCnCca ndash unreduced gametes gametes with the somatic chromosome

number and cross with B juncea (AjAjBjBj) to obtain allohexaploids (AnAjBcaBjCnCca

(b) Cross between B napus (AnAnCnCn) and B juncea (AjAjBjBj) to produce unbalanced

allotetraploids (AnAjBjCn ndash unreduced gametes) and cross with B carinata (BcaBcaCcaCca) to

obtain allohexaploids (AnAjBcaBjCnCca)

(c) Cross between B carinata (BcaBcaCcaCca) and B juncea (AjAjBjBj) to produce unbalanced

allotetraploids (AjBcaBjCca - ndash unreduced gametes) and cross with B napus (AnAnCnCn) to obtain

allohexaploids (AnAjBcaBjCnCca)

Approach 3 Use three diploids as parents (2X ndash 2X ndash 2X) Cross between B rapa (ArAr) B

nigra (BniBni) and B oleracea (CoCo) sequentially to obtain hexaploid hybrids (ArArBniBniCoCo)

43

Continuehellip

Guijun Yan 2012

44

Applications of Genomic

tools in Super-Domestication

45

Genome Sequencing

Potential methods of sequencing

1 Clone by clone approach

2 Whole genome shotgun approach

3 Combination of the two methods

Till today no of cultivated plants completely sequenced -85

2016- Arachis duranensis

2015- Solanum cumersonii (Wild potato)

(Ref- NCBI)

46

GWAS

It is a study design in which many markers spread across a genome

are genotyped and test a statistical association with a phenotype are

performed locally along the genome

It is also an examination of many common genetic variants in different

individuals to see if any variant is associated with a trait

Used in successfully studying maize sorghum and barley

Method is efficient for large scale low cost genotyping (even with the

minimum number of SNPs)

Cannot be utilized generally because it needs large population size

GWAS identify rare alleles more precisely

If small population we can opt NAM

47

GWAS and whole genome prediction

Xuehui Huang and Bin Han 2014

48

Five high throuput genotyping methods

Xuehui Huang and Bin Han 2014

49

Role of NGS in domestication Capture of novel genes from wild species will be made easier by

understanding the molecular events associated with crop domestication

Re-sequencing of domesticated species can identify low diversity regions

resulting from selection during domestication

To identify gene-specific sequences to aid the cloning of homologues of key

domestication genes from wild relatives

Candidate genes from wild and domesticated plant populations can define

diversity of target genes in wild populations and lead to the discovery of key

genes for important traits by association analysis

NGS of amplicons of large numbers of candidate genes from wild and

domesticated plant populations can define diversity of target genes in

wild populations and lead to the discovery of key genes for important

traits by association analysis

50

NGS

supports the rapid domestication of new plant species and the efficient

identification and capture of novel genetic variation from related species

Allows whole-genome analysis to determine the genetic basis of

phenotypic differences

NGS allows rapid expansion of genomic analysis to investigation of non-

model species

Made rice study easy by related grass

cost-effective method for plant identification

useful strategy to analysis the chloroplast genome sequence from whole-

genome shot-gun sequencing

facilitates managing this diversity and any changes in crop performance

over time due to genetic drift

Patterns of gene expression have been evaluated in hybrids using NGS

51

Two Approaches to Finding Adaptive Genes

Ross-Ibarra et al2007

52

Techniques to re-wild the plants (transgene free)

1 Introgression

breeding

2 Specific

insertion of lost genes

3 Precision

mutagenesis

Palmgren et al2014

53

Process of rewilding

Palmgren et al2014

54

Synthetic biology projects(i) Modifying cereals including wheat to fix atmospheric nitrogen

(ii) Redesigning metabolic pathways to increase the yield of

secondary metabolites or to generate compounds with enhanced

properties

(iii) Transferring the C4 photosynthesis pathway to rice

(iv) Modifying the glycosylation pathway in plants to accommodate

production of therapeutic proteins

(v) Introducing synthetic signal transduction systems that respond to

external cues

55

Synthetic biology projects

Nicholas J Baltes et al 2015

56

Refactoring the N fixation gene cluster from Klebsiella

Karsten Temme et al 2012

Solanum pimpinellifolium

Solanum lycopersicum19

Domestication of carrot

Queen Annes Lace

Daucus carota

20

Domestication of peanut

A villosulicarpa Hoehne andA Stenosperma (Brazil)

AABB

21

Domestication of Chilli

22

StrawberryBanana

Musa acuminata Musa balbisiana (2n=3x=33) AB genomeFRAGARIA X ANANASSA

Wood berries (F vesca) and Musky strawberries (F moschata)23

Wild SoybeanGlycin soja2n=40

Cultivated soybeanGlycin max 2n=40

24

Increased in domesticate

seed germination

determinate growth

longer pods

bigger (heavier) seeds

earliness

harvest index (seed yieldbiomass)

Decreased in domesticate

seed dispersal

seed dormancy

twining

number of nodes

length of internode

number of pods

photoperiod sensitivity

Common Bean Phaseolus vulgarishttpwwwplantsciencesucdavisedugeptspb143pb143htm

copy Paul Gepts

25

Wild pigeon peaCajanus cajanifolius

Cultivated pigeon pea

26

27

28

WHY OTHERS ARE NOT DOMESTICATED

bull 350000 plants

bull 4629 mammals

bull 9200 birds

bull 10000000 insects

bull 500000 fungi

bull But only 200 plants

bull 15 mammals 5 birds and

bull 2 insects are domesticated

bull Spread of these few species

bull Little change since early

agriculture

bull Repeated domestication of these

species (sometimes)

bull Lack of new species even with

attempts with species known to be

valuable Some groups are good

candidates with no domestication

eg ferns sub-Saharan mammals

29

WHY OTHERS HAVE TO BE DOMESTICATED

New uses and demands ndash biofuels animal feed

medicinalneutraceutical waterclimate food changes

Knowledge why species arenrsquot suitable for domestication or

were not useful

Better understanding of genetics and selection

Sustainability of production

Reliability of production

To meet the food demand in an alternative way

WHY OTHERS HAVE TO BE DOMESTICATED

30

Reallocate biomass for human use

More efficient metabolism and photosynthesis increase

leaf surface decrease root system increase leaf

longevity

Grains more fertile florets larger inflorescence OR

number of ears different ways to get more seed

Larger seeds (automatic vs deliberate selection)

Oil plants increased oil content or more seed

Fiber plants long strong fibers

Domestication syndrome

31

Centers of Domestication

Fuller 2011

32

Centers of Domestication in India

Fuller 2011

33

Indian centers of domestication South India (Deccan centre) Vigna radiate Vigna mungo

Macrotyloma uniflorum (Horse gram) Sataria verticillata S plumila

wheat (macaroni) and two rowed barleybrachiaria ramosa

Orissa (Mahanadi river) Pegion pea Horsegram mung small millets

like Echinichloa Paspalum and Sataria

The Middle Ganges (Harappan civilization) Oryza nivara O rufipogon

and wild sativa Sateria pumia Cannabis sativa even the diffusion of

japonica rice

Saurashtra (Harappan civilization) Eleucine coracana Sateria italica

Paicum spp Brachypodia pearl millet and sorghum Dollicos lablab

The Himalayan foothills of the Punjab region Was a centre of

diversity for Japonica type rice and many temperate fruits and

vegetables

34

DOMESTICATION RELATED TRAITS CONTROLLED BY ONLY FEW GENES

Trait Crops

Plant architecturegrowth habit Ricemaizemilletsbeantomato

Flowering timephotoperiod sensitivity Ricemaizesorghumbeantomato

Fruit size Tomato egg plant

Grain size Ricemaizesorghumbean

Seed dispersal Brassica rice

Inflorescence modification Brassica

Dormancy Bean

35

Genes Crop Moleular and phenotypic function Causative change

Genes identified as controlling domestication traits

tb1 Maize Transcriptional regulator (TCP) plant and

inflorescence structure

regulatory change

tga1 Maize Transcriptional regulator (SBP) seed casing amino acid change

qSH1 Rice Transcriptional regulator (homeodomain)

abscission layer formation shattering

regulatory change

Rc Rice Transcriptional regulator (bHLH) seed color disrupted coding

sequence

sh4 Rice Transcriptional regulator (Myb3) abscission

layer formation shattering

regulatoryamino

acid change

fw22 Tomato Cell signaling fruit weight regulatory change

Q Wheat Transcriptional regulator (AP2) inflorescence

structure

regulatoryamino

acid change

Vrs1 Barley Inflorescence structure Premature stop Amino acid change

Genes of interest in crop domestication and improvement

36

Genes Crop Moleular and phenotypic function Causative change

c1

r1

Maize Transcriptional regulator (MYB) kernel color and

Transcriptional regulator (bHLH) kernel color

regulatory change

sh2 Maize pyrophosphorylase supersweet sweet corn transposon

insertion

su1 Maize isoamylase sweet corn gene amino acid change

brix9-2-5 Tomato Invertase fruit soluble solid content amino acid change

ovate Tomato Unknown fruit shap early stop codon

R Pea Starch branching enzyme seed sugar content transposon

insertion

ehd1 Rice B-type response regulator flowering time amino acid change

hd1 Rice Transcriptional regulator (zinc finger) flowering

time

disrupted coding

sequence

waxy Rice Starch synthase sticky grains intron splicing

defect

rht Wheat Transcriptional regulator (SH2) plant height early stop codon

vrn1 Wheat Transcriptional regulator (MADS) vernalization regulatory change

vrn2 Wheat Transcriptional regulator (ZCCT) vernalization amino acid change

Genes Identified as Controlling Varietal Differences

37

Process of domestication over the yearshellip

Rachel S Meyer 2012

38

Genetic bottleneck

Cultivated crops undergone with narrowing of diversity problem

But this is not the case in weeds

Weeds are the major threats from the beginning of domestication till

today

Problem arose due to

1 Crop mimicry

2 Genetic assimilation

3 Genetic evolution

39

Super- Domestication Vaughn et al (2007) first used the term super-domestication

The processes that lead to a domesticate with dramatically

increased yield that could not be selected in natural environments

from naturally occurring variation without recourse to new

technologies

Super-domesticates can be constructed with knowledge led

approaches based on current needs using the range of new

technologies now available

Plants exploited for continuous selection introduction hybridization

etc which boosted the process of domestication but now the plant

genetic engineering approach is exploiting plants towards synthetic

biology

40

How to use diversitybull Cross two varieties

bull Genome manipulations

Cell fusion hybrids

bull Chromosome manipulation Backcross a new species

bull Generate recombinants Chromosome recombinations

bull Use a new species wild germplasm

Transgenic approach Modern mutagenesis synthetic gene

construction by utilizing green florescent protein genome editing

NGS GWAS sequencing etchelliphelliphelliphelliphellip

41

Reduce genetic bottlenecks through polyplodization

More vigour

SC

Buffering capacity

Heterotic advantage

Enhaced vegetative

charachers

Enhanced oil

Meiotic stability

42

Approach 1 Use one tetraploid and one diploid as parents (4X ndash 2X) followed by the

chromosome doubling of triploid hybrids (Chrom doubling)

a) Cross between B juncea (AjAjBjBj ) and B oleracea (CoCo) to produce hexaploids

(AjAjBjBjCoCo)

(b) Cross between B napus (AnAnCnCn) and B nigra (BniBni) to produce hexaploids

(AnAnBniBniCnCn)

(c) Cross between B carinata (BcaBcaCcaCca) and B rapa (ArAr) to produce hexaploids

(ArArBcaBcaCcaCca)

Approach 2 Use three tetraploids as parents

(a) Cross between B napus (AnAnCnCn) and B carinata (BcaBcaCcaCca) to produce unbalanced

allotetraploids (AnBcaCnCca ndash unreduced gametes gametes with the somatic chromosome

number and cross with B juncea (AjAjBjBj) to obtain allohexaploids (AnAjBcaBjCnCca

(b) Cross between B napus (AnAnCnCn) and B juncea (AjAjBjBj) to produce unbalanced

allotetraploids (AnAjBjCn ndash unreduced gametes) and cross with B carinata (BcaBcaCcaCca) to

obtain allohexaploids (AnAjBcaBjCnCca)

(c) Cross between B carinata (BcaBcaCcaCca) and B juncea (AjAjBjBj) to produce unbalanced

allotetraploids (AjBcaBjCca - ndash unreduced gametes) and cross with B napus (AnAnCnCn) to obtain

allohexaploids (AnAjBcaBjCnCca)

Approach 3 Use three diploids as parents (2X ndash 2X ndash 2X) Cross between B rapa (ArAr) B

nigra (BniBni) and B oleracea (CoCo) sequentially to obtain hexaploid hybrids (ArArBniBniCoCo)

43

Continuehellip

Guijun Yan 2012

44

Applications of Genomic

tools in Super-Domestication

45

Genome Sequencing

Potential methods of sequencing

1 Clone by clone approach

2 Whole genome shotgun approach

3 Combination of the two methods

Till today no of cultivated plants completely sequenced -85

2016- Arachis duranensis

2015- Solanum cumersonii (Wild potato)

(Ref- NCBI)

46

GWAS

It is a study design in which many markers spread across a genome

are genotyped and test a statistical association with a phenotype are

performed locally along the genome

It is also an examination of many common genetic variants in different

individuals to see if any variant is associated with a trait

Used in successfully studying maize sorghum and barley

Method is efficient for large scale low cost genotyping (even with the

minimum number of SNPs)

Cannot be utilized generally because it needs large population size

GWAS identify rare alleles more precisely

If small population we can opt NAM

47

GWAS and whole genome prediction

Xuehui Huang and Bin Han 2014

48

Five high throuput genotyping methods

Xuehui Huang and Bin Han 2014

49

Role of NGS in domestication Capture of novel genes from wild species will be made easier by

understanding the molecular events associated with crop domestication

Re-sequencing of domesticated species can identify low diversity regions

resulting from selection during domestication

To identify gene-specific sequences to aid the cloning of homologues of key

domestication genes from wild relatives

Candidate genes from wild and domesticated plant populations can define

diversity of target genes in wild populations and lead to the discovery of key

genes for important traits by association analysis

NGS of amplicons of large numbers of candidate genes from wild and

domesticated plant populations can define diversity of target genes in

wild populations and lead to the discovery of key genes for important

traits by association analysis

50

NGS

supports the rapid domestication of new plant species and the efficient

identification and capture of novel genetic variation from related species

Allows whole-genome analysis to determine the genetic basis of

phenotypic differences

NGS allows rapid expansion of genomic analysis to investigation of non-

model species

Made rice study easy by related grass

cost-effective method for plant identification

useful strategy to analysis the chloroplast genome sequence from whole-

genome shot-gun sequencing

facilitates managing this diversity and any changes in crop performance

over time due to genetic drift

Patterns of gene expression have been evaluated in hybrids using NGS

51

Two Approaches to Finding Adaptive Genes

Ross-Ibarra et al2007

52

Techniques to re-wild the plants (transgene free)

1 Introgression

breeding

2 Specific

insertion of lost genes

3 Precision

mutagenesis

Palmgren et al2014

53

Process of rewilding

Palmgren et al2014

54

Synthetic biology projects(i) Modifying cereals including wheat to fix atmospheric nitrogen

(ii) Redesigning metabolic pathways to increase the yield of

secondary metabolites or to generate compounds with enhanced

properties

(iii) Transferring the C4 photosynthesis pathway to rice

(iv) Modifying the glycosylation pathway in plants to accommodate

production of therapeutic proteins

(v) Introducing synthetic signal transduction systems that respond to

external cues

55

Synthetic biology projects

Nicholas J Baltes et al 2015

56

Refactoring the N fixation gene cluster from Klebsiella

Karsten Temme et al 2012

Domestication of carrot

Queen Annes Lace

Daucus carota

20

Domestication of peanut

A villosulicarpa Hoehne andA Stenosperma (Brazil)

AABB

21

Domestication of Chilli

22

StrawberryBanana

Musa acuminata Musa balbisiana (2n=3x=33) AB genomeFRAGARIA X ANANASSA

Wood berries (F vesca) and Musky strawberries (F moschata)23

Wild SoybeanGlycin soja2n=40

Cultivated soybeanGlycin max 2n=40

24

Increased in domesticate

seed germination

determinate growth

longer pods

bigger (heavier) seeds

earliness

harvest index (seed yieldbiomass)

Decreased in domesticate

seed dispersal

seed dormancy

twining

number of nodes

length of internode

number of pods

photoperiod sensitivity

Common Bean Phaseolus vulgarishttpwwwplantsciencesucdavisedugeptspb143pb143htm

copy Paul Gepts

25

Wild pigeon peaCajanus cajanifolius

Cultivated pigeon pea

26

27

28

WHY OTHERS ARE NOT DOMESTICATED

bull 350000 plants

bull 4629 mammals

bull 9200 birds

bull 10000000 insects

bull 500000 fungi

bull But only 200 plants

bull 15 mammals 5 birds and

bull 2 insects are domesticated

bull Spread of these few species

bull Little change since early

agriculture

bull Repeated domestication of these

species (sometimes)

bull Lack of new species even with

attempts with species known to be

valuable Some groups are good

candidates with no domestication

eg ferns sub-Saharan mammals

29

WHY OTHERS HAVE TO BE DOMESTICATED

New uses and demands ndash biofuels animal feed

medicinalneutraceutical waterclimate food changes

Knowledge why species arenrsquot suitable for domestication or

were not useful

Better understanding of genetics and selection

Sustainability of production

Reliability of production

To meet the food demand in an alternative way

WHY OTHERS HAVE TO BE DOMESTICATED

30

Reallocate biomass for human use

More efficient metabolism and photosynthesis increase

leaf surface decrease root system increase leaf

longevity

Grains more fertile florets larger inflorescence OR

number of ears different ways to get more seed

Larger seeds (automatic vs deliberate selection)

Oil plants increased oil content or more seed

Fiber plants long strong fibers

Domestication syndrome

31

Centers of Domestication

Fuller 2011

32

Centers of Domestication in India

Fuller 2011

33

Indian centers of domestication South India (Deccan centre) Vigna radiate Vigna mungo

Macrotyloma uniflorum (Horse gram) Sataria verticillata S plumila

wheat (macaroni) and two rowed barleybrachiaria ramosa

Orissa (Mahanadi river) Pegion pea Horsegram mung small millets

like Echinichloa Paspalum and Sataria

The Middle Ganges (Harappan civilization) Oryza nivara O rufipogon

and wild sativa Sateria pumia Cannabis sativa even the diffusion of

japonica rice

Saurashtra (Harappan civilization) Eleucine coracana Sateria italica

Paicum spp Brachypodia pearl millet and sorghum Dollicos lablab

The Himalayan foothills of the Punjab region Was a centre of

diversity for Japonica type rice and many temperate fruits and

vegetables

34

DOMESTICATION RELATED TRAITS CONTROLLED BY ONLY FEW GENES

Trait Crops

Plant architecturegrowth habit Ricemaizemilletsbeantomato

Flowering timephotoperiod sensitivity Ricemaizesorghumbeantomato

Fruit size Tomato egg plant

Grain size Ricemaizesorghumbean

Seed dispersal Brassica rice

Inflorescence modification Brassica

Dormancy Bean

35

Genes Crop Moleular and phenotypic function Causative change

Genes identified as controlling domestication traits

tb1 Maize Transcriptional regulator (TCP) plant and

inflorescence structure

regulatory change

tga1 Maize Transcriptional regulator (SBP) seed casing amino acid change

qSH1 Rice Transcriptional regulator (homeodomain)

abscission layer formation shattering

regulatory change

Rc Rice Transcriptional regulator (bHLH) seed color disrupted coding

sequence

sh4 Rice Transcriptional regulator (Myb3) abscission

layer formation shattering

regulatoryamino

acid change

fw22 Tomato Cell signaling fruit weight regulatory change

Q Wheat Transcriptional regulator (AP2) inflorescence

structure

regulatoryamino

acid change

Vrs1 Barley Inflorescence structure Premature stop Amino acid change

Genes of interest in crop domestication and improvement

36

Genes Crop Moleular and phenotypic function Causative change

c1

r1

Maize Transcriptional regulator (MYB) kernel color and

Transcriptional regulator (bHLH) kernel color

regulatory change

sh2 Maize pyrophosphorylase supersweet sweet corn transposon

insertion

su1 Maize isoamylase sweet corn gene amino acid change

brix9-2-5 Tomato Invertase fruit soluble solid content amino acid change

ovate Tomato Unknown fruit shap early stop codon

R Pea Starch branching enzyme seed sugar content transposon

insertion

ehd1 Rice B-type response regulator flowering time amino acid change

hd1 Rice Transcriptional regulator (zinc finger) flowering

time

disrupted coding

sequence

waxy Rice Starch synthase sticky grains intron splicing

defect

rht Wheat Transcriptional regulator (SH2) plant height early stop codon

vrn1 Wheat Transcriptional regulator (MADS) vernalization regulatory change

vrn2 Wheat Transcriptional regulator (ZCCT) vernalization amino acid change

Genes Identified as Controlling Varietal Differences

37

Process of domestication over the yearshellip

Rachel S Meyer 2012

38

Genetic bottleneck

Cultivated crops undergone with narrowing of diversity problem

But this is not the case in weeds

Weeds are the major threats from the beginning of domestication till

today

Problem arose due to

1 Crop mimicry

2 Genetic assimilation

3 Genetic evolution

39

Super- Domestication Vaughn et al (2007) first used the term super-domestication

The processes that lead to a domesticate with dramatically

increased yield that could not be selected in natural environments

from naturally occurring variation without recourse to new

technologies

Super-domesticates can be constructed with knowledge led

approaches based on current needs using the range of new

technologies now available

Plants exploited for continuous selection introduction hybridization

etc which boosted the process of domestication but now the plant

genetic engineering approach is exploiting plants towards synthetic

biology

40

How to use diversitybull Cross two varieties

bull Genome manipulations

Cell fusion hybrids

bull Chromosome manipulation Backcross a new species

bull Generate recombinants Chromosome recombinations

bull Use a new species wild germplasm

Transgenic approach Modern mutagenesis synthetic gene

construction by utilizing green florescent protein genome editing

NGS GWAS sequencing etchelliphelliphelliphelliphellip

41

Reduce genetic bottlenecks through polyplodization

More vigour

SC

Buffering capacity

Heterotic advantage

Enhaced vegetative

charachers

Enhanced oil

Meiotic stability

42

Approach 1 Use one tetraploid and one diploid as parents (4X ndash 2X) followed by the

chromosome doubling of triploid hybrids (Chrom doubling)

a) Cross between B juncea (AjAjBjBj ) and B oleracea (CoCo) to produce hexaploids

(AjAjBjBjCoCo)

(b) Cross between B napus (AnAnCnCn) and B nigra (BniBni) to produce hexaploids

(AnAnBniBniCnCn)

(c) Cross between B carinata (BcaBcaCcaCca) and B rapa (ArAr) to produce hexaploids

(ArArBcaBcaCcaCca)

Approach 2 Use three tetraploids as parents

(a) Cross between B napus (AnAnCnCn) and B carinata (BcaBcaCcaCca) to produce unbalanced

allotetraploids (AnBcaCnCca ndash unreduced gametes gametes with the somatic chromosome

number and cross with B juncea (AjAjBjBj) to obtain allohexaploids (AnAjBcaBjCnCca

(b) Cross between B napus (AnAnCnCn) and B juncea (AjAjBjBj) to produce unbalanced

allotetraploids (AnAjBjCn ndash unreduced gametes) and cross with B carinata (BcaBcaCcaCca) to

obtain allohexaploids (AnAjBcaBjCnCca)

(c) Cross between B carinata (BcaBcaCcaCca) and B juncea (AjAjBjBj) to produce unbalanced

allotetraploids (AjBcaBjCca - ndash unreduced gametes) and cross with B napus (AnAnCnCn) to obtain

allohexaploids (AnAjBcaBjCnCca)

Approach 3 Use three diploids as parents (2X ndash 2X ndash 2X) Cross between B rapa (ArAr) B

nigra (BniBni) and B oleracea (CoCo) sequentially to obtain hexaploid hybrids (ArArBniBniCoCo)

43

Continuehellip

Guijun Yan 2012

44

Applications of Genomic

tools in Super-Domestication

45

Genome Sequencing

Potential methods of sequencing

1 Clone by clone approach

2 Whole genome shotgun approach

3 Combination of the two methods

Till today no of cultivated plants completely sequenced -85

2016- Arachis duranensis

2015- Solanum cumersonii (Wild potato)

(Ref- NCBI)

46

GWAS

It is a study design in which many markers spread across a genome

are genotyped and test a statistical association with a phenotype are

performed locally along the genome

It is also an examination of many common genetic variants in different

individuals to see if any variant is associated with a trait

Used in successfully studying maize sorghum and barley

Method is efficient for large scale low cost genotyping (even with the

minimum number of SNPs)

Cannot be utilized generally because it needs large population size

GWAS identify rare alleles more precisely

If small population we can opt NAM

47

GWAS and whole genome prediction

Xuehui Huang and Bin Han 2014

48

Five high throuput genotyping methods

Xuehui Huang and Bin Han 2014

49

Role of NGS in domestication Capture of novel genes from wild species will be made easier by

understanding the molecular events associated with crop domestication

Re-sequencing of domesticated species can identify low diversity regions

resulting from selection during domestication

To identify gene-specific sequences to aid the cloning of homologues of key

domestication genes from wild relatives

Candidate genes from wild and domesticated plant populations can define

diversity of target genes in wild populations and lead to the discovery of key

genes for important traits by association analysis

NGS of amplicons of large numbers of candidate genes from wild and

domesticated plant populations can define diversity of target genes in

wild populations and lead to the discovery of key genes for important

traits by association analysis

50

NGS

supports the rapid domestication of new plant species and the efficient

identification and capture of novel genetic variation from related species

Allows whole-genome analysis to determine the genetic basis of

phenotypic differences

NGS allows rapid expansion of genomic analysis to investigation of non-

model species

Made rice study easy by related grass

cost-effective method for plant identification

useful strategy to analysis the chloroplast genome sequence from whole-

genome shot-gun sequencing

facilitates managing this diversity and any changes in crop performance

over time due to genetic drift

Patterns of gene expression have been evaluated in hybrids using NGS

51

Two Approaches to Finding Adaptive Genes

Ross-Ibarra et al2007

52

Techniques to re-wild the plants (transgene free)

1 Introgression

breeding

2 Specific

insertion of lost genes

3 Precision

mutagenesis

Palmgren et al2014

53

Process of rewilding

Palmgren et al2014

54

Synthetic biology projects(i) Modifying cereals including wheat to fix atmospheric nitrogen

(ii) Redesigning metabolic pathways to increase the yield of

secondary metabolites or to generate compounds with enhanced

properties

(iii) Transferring the C4 photosynthesis pathway to rice

(iv) Modifying the glycosylation pathway in plants to accommodate

production of therapeutic proteins

(v) Introducing synthetic signal transduction systems that respond to

external cues

55

Synthetic biology projects

Nicholas J Baltes et al 2015

56

Refactoring the N fixation gene cluster from Klebsiella

Karsten Temme et al 2012

Domestication of peanut

A villosulicarpa Hoehne andA Stenosperma (Brazil)

AABB

21

Domestication of Chilli

22

StrawberryBanana

Musa acuminata Musa balbisiana (2n=3x=33) AB genomeFRAGARIA X ANANASSA

Wood berries (F vesca) and Musky strawberries (F moschata)23

Wild SoybeanGlycin soja2n=40

Cultivated soybeanGlycin max 2n=40

24

Increased in domesticate

seed germination

determinate growth

longer pods

bigger (heavier) seeds

earliness

harvest index (seed yieldbiomass)

Decreased in domesticate

seed dispersal

seed dormancy

twining

number of nodes

length of internode

number of pods

photoperiod sensitivity

Common Bean Phaseolus vulgarishttpwwwplantsciencesucdavisedugeptspb143pb143htm

copy Paul Gepts

25

Wild pigeon peaCajanus cajanifolius

Cultivated pigeon pea

26

27

28

WHY OTHERS ARE NOT DOMESTICATED

bull 350000 plants

bull 4629 mammals

bull 9200 birds

bull 10000000 insects

bull 500000 fungi

bull But only 200 plants

bull 15 mammals 5 birds and

bull 2 insects are domesticated

bull Spread of these few species

bull Little change since early

agriculture

bull Repeated domestication of these

species (sometimes)

bull Lack of new species even with

attempts with species known to be

valuable Some groups are good

candidates with no domestication

eg ferns sub-Saharan mammals

29

WHY OTHERS HAVE TO BE DOMESTICATED

New uses and demands ndash biofuels animal feed

medicinalneutraceutical waterclimate food changes

Knowledge why species arenrsquot suitable for domestication or

were not useful

Better understanding of genetics and selection

Sustainability of production

Reliability of production

To meet the food demand in an alternative way

WHY OTHERS HAVE TO BE DOMESTICATED

30

Reallocate biomass for human use

More efficient metabolism and photosynthesis increase

leaf surface decrease root system increase leaf

longevity

Grains more fertile florets larger inflorescence OR

number of ears different ways to get more seed

Larger seeds (automatic vs deliberate selection)

Oil plants increased oil content or more seed

Fiber plants long strong fibers

Domestication syndrome

31

Centers of Domestication

Fuller 2011

32

Centers of Domestication in India

Fuller 2011

33

Indian centers of domestication South India (Deccan centre) Vigna radiate Vigna mungo

Macrotyloma uniflorum (Horse gram) Sataria verticillata S plumila

wheat (macaroni) and two rowed barleybrachiaria ramosa

Orissa (Mahanadi river) Pegion pea Horsegram mung small millets

like Echinichloa Paspalum and Sataria

The Middle Ganges (Harappan civilization) Oryza nivara O rufipogon

and wild sativa Sateria pumia Cannabis sativa even the diffusion of

japonica rice

Saurashtra (Harappan civilization) Eleucine coracana Sateria italica

Paicum spp Brachypodia pearl millet and sorghum Dollicos lablab

The Himalayan foothills of the Punjab region Was a centre of

diversity for Japonica type rice and many temperate fruits and

vegetables

34

DOMESTICATION RELATED TRAITS CONTROLLED BY ONLY FEW GENES

Trait Crops

Plant architecturegrowth habit Ricemaizemilletsbeantomato

Flowering timephotoperiod sensitivity Ricemaizesorghumbeantomato

Fruit size Tomato egg plant

Grain size Ricemaizesorghumbean

Seed dispersal Brassica rice

Inflorescence modification Brassica

Dormancy Bean

35

Genes Crop Moleular and phenotypic function Causative change

Genes identified as controlling domestication traits

tb1 Maize Transcriptional regulator (TCP) plant and

inflorescence structure

regulatory change

tga1 Maize Transcriptional regulator (SBP) seed casing amino acid change

qSH1 Rice Transcriptional regulator (homeodomain)

abscission layer formation shattering

regulatory change

Rc Rice Transcriptional regulator (bHLH) seed color disrupted coding

sequence

sh4 Rice Transcriptional regulator (Myb3) abscission

layer formation shattering

regulatoryamino

acid change

fw22 Tomato Cell signaling fruit weight regulatory change

Q Wheat Transcriptional regulator (AP2) inflorescence

structure

regulatoryamino

acid change

Vrs1 Barley Inflorescence structure Premature stop Amino acid change

Genes of interest in crop domestication and improvement

36

Genes Crop Moleular and phenotypic function Causative change

c1

r1

Maize Transcriptional regulator (MYB) kernel color and

Transcriptional regulator (bHLH) kernel color

regulatory change

sh2 Maize pyrophosphorylase supersweet sweet corn transposon

insertion

su1 Maize isoamylase sweet corn gene amino acid change

brix9-2-5 Tomato Invertase fruit soluble solid content amino acid change

ovate Tomato Unknown fruit shap early stop codon

R Pea Starch branching enzyme seed sugar content transposon

insertion

ehd1 Rice B-type response regulator flowering time amino acid change

hd1 Rice Transcriptional regulator (zinc finger) flowering

time

disrupted coding

sequence

waxy Rice Starch synthase sticky grains intron splicing

defect

rht Wheat Transcriptional regulator (SH2) plant height early stop codon

vrn1 Wheat Transcriptional regulator (MADS) vernalization regulatory change

vrn2 Wheat Transcriptional regulator (ZCCT) vernalization amino acid change

Genes Identified as Controlling Varietal Differences

37

Process of domestication over the yearshellip

Rachel S Meyer 2012

38

Genetic bottleneck

Cultivated crops undergone with narrowing of diversity problem

But this is not the case in weeds

Weeds are the major threats from the beginning of domestication till

today

Problem arose due to

1 Crop mimicry

2 Genetic assimilation

3 Genetic evolution

39

Super- Domestication Vaughn et al (2007) first used the term super-domestication

The processes that lead to a domesticate with dramatically

increased yield that could not be selected in natural environments

from naturally occurring variation without recourse to new

technologies

Super-domesticates can be constructed with knowledge led

approaches based on current needs using the range of new

technologies now available

Plants exploited for continuous selection introduction hybridization

etc which boosted the process of domestication but now the plant

genetic engineering approach is exploiting plants towards synthetic

biology

40

How to use diversitybull Cross two varieties

bull Genome manipulations

Cell fusion hybrids

bull Chromosome manipulation Backcross a new species

bull Generate recombinants Chromosome recombinations

bull Use a new species wild germplasm

Transgenic approach Modern mutagenesis synthetic gene

construction by utilizing green florescent protein genome editing

NGS GWAS sequencing etchelliphelliphelliphelliphellip

41

Reduce genetic bottlenecks through polyplodization

More vigour

SC

Buffering capacity

Heterotic advantage

Enhaced vegetative

charachers

Enhanced oil

Meiotic stability

42

Approach 1 Use one tetraploid and one diploid as parents (4X ndash 2X) followed by the

chromosome doubling of triploid hybrids (Chrom doubling)

a) Cross between B juncea (AjAjBjBj ) and B oleracea (CoCo) to produce hexaploids

(AjAjBjBjCoCo)

(b) Cross between B napus (AnAnCnCn) and B nigra (BniBni) to produce hexaploids

(AnAnBniBniCnCn)

(c) Cross between B carinata (BcaBcaCcaCca) and B rapa (ArAr) to produce hexaploids

(ArArBcaBcaCcaCca)

Approach 2 Use three tetraploids as parents

(a) Cross between B napus (AnAnCnCn) and B carinata (BcaBcaCcaCca) to produce unbalanced

allotetraploids (AnBcaCnCca ndash unreduced gametes gametes with the somatic chromosome

number and cross with B juncea (AjAjBjBj) to obtain allohexaploids (AnAjBcaBjCnCca

(b) Cross between B napus (AnAnCnCn) and B juncea (AjAjBjBj) to produce unbalanced

allotetraploids (AnAjBjCn ndash unreduced gametes) and cross with B carinata (BcaBcaCcaCca) to

obtain allohexaploids (AnAjBcaBjCnCca)

(c) Cross between B carinata (BcaBcaCcaCca) and B juncea (AjAjBjBj) to produce unbalanced

allotetraploids (AjBcaBjCca - ndash unreduced gametes) and cross with B napus (AnAnCnCn) to obtain

allohexaploids (AnAjBcaBjCnCca)

Approach 3 Use three diploids as parents (2X ndash 2X ndash 2X) Cross between B rapa (ArAr) B

nigra (BniBni) and B oleracea (CoCo) sequentially to obtain hexaploid hybrids (ArArBniBniCoCo)

43

Continuehellip

Guijun Yan 2012

44

Applications of Genomic

tools in Super-Domestication

45

Genome Sequencing

Potential methods of sequencing

1 Clone by clone approach

2 Whole genome shotgun approach

3 Combination of the two methods

Till today no of cultivated plants completely sequenced -85

2016- Arachis duranensis

2015- Solanum cumersonii (Wild potato)

(Ref- NCBI)

46

GWAS

It is a study design in which many markers spread across a genome

are genotyped and test a statistical association with a phenotype are

performed locally along the genome

It is also an examination of many common genetic variants in different

individuals to see if any variant is associated with a trait

Used in successfully studying maize sorghum and barley

Method is efficient for large scale low cost genotyping (even with the

minimum number of SNPs)

Cannot be utilized generally because it needs large population size

GWAS identify rare alleles more precisely

If small population we can opt NAM

47

GWAS and whole genome prediction

Xuehui Huang and Bin Han 2014

48

Five high throuput genotyping methods

Xuehui Huang and Bin Han 2014

49

Role of NGS in domestication Capture of novel genes from wild species will be made easier by

understanding the molecular events associated with crop domestication

Re-sequencing of domesticated species can identify low diversity regions

resulting from selection during domestication

To identify gene-specific sequences to aid the cloning of homologues of key

domestication genes from wild relatives

Candidate genes from wild and domesticated plant populations can define

diversity of target genes in wild populations and lead to the discovery of key

genes for important traits by association analysis

NGS of amplicons of large numbers of candidate genes from wild and

domesticated plant populations can define diversity of target genes in

wild populations and lead to the discovery of key genes for important

traits by association analysis

50

NGS

supports the rapid domestication of new plant species and the efficient

identification and capture of novel genetic variation from related species

Allows whole-genome analysis to determine the genetic basis of

phenotypic differences

NGS allows rapid expansion of genomic analysis to investigation of non-

model species

Made rice study easy by related grass

cost-effective method for plant identification

useful strategy to analysis the chloroplast genome sequence from whole-

genome shot-gun sequencing

facilitates managing this diversity and any changes in crop performance

over time due to genetic drift

Patterns of gene expression have been evaluated in hybrids using NGS

51

Two Approaches to Finding Adaptive Genes

Ross-Ibarra et al2007

52

Techniques to re-wild the plants (transgene free)

1 Introgression

breeding

2 Specific

insertion of lost genes

3 Precision

mutagenesis

Palmgren et al2014

53

Process of rewilding

Palmgren et al2014

54

Synthetic biology projects(i) Modifying cereals including wheat to fix atmospheric nitrogen

(ii) Redesigning metabolic pathways to increase the yield of

secondary metabolites or to generate compounds with enhanced

properties

(iii) Transferring the C4 photosynthesis pathway to rice

(iv) Modifying the glycosylation pathway in plants to accommodate

production of therapeutic proteins

(v) Introducing synthetic signal transduction systems that respond to

external cues

55

Synthetic biology projects

Nicholas J Baltes et al 2015

56

Refactoring the N fixation gene cluster from Klebsiella

Karsten Temme et al 2012

Domestication of Chilli

22

StrawberryBanana

Musa acuminata Musa balbisiana (2n=3x=33) AB genomeFRAGARIA X ANANASSA

Wood berries (F vesca) and Musky strawberries (F moschata)23

Wild SoybeanGlycin soja2n=40

Cultivated soybeanGlycin max 2n=40

24

Increased in domesticate

seed germination

determinate growth

longer pods

bigger (heavier) seeds

earliness

harvest index (seed yieldbiomass)

Decreased in domesticate

seed dispersal

seed dormancy

twining

number of nodes

length of internode

number of pods

photoperiod sensitivity

Common Bean Phaseolus vulgarishttpwwwplantsciencesucdavisedugeptspb143pb143htm

copy Paul Gepts

25

Wild pigeon peaCajanus cajanifolius

Cultivated pigeon pea

26

27

28

WHY OTHERS ARE NOT DOMESTICATED

bull 350000 plants

bull 4629 mammals

bull 9200 birds

bull 10000000 insects

bull 500000 fungi

bull But only 200 plants

bull 15 mammals 5 birds and

bull 2 insects are domesticated

bull Spread of these few species

bull Little change since early

agriculture

bull Repeated domestication of these

species (sometimes)

bull Lack of new species even with

attempts with species known to be

valuable Some groups are good

candidates with no domestication

eg ferns sub-Saharan mammals

29

WHY OTHERS HAVE TO BE DOMESTICATED

New uses and demands ndash biofuels animal feed

medicinalneutraceutical waterclimate food changes

Knowledge why species arenrsquot suitable for domestication or

were not useful

Better understanding of genetics and selection

Sustainability of production

Reliability of production

To meet the food demand in an alternative way

WHY OTHERS HAVE TO BE DOMESTICATED

30

Reallocate biomass for human use

More efficient metabolism and photosynthesis increase

leaf surface decrease root system increase leaf

longevity

Grains more fertile florets larger inflorescence OR

number of ears different ways to get more seed

Larger seeds (automatic vs deliberate selection)

Oil plants increased oil content or more seed

Fiber plants long strong fibers

Domestication syndrome

31

Centers of Domestication

Fuller 2011

32

Centers of Domestication in India

Fuller 2011

33

Indian centers of domestication South India (Deccan centre) Vigna radiate Vigna mungo

Macrotyloma uniflorum (Horse gram) Sataria verticillata S plumila

wheat (macaroni) and two rowed barleybrachiaria ramosa

Orissa (Mahanadi river) Pegion pea Horsegram mung small millets

like Echinichloa Paspalum and Sataria

The Middle Ganges (Harappan civilization) Oryza nivara O rufipogon

and wild sativa Sateria pumia Cannabis sativa even the diffusion of

japonica rice

Saurashtra (Harappan civilization) Eleucine coracana Sateria italica

Paicum spp Brachypodia pearl millet and sorghum Dollicos lablab

The Himalayan foothills of the Punjab region Was a centre of

diversity for Japonica type rice and many temperate fruits and

vegetables

34

DOMESTICATION RELATED TRAITS CONTROLLED BY ONLY FEW GENES

Trait Crops

Plant architecturegrowth habit Ricemaizemilletsbeantomato

Flowering timephotoperiod sensitivity Ricemaizesorghumbeantomato

Fruit size Tomato egg plant

Grain size Ricemaizesorghumbean

Seed dispersal Brassica rice

Inflorescence modification Brassica

Dormancy Bean

35

Genes Crop Moleular and phenotypic function Causative change

Genes identified as controlling domestication traits

tb1 Maize Transcriptional regulator (TCP) plant and

inflorescence structure

regulatory change

tga1 Maize Transcriptional regulator (SBP) seed casing amino acid change

qSH1 Rice Transcriptional regulator (homeodomain)

abscission layer formation shattering

regulatory change

Rc Rice Transcriptional regulator (bHLH) seed color disrupted coding

sequence

sh4 Rice Transcriptional regulator (Myb3) abscission

layer formation shattering

regulatoryamino

acid change

fw22 Tomato Cell signaling fruit weight regulatory change

Q Wheat Transcriptional regulator (AP2) inflorescence

structure

regulatoryamino

acid change

Vrs1 Barley Inflorescence structure Premature stop Amino acid change

Genes of interest in crop domestication and improvement

36

Genes Crop Moleular and phenotypic function Causative change

c1

r1

Maize Transcriptional regulator (MYB) kernel color and

Transcriptional regulator (bHLH) kernel color

regulatory change

sh2 Maize pyrophosphorylase supersweet sweet corn transposon

insertion

su1 Maize isoamylase sweet corn gene amino acid change

brix9-2-5 Tomato Invertase fruit soluble solid content amino acid change

ovate Tomato Unknown fruit shap early stop codon

R Pea Starch branching enzyme seed sugar content transposon

insertion

ehd1 Rice B-type response regulator flowering time amino acid change

hd1 Rice Transcriptional regulator (zinc finger) flowering

time

disrupted coding

sequence

waxy Rice Starch synthase sticky grains intron splicing

defect

rht Wheat Transcriptional regulator (SH2) plant height early stop codon

vrn1 Wheat Transcriptional regulator (MADS) vernalization regulatory change

vrn2 Wheat Transcriptional regulator (ZCCT) vernalization amino acid change

Genes Identified as Controlling Varietal Differences

37

Process of domestication over the yearshellip

Rachel S Meyer 2012

38

Genetic bottleneck

Cultivated crops undergone with narrowing of diversity problem

But this is not the case in weeds

Weeds are the major threats from the beginning of domestication till

today

Problem arose due to

1 Crop mimicry

2 Genetic assimilation

3 Genetic evolution

39

Super- Domestication Vaughn et al (2007) first used the term super-domestication

The processes that lead to a domesticate with dramatically

increased yield that could not be selected in natural environments

from naturally occurring variation without recourse to new

technologies

Super-domesticates can be constructed with knowledge led

approaches based on current needs using the range of new

technologies now available

Plants exploited for continuous selection introduction hybridization

etc which boosted the process of domestication but now the plant

genetic engineering approach is exploiting plants towards synthetic

biology

40

How to use diversitybull Cross two varieties

bull Genome manipulations

Cell fusion hybrids

bull Chromosome manipulation Backcross a new species

bull Generate recombinants Chromosome recombinations

bull Use a new species wild germplasm

Transgenic approach Modern mutagenesis synthetic gene

construction by utilizing green florescent protein genome editing

NGS GWAS sequencing etchelliphelliphelliphelliphellip

41

Reduce genetic bottlenecks through polyplodization

More vigour

SC

Buffering capacity

Heterotic advantage

Enhaced vegetative

charachers

Enhanced oil

Meiotic stability

42

Approach 1 Use one tetraploid and one diploid as parents (4X ndash 2X) followed by the

chromosome doubling of triploid hybrids (Chrom doubling)

a) Cross between B juncea (AjAjBjBj ) and B oleracea (CoCo) to produce hexaploids

(AjAjBjBjCoCo)

(b) Cross between B napus (AnAnCnCn) and B nigra (BniBni) to produce hexaploids

(AnAnBniBniCnCn)

(c) Cross between B carinata (BcaBcaCcaCca) and B rapa (ArAr) to produce hexaploids

(ArArBcaBcaCcaCca)

Approach 2 Use three tetraploids as parents

(a) Cross between B napus (AnAnCnCn) and B carinata (BcaBcaCcaCca) to produce unbalanced

allotetraploids (AnBcaCnCca ndash unreduced gametes gametes with the somatic chromosome

number and cross with B juncea (AjAjBjBj) to obtain allohexaploids (AnAjBcaBjCnCca

(b) Cross between B napus (AnAnCnCn) and B juncea (AjAjBjBj) to produce unbalanced

allotetraploids (AnAjBjCn ndash unreduced gametes) and cross with B carinata (BcaBcaCcaCca) to

obtain allohexaploids (AnAjBcaBjCnCca)

(c) Cross between B carinata (BcaBcaCcaCca) and B juncea (AjAjBjBj) to produce unbalanced

allotetraploids (AjBcaBjCca - ndash unreduced gametes) and cross with B napus (AnAnCnCn) to obtain

allohexaploids (AnAjBcaBjCnCca)

Approach 3 Use three diploids as parents (2X ndash 2X ndash 2X) Cross between B rapa (ArAr) B

nigra (BniBni) and B oleracea (CoCo) sequentially to obtain hexaploid hybrids (ArArBniBniCoCo)

43

Continuehellip

Guijun Yan 2012

44

Applications of Genomic

tools in Super-Domestication

45

Genome Sequencing

Potential methods of sequencing

1 Clone by clone approach

2 Whole genome shotgun approach

3 Combination of the two methods

Till today no of cultivated plants completely sequenced -85

2016- Arachis duranensis

2015- Solanum cumersonii (Wild potato)

(Ref- NCBI)

46

GWAS

It is a study design in which many markers spread across a genome

are genotyped and test a statistical association with a phenotype are

performed locally along the genome

It is also an examination of many common genetic variants in different

individuals to see if any variant is associated with a trait

Used in successfully studying maize sorghum and barley

Method is efficient for large scale low cost genotyping (even with the

minimum number of SNPs)

Cannot be utilized generally because it needs large population size

GWAS identify rare alleles more precisely

If small population we can opt NAM

47

GWAS and whole genome prediction

Xuehui Huang and Bin Han 2014

48

Five high throuput genotyping methods

Xuehui Huang and Bin Han 2014

49

Role of NGS in domestication Capture of novel genes from wild species will be made easier by

understanding the molecular events associated with crop domestication

Re-sequencing of domesticated species can identify low diversity regions

resulting from selection during domestication

To identify gene-specific sequences to aid the cloning of homologues of key

domestication genes from wild relatives

Candidate genes from wild and domesticated plant populations can define

diversity of target genes in wild populations and lead to the discovery of key

genes for important traits by association analysis

NGS of amplicons of large numbers of candidate genes from wild and

domesticated plant populations can define diversity of target genes in

wild populations and lead to the discovery of key genes for important

traits by association analysis

50

NGS

supports the rapid domestication of new plant species and the efficient

identification and capture of novel genetic variation from related species

Allows whole-genome analysis to determine the genetic basis of

phenotypic differences

NGS allows rapid expansion of genomic analysis to investigation of non-

model species

Made rice study easy by related grass

cost-effective method for plant identification

useful strategy to analysis the chloroplast genome sequence from whole-

genome shot-gun sequencing

facilitates managing this diversity and any changes in crop performance

over time due to genetic drift

Patterns of gene expression have been evaluated in hybrids using NGS

51

Two Approaches to Finding Adaptive Genes

Ross-Ibarra et al2007

52

Techniques to re-wild the plants (transgene free)

1 Introgression

breeding

2 Specific

insertion of lost genes

3 Precision

mutagenesis

Palmgren et al2014

53

Process of rewilding

Palmgren et al2014

54

Synthetic biology projects(i) Modifying cereals including wheat to fix atmospheric nitrogen

(ii) Redesigning metabolic pathways to increase the yield of

secondary metabolites or to generate compounds with enhanced

properties

(iii) Transferring the C4 photosynthesis pathway to rice

(iv) Modifying the glycosylation pathway in plants to accommodate

production of therapeutic proteins

(v) Introducing synthetic signal transduction systems that respond to

external cues

55

Synthetic biology projects

Nicholas J Baltes et al 2015

56

Refactoring the N fixation gene cluster from Klebsiella

Karsten Temme et al 2012

StrawberryBanana

Musa acuminata Musa balbisiana (2n=3x=33) AB genomeFRAGARIA X ANANASSA

Wood berries (F vesca) and Musky strawberries (F moschata)23

Wild SoybeanGlycin soja2n=40

Cultivated soybeanGlycin max 2n=40

24

Increased in domesticate

seed germination

determinate growth

longer pods

bigger (heavier) seeds

earliness

harvest index (seed yieldbiomass)

Decreased in domesticate

seed dispersal

seed dormancy

twining

number of nodes

length of internode

number of pods

photoperiod sensitivity

Common Bean Phaseolus vulgarishttpwwwplantsciencesucdavisedugeptspb143pb143htm

copy Paul Gepts

25

Wild pigeon peaCajanus cajanifolius

Cultivated pigeon pea

26

27

28

WHY OTHERS ARE NOT DOMESTICATED

bull 350000 plants

bull 4629 mammals

bull 9200 birds

bull 10000000 insects

bull 500000 fungi

bull But only 200 plants

bull 15 mammals 5 birds and

bull 2 insects are domesticated

bull Spread of these few species

bull Little change since early

agriculture

bull Repeated domestication of these

species (sometimes)

bull Lack of new species even with

attempts with species known to be

valuable Some groups are good

candidates with no domestication

eg ferns sub-Saharan mammals

29

WHY OTHERS HAVE TO BE DOMESTICATED

New uses and demands ndash biofuels animal feed

medicinalneutraceutical waterclimate food changes

Knowledge why species arenrsquot suitable for domestication or

were not useful

Better understanding of genetics and selection

Sustainability of production

Reliability of production

To meet the food demand in an alternative way

WHY OTHERS HAVE TO BE DOMESTICATED

30

Reallocate biomass for human use

More efficient metabolism and photosynthesis increase

leaf surface decrease root system increase leaf

longevity

Grains more fertile florets larger inflorescence OR

number of ears different ways to get more seed

Larger seeds (automatic vs deliberate selection)

Oil plants increased oil content or more seed

Fiber plants long strong fibers

Domestication syndrome

31

Centers of Domestication

Fuller 2011

32

Centers of Domestication in India

Fuller 2011

33

Indian centers of domestication South India (Deccan centre) Vigna radiate Vigna mungo

Macrotyloma uniflorum (Horse gram) Sataria verticillata S plumila

wheat (macaroni) and two rowed barleybrachiaria ramosa

Orissa (Mahanadi river) Pegion pea Horsegram mung small millets

like Echinichloa Paspalum and Sataria

The Middle Ganges (Harappan civilization) Oryza nivara O rufipogon

and wild sativa Sateria pumia Cannabis sativa even the diffusion of

japonica rice

Saurashtra (Harappan civilization) Eleucine coracana Sateria italica

Paicum spp Brachypodia pearl millet and sorghum Dollicos lablab

The Himalayan foothills of the Punjab region Was a centre of

diversity for Japonica type rice and many temperate fruits and

vegetables

34

DOMESTICATION RELATED TRAITS CONTROLLED BY ONLY FEW GENES

Trait Crops

Plant architecturegrowth habit Ricemaizemilletsbeantomato

Flowering timephotoperiod sensitivity Ricemaizesorghumbeantomato

Fruit size Tomato egg plant

Grain size Ricemaizesorghumbean

Seed dispersal Brassica rice

Inflorescence modification Brassica

Dormancy Bean

35

Genes Crop Moleular and phenotypic function Causative change

Genes identified as controlling domestication traits

tb1 Maize Transcriptional regulator (TCP) plant and

inflorescence structure

regulatory change

tga1 Maize Transcriptional regulator (SBP) seed casing amino acid change

qSH1 Rice Transcriptional regulator (homeodomain)

abscission layer formation shattering

regulatory change

Rc Rice Transcriptional regulator (bHLH) seed color disrupted coding

sequence

sh4 Rice Transcriptional regulator (Myb3) abscission

layer formation shattering

regulatoryamino

acid change

fw22 Tomato Cell signaling fruit weight regulatory change

Q Wheat Transcriptional regulator (AP2) inflorescence

structure

regulatoryamino

acid change

Vrs1 Barley Inflorescence structure Premature stop Amino acid change

Genes of interest in crop domestication and improvement

36

Genes Crop Moleular and phenotypic function Causative change

c1

r1

Maize Transcriptional regulator (MYB) kernel color and

Transcriptional regulator (bHLH) kernel color

regulatory change

sh2 Maize pyrophosphorylase supersweet sweet corn transposon

insertion

su1 Maize isoamylase sweet corn gene amino acid change

brix9-2-5 Tomato Invertase fruit soluble solid content amino acid change

ovate Tomato Unknown fruit shap early stop codon

R Pea Starch branching enzyme seed sugar content transposon

insertion

ehd1 Rice B-type response regulator flowering time amino acid change

hd1 Rice Transcriptional regulator (zinc finger) flowering

time

disrupted coding

sequence

waxy Rice Starch synthase sticky grains intron splicing

defect

rht Wheat Transcriptional regulator (SH2) plant height early stop codon

vrn1 Wheat Transcriptional regulator (MADS) vernalization regulatory change

vrn2 Wheat Transcriptional regulator (ZCCT) vernalization amino acid change

Genes Identified as Controlling Varietal Differences

37

Process of domestication over the yearshellip

Rachel S Meyer 2012

38

Genetic bottleneck

Cultivated crops undergone with narrowing of diversity problem

But this is not the case in weeds

Weeds are the major threats from the beginning of domestication till

today

Problem arose due to

1 Crop mimicry

2 Genetic assimilation

3 Genetic evolution

39

Super- Domestication Vaughn et al (2007) first used the term super-domestication

The processes that lead to a domesticate with dramatically

increased yield that could not be selected in natural environments

from naturally occurring variation without recourse to new

technologies

Super-domesticates can be constructed with knowledge led

approaches based on current needs using the range of new

technologies now available

Plants exploited for continuous selection introduction hybridization

etc which boosted the process of domestication but now the plant

genetic engineering approach is exploiting plants towards synthetic

biology

40

How to use diversitybull Cross two varieties

bull Genome manipulations

Cell fusion hybrids

bull Chromosome manipulation Backcross a new species

bull Generate recombinants Chromosome recombinations

bull Use a new species wild germplasm

Transgenic approach Modern mutagenesis synthetic gene

construction by utilizing green florescent protein genome editing

NGS GWAS sequencing etchelliphelliphelliphelliphellip

41

Reduce genetic bottlenecks through polyplodization

More vigour

SC

Buffering capacity

Heterotic advantage

Enhaced vegetative

charachers

Enhanced oil

Meiotic stability

42

Approach 1 Use one tetraploid and one diploid as parents (4X ndash 2X) followed by the

chromosome doubling of triploid hybrids (Chrom doubling)

a) Cross between B juncea (AjAjBjBj ) and B oleracea (CoCo) to produce hexaploids

(AjAjBjBjCoCo)

(b) Cross between B napus (AnAnCnCn) and B nigra (BniBni) to produce hexaploids

(AnAnBniBniCnCn)

(c) Cross between B carinata (BcaBcaCcaCca) and B rapa (ArAr) to produce hexaploids

(ArArBcaBcaCcaCca)

Approach 2 Use three tetraploids as parents

(a) Cross between B napus (AnAnCnCn) and B carinata (BcaBcaCcaCca) to produce unbalanced

allotetraploids (AnBcaCnCca ndash unreduced gametes gametes with the somatic chromosome

number and cross with B juncea (AjAjBjBj) to obtain allohexaploids (AnAjBcaBjCnCca

(b) Cross between B napus (AnAnCnCn) and B juncea (AjAjBjBj) to produce unbalanced

allotetraploids (AnAjBjCn ndash unreduced gametes) and cross with B carinata (BcaBcaCcaCca) to

obtain allohexaploids (AnAjBcaBjCnCca)

(c) Cross between B carinata (BcaBcaCcaCca) and B juncea (AjAjBjBj) to produce unbalanced

allotetraploids (AjBcaBjCca - ndash unreduced gametes) and cross with B napus (AnAnCnCn) to obtain

allohexaploids (AnAjBcaBjCnCca)

Approach 3 Use three diploids as parents (2X ndash 2X ndash 2X) Cross between B rapa (ArAr) B

nigra (BniBni) and B oleracea (CoCo) sequentially to obtain hexaploid hybrids (ArArBniBniCoCo)

43

Continuehellip

Guijun Yan 2012

44

Applications of Genomic

tools in Super-Domestication

45

Genome Sequencing

Potential methods of sequencing

1 Clone by clone approach

2 Whole genome shotgun approach

3 Combination of the two methods

Till today no of cultivated plants completely sequenced -85

2016- Arachis duranensis

2015- Solanum cumersonii (Wild potato)

(Ref- NCBI)

46

GWAS

It is a study design in which many markers spread across a genome

are genotyped and test a statistical association with a phenotype are

performed locally along the genome

It is also an examination of many common genetic variants in different

individuals to see if any variant is associated with a trait

Used in successfully studying maize sorghum and barley

Method is efficient for large scale low cost genotyping (even with the

minimum number of SNPs)

Cannot be utilized generally because it needs large population size

GWAS identify rare alleles more precisely

If small population we can opt NAM

47

GWAS and whole genome prediction

Xuehui Huang and Bin Han 2014

48

Five high throuput genotyping methods

Xuehui Huang and Bin Han 2014

49

Role of NGS in domestication Capture of novel genes from wild species will be made easier by

understanding the molecular events associated with crop domestication

Re-sequencing of domesticated species can identify low diversity regions

resulting from selection during domestication

To identify gene-specific sequences to aid the cloning of homologues of key

domestication genes from wild relatives

Candidate genes from wild and domesticated plant populations can define

diversity of target genes in wild populations and lead to the discovery of key

genes for important traits by association analysis

NGS of amplicons of large numbers of candidate genes from wild and

domesticated plant populations can define diversity of target genes in

wild populations and lead to the discovery of key genes for important

traits by association analysis

50

NGS

supports the rapid domestication of new plant species and the efficient

identification and capture of novel genetic variation from related species

Allows whole-genome analysis to determine the genetic basis of

phenotypic differences

NGS allows rapid expansion of genomic analysis to investigation of non-

model species

Made rice study easy by related grass

cost-effective method for plant identification

useful strategy to analysis the chloroplast genome sequence from whole-

genome shot-gun sequencing

facilitates managing this diversity and any changes in crop performance

over time due to genetic drift

Patterns of gene expression have been evaluated in hybrids using NGS

51

Two Approaches to Finding Adaptive Genes

Ross-Ibarra et al2007

52

Techniques to re-wild the plants (transgene free)

1 Introgression

breeding

2 Specific

insertion of lost genes

3 Precision

mutagenesis

Palmgren et al2014

53

Process of rewilding

Palmgren et al2014

54

Synthetic biology projects(i) Modifying cereals including wheat to fix atmospheric nitrogen

(ii) Redesigning metabolic pathways to increase the yield of

secondary metabolites or to generate compounds with enhanced

properties

(iii) Transferring the C4 photosynthesis pathway to rice

(iv) Modifying the glycosylation pathway in plants to accommodate

production of therapeutic proteins

(v) Introducing synthetic signal transduction systems that respond to

external cues

55

Synthetic biology projects

Nicholas J Baltes et al 2015

56

Refactoring the N fixation gene cluster from Klebsiella

Karsten Temme et al 2012

Wild SoybeanGlycin soja2n=40

Cultivated soybeanGlycin max 2n=40

24

Increased in domesticate

seed germination

determinate growth

longer pods

bigger (heavier) seeds

earliness

harvest index (seed yieldbiomass)

Decreased in domesticate

seed dispersal

seed dormancy

twining

number of nodes

length of internode

number of pods

photoperiod sensitivity

Common Bean Phaseolus vulgarishttpwwwplantsciencesucdavisedugeptspb143pb143htm

copy Paul Gepts

25

Wild pigeon peaCajanus cajanifolius

Cultivated pigeon pea

26

27

28

WHY OTHERS ARE NOT DOMESTICATED

bull 350000 plants

bull 4629 mammals

bull 9200 birds

bull 10000000 insects

bull 500000 fungi

bull But only 200 plants

bull 15 mammals 5 birds and

bull 2 insects are domesticated

bull Spread of these few species

bull Little change since early

agriculture

bull Repeated domestication of these

species (sometimes)

bull Lack of new species even with

attempts with species known to be

valuable Some groups are good

candidates with no domestication

eg ferns sub-Saharan mammals

29

WHY OTHERS HAVE TO BE DOMESTICATED

New uses and demands ndash biofuels animal feed

medicinalneutraceutical waterclimate food changes

Knowledge why species arenrsquot suitable for domestication or

were not useful

Better understanding of genetics and selection

Sustainability of production

Reliability of production

To meet the food demand in an alternative way

WHY OTHERS HAVE TO BE DOMESTICATED

30

Reallocate biomass for human use

More efficient metabolism and photosynthesis increase

leaf surface decrease root system increase leaf

longevity

Grains more fertile florets larger inflorescence OR

number of ears different ways to get more seed

Larger seeds (automatic vs deliberate selection)

Oil plants increased oil content or more seed

Fiber plants long strong fibers

Domestication syndrome

31

Centers of Domestication

Fuller 2011

32

Centers of Domestication in India

Fuller 2011

33

Indian centers of domestication South India (Deccan centre) Vigna radiate Vigna mungo

Macrotyloma uniflorum (Horse gram) Sataria verticillata S plumila

wheat (macaroni) and two rowed barleybrachiaria ramosa

Orissa (Mahanadi river) Pegion pea Horsegram mung small millets

like Echinichloa Paspalum and Sataria

The Middle Ganges (Harappan civilization) Oryza nivara O rufipogon

and wild sativa Sateria pumia Cannabis sativa even the diffusion of

japonica rice

Saurashtra (Harappan civilization) Eleucine coracana Sateria italica

Paicum spp Brachypodia pearl millet and sorghum Dollicos lablab

The Himalayan foothills of the Punjab region Was a centre of

diversity for Japonica type rice and many temperate fruits and

vegetables

34

DOMESTICATION RELATED TRAITS CONTROLLED BY ONLY FEW GENES

Trait Crops

Plant architecturegrowth habit Ricemaizemilletsbeantomato

Flowering timephotoperiod sensitivity Ricemaizesorghumbeantomato

Fruit size Tomato egg plant

Grain size Ricemaizesorghumbean

Seed dispersal Brassica rice

Inflorescence modification Brassica

Dormancy Bean

35

Genes Crop Moleular and phenotypic function Causative change

Genes identified as controlling domestication traits

tb1 Maize Transcriptional regulator (TCP) plant and

inflorescence structure

regulatory change

tga1 Maize Transcriptional regulator (SBP) seed casing amino acid change

qSH1 Rice Transcriptional regulator (homeodomain)

abscission layer formation shattering

regulatory change

Rc Rice Transcriptional regulator (bHLH) seed color disrupted coding

sequence

sh4 Rice Transcriptional regulator (Myb3) abscission

layer formation shattering

regulatoryamino

acid change

fw22 Tomato Cell signaling fruit weight regulatory change

Q Wheat Transcriptional regulator (AP2) inflorescence

structure

regulatoryamino

acid change

Vrs1 Barley Inflorescence structure Premature stop Amino acid change

Genes of interest in crop domestication and improvement

36

Genes Crop Moleular and phenotypic function Causative change

c1

r1

Maize Transcriptional regulator (MYB) kernel color and

Transcriptional regulator (bHLH) kernel color

regulatory change

sh2 Maize pyrophosphorylase supersweet sweet corn transposon

insertion

su1 Maize isoamylase sweet corn gene amino acid change

brix9-2-5 Tomato Invertase fruit soluble solid content amino acid change

ovate Tomato Unknown fruit shap early stop codon

R Pea Starch branching enzyme seed sugar content transposon

insertion

ehd1 Rice B-type response regulator flowering time amino acid change

hd1 Rice Transcriptional regulator (zinc finger) flowering

time

disrupted coding

sequence

waxy Rice Starch synthase sticky grains intron splicing

defect

rht Wheat Transcriptional regulator (SH2) plant height early stop codon

vrn1 Wheat Transcriptional regulator (MADS) vernalization regulatory change

vrn2 Wheat Transcriptional regulator (ZCCT) vernalization amino acid change

Genes Identified as Controlling Varietal Differences

37

Process of domestication over the yearshellip

Rachel S Meyer 2012

38

Genetic bottleneck

Cultivated crops undergone with narrowing of diversity problem

But this is not the case in weeds

Weeds are the major threats from the beginning of domestication till

today

Problem arose due to

1 Crop mimicry

2 Genetic assimilation

3 Genetic evolution

39

Super- Domestication Vaughn et al (2007) first used the term super-domestication

The processes that lead to a domesticate with dramatically

increased yield that could not be selected in natural environments

from naturally occurring variation without recourse to new

technologies

Super-domesticates can be constructed with knowledge led

approaches based on current needs using the range of new

technologies now available

Plants exploited for continuous selection introduction hybridization

etc which boosted the process of domestication but now the plant

genetic engineering approach is exploiting plants towards synthetic

biology

40

How to use diversitybull Cross two varieties

bull Genome manipulations

Cell fusion hybrids

bull Chromosome manipulation Backcross a new species

bull Generate recombinants Chromosome recombinations

bull Use a new species wild germplasm

Transgenic approach Modern mutagenesis synthetic gene

construction by utilizing green florescent protein genome editing

NGS GWAS sequencing etchelliphelliphelliphelliphellip

41

Reduce genetic bottlenecks through polyplodization

More vigour

SC

Buffering capacity

Heterotic advantage

Enhaced vegetative

charachers

Enhanced oil

Meiotic stability

42

Approach 1 Use one tetraploid and one diploid as parents (4X ndash 2X) followed by the

chromosome doubling of triploid hybrids (Chrom doubling)

a) Cross between B juncea (AjAjBjBj ) and B oleracea (CoCo) to produce hexaploids

(AjAjBjBjCoCo)

(b) Cross between B napus (AnAnCnCn) and B nigra (BniBni) to produce hexaploids

(AnAnBniBniCnCn)

(c) Cross between B carinata (BcaBcaCcaCca) and B rapa (ArAr) to produce hexaploids

(ArArBcaBcaCcaCca)

Approach 2 Use three tetraploids as parents

(a) Cross between B napus (AnAnCnCn) and B carinata (BcaBcaCcaCca) to produce unbalanced

allotetraploids (AnBcaCnCca ndash unreduced gametes gametes with the somatic chromosome

number and cross with B juncea (AjAjBjBj) to obtain allohexaploids (AnAjBcaBjCnCca

(b) Cross between B napus (AnAnCnCn) and B juncea (AjAjBjBj) to produce unbalanced

allotetraploids (AnAjBjCn ndash unreduced gametes) and cross with B carinata (BcaBcaCcaCca) to

obtain allohexaploids (AnAjBcaBjCnCca)

(c) Cross between B carinata (BcaBcaCcaCca) and B juncea (AjAjBjBj) to produce unbalanced

allotetraploids (AjBcaBjCca - ndash unreduced gametes) and cross with B napus (AnAnCnCn) to obtain

allohexaploids (AnAjBcaBjCnCca)

Approach 3 Use three diploids as parents (2X ndash 2X ndash 2X) Cross between B rapa (ArAr) B

nigra (BniBni) and B oleracea (CoCo) sequentially to obtain hexaploid hybrids (ArArBniBniCoCo)

43

Continuehellip

Guijun Yan 2012

44

Applications of Genomic

tools in Super-Domestication

45

Genome Sequencing

Potential methods of sequencing

1 Clone by clone approach

2 Whole genome shotgun approach

3 Combination of the two methods

Till today no of cultivated plants completely sequenced -85

2016- Arachis duranensis

2015- Solanum cumersonii (Wild potato)

(Ref- NCBI)

46

GWAS

It is a study design in which many markers spread across a genome

are genotyped and test a statistical association with a phenotype are

performed locally along the genome

It is also an examination of many common genetic variants in different

individuals to see if any variant is associated with a trait

Used in successfully studying maize sorghum and barley

Method is efficient for large scale low cost genotyping (even with the

minimum number of SNPs)

Cannot be utilized generally because it needs large population size

GWAS identify rare alleles more precisely

If small population we can opt NAM

47

GWAS and whole genome prediction

Xuehui Huang and Bin Han 2014

48

Five high throuput genotyping methods

Xuehui Huang and Bin Han 2014

49

Role of NGS in domestication Capture of novel genes from wild species will be made easier by

understanding the molecular events associated with crop domestication

Re-sequencing of domesticated species can identify low diversity regions

resulting from selection during domestication

To identify gene-specific sequences to aid the cloning of homologues of key

domestication genes from wild relatives

Candidate genes from wild and domesticated plant populations can define

diversity of target genes in wild populations and lead to the discovery of key

genes for important traits by association analysis

NGS of amplicons of large numbers of candidate genes from wild and

domesticated plant populations can define diversity of target genes in

wild populations and lead to the discovery of key genes for important

traits by association analysis

50

NGS

supports the rapid domestication of new plant species and the efficient

identification and capture of novel genetic variation from related species

Allows whole-genome analysis to determine the genetic basis of

phenotypic differences

NGS allows rapid expansion of genomic analysis to investigation of non-

model species

Made rice study easy by related grass

cost-effective method for plant identification

useful strategy to analysis the chloroplast genome sequence from whole-

genome shot-gun sequencing

facilitates managing this diversity and any changes in crop performance

over time due to genetic drift

Patterns of gene expression have been evaluated in hybrids using NGS

51

Two Approaches to Finding Adaptive Genes

Ross-Ibarra et al2007

52

Techniques to re-wild the plants (transgene free)

1 Introgression

breeding

2 Specific

insertion of lost genes

3 Precision

mutagenesis

Palmgren et al2014

53

Process of rewilding

Palmgren et al2014

54

Synthetic biology projects(i) Modifying cereals including wheat to fix atmospheric nitrogen

(ii) Redesigning metabolic pathways to increase the yield of

secondary metabolites or to generate compounds with enhanced

properties

(iii) Transferring the C4 photosynthesis pathway to rice

(iv) Modifying the glycosylation pathway in plants to accommodate

production of therapeutic proteins

(v) Introducing synthetic signal transduction systems that respond to

external cues

55

Synthetic biology projects

Nicholas J Baltes et al 2015

56

Refactoring the N fixation gene cluster from Klebsiella

Karsten Temme et al 2012

Increased in domesticate

seed germination

determinate growth

longer pods

bigger (heavier) seeds

earliness

harvest index (seed yieldbiomass)

Decreased in domesticate

seed dispersal

seed dormancy

twining

number of nodes

length of internode

number of pods

photoperiod sensitivity

Common Bean Phaseolus vulgarishttpwwwplantsciencesucdavisedugeptspb143pb143htm

copy Paul Gepts

25

Wild pigeon peaCajanus cajanifolius

Cultivated pigeon pea

26

27

28

WHY OTHERS ARE NOT DOMESTICATED

bull 350000 plants

bull 4629 mammals

bull 9200 birds

bull 10000000 insects

bull 500000 fungi

bull But only 200 plants

bull 15 mammals 5 birds and

bull 2 insects are domesticated

bull Spread of these few species

bull Little change since early

agriculture

bull Repeated domestication of these

species (sometimes)

bull Lack of new species even with

attempts with species known to be

valuable Some groups are good

candidates with no domestication

eg ferns sub-Saharan mammals

29

WHY OTHERS HAVE TO BE DOMESTICATED

New uses and demands ndash biofuels animal feed

medicinalneutraceutical waterclimate food changes

Knowledge why species arenrsquot suitable for domestication or

were not useful

Better understanding of genetics and selection

Sustainability of production

Reliability of production

To meet the food demand in an alternative way

WHY OTHERS HAVE TO BE DOMESTICATED

30

Reallocate biomass for human use

More efficient metabolism and photosynthesis increase

leaf surface decrease root system increase leaf

longevity

Grains more fertile florets larger inflorescence OR

number of ears different ways to get more seed

Larger seeds (automatic vs deliberate selection)

Oil plants increased oil content or more seed

Fiber plants long strong fibers

Domestication syndrome

31

Centers of Domestication

Fuller 2011

32

Centers of Domestication in India

Fuller 2011

33

Indian centers of domestication South India (Deccan centre) Vigna radiate Vigna mungo

Macrotyloma uniflorum (Horse gram) Sataria verticillata S plumila

wheat (macaroni) and two rowed barleybrachiaria ramosa

Orissa (Mahanadi river) Pegion pea Horsegram mung small millets

like Echinichloa Paspalum and Sataria

The Middle Ganges (Harappan civilization) Oryza nivara O rufipogon

and wild sativa Sateria pumia Cannabis sativa even the diffusion of

japonica rice

Saurashtra (Harappan civilization) Eleucine coracana Sateria italica

Paicum spp Brachypodia pearl millet and sorghum Dollicos lablab

The Himalayan foothills of the Punjab region Was a centre of

diversity for Japonica type rice and many temperate fruits and

vegetables

34

DOMESTICATION RELATED TRAITS CONTROLLED BY ONLY FEW GENES

Trait Crops

Plant architecturegrowth habit Ricemaizemilletsbeantomato

Flowering timephotoperiod sensitivity Ricemaizesorghumbeantomato

Fruit size Tomato egg plant

Grain size Ricemaizesorghumbean

Seed dispersal Brassica rice

Inflorescence modification Brassica

Dormancy Bean

35

Genes Crop Moleular and phenotypic function Causative change

Genes identified as controlling domestication traits

tb1 Maize Transcriptional regulator (TCP) plant and

inflorescence structure

regulatory change

tga1 Maize Transcriptional regulator (SBP) seed casing amino acid change

qSH1 Rice Transcriptional regulator (homeodomain)

abscission layer formation shattering

regulatory change

Rc Rice Transcriptional regulator (bHLH) seed color disrupted coding

sequence

sh4 Rice Transcriptional regulator (Myb3) abscission

layer formation shattering

regulatoryamino

acid change

fw22 Tomato Cell signaling fruit weight regulatory change

Q Wheat Transcriptional regulator (AP2) inflorescence

structure

regulatoryamino

acid change

Vrs1 Barley Inflorescence structure Premature stop Amino acid change

Genes of interest in crop domestication and improvement

36

Genes Crop Moleular and phenotypic function Causative change

c1

r1

Maize Transcriptional regulator (MYB) kernel color and

Transcriptional regulator (bHLH) kernel color

regulatory change

sh2 Maize pyrophosphorylase supersweet sweet corn transposon

insertion

su1 Maize isoamylase sweet corn gene amino acid change

brix9-2-5 Tomato Invertase fruit soluble solid content amino acid change

ovate Tomato Unknown fruit shap early stop codon

R Pea Starch branching enzyme seed sugar content transposon

insertion

ehd1 Rice B-type response regulator flowering time amino acid change

hd1 Rice Transcriptional regulator (zinc finger) flowering

time

disrupted coding

sequence

waxy Rice Starch synthase sticky grains intron splicing

defect

rht Wheat Transcriptional regulator (SH2) plant height early stop codon

vrn1 Wheat Transcriptional regulator (MADS) vernalization regulatory change

vrn2 Wheat Transcriptional regulator (ZCCT) vernalization amino acid change

Genes Identified as Controlling Varietal Differences

37

Process of domestication over the yearshellip

Rachel S Meyer 2012

38

Genetic bottleneck

Cultivated crops undergone with narrowing of diversity problem

But this is not the case in weeds

Weeds are the major threats from the beginning of domestication till

today

Problem arose due to

1 Crop mimicry

2 Genetic assimilation

3 Genetic evolution

39

Super- Domestication Vaughn et al (2007) first used the term super-domestication

The processes that lead to a domesticate with dramatically

increased yield that could not be selected in natural environments

from naturally occurring variation without recourse to new

technologies

Super-domesticates can be constructed with knowledge led

approaches based on current needs using the range of new

technologies now available

Plants exploited for continuous selection introduction hybridization

etc which boosted the process of domestication but now the plant

genetic engineering approach is exploiting plants towards synthetic

biology

40

How to use diversitybull Cross two varieties

bull Genome manipulations

Cell fusion hybrids

bull Chromosome manipulation Backcross a new species

bull Generate recombinants Chromosome recombinations

bull Use a new species wild germplasm

Transgenic approach Modern mutagenesis synthetic gene

construction by utilizing green florescent protein genome editing

NGS GWAS sequencing etchelliphelliphelliphelliphellip

41

Reduce genetic bottlenecks through polyplodization

More vigour

SC

Buffering capacity

Heterotic advantage

Enhaced vegetative

charachers

Enhanced oil

Meiotic stability

42

Approach 1 Use one tetraploid and one diploid as parents (4X ndash 2X) followed by the

chromosome doubling of triploid hybrids (Chrom doubling)

a) Cross between B juncea (AjAjBjBj ) and B oleracea (CoCo) to produce hexaploids

(AjAjBjBjCoCo)

(b) Cross between B napus (AnAnCnCn) and B nigra (BniBni) to produce hexaploids

(AnAnBniBniCnCn)

(c) Cross between B carinata (BcaBcaCcaCca) and B rapa (ArAr) to produce hexaploids

(ArArBcaBcaCcaCca)

Approach 2 Use three tetraploids as parents

(a) Cross between B napus (AnAnCnCn) and B carinata (BcaBcaCcaCca) to produce unbalanced

allotetraploids (AnBcaCnCca ndash unreduced gametes gametes with the somatic chromosome

number and cross with B juncea (AjAjBjBj) to obtain allohexaploids (AnAjBcaBjCnCca

(b) Cross between B napus (AnAnCnCn) and B juncea (AjAjBjBj) to produce unbalanced

allotetraploids (AnAjBjCn ndash unreduced gametes) and cross with B carinata (BcaBcaCcaCca) to

obtain allohexaploids (AnAjBcaBjCnCca)

(c) Cross between B carinata (BcaBcaCcaCca) and B juncea (AjAjBjBj) to produce unbalanced

allotetraploids (AjBcaBjCca - ndash unreduced gametes) and cross with B napus (AnAnCnCn) to obtain

allohexaploids (AnAjBcaBjCnCca)

Approach 3 Use three diploids as parents (2X ndash 2X ndash 2X) Cross between B rapa (ArAr) B

nigra (BniBni) and B oleracea (CoCo) sequentially to obtain hexaploid hybrids (ArArBniBniCoCo)

43

Continuehellip

Guijun Yan 2012

44

Applications of Genomic

tools in Super-Domestication

45

Genome Sequencing

Potential methods of sequencing

1 Clone by clone approach

2 Whole genome shotgun approach

3 Combination of the two methods

Till today no of cultivated plants completely sequenced -85

2016- Arachis duranensis

2015- Solanum cumersonii (Wild potato)

(Ref- NCBI)

46

GWAS

It is a study design in which many markers spread across a genome

are genotyped and test a statistical association with a phenotype are

performed locally along the genome

It is also an examination of many common genetic variants in different

individuals to see if any variant is associated with a trait

Used in successfully studying maize sorghum and barley

Method is efficient for large scale low cost genotyping (even with the

minimum number of SNPs)

Cannot be utilized generally because it needs large population size

GWAS identify rare alleles more precisely

If small population we can opt NAM

47

GWAS and whole genome prediction

Xuehui Huang and Bin Han 2014

48

Five high throuput genotyping methods

Xuehui Huang and Bin Han 2014

49

Role of NGS in domestication Capture of novel genes from wild species will be made easier by

understanding the molecular events associated with crop domestication

Re-sequencing of domesticated species can identify low diversity regions

resulting from selection during domestication

To identify gene-specific sequences to aid the cloning of homologues of key

domestication genes from wild relatives

Candidate genes from wild and domesticated plant populations can define

diversity of target genes in wild populations and lead to the discovery of key

genes for important traits by association analysis

NGS of amplicons of large numbers of candidate genes from wild and

domesticated plant populations can define diversity of target genes in

wild populations and lead to the discovery of key genes for important

traits by association analysis

50

NGS

supports the rapid domestication of new plant species and the efficient

identification and capture of novel genetic variation from related species

Allows whole-genome analysis to determine the genetic basis of

phenotypic differences

NGS allows rapid expansion of genomic analysis to investigation of non-

model species

Made rice study easy by related grass

cost-effective method for plant identification

useful strategy to analysis the chloroplast genome sequence from whole-

genome shot-gun sequencing

facilitates managing this diversity and any changes in crop performance

over time due to genetic drift

Patterns of gene expression have been evaluated in hybrids using NGS

51

Two Approaches to Finding Adaptive Genes

Ross-Ibarra et al2007

52

Techniques to re-wild the plants (transgene free)

1 Introgression

breeding

2 Specific

insertion of lost genes

3 Precision

mutagenesis

Palmgren et al2014

53

Process of rewilding

Palmgren et al2014

54

Synthetic biology projects(i) Modifying cereals including wheat to fix atmospheric nitrogen

(ii) Redesigning metabolic pathways to increase the yield of

secondary metabolites or to generate compounds with enhanced

properties

(iii) Transferring the C4 photosynthesis pathway to rice

(iv) Modifying the glycosylation pathway in plants to accommodate

production of therapeutic proteins

(v) Introducing synthetic signal transduction systems that respond to

external cues

55

Synthetic biology projects

Nicholas J Baltes et al 2015

56

Refactoring the N fixation gene cluster from Klebsiella

Karsten Temme et al 2012

Wild pigeon peaCajanus cajanifolius

Cultivated pigeon pea

26

27

28

WHY OTHERS ARE NOT DOMESTICATED

bull 350000 plants

bull 4629 mammals

bull 9200 birds

bull 10000000 insects

bull 500000 fungi

bull But only 200 plants

bull 15 mammals 5 birds and

bull 2 insects are domesticated

bull Spread of these few species

bull Little change since early

agriculture

bull Repeated domestication of these

species (sometimes)

bull Lack of new species even with

attempts with species known to be

valuable Some groups are good

candidates with no domestication

eg ferns sub-Saharan mammals

29

WHY OTHERS HAVE TO BE DOMESTICATED

New uses and demands ndash biofuels animal feed

medicinalneutraceutical waterclimate food changes

Knowledge why species arenrsquot suitable for domestication or

were not useful

Better understanding of genetics and selection

Sustainability of production

Reliability of production

To meet the food demand in an alternative way

WHY OTHERS HAVE TO BE DOMESTICATED

30

Reallocate biomass for human use

More efficient metabolism and photosynthesis increase

leaf surface decrease root system increase leaf

longevity

Grains more fertile florets larger inflorescence OR

number of ears different ways to get more seed

Larger seeds (automatic vs deliberate selection)

Oil plants increased oil content or more seed

Fiber plants long strong fibers

Domestication syndrome

31

Centers of Domestication

Fuller 2011

32

Centers of Domestication in India

Fuller 2011

33

Indian centers of domestication South India (Deccan centre) Vigna radiate Vigna mungo

Macrotyloma uniflorum (Horse gram) Sataria verticillata S plumila

wheat (macaroni) and two rowed barleybrachiaria ramosa

Orissa (Mahanadi river) Pegion pea Horsegram mung small millets

like Echinichloa Paspalum and Sataria

The Middle Ganges (Harappan civilization) Oryza nivara O rufipogon

and wild sativa Sateria pumia Cannabis sativa even the diffusion of

japonica rice

Saurashtra (Harappan civilization) Eleucine coracana Sateria italica

Paicum spp Brachypodia pearl millet and sorghum Dollicos lablab

The Himalayan foothills of the Punjab region Was a centre of

diversity for Japonica type rice and many temperate fruits and

vegetables

34

DOMESTICATION RELATED TRAITS CONTROLLED BY ONLY FEW GENES

Trait Crops

Plant architecturegrowth habit Ricemaizemilletsbeantomato

Flowering timephotoperiod sensitivity Ricemaizesorghumbeantomato

Fruit size Tomato egg plant

Grain size Ricemaizesorghumbean

Seed dispersal Brassica rice

Inflorescence modification Brassica

Dormancy Bean

35

Genes Crop Moleular and phenotypic function Causative change

Genes identified as controlling domestication traits

tb1 Maize Transcriptional regulator (TCP) plant and

inflorescence structure

regulatory change

tga1 Maize Transcriptional regulator (SBP) seed casing amino acid change

qSH1 Rice Transcriptional regulator (homeodomain)

abscission layer formation shattering

regulatory change

Rc Rice Transcriptional regulator (bHLH) seed color disrupted coding

sequence

sh4 Rice Transcriptional regulator (Myb3) abscission

layer formation shattering

regulatoryamino

acid change

fw22 Tomato Cell signaling fruit weight regulatory change

Q Wheat Transcriptional regulator (AP2) inflorescence

structure

regulatoryamino

acid change

Vrs1 Barley Inflorescence structure Premature stop Amino acid change

Genes of interest in crop domestication and improvement

36

Genes Crop Moleular and phenotypic function Causative change

c1

r1

Maize Transcriptional regulator (MYB) kernel color and

Transcriptional regulator (bHLH) kernel color

regulatory change

sh2 Maize pyrophosphorylase supersweet sweet corn transposon

insertion

su1 Maize isoamylase sweet corn gene amino acid change

brix9-2-5 Tomato Invertase fruit soluble solid content amino acid change

ovate Tomato Unknown fruit shap early stop codon

R Pea Starch branching enzyme seed sugar content transposon

insertion

ehd1 Rice B-type response regulator flowering time amino acid change

hd1 Rice Transcriptional regulator (zinc finger) flowering

time

disrupted coding

sequence

waxy Rice Starch synthase sticky grains intron splicing

defect

rht Wheat Transcriptional regulator (SH2) plant height early stop codon

vrn1 Wheat Transcriptional regulator (MADS) vernalization regulatory change

vrn2 Wheat Transcriptional regulator (ZCCT) vernalization amino acid change

Genes Identified as Controlling Varietal Differences

37

Process of domestication over the yearshellip

Rachel S Meyer 2012

38

Genetic bottleneck

Cultivated crops undergone with narrowing of diversity problem

But this is not the case in weeds

Weeds are the major threats from the beginning of domestication till

today

Problem arose due to

1 Crop mimicry

2 Genetic assimilation

3 Genetic evolution

39

Super- Domestication Vaughn et al (2007) first used the term super-domestication

The processes that lead to a domesticate with dramatically

increased yield that could not be selected in natural environments

from naturally occurring variation without recourse to new

technologies

Super-domesticates can be constructed with knowledge led

approaches based on current needs using the range of new

technologies now available

Plants exploited for continuous selection introduction hybridization

etc which boosted the process of domestication but now the plant

genetic engineering approach is exploiting plants towards synthetic

biology

40

How to use diversitybull Cross two varieties

bull Genome manipulations

Cell fusion hybrids

bull Chromosome manipulation Backcross a new species

bull Generate recombinants Chromosome recombinations

bull Use a new species wild germplasm

Transgenic approach Modern mutagenesis synthetic gene

construction by utilizing green florescent protein genome editing

NGS GWAS sequencing etchelliphelliphelliphelliphellip

41

Reduce genetic bottlenecks through polyplodization

More vigour

SC

Buffering capacity

Heterotic advantage

Enhaced vegetative

charachers

Enhanced oil

Meiotic stability

42

Approach 1 Use one tetraploid and one diploid as parents (4X ndash 2X) followed by the

chromosome doubling of triploid hybrids (Chrom doubling)

a) Cross between B juncea (AjAjBjBj ) and B oleracea (CoCo) to produce hexaploids

(AjAjBjBjCoCo)

(b) Cross between B napus (AnAnCnCn) and B nigra (BniBni) to produce hexaploids

(AnAnBniBniCnCn)

(c) Cross between B carinata (BcaBcaCcaCca) and B rapa (ArAr) to produce hexaploids

(ArArBcaBcaCcaCca)

Approach 2 Use three tetraploids as parents

(a) Cross between B napus (AnAnCnCn) and B carinata (BcaBcaCcaCca) to produce unbalanced

allotetraploids (AnBcaCnCca ndash unreduced gametes gametes with the somatic chromosome

number and cross with B juncea (AjAjBjBj) to obtain allohexaploids (AnAjBcaBjCnCca

(b) Cross between B napus (AnAnCnCn) and B juncea (AjAjBjBj) to produce unbalanced

allotetraploids (AnAjBjCn ndash unreduced gametes) and cross with B carinata (BcaBcaCcaCca) to

obtain allohexaploids (AnAjBcaBjCnCca)

(c) Cross between B carinata (BcaBcaCcaCca) and B juncea (AjAjBjBj) to produce unbalanced

allotetraploids (AjBcaBjCca - ndash unreduced gametes) and cross with B napus (AnAnCnCn) to obtain

allohexaploids (AnAjBcaBjCnCca)

Approach 3 Use three diploids as parents (2X ndash 2X ndash 2X) Cross between B rapa (ArAr) B

nigra (BniBni) and B oleracea (CoCo) sequentially to obtain hexaploid hybrids (ArArBniBniCoCo)

43

Continuehellip

Guijun Yan 2012

44

Applications of Genomic

tools in Super-Domestication

45

Genome Sequencing

Potential methods of sequencing

1 Clone by clone approach

2 Whole genome shotgun approach

3 Combination of the two methods

Till today no of cultivated plants completely sequenced -85

2016- Arachis duranensis

2015- Solanum cumersonii (Wild potato)

(Ref- NCBI)

46

GWAS

It is a study design in which many markers spread across a genome

are genotyped and test a statistical association with a phenotype are

performed locally along the genome

It is also an examination of many common genetic variants in different

individuals to see if any variant is associated with a trait

Used in successfully studying maize sorghum and barley

Method is efficient for large scale low cost genotyping (even with the

minimum number of SNPs)

Cannot be utilized generally because it needs large population size

GWAS identify rare alleles more precisely

If small population we can opt NAM

47

GWAS and whole genome prediction

Xuehui Huang and Bin Han 2014

48

Five high throuput genotyping methods

Xuehui Huang and Bin Han 2014

49

Role of NGS in domestication Capture of novel genes from wild species will be made easier by

understanding the molecular events associated with crop domestication

Re-sequencing of domesticated species can identify low diversity regions

resulting from selection during domestication

To identify gene-specific sequences to aid the cloning of homologues of key

domestication genes from wild relatives

Candidate genes from wild and domesticated plant populations can define

diversity of target genes in wild populations and lead to the discovery of key

genes for important traits by association analysis

NGS of amplicons of large numbers of candidate genes from wild and

domesticated plant populations can define diversity of target genes in

wild populations and lead to the discovery of key genes for important

traits by association analysis

50

NGS

supports the rapid domestication of new plant species and the efficient

identification and capture of novel genetic variation from related species

Allows whole-genome analysis to determine the genetic basis of

phenotypic differences

NGS allows rapid expansion of genomic analysis to investigation of non-

model species

Made rice study easy by related grass

cost-effective method for plant identification

useful strategy to analysis the chloroplast genome sequence from whole-

genome shot-gun sequencing

facilitates managing this diversity and any changes in crop performance

over time due to genetic drift

Patterns of gene expression have been evaluated in hybrids using NGS

51

Two Approaches to Finding Adaptive Genes

Ross-Ibarra et al2007

52

Techniques to re-wild the plants (transgene free)

1 Introgression

breeding

2 Specific

insertion of lost genes

3 Precision

mutagenesis

Palmgren et al2014

53

Process of rewilding

Palmgren et al2014

54

Synthetic biology projects(i) Modifying cereals including wheat to fix atmospheric nitrogen

(ii) Redesigning metabolic pathways to increase the yield of

secondary metabolites or to generate compounds with enhanced

properties

(iii) Transferring the C4 photosynthesis pathway to rice

(iv) Modifying the glycosylation pathway in plants to accommodate

production of therapeutic proteins

(v) Introducing synthetic signal transduction systems that respond to

external cues

55

Synthetic biology projects

Nicholas J Baltes et al 2015

56

Refactoring the N fixation gene cluster from Klebsiella

Karsten Temme et al 2012

27

28

WHY OTHERS ARE NOT DOMESTICATED

bull 350000 plants

bull 4629 mammals

bull 9200 birds

bull 10000000 insects

bull 500000 fungi

bull But only 200 plants

bull 15 mammals 5 birds and

bull 2 insects are domesticated

bull Spread of these few species

bull Little change since early

agriculture

bull Repeated domestication of these

species (sometimes)

bull Lack of new species even with

attempts with species known to be

valuable Some groups are good

candidates with no domestication

eg ferns sub-Saharan mammals

29

WHY OTHERS HAVE TO BE DOMESTICATED

New uses and demands ndash biofuels animal feed

medicinalneutraceutical waterclimate food changes

Knowledge why species arenrsquot suitable for domestication or

were not useful

Better understanding of genetics and selection

Sustainability of production

Reliability of production

To meet the food demand in an alternative way

WHY OTHERS HAVE TO BE DOMESTICATED

30

Reallocate biomass for human use

More efficient metabolism and photosynthesis increase

leaf surface decrease root system increase leaf

longevity

Grains more fertile florets larger inflorescence OR

number of ears different ways to get more seed

Larger seeds (automatic vs deliberate selection)

Oil plants increased oil content or more seed

Fiber plants long strong fibers

Domestication syndrome

31

Centers of Domestication

Fuller 2011

32

Centers of Domestication in India

Fuller 2011

33

Indian centers of domestication South India (Deccan centre) Vigna radiate Vigna mungo

Macrotyloma uniflorum (Horse gram) Sataria verticillata S plumila

wheat (macaroni) and two rowed barleybrachiaria ramosa

Orissa (Mahanadi river) Pegion pea Horsegram mung small millets

like Echinichloa Paspalum and Sataria

The Middle Ganges (Harappan civilization) Oryza nivara O rufipogon

and wild sativa Sateria pumia Cannabis sativa even the diffusion of

japonica rice

Saurashtra (Harappan civilization) Eleucine coracana Sateria italica

Paicum spp Brachypodia pearl millet and sorghum Dollicos lablab

The Himalayan foothills of the Punjab region Was a centre of

diversity for Japonica type rice and many temperate fruits and

vegetables

34

DOMESTICATION RELATED TRAITS CONTROLLED BY ONLY FEW GENES

Trait Crops

Plant architecturegrowth habit Ricemaizemilletsbeantomato

Flowering timephotoperiod sensitivity Ricemaizesorghumbeantomato

Fruit size Tomato egg plant

Grain size Ricemaizesorghumbean

Seed dispersal Brassica rice

Inflorescence modification Brassica

Dormancy Bean

35

Genes Crop Moleular and phenotypic function Causative change

Genes identified as controlling domestication traits

tb1 Maize Transcriptional regulator (TCP) plant and

inflorescence structure

regulatory change

tga1 Maize Transcriptional regulator (SBP) seed casing amino acid change

qSH1 Rice Transcriptional regulator (homeodomain)

abscission layer formation shattering

regulatory change

Rc Rice Transcriptional regulator (bHLH) seed color disrupted coding

sequence

sh4 Rice Transcriptional regulator (Myb3) abscission

layer formation shattering

regulatoryamino

acid change

fw22 Tomato Cell signaling fruit weight regulatory change

Q Wheat Transcriptional regulator (AP2) inflorescence

structure

regulatoryamino

acid change

Vrs1 Barley Inflorescence structure Premature stop Amino acid change

Genes of interest in crop domestication and improvement

36

Genes Crop Moleular and phenotypic function Causative change

c1

r1

Maize Transcriptional regulator (MYB) kernel color and

Transcriptional regulator (bHLH) kernel color

regulatory change

sh2 Maize pyrophosphorylase supersweet sweet corn transposon

insertion

su1 Maize isoamylase sweet corn gene amino acid change

brix9-2-5 Tomato Invertase fruit soluble solid content amino acid change

ovate Tomato Unknown fruit shap early stop codon

R Pea Starch branching enzyme seed sugar content transposon

insertion

ehd1 Rice B-type response regulator flowering time amino acid change

hd1 Rice Transcriptional regulator (zinc finger) flowering

time

disrupted coding

sequence

waxy Rice Starch synthase sticky grains intron splicing

defect

rht Wheat Transcriptional regulator (SH2) plant height early stop codon

vrn1 Wheat Transcriptional regulator (MADS) vernalization regulatory change

vrn2 Wheat Transcriptional regulator (ZCCT) vernalization amino acid change

Genes Identified as Controlling Varietal Differences

37

Process of domestication over the yearshellip

Rachel S Meyer 2012

38

Genetic bottleneck

Cultivated crops undergone with narrowing of diversity problem

But this is not the case in weeds

Weeds are the major threats from the beginning of domestication till

today

Problem arose due to

1 Crop mimicry

2 Genetic assimilation

3 Genetic evolution

39

Super- Domestication Vaughn et al (2007) first used the term super-domestication

The processes that lead to a domesticate with dramatically

increased yield that could not be selected in natural environments

from naturally occurring variation without recourse to new

technologies

Super-domesticates can be constructed with knowledge led

approaches based on current needs using the range of new

technologies now available

Plants exploited for continuous selection introduction hybridization

etc which boosted the process of domestication but now the plant

genetic engineering approach is exploiting plants towards synthetic

biology

40

How to use diversitybull Cross two varieties

bull Genome manipulations

Cell fusion hybrids

bull Chromosome manipulation Backcross a new species

bull Generate recombinants Chromosome recombinations

bull Use a new species wild germplasm

Transgenic approach Modern mutagenesis synthetic gene

construction by utilizing green florescent protein genome editing

NGS GWAS sequencing etchelliphelliphelliphelliphellip

41

Reduce genetic bottlenecks through polyplodization

More vigour

SC

Buffering capacity

Heterotic advantage

Enhaced vegetative

charachers

Enhanced oil

Meiotic stability

42

Approach 1 Use one tetraploid and one diploid as parents (4X ndash 2X) followed by the

chromosome doubling of triploid hybrids (Chrom doubling)

a) Cross between B juncea (AjAjBjBj ) and B oleracea (CoCo) to produce hexaploids

(AjAjBjBjCoCo)

(b) Cross between B napus (AnAnCnCn) and B nigra (BniBni) to produce hexaploids

(AnAnBniBniCnCn)

(c) Cross between B carinata (BcaBcaCcaCca) and B rapa (ArAr) to produce hexaploids

(ArArBcaBcaCcaCca)

Approach 2 Use three tetraploids as parents

(a) Cross between B napus (AnAnCnCn) and B carinata (BcaBcaCcaCca) to produce unbalanced

allotetraploids (AnBcaCnCca ndash unreduced gametes gametes with the somatic chromosome

number and cross with B juncea (AjAjBjBj) to obtain allohexaploids (AnAjBcaBjCnCca

(b) Cross between B napus (AnAnCnCn) and B juncea (AjAjBjBj) to produce unbalanced

allotetraploids (AnAjBjCn ndash unreduced gametes) and cross with B carinata (BcaBcaCcaCca) to

obtain allohexaploids (AnAjBcaBjCnCca)

(c) Cross between B carinata (BcaBcaCcaCca) and B juncea (AjAjBjBj) to produce unbalanced

allotetraploids (AjBcaBjCca - ndash unreduced gametes) and cross with B napus (AnAnCnCn) to obtain

allohexaploids (AnAjBcaBjCnCca)

Approach 3 Use three diploids as parents (2X ndash 2X ndash 2X) Cross between B rapa (ArAr) B

nigra (BniBni) and B oleracea (CoCo) sequentially to obtain hexaploid hybrids (ArArBniBniCoCo)

43

Continuehellip

Guijun Yan 2012

44

Applications of Genomic

tools in Super-Domestication

45

Genome Sequencing

Potential methods of sequencing

1 Clone by clone approach

2 Whole genome shotgun approach

3 Combination of the two methods

Till today no of cultivated plants completely sequenced -85

2016- Arachis duranensis

2015- Solanum cumersonii (Wild potato)

(Ref- NCBI)

46

GWAS

It is a study design in which many markers spread across a genome

are genotyped and test a statistical association with a phenotype are

performed locally along the genome

It is also an examination of many common genetic variants in different

individuals to see if any variant is associated with a trait

Used in successfully studying maize sorghum and barley

Method is efficient for large scale low cost genotyping (even with the

minimum number of SNPs)

Cannot be utilized generally because it needs large population size

GWAS identify rare alleles more precisely

If small population we can opt NAM

47

GWAS and whole genome prediction

Xuehui Huang and Bin Han 2014

48

Five high throuput genotyping methods

Xuehui Huang and Bin Han 2014

49

Role of NGS in domestication Capture of novel genes from wild species will be made easier by

understanding the molecular events associated with crop domestication

Re-sequencing of domesticated species can identify low diversity regions

resulting from selection during domestication

To identify gene-specific sequences to aid the cloning of homologues of key

domestication genes from wild relatives

Candidate genes from wild and domesticated plant populations can define

diversity of target genes in wild populations and lead to the discovery of key

genes for important traits by association analysis

NGS of amplicons of large numbers of candidate genes from wild and

domesticated plant populations can define diversity of target genes in

wild populations and lead to the discovery of key genes for important

traits by association analysis

50

NGS

supports the rapid domestication of new plant species and the efficient

identification and capture of novel genetic variation from related species

Allows whole-genome analysis to determine the genetic basis of

phenotypic differences

NGS allows rapid expansion of genomic analysis to investigation of non-

model species

Made rice study easy by related grass

cost-effective method for plant identification

useful strategy to analysis the chloroplast genome sequence from whole-

genome shot-gun sequencing

facilitates managing this diversity and any changes in crop performance

over time due to genetic drift

Patterns of gene expression have been evaluated in hybrids using NGS

51

Two Approaches to Finding Adaptive Genes

Ross-Ibarra et al2007

52

Techniques to re-wild the plants (transgene free)

1 Introgression

breeding

2 Specific

insertion of lost genes

3 Precision

mutagenesis

Palmgren et al2014

53

Process of rewilding

Palmgren et al2014

54

Synthetic biology projects(i) Modifying cereals including wheat to fix atmospheric nitrogen

(ii) Redesigning metabolic pathways to increase the yield of

secondary metabolites or to generate compounds with enhanced

properties

(iii) Transferring the C4 photosynthesis pathway to rice

(iv) Modifying the glycosylation pathway in plants to accommodate

production of therapeutic proteins

(v) Introducing synthetic signal transduction systems that respond to

external cues

55

Synthetic biology projects

Nicholas J Baltes et al 2015

56

Refactoring the N fixation gene cluster from Klebsiella

Karsten Temme et al 2012

28

WHY OTHERS ARE NOT DOMESTICATED

bull 350000 plants

bull 4629 mammals

bull 9200 birds

bull 10000000 insects

bull 500000 fungi

bull But only 200 plants

bull 15 mammals 5 birds and

bull 2 insects are domesticated

bull Spread of these few species

bull Little change since early

agriculture

bull Repeated domestication of these

species (sometimes)

bull Lack of new species even with

attempts with species known to be

valuable Some groups are good

candidates with no domestication

eg ferns sub-Saharan mammals

29

WHY OTHERS HAVE TO BE DOMESTICATED

New uses and demands ndash biofuels animal feed

medicinalneutraceutical waterclimate food changes

Knowledge why species arenrsquot suitable for domestication or

were not useful

Better understanding of genetics and selection

Sustainability of production

Reliability of production

To meet the food demand in an alternative way

WHY OTHERS HAVE TO BE DOMESTICATED

30

Reallocate biomass for human use

More efficient metabolism and photosynthesis increase

leaf surface decrease root system increase leaf

longevity

Grains more fertile florets larger inflorescence OR

number of ears different ways to get more seed

Larger seeds (automatic vs deliberate selection)

Oil plants increased oil content or more seed

Fiber plants long strong fibers

Domestication syndrome

31

Centers of Domestication

Fuller 2011

32

Centers of Domestication in India

Fuller 2011

33

Indian centers of domestication South India (Deccan centre) Vigna radiate Vigna mungo

Macrotyloma uniflorum (Horse gram) Sataria verticillata S plumila

wheat (macaroni) and two rowed barleybrachiaria ramosa

Orissa (Mahanadi river) Pegion pea Horsegram mung small millets

like Echinichloa Paspalum and Sataria

The Middle Ganges (Harappan civilization) Oryza nivara O rufipogon

and wild sativa Sateria pumia Cannabis sativa even the diffusion of

japonica rice

Saurashtra (Harappan civilization) Eleucine coracana Sateria italica

Paicum spp Brachypodia pearl millet and sorghum Dollicos lablab

The Himalayan foothills of the Punjab region Was a centre of

diversity for Japonica type rice and many temperate fruits and

vegetables

34

DOMESTICATION RELATED TRAITS CONTROLLED BY ONLY FEW GENES

Trait Crops

Plant architecturegrowth habit Ricemaizemilletsbeantomato

Flowering timephotoperiod sensitivity Ricemaizesorghumbeantomato

Fruit size Tomato egg plant

Grain size Ricemaizesorghumbean

Seed dispersal Brassica rice

Inflorescence modification Brassica

Dormancy Bean

35

Genes Crop Moleular and phenotypic function Causative change

Genes identified as controlling domestication traits

tb1 Maize Transcriptional regulator (TCP) plant and

inflorescence structure

regulatory change

tga1 Maize Transcriptional regulator (SBP) seed casing amino acid change

qSH1 Rice Transcriptional regulator (homeodomain)

abscission layer formation shattering

regulatory change

Rc Rice Transcriptional regulator (bHLH) seed color disrupted coding

sequence

sh4 Rice Transcriptional regulator (Myb3) abscission

layer formation shattering

regulatoryamino

acid change

fw22 Tomato Cell signaling fruit weight regulatory change

Q Wheat Transcriptional regulator (AP2) inflorescence

structure

regulatoryamino

acid change

Vrs1 Barley Inflorescence structure Premature stop Amino acid change

Genes of interest in crop domestication and improvement

36

Genes Crop Moleular and phenotypic function Causative change

c1

r1

Maize Transcriptional regulator (MYB) kernel color and

Transcriptional regulator (bHLH) kernel color

regulatory change

sh2 Maize pyrophosphorylase supersweet sweet corn transposon

insertion

su1 Maize isoamylase sweet corn gene amino acid change

brix9-2-5 Tomato Invertase fruit soluble solid content amino acid change

ovate Tomato Unknown fruit shap early stop codon

R Pea Starch branching enzyme seed sugar content transposon

insertion

ehd1 Rice B-type response regulator flowering time amino acid change

hd1 Rice Transcriptional regulator (zinc finger) flowering

time

disrupted coding

sequence

waxy Rice Starch synthase sticky grains intron splicing

defect

rht Wheat Transcriptional regulator (SH2) plant height early stop codon

vrn1 Wheat Transcriptional regulator (MADS) vernalization regulatory change

vrn2 Wheat Transcriptional regulator (ZCCT) vernalization amino acid change

Genes Identified as Controlling Varietal Differences

37

Process of domestication over the yearshellip

Rachel S Meyer 2012

38

Genetic bottleneck

Cultivated crops undergone with narrowing of diversity problem

But this is not the case in weeds

Weeds are the major threats from the beginning of domestication till

today

Problem arose due to

1 Crop mimicry

2 Genetic assimilation

3 Genetic evolution

39

Super- Domestication Vaughn et al (2007) first used the term super-domestication

The processes that lead to a domesticate with dramatically

increased yield that could not be selected in natural environments

from naturally occurring variation without recourse to new

technologies

Super-domesticates can be constructed with knowledge led

approaches based on current needs using the range of new

technologies now available

Plants exploited for continuous selection introduction hybridization

etc which boosted the process of domestication but now the plant

genetic engineering approach is exploiting plants towards synthetic

biology

40

How to use diversitybull Cross two varieties

bull Genome manipulations

Cell fusion hybrids

bull Chromosome manipulation Backcross a new species

bull Generate recombinants Chromosome recombinations

bull Use a new species wild germplasm

Transgenic approach Modern mutagenesis synthetic gene

construction by utilizing green florescent protein genome editing

NGS GWAS sequencing etchelliphelliphelliphelliphellip

41

Reduce genetic bottlenecks through polyplodization

More vigour

SC

Buffering capacity

Heterotic advantage

Enhaced vegetative

charachers

Enhanced oil

Meiotic stability

42

Approach 1 Use one tetraploid and one diploid as parents (4X ndash 2X) followed by the

chromosome doubling of triploid hybrids (Chrom doubling)

a) Cross between B juncea (AjAjBjBj ) and B oleracea (CoCo) to produce hexaploids

(AjAjBjBjCoCo)

(b) Cross between B napus (AnAnCnCn) and B nigra (BniBni) to produce hexaploids

(AnAnBniBniCnCn)

(c) Cross between B carinata (BcaBcaCcaCca) and B rapa (ArAr) to produce hexaploids

(ArArBcaBcaCcaCca)

Approach 2 Use three tetraploids as parents

(a) Cross between B napus (AnAnCnCn) and B carinata (BcaBcaCcaCca) to produce unbalanced

allotetraploids (AnBcaCnCca ndash unreduced gametes gametes with the somatic chromosome

number and cross with B juncea (AjAjBjBj) to obtain allohexaploids (AnAjBcaBjCnCca

(b) Cross between B napus (AnAnCnCn) and B juncea (AjAjBjBj) to produce unbalanced

allotetraploids (AnAjBjCn ndash unreduced gametes) and cross with B carinata (BcaBcaCcaCca) to

obtain allohexaploids (AnAjBcaBjCnCca)

(c) Cross between B carinata (BcaBcaCcaCca) and B juncea (AjAjBjBj) to produce unbalanced

allotetraploids (AjBcaBjCca - ndash unreduced gametes) and cross with B napus (AnAnCnCn) to obtain

allohexaploids (AnAjBcaBjCnCca)

Approach 3 Use three diploids as parents (2X ndash 2X ndash 2X) Cross between B rapa (ArAr) B

nigra (BniBni) and B oleracea (CoCo) sequentially to obtain hexaploid hybrids (ArArBniBniCoCo)

43

Continuehellip

Guijun Yan 2012

44

Applications of Genomic

tools in Super-Domestication

45

Genome Sequencing

Potential methods of sequencing

1 Clone by clone approach

2 Whole genome shotgun approach

3 Combination of the two methods

Till today no of cultivated plants completely sequenced -85

2016- Arachis duranensis

2015- Solanum cumersonii (Wild potato)

(Ref- NCBI)

46

GWAS

It is a study design in which many markers spread across a genome

are genotyped and test a statistical association with a phenotype are

performed locally along the genome

It is also an examination of many common genetic variants in different

individuals to see if any variant is associated with a trait

Used in successfully studying maize sorghum and barley

Method is efficient for large scale low cost genotyping (even with the

minimum number of SNPs)

Cannot be utilized generally because it needs large population size

GWAS identify rare alleles more precisely

If small population we can opt NAM

47

GWAS and whole genome prediction

Xuehui Huang and Bin Han 2014

48

Five high throuput genotyping methods

Xuehui Huang and Bin Han 2014

49

Role of NGS in domestication Capture of novel genes from wild species will be made easier by

understanding the molecular events associated with crop domestication

Re-sequencing of domesticated species can identify low diversity regions

resulting from selection during domestication

To identify gene-specific sequences to aid the cloning of homologues of key

domestication genes from wild relatives

Candidate genes from wild and domesticated plant populations can define

diversity of target genes in wild populations and lead to the discovery of key

genes for important traits by association analysis

NGS of amplicons of large numbers of candidate genes from wild and

domesticated plant populations can define diversity of target genes in

wild populations and lead to the discovery of key genes for important

traits by association analysis

50

NGS

supports the rapid domestication of new plant species and the efficient

identification and capture of novel genetic variation from related species

Allows whole-genome analysis to determine the genetic basis of

phenotypic differences

NGS allows rapid expansion of genomic analysis to investigation of non-

model species

Made rice study easy by related grass

cost-effective method for plant identification

useful strategy to analysis the chloroplast genome sequence from whole-

genome shot-gun sequencing

facilitates managing this diversity and any changes in crop performance

over time due to genetic drift

Patterns of gene expression have been evaluated in hybrids using NGS

51

Two Approaches to Finding Adaptive Genes

Ross-Ibarra et al2007

52

Techniques to re-wild the plants (transgene free)

1 Introgression

breeding

2 Specific

insertion of lost genes

3 Precision

mutagenesis

Palmgren et al2014

53

Process of rewilding

Palmgren et al2014

54

Synthetic biology projects(i) Modifying cereals including wheat to fix atmospheric nitrogen

(ii) Redesigning metabolic pathways to increase the yield of

secondary metabolites or to generate compounds with enhanced

properties

(iii) Transferring the C4 photosynthesis pathway to rice

(iv) Modifying the glycosylation pathway in plants to accommodate

production of therapeutic proteins

(v) Introducing synthetic signal transduction systems that respond to

external cues

55

Synthetic biology projects

Nicholas J Baltes et al 2015

56

Refactoring the N fixation gene cluster from Klebsiella

Karsten Temme et al 2012

29

WHY OTHERS HAVE TO BE DOMESTICATED

New uses and demands ndash biofuels animal feed

medicinalneutraceutical waterclimate food changes

Knowledge why species arenrsquot suitable for domestication or

were not useful

Better understanding of genetics and selection

Sustainability of production

Reliability of production

To meet the food demand in an alternative way

WHY OTHERS HAVE TO BE DOMESTICATED

30

Reallocate biomass for human use

More efficient metabolism and photosynthesis increase

leaf surface decrease root system increase leaf

longevity

Grains more fertile florets larger inflorescence OR

number of ears different ways to get more seed

Larger seeds (automatic vs deliberate selection)

Oil plants increased oil content or more seed

Fiber plants long strong fibers

Domestication syndrome

31

Centers of Domestication

Fuller 2011

32

Centers of Domestication in India

Fuller 2011

33

Indian centers of domestication South India (Deccan centre) Vigna radiate Vigna mungo

Macrotyloma uniflorum (Horse gram) Sataria verticillata S plumila

wheat (macaroni) and two rowed barleybrachiaria ramosa

Orissa (Mahanadi river) Pegion pea Horsegram mung small millets

like Echinichloa Paspalum and Sataria

The Middle Ganges (Harappan civilization) Oryza nivara O rufipogon

and wild sativa Sateria pumia Cannabis sativa even the diffusion of

japonica rice

Saurashtra (Harappan civilization) Eleucine coracana Sateria italica

Paicum spp Brachypodia pearl millet and sorghum Dollicos lablab

The Himalayan foothills of the Punjab region Was a centre of

diversity for Japonica type rice and many temperate fruits and

vegetables

34

DOMESTICATION RELATED TRAITS CONTROLLED BY ONLY FEW GENES

Trait Crops

Plant architecturegrowth habit Ricemaizemilletsbeantomato

Flowering timephotoperiod sensitivity Ricemaizesorghumbeantomato

Fruit size Tomato egg plant

Grain size Ricemaizesorghumbean

Seed dispersal Brassica rice

Inflorescence modification Brassica

Dormancy Bean

35

Genes Crop Moleular and phenotypic function Causative change

Genes identified as controlling domestication traits

tb1 Maize Transcriptional regulator (TCP) plant and

inflorescence structure

regulatory change

tga1 Maize Transcriptional regulator (SBP) seed casing amino acid change

qSH1 Rice Transcriptional regulator (homeodomain)

abscission layer formation shattering

regulatory change

Rc Rice Transcriptional regulator (bHLH) seed color disrupted coding

sequence

sh4 Rice Transcriptional regulator (Myb3) abscission

layer formation shattering

regulatoryamino

acid change

fw22 Tomato Cell signaling fruit weight regulatory change

Q Wheat Transcriptional regulator (AP2) inflorescence

structure

regulatoryamino

acid change

Vrs1 Barley Inflorescence structure Premature stop Amino acid change

Genes of interest in crop domestication and improvement

36

Genes Crop Moleular and phenotypic function Causative change

c1

r1

Maize Transcriptional regulator (MYB) kernel color and

Transcriptional regulator (bHLH) kernel color

regulatory change

sh2 Maize pyrophosphorylase supersweet sweet corn transposon

insertion

su1 Maize isoamylase sweet corn gene amino acid change

brix9-2-5 Tomato Invertase fruit soluble solid content amino acid change

ovate Tomato Unknown fruit shap early stop codon

R Pea Starch branching enzyme seed sugar content transposon

insertion

ehd1 Rice B-type response regulator flowering time amino acid change

hd1 Rice Transcriptional regulator (zinc finger) flowering

time

disrupted coding

sequence

waxy Rice Starch synthase sticky grains intron splicing

defect

rht Wheat Transcriptional regulator (SH2) plant height early stop codon

vrn1 Wheat Transcriptional regulator (MADS) vernalization regulatory change

vrn2 Wheat Transcriptional regulator (ZCCT) vernalization amino acid change

Genes Identified as Controlling Varietal Differences

37

Process of domestication over the yearshellip

Rachel S Meyer 2012

38

Genetic bottleneck

Cultivated crops undergone with narrowing of diversity problem

But this is not the case in weeds

Weeds are the major threats from the beginning of domestication till

today

Problem arose due to

1 Crop mimicry

2 Genetic assimilation

3 Genetic evolution

39

Super- Domestication Vaughn et al (2007) first used the term super-domestication

The processes that lead to a domesticate with dramatically

increased yield that could not be selected in natural environments

from naturally occurring variation without recourse to new

technologies

Super-domesticates can be constructed with knowledge led

approaches based on current needs using the range of new

technologies now available

Plants exploited for continuous selection introduction hybridization

etc which boosted the process of domestication but now the plant

genetic engineering approach is exploiting plants towards synthetic

biology

40

How to use diversitybull Cross two varieties

bull Genome manipulations

Cell fusion hybrids

bull Chromosome manipulation Backcross a new species

bull Generate recombinants Chromosome recombinations

bull Use a new species wild germplasm

Transgenic approach Modern mutagenesis synthetic gene

construction by utilizing green florescent protein genome editing

NGS GWAS sequencing etchelliphelliphelliphelliphellip

41

Reduce genetic bottlenecks through polyplodization

More vigour

SC

Buffering capacity

Heterotic advantage

Enhaced vegetative

charachers

Enhanced oil

Meiotic stability

42

Approach 1 Use one tetraploid and one diploid as parents (4X ndash 2X) followed by the

chromosome doubling of triploid hybrids (Chrom doubling)

a) Cross between B juncea (AjAjBjBj ) and B oleracea (CoCo) to produce hexaploids

(AjAjBjBjCoCo)

(b) Cross between B napus (AnAnCnCn) and B nigra (BniBni) to produce hexaploids

(AnAnBniBniCnCn)

(c) Cross between B carinata (BcaBcaCcaCca) and B rapa (ArAr) to produce hexaploids

(ArArBcaBcaCcaCca)

Approach 2 Use three tetraploids as parents

(a) Cross between B napus (AnAnCnCn) and B carinata (BcaBcaCcaCca) to produce unbalanced

allotetraploids (AnBcaCnCca ndash unreduced gametes gametes with the somatic chromosome

number and cross with B juncea (AjAjBjBj) to obtain allohexaploids (AnAjBcaBjCnCca

(b) Cross between B napus (AnAnCnCn) and B juncea (AjAjBjBj) to produce unbalanced

allotetraploids (AnAjBjCn ndash unreduced gametes) and cross with B carinata (BcaBcaCcaCca) to

obtain allohexaploids (AnAjBcaBjCnCca)

(c) Cross between B carinata (BcaBcaCcaCca) and B juncea (AjAjBjBj) to produce unbalanced

allotetraploids (AjBcaBjCca - ndash unreduced gametes) and cross with B napus (AnAnCnCn) to obtain

allohexaploids (AnAjBcaBjCnCca)

Approach 3 Use three diploids as parents (2X ndash 2X ndash 2X) Cross between B rapa (ArAr) B

nigra (BniBni) and B oleracea (CoCo) sequentially to obtain hexaploid hybrids (ArArBniBniCoCo)

43

Continuehellip

Guijun Yan 2012

44

Applications of Genomic

tools in Super-Domestication

45

Genome Sequencing

Potential methods of sequencing

1 Clone by clone approach

2 Whole genome shotgun approach

3 Combination of the two methods

Till today no of cultivated plants completely sequenced -85

2016- Arachis duranensis

2015- Solanum cumersonii (Wild potato)

(Ref- NCBI)

46

GWAS

It is a study design in which many markers spread across a genome

are genotyped and test a statistical association with a phenotype are

performed locally along the genome

It is also an examination of many common genetic variants in different

individuals to see if any variant is associated with a trait

Used in successfully studying maize sorghum and barley

Method is efficient for large scale low cost genotyping (even with the

minimum number of SNPs)

Cannot be utilized generally because it needs large population size

GWAS identify rare alleles more precisely

If small population we can opt NAM

47

GWAS and whole genome prediction

Xuehui Huang and Bin Han 2014

48

Five high throuput genotyping methods

Xuehui Huang and Bin Han 2014

49

Role of NGS in domestication Capture of novel genes from wild species will be made easier by

understanding the molecular events associated with crop domestication

Re-sequencing of domesticated species can identify low diversity regions

resulting from selection during domestication

To identify gene-specific sequences to aid the cloning of homologues of key

domestication genes from wild relatives

Candidate genes from wild and domesticated plant populations can define

diversity of target genes in wild populations and lead to the discovery of key

genes for important traits by association analysis

NGS of amplicons of large numbers of candidate genes from wild and

domesticated plant populations can define diversity of target genes in

wild populations and lead to the discovery of key genes for important

traits by association analysis

50

NGS

supports the rapid domestication of new plant species and the efficient

identification and capture of novel genetic variation from related species

Allows whole-genome analysis to determine the genetic basis of

phenotypic differences

NGS allows rapid expansion of genomic analysis to investigation of non-

model species

Made rice study easy by related grass

cost-effective method for plant identification

useful strategy to analysis the chloroplast genome sequence from whole-

genome shot-gun sequencing

facilitates managing this diversity and any changes in crop performance

over time due to genetic drift

Patterns of gene expression have been evaluated in hybrids using NGS

51

Two Approaches to Finding Adaptive Genes

Ross-Ibarra et al2007

52

Techniques to re-wild the plants (transgene free)

1 Introgression

breeding

2 Specific

insertion of lost genes

3 Precision

mutagenesis

Palmgren et al2014

53

Process of rewilding

Palmgren et al2014

54

Synthetic biology projects(i) Modifying cereals including wheat to fix atmospheric nitrogen

(ii) Redesigning metabolic pathways to increase the yield of

secondary metabolites or to generate compounds with enhanced

properties

(iii) Transferring the C4 photosynthesis pathway to rice

(iv) Modifying the glycosylation pathway in plants to accommodate

production of therapeutic proteins

(v) Introducing synthetic signal transduction systems that respond to

external cues

55

Synthetic biology projects

Nicholas J Baltes et al 2015

56

Refactoring the N fixation gene cluster from Klebsiella

Karsten Temme et al 2012

30

Reallocate biomass for human use

More efficient metabolism and photosynthesis increase

leaf surface decrease root system increase leaf

longevity

Grains more fertile florets larger inflorescence OR

number of ears different ways to get more seed

Larger seeds (automatic vs deliberate selection)

Oil plants increased oil content or more seed

Fiber plants long strong fibers

Domestication syndrome

31

Centers of Domestication

Fuller 2011

32

Centers of Domestication in India

Fuller 2011

33

Indian centers of domestication South India (Deccan centre) Vigna radiate Vigna mungo

Macrotyloma uniflorum (Horse gram) Sataria verticillata S plumila

wheat (macaroni) and two rowed barleybrachiaria ramosa

Orissa (Mahanadi river) Pegion pea Horsegram mung small millets

like Echinichloa Paspalum and Sataria

The Middle Ganges (Harappan civilization) Oryza nivara O rufipogon

and wild sativa Sateria pumia Cannabis sativa even the diffusion of

japonica rice

Saurashtra (Harappan civilization) Eleucine coracana Sateria italica

Paicum spp Brachypodia pearl millet and sorghum Dollicos lablab

The Himalayan foothills of the Punjab region Was a centre of

diversity for Japonica type rice and many temperate fruits and

vegetables

34

DOMESTICATION RELATED TRAITS CONTROLLED BY ONLY FEW GENES

Trait Crops

Plant architecturegrowth habit Ricemaizemilletsbeantomato

Flowering timephotoperiod sensitivity Ricemaizesorghumbeantomato

Fruit size Tomato egg plant

Grain size Ricemaizesorghumbean

Seed dispersal Brassica rice

Inflorescence modification Brassica

Dormancy Bean

35

Genes Crop Moleular and phenotypic function Causative change

Genes identified as controlling domestication traits

tb1 Maize Transcriptional regulator (TCP) plant and

inflorescence structure

regulatory change

tga1 Maize Transcriptional regulator (SBP) seed casing amino acid change

qSH1 Rice Transcriptional regulator (homeodomain)

abscission layer formation shattering

regulatory change

Rc Rice Transcriptional regulator (bHLH) seed color disrupted coding

sequence

sh4 Rice Transcriptional regulator (Myb3) abscission

layer formation shattering

regulatoryamino

acid change

fw22 Tomato Cell signaling fruit weight regulatory change

Q Wheat Transcriptional regulator (AP2) inflorescence

structure

regulatoryamino

acid change

Vrs1 Barley Inflorescence structure Premature stop Amino acid change

Genes of interest in crop domestication and improvement

36

Genes Crop Moleular and phenotypic function Causative change

c1

r1

Maize Transcriptional regulator (MYB) kernel color and

Transcriptional regulator (bHLH) kernel color

regulatory change

sh2 Maize pyrophosphorylase supersweet sweet corn transposon

insertion

su1 Maize isoamylase sweet corn gene amino acid change

brix9-2-5 Tomato Invertase fruit soluble solid content amino acid change

ovate Tomato Unknown fruit shap early stop codon

R Pea Starch branching enzyme seed sugar content transposon

insertion

ehd1 Rice B-type response regulator flowering time amino acid change

hd1 Rice Transcriptional regulator (zinc finger) flowering

time

disrupted coding

sequence

waxy Rice Starch synthase sticky grains intron splicing

defect

rht Wheat Transcriptional regulator (SH2) plant height early stop codon

vrn1 Wheat Transcriptional regulator (MADS) vernalization regulatory change

vrn2 Wheat Transcriptional regulator (ZCCT) vernalization amino acid change

Genes Identified as Controlling Varietal Differences

37

Process of domestication over the yearshellip

Rachel S Meyer 2012

38

Genetic bottleneck

Cultivated crops undergone with narrowing of diversity problem

But this is not the case in weeds

Weeds are the major threats from the beginning of domestication till

today

Problem arose due to

1 Crop mimicry

2 Genetic assimilation

3 Genetic evolution

39

Super- Domestication Vaughn et al (2007) first used the term super-domestication

The processes that lead to a domesticate with dramatically

increased yield that could not be selected in natural environments

from naturally occurring variation without recourse to new

technologies

Super-domesticates can be constructed with knowledge led

approaches based on current needs using the range of new

technologies now available

Plants exploited for continuous selection introduction hybridization

etc which boosted the process of domestication but now the plant

genetic engineering approach is exploiting plants towards synthetic

biology

40

How to use diversitybull Cross two varieties

bull Genome manipulations

Cell fusion hybrids

bull Chromosome manipulation Backcross a new species

bull Generate recombinants Chromosome recombinations

bull Use a new species wild germplasm

Transgenic approach Modern mutagenesis synthetic gene

construction by utilizing green florescent protein genome editing

NGS GWAS sequencing etchelliphelliphelliphelliphellip

41

Reduce genetic bottlenecks through polyplodization

More vigour

SC

Buffering capacity

Heterotic advantage

Enhaced vegetative

charachers

Enhanced oil

Meiotic stability

42

Approach 1 Use one tetraploid and one diploid as parents (4X ndash 2X) followed by the

chromosome doubling of triploid hybrids (Chrom doubling)

a) Cross between B juncea (AjAjBjBj ) and B oleracea (CoCo) to produce hexaploids

(AjAjBjBjCoCo)

(b) Cross between B napus (AnAnCnCn) and B nigra (BniBni) to produce hexaploids

(AnAnBniBniCnCn)

(c) Cross between B carinata (BcaBcaCcaCca) and B rapa (ArAr) to produce hexaploids

(ArArBcaBcaCcaCca)

Approach 2 Use three tetraploids as parents

(a) Cross between B napus (AnAnCnCn) and B carinata (BcaBcaCcaCca) to produce unbalanced

allotetraploids (AnBcaCnCca ndash unreduced gametes gametes with the somatic chromosome

number and cross with B juncea (AjAjBjBj) to obtain allohexaploids (AnAjBcaBjCnCca

(b) Cross between B napus (AnAnCnCn) and B juncea (AjAjBjBj) to produce unbalanced

allotetraploids (AnAjBjCn ndash unreduced gametes) and cross with B carinata (BcaBcaCcaCca) to

obtain allohexaploids (AnAjBcaBjCnCca)

(c) Cross between B carinata (BcaBcaCcaCca) and B juncea (AjAjBjBj) to produce unbalanced

allotetraploids (AjBcaBjCca - ndash unreduced gametes) and cross with B napus (AnAnCnCn) to obtain

allohexaploids (AnAjBcaBjCnCca)

Approach 3 Use three diploids as parents (2X ndash 2X ndash 2X) Cross between B rapa (ArAr) B

nigra (BniBni) and B oleracea (CoCo) sequentially to obtain hexaploid hybrids (ArArBniBniCoCo)

43

Continuehellip

Guijun Yan 2012

44

Applications of Genomic

tools in Super-Domestication

45

Genome Sequencing

Potential methods of sequencing

1 Clone by clone approach

2 Whole genome shotgun approach

3 Combination of the two methods

Till today no of cultivated plants completely sequenced -85

2016- Arachis duranensis

2015- Solanum cumersonii (Wild potato)

(Ref- NCBI)

46

GWAS

It is a study design in which many markers spread across a genome

are genotyped and test a statistical association with a phenotype are

performed locally along the genome

It is also an examination of many common genetic variants in different

individuals to see if any variant is associated with a trait

Used in successfully studying maize sorghum and barley

Method is efficient for large scale low cost genotyping (even with the

minimum number of SNPs)

Cannot be utilized generally because it needs large population size

GWAS identify rare alleles more precisely

If small population we can opt NAM

47

GWAS and whole genome prediction

Xuehui Huang and Bin Han 2014

48

Five high throuput genotyping methods

Xuehui Huang and Bin Han 2014

49

Role of NGS in domestication Capture of novel genes from wild species will be made easier by

understanding the molecular events associated with crop domestication

Re-sequencing of domesticated species can identify low diversity regions

resulting from selection during domestication

To identify gene-specific sequences to aid the cloning of homologues of key

domestication genes from wild relatives

Candidate genes from wild and domesticated plant populations can define

diversity of target genes in wild populations and lead to the discovery of key

genes for important traits by association analysis

NGS of amplicons of large numbers of candidate genes from wild and

domesticated plant populations can define diversity of target genes in

wild populations and lead to the discovery of key genes for important

traits by association analysis

50

NGS

supports the rapid domestication of new plant species and the efficient

identification and capture of novel genetic variation from related species

Allows whole-genome analysis to determine the genetic basis of

phenotypic differences

NGS allows rapid expansion of genomic analysis to investigation of non-

model species

Made rice study easy by related grass

cost-effective method for plant identification

useful strategy to analysis the chloroplast genome sequence from whole-

genome shot-gun sequencing

facilitates managing this diversity and any changes in crop performance

over time due to genetic drift

Patterns of gene expression have been evaluated in hybrids using NGS

51

Two Approaches to Finding Adaptive Genes

Ross-Ibarra et al2007

52

Techniques to re-wild the plants (transgene free)

1 Introgression

breeding

2 Specific

insertion of lost genes

3 Precision

mutagenesis

Palmgren et al2014

53

Process of rewilding

Palmgren et al2014

54

Synthetic biology projects(i) Modifying cereals including wheat to fix atmospheric nitrogen

(ii) Redesigning metabolic pathways to increase the yield of

secondary metabolites or to generate compounds with enhanced

properties

(iii) Transferring the C4 photosynthesis pathway to rice

(iv) Modifying the glycosylation pathway in plants to accommodate

production of therapeutic proteins

(v) Introducing synthetic signal transduction systems that respond to

external cues

55

Synthetic biology projects

Nicholas J Baltes et al 2015

56

Refactoring the N fixation gene cluster from Klebsiella

Karsten Temme et al 2012

31

Centers of Domestication

Fuller 2011

32

Centers of Domestication in India

Fuller 2011

33

Indian centers of domestication South India (Deccan centre) Vigna radiate Vigna mungo

Macrotyloma uniflorum (Horse gram) Sataria verticillata S plumila

wheat (macaroni) and two rowed barleybrachiaria ramosa

Orissa (Mahanadi river) Pegion pea Horsegram mung small millets

like Echinichloa Paspalum and Sataria

The Middle Ganges (Harappan civilization) Oryza nivara O rufipogon

and wild sativa Sateria pumia Cannabis sativa even the diffusion of

japonica rice

Saurashtra (Harappan civilization) Eleucine coracana Sateria italica

Paicum spp Brachypodia pearl millet and sorghum Dollicos lablab

The Himalayan foothills of the Punjab region Was a centre of

diversity for Japonica type rice and many temperate fruits and

vegetables

34

DOMESTICATION RELATED TRAITS CONTROLLED BY ONLY FEW GENES

Trait Crops

Plant architecturegrowth habit Ricemaizemilletsbeantomato

Flowering timephotoperiod sensitivity Ricemaizesorghumbeantomato

Fruit size Tomato egg plant

Grain size Ricemaizesorghumbean

Seed dispersal Brassica rice

Inflorescence modification Brassica

Dormancy Bean

35

Genes Crop Moleular and phenotypic function Causative change

Genes identified as controlling domestication traits

tb1 Maize Transcriptional regulator (TCP) plant and

inflorescence structure

regulatory change

tga1 Maize Transcriptional regulator (SBP) seed casing amino acid change

qSH1 Rice Transcriptional regulator (homeodomain)

abscission layer formation shattering

regulatory change

Rc Rice Transcriptional regulator (bHLH) seed color disrupted coding

sequence

sh4 Rice Transcriptional regulator (Myb3) abscission

layer formation shattering

regulatoryamino

acid change

fw22 Tomato Cell signaling fruit weight regulatory change

Q Wheat Transcriptional regulator (AP2) inflorescence

structure

regulatoryamino

acid change

Vrs1 Barley Inflorescence structure Premature stop Amino acid change

Genes of interest in crop domestication and improvement

36

Genes Crop Moleular and phenotypic function Causative change

c1

r1

Maize Transcriptional regulator (MYB) kernel color and

Transcriptional regulator (bHLH) kernel color

regulatory change

sh2 Maize pyrophosphorylase supersweet sweet corn transposon

insertion

su1 Maize isoamylase sweet corn gene amino acid change

brix9-2-5 Tomato Invertase fruit soluble solid content amino acid change

ovate Tomato Unknown fruit shap early stop codon

R Pea Starch branching enzyme seed sugar content transposon

insertion

ehd1 Rice B-type response regulator flowering time amino acid change

hd1 Rice Transcriptional regulator (zinc finger) flowering

time

disrupted coding

sequence

waxy Rice Starch synthase sticky grains intron splicing

defect

rht Wheat Transcriptional regulator (SH2) plant height early stop codon

vrn1 Wheat Transcriptional regulator (MADS) vernalization regulatory change

vrn2 Wheat Transcriptional regulator (ZCCT) vernalization amino acid change

Genes Identified as Controlling Varietal Differences

37

Process of domestication over the yearshellip

Rachel S Meyer 2012

38

Genetic bottleneck

Cultivated crops undergone with narrowing of diversity problem

But this is not the case in weeds

Weeds are the major threats from the beginning of domestication till

today

Problem arose due to

1 Crop mimicry

2 Genetic assimilation

3 Genetic evolution

39

Super- Domestication Vaughn et al (2007) first used the term super-domestication

The processes that lead to a domesticate with dramatically

increased yield that could not be selected in natural environments

from naturally occurring variation without recourse to new

technologies

Super-domesticates can be constructed with knowledge led

approaches based on current needs using the range of new

technologies now available

Plants exploited for continuous selection introduction hybridization

etc which boosted the process of domestication but now the plant

genetic engineering approach is exploiting plants towards synthetic

biology

40

How to use diversitybull Cross two varieties

bull Genome manipulations

Cell fusion hybrids

bull Chromosome manipulation Backcross a new species

bull Generate recombinants Chromosome recombinations

bull Use a new species wild germplasm

Transgenic approach Modern mutagenesis synthetic gene

construction by utilizing green florescent protein genome editing

NGS GWAS sequencing etchelliphelliphelliphelliphellip

41

Reduce genetic bottlenecks through polyplodization

More vigour

SC

Buffering capacity

Heterotic advantage

Enhaced vegetative

charachers

Enhanced oil

Meiotic stability

42

Approach 1 Use one tetraploid and one diploid as parents (4X ndash 2X) followed by the

chromosome doubling of triploid hybrids (Chrom doubling)

a) Cross between B juncea (AjAjBjBj ) and B oleracea (CoCo) to produce hexaploids

(AjAjBjBjCoCo)

(b) Cross between B napus (AnAnCnCn) and B nigra (BniBni) to produce hexaploids

(AnAnBniBniCnCn)

(c) Cross between B carinata (BcaBcaCcaCca) and B rapa (ArAr) to produce hexaploids

(ArArBcaBcaCcaCca)

Approach 2 Use three tetraploids as parents

(a) Cross between B napus (AnAnCnCn) and B carinata (BcaBcaCcaCca) to produce unbalanced

allotetraploids (AnBcaCnCca ndash unreduced gametes gametes with the somatic chromosome

number and cross with B juncea (AjAjBjBj) to obtain allohexaploids (AnAjBcaBjCnCca

(b) Cross between B napus (AnAnCnCn) and B juncea (AjAjBjBj) to produce unbalanced

allotetraploids (AnAjBjCn ndash unreduced gametes) and cross with B carinata (BcaBcaCcaCca) to

obtain allohexaploids (AnAjBcaBjCnCca)

(c) Cross between B carinata (BcaBcaCcaCca) and B juncea (AjAjBjBj) to produce unbalanced

allotetraploids (AjBcaBjCca - ndash unreduced gametes) and cross with B napus (AnAnCnCn) to obtain

allohexaploids (AnAjBcaBjCnCca)

Approach 3 Use three diploids as parents (2X ndash 2X ndash 2X) Cross between B rapa (ArAr) B

nigra (BniBni) and B oleracea (CoCo) sequentially to obtain hexaploid hybrids (ArArBniBniCoCo)

43

Continuehellip

Guijun Yan 2012

44

Applications of Genomic

tools in Super-Domestication

45

Genome Sequencing

Potential methods of sequencing

1 Clone by clone approach

2 Whole genome shotgun approach

3 Combination of the two methods

Till today no of cultivated plants completely sequenced -85

2016- Arachis duranensis

2015- Solanum cumersonii (Wild potato)

(Ref- NCBI)

46

GWAS

It is a study design in which many markers spread across a genome

are genotyped and test a statistical association with a phenotype are

performed locally along the genome

It is also an examination of many common genetic variants in different

individuals to see if any variant is associated with a trait

Used in successfully studying maize sorghum and barley

Method is efficient for large scale low cost genotyping (even with the

minimum number of SNPs)

Cannot be utilized generally because it needs large population size

GWAS identify rare alleles more precisely

If small population we can opt NAM

47

GWAS and whole genome prediction

Xuehui Huang and Bin Han 2014

48

Five high throuput genotyping methods

Xuehui Huang and Bin Han 2014

49

Role of NGS in domestication Capture of novel genes from wild species will be made easier by

understanding the molecular events associated with crop domestication

Re-sequencing of domesticated species can identify low diversity regions

resulting from selection during domestication

To identify gene-specific sequences to aid the cloning of homologues of key

domestication genes from wild relatives

Candidate genes from wild and domesticated plant populations can define

diversity of target genes in wild populations and lead to the discovery of key

genes for important traits by association analysis

NGS of amplicons of large numbers of candidate genes from wild and

domesticated plant populations can define diversity of target genes in

wild populations and lead to the discovery of key genes for important

traits by association analysis

50

NGS

supports the rapid domestication of new plant species and the efficient

identification and capture of novel genetic variation from related species

Allows whole-genome analysis to determine the genetic basis of

phenotypic differences

NGS allows rapid expansion of genomic analysis to investigation of non-

model species

Made rice study easy by related grass

cost-effective method for plant identification

useful strategy to analysis the chloroplast genome sequence from whole-

genome shot-gun sequencing

facilitates managing this diversity and any changes in crop performance

over time due to genetic drift

Patterns of gene expression have been evaluated in hybrids using NGS

51

Two Approaches to Finding Adaptive Genes

Ross-Ibarra et al2007

52

Techniques to re-wild the plants (transgene free)

1 Introgression

breeding

2 Specific

insertion of lost genes

3 Precision

mutagenesis

Palmgren et al2014

53

Process of rewilding

Palmgren et al2014

54

Synthetic biology projects(i) Modifying cereals including wheat to fix atmospheric nitrogen

(ii) Redesigning metabolic pathways to increase the yield of

secondary metabolites or to generate compounds with enhanced

properties

(iii) Transferring the C4 photosynthesis pathway to rice

(iv) Modifying the glycosylation pathway in plants to accommodate

production of therapeutic proteins

(v) Introducing synthetic signal transduction systems that respond to

external cues

55

Synthetic biology projects

Nicholas J Baltes et al 2015

56

Refactoring the N fixation gene cluster from Klebsiella

Karsten Temme et al 2012

32

Centers of Domestication in India

Fuller 2011

33

Indian centers of domestication South India (Deccan centre) Vigna radiate Vigna mungo

Macrotyloma uniflorum (Horse gram) Sataria verticillata S plumila

wheat (macaroni) and two rowed barleybrachiaria ramosa

Orissa (Mahanadi river) Pegion pea Horsegram mung small millets

like Echinichloa Paspalum and Sataria

The Middle Ganges (Harappan civilization) Oryza nivara O rufipogon

and wild sativa Sateria pumia Cannabis sativa even the diffusion of

japonica rice

Saurashtra (Harappan civilization) Eleucine coracana Sateria italica

Paicum spp Brachypodia pearl millet and sorghum Dollicos lablab

The Himalayan foothills of the Punjab region Was a centre of

diversity for Japonica type rice and many temperate fruits and

vegetables

34

DOMESTICATION RELATED TRAITS CONTROLLED BY ONLY FEW GENES

Trait Crops

Plant architecturegrowth habit Ricemaizemilletsbeantomato

Flowering timephotoperiod sensitivity Ricemaizesorghumbeantomato

Fruit size Tomato egg plant

Grain size Ricemaizesorghumbean

Seed dispersal Brassica rice

Inflorescence modification Brassica

Dormancy Bean

35

Genes Crop Moleular and phenotypic function Causative change

Genes identified as controlling domestication traits

tb1 Maize Transcriptional regulator (TCP) plant and

inflorescence structure

regulatory change

tga1 Maize Transcriptional regulator (SBP) seed casing amino acid change

qSH1 Rice Transcriptional regulator (homeodomain)

abscission layer formation shattering

regulatory change

Rc Rice Transcriptional regulator (bHLH) seed color disrupted coding

sequence

sh4 Rice Transcriptional regulator (Myb3) abscission

layer formation shattering

regulatoryamino

acid change

fw22 Tomato Cell signaling fruit weight regulatory change

Q Wheat Transcriptional regulator (AP2) inflorescence

structure

regulatoryamino

acid change

Vrs1 Barley Inflorescence structure Premature stop Amino acid change

Genes of interest in crop domestication and improvement

36

Genes Crop Moleular and phenotypic function Causative change

c1

r1

Maize Transcriptional regulator (MYB) kernel color and

Transcriptional regulator (bHLH) kernel color

regulatory change

sh2 Maize pyrophosphorylase supersweet sweet corn transposon

insertion

su1 Maize isoamylase sweet corn gene amino acid change

brix9-2-5 Tomato Invertase fruit soluble solid content amino acid change

ovate Tomato Unknown fruit shap early stop codon

R Pea Starch branching enzyme seed sugar content transposon

insertion

ehd1 Rice B-type response regulator flowering time amino acid change

hd1 Rice Transcriptional regulator (zinc finger) flowering

time

disrupted coding

sequence

waxy Rice Starch synthase sticky grains intron splicing

defect

rht Wheat Transcriptional regulator (SH2) plant height early stop codon

vrn1 Wheat Transcriptional regulator (MADS) vernalization regulatory change

vrn2 Wheat Transcriptional regulator (ZCCT) vernalization amino acid change

Genes Identified as Controlling Varietal Differences

37

Process of domestication over the yearshellip

Rachel S Meyer 2012

38

Genetic bottleneck

Cultivated crops undergone with narrowing of diversity problem

But this is not the case in weeds

Weeds are the major threats from the beginning of domestication till

today

Problem arose due to

1 Crop mimicry

2 Genetic assimilation

3 Genetic evolution

39

Super- Domestication Vaughn et al (2007) first used the term super-domestication

The processes that lead to a domesticate with dramatically

increased yield that could not be selected in natural environments

from naturally occurring variation without recourse to new

technologies

Super-domesticates can be constructed with knowledge led

approaches based on current needs using the range of new

technologies now available

Plants exploited for continuous selection introduction hybridization

etc which boosted the process of domestication but now the plant

genetic engineering approach is exploiting plants towards synthetic

biology

40

How to use diversitybull Cross two varieties

bull Genome manipulations

Cell fusion hybrids

bull Chromosome manipulation Backcross a new species

bull Generate recombinants Chromosome recombinations

bull Use a new species wild germplasm

Transgenic approach Modern mutagenesis synthetic gene

construction by utilizing green florescent protein genome editing

NGS GWAS sequencing etchelliphelliphelliphelliphellip

41

Reduce genetic bottlenecks through polyplodization

More vigour

SC

Buffering capacity

Heterotic advantage

Enhaced vegetative

charachers

Enhanced oil

Meiotic stability

42

Approach 1 Use one tetraploid and one diploid as parents (4X ndash 2X) followed by the

chromosome doubling of triploid hybrids (Chrom doubling)

a) Cross between B juncea (AjAjBjBj ) and B oleracea (CoCo) to produce hexaploids

(AjAjBjBjCoCo)

(b) Cross between B napus (AnAnCnCn) and B nigra (BniBni) to produce hexaploids

(AnAnBniBniCnCn)

(c) Cross between B carinata (BcaBcaCcaCca) and B rapa (ArAr) to produce hexaploids

(ArArBcaBcaCcaCca)

Approach 2 Use three tetraploids as parents

(a) Cross between B napus (AnAnCnCn) and B carinata (BcaBcaCcaCca) to produce unbalanced

allotetraploids (AnBcaCnCca ndash unreduced gametes gametes with the somatic chromosome

number and cross with B juncea (AjAjBjBj) to obtain allohexaploids (AnAjBcaBjCnCca

(b) Cross between B napus (AnAnCnCn) and B juncea (AjAjBjBj) to produce unbalanced

allotetraploids (AnAjBjCn ndash unreduced gametes) and cross with B carinata (BcaBcaCcaCca) to

obtain allohexaploids (AnAjBcaBjCnCca)

(c) Cross between B carinata (BcaBcaCcaCca) and B juncea (AjAjBjBj) to produce unbalanced

allotetraploids (AjBcaBjCca - ndash unreduced gametes) and cross with B napus (AnAnCnCn) to obtain

allohexaploids (AnAjBcaBjCnCca)

Approach 3 Use three diploids as parents (2X ndash 2X ndash 2X) Cross between B rapa (ArAr) B

nigra (BniBni) and B oleracea (CoCo) sequentially to obtain hexaploid hybrids (ArArBniBniCoCo)

43

Continuehellip

Guijun Yan 2012

44

Applications of Genomic

tools in Super-Domestication

45

Genome Sequencing

Potential methods of sequencing

1 Clone by clone approach

2 Whole genome shotgun approach

3 Combination of the two methods

Till today no of cultivated plants completely sequenced -85

2016- Arachis duranensis

2015- Solanum cumersonii (Wild potato)

(Ref- NCBI)

46

GWAS

It is a study design in which many markers spread across a genome

are genotyped and test a statistical association with a phenotype are

performed locally along the genome

It is also an examination of many common genetic variants in different

individuals to see if any variant is associated with a trait

Used in successfully studying maize sorghum and barley

Method is efficient for large scale low cost genotyping (even with the

minimum number of SNPs)

Cannot be utilized generally because it needs large population size

GWAS identify rare alleles more precisely

If small population we can opt NAM

47

GWAS and whole genome prediction

Xuehui Huang and Bin Han 2014

48

Five high throuput genotyping methods

Xuehui Huang and Bin Han 2014

49

Role of NGS in domestication Capture of novel genes from wild species will be made easier by

understanding the molecular events associated with crop domestication

Re-sequencing of domesticated species can identify low diversity regions

resulting from selection during domestication

To identify gene-specific sequences to aid the cloning of homologues of key

domestication genes from wild relatives

Candidate genes from wild and domesticated plant populations can define

diversity of target genes in wild populations and lead to the discovery of key

genes for important traits by association analysis

NGS of amplicons of large numbers of candidate genes from wild and

domesticated plant populations can define diversity of target genes in

wild populations and lead to the discovery of key genes for important

traits by association analysis

50

NGS

supports the rapid domestication of new plant species and the efficient

identification and capture of novel genetic variation from related species

Allows whole-genome analysis to determine the genetic basis of

phenotypic differences

NGS allows rapid expansion of genomic analysis to investigation of non-

model species

Made rice study easy by related grass

cost-effective method for plant identification

useful strategy to analysis the chloroplast genome sequence from whole-

genome shot-gun sequencing

facilitates managing this diversity and any changes in crop performance

over time due to genetic drift

Patterns of gene expression have been evaluated in hybrids using NGS

51

Two Approaches to Finding Adaptive Genes

Ross-Ibarra et al2007

52

Techniques to re-wild the plants (transgene free)

1 Introgression

breeding

2 Specific

insertion of lost genes

3 Precision

mutagenesis

Palmgren et al2014

53

Process of rewilding

Palmgren et al2014

54

Synthetic biology projects(i) Modifying cereals including wheat to fix atmospheric nitrogen

(ii) Redesigning metabolic pathways to increase the yield of

secondary metabolites or to generate compounds with enhanced

properties

(iii) Transferring the C4 photosynthesis pathway to rice

(iv) Modifying the glycosylation pathway in plants to accommodate

production of therapeutic proteins

(v) Introducing synthetic signal transduction systems that respond to

external cues

55

Synthetic biology projects

Nicholas J Baltes et al 2015

56

Refactoring the N fixation gene cluster from Klebsiella

Karsten Temme et al 2012

33

Indian centers of domestication South India (Deccan centre) Vigna radiate Vigna mungo

Macrotyloma uniflorum (Horse gram) Sataria verticillata S plumila

wheat (macaroni) and two rowed barleybrachiaria ramosa

Orissa (Mahanadi river) Pegion pea Horsegram mung small millets

like Echinichloa Paspalum and Sataria

The Middle Ganges (Harappan civilization) Oryza nivara O rufipogon

and wild sativa Sateria pumia Cannabis sativa even the diffusion of

japonica rice

Saurashtra (Harappan civilization) Eleucine coracana Sateria italica

Paicum spp Brachypodia pearl millet and sorghum Dollicos lablab

The Himalayan foothills of the Punjab region Was a centre of

diversity for Japonica type rice and many temperate fruits and

vegetables

34

DOMESTICATION RELATED TRAITS CONTROLLED BY ONLY FEW GENES

Trait Crops

Plant architecturegrowth habit Ricemaizemilletsbeantomato

Flowering timephotoperiod sensitivity Ricemaizesorghumbeantomato

Fruit size Tomato egg plant

Grain size Ricemaizesorghumbean

Seed dispersal Brassica rice

Inflorescence modification Brassica

Dormancy Bean

35

Genes Crop Moleular and phenotypic function Causative change

Genes identified as controlling domestication traits

tb1 Maize Transcriptional regulator (TCP) plant and

inflorescence structure

regulatory change

tga1 Maize Transcriptional regulator (SBP) seed casing amino acid change

qSH1 Rice Transcriptional regulator (homeodomain)

abscission layer formation shattering

regulatory change

Rc Rice Transcriptional regulator (bHLH) seed color disrupted coding

sequence

sh4 Rice Transcriptional regulator (Myb3) abscission

layer formation shattering

regulatoryamino

acid change

fw22 Tomato Cell signaling fruit weight regulatory change

Q Wheat Transcriptional regulator (AP2) inflorescence

structure

regulatoryamino

acid change

Vrs1 Barley Inflorescence structure Premature stop Amino acid change

Genes of interest in crop domestication and improvement

36

Genes Crop Moleular and phenotypic function Causative change

c1

r1

Maize Transcriptional regulator (MYB) kernel color and

Transcriptional regulator (bHLH) kernel color

regulatory change

sh2 Maize pyrophosphorylase supersweet sweet corn transposon

insertion

su1 Maize isoamylase sweet corn gene amino acid change

brix9-2-5 Tomato Invertase fruit soluble solid content amino acid change

ovate Tomato Unknown fruit shap early stop codon

R Pea Starch branching enzyme seed sugar content transposon

insertion

ehd1 Rice B-type response regulator flowering time amino acid change

hd1 Rice Transcriptional regulator (zinc finger) flowering

time

disrupted coding

sequence

waxy Rice Starch synthase sticky grains intron splicing

defect

rht Wheat Transcriptional regulator (SH2) plant height early stop codon

vrn1 Wheat Transcriptional regulator (MADS) vernalization regulatory change

vrn2 Wheat Transcriptional regulator (ZCCT) vernalization amino acid change

Genes Identified as Controlling Varietal Differences

37

Process of domestication over the yearshellip

Rachel S Meyer 2012

38

Genetic bottleneck

Cultivated crops undergone with narrowing of diversity problem

But this is not the case in weeds

Weeds are the major threats from the beginning of domestication till

today

Problem arose due to

1 Crop mimicry

2 Genetic assimilation

3 Genetic evolution

39

Super- Domestication Vaughn et al (2007) first used the term super-domestication

The processes that lead to a domesticate with dramatically

increased yield that could not be selected in natural environments

from naturally occurring variation without recourse to new

technologies

Super-domesticates can be constructed with knowledge led

approaches based on current needs using the range of new

technologies now available

Plants exploited for continuous selection introduction hybridization

etc which boosted the process of domestication but now the plant

genetic engineering approach is exploiting plants towards synthetic

biology

40

How to use diversitybull Cross two varieties

bull Genome manipulations

Cell fusion hybrids

bull Chromosome manipulation Backcross a new species

bull Generate recombinants Chromosome recombinations

bull Use a new species wild germplasm

Transgenic approach Modern mutagenesis synthetic gene

construction by utilizing green florescent protein genome editing

NGS GWAS sequencing etchelliphelliphelliphelliphellip

41

Reduce genetic bottlenecks through polyplodization

More vigour

SC

Buffering capacity

Heterotic advantage

Enhaced vegetative

charachers

Enhanced oil

Meiotic stability

42

Approach 1 Use one tetraploid and one diploid as parents (4X ndash 2X) followed by the

chromosome doubling of triploid hybrids (Chrom doubling)

a) Cross between B juncea (AjAjBjBj ) and B oleracea (CoCo) to produce hexaploids

(AjAjBjBjCoCo)

(b) Cross between B napus (AnAnCnCn) and B nigra (BniBni) to produce hexaploids

(AnAnBniBniCnCn)

(c) Cross between B carinata (BcaBcaCcaCca) and B rapa (ArAr) to produce hexaploids

(ArArBcaBcaCcaCca)

Approach 2 Use three tetraploids as parents

(a) Cross between B napus (AnAnCnCn) and B carinata (BcaBcaCcaCca) to produce unbalanced

allotetraploids (AnBcaCnCca ndash unreduced gametes gametes with the somatic chromosome

number and cross with B juncea (AjAjBjBj) to obtain allohexaploids (AnAjBcaBjCnCca

(b) Cross between B napus (AnAnCnCn) and B juncea (AjAjBjBj) to produce unbalanced

allotetraploids (AnAjBjCn ndash unreduced gametes) and cross with B carinata (BcaBcaCcaCca) to

obtain allohexaploids (AnAjBcaBjCnCca)

(c) Cross between B carinata (BcaBcaCcaCca) and B juncea (AjAjBjBj) to produce unbalanced

allotetraploids (AjBcaBjCca - ndash unreduced gametes) and cross with B napus (AnAnCnCn) to obtain

allohexaploids (AnAjBcaBjCnCca)

Approach 3 Use three diploids as parents (2X ndash 2X ndash 2X) Cross between B rapa (ArAr) B

nigra (BniBni) and B oleracea (CoCo) sequentially to obtain hexaploid hybrids (ArArBniBniCoCo)

43

Continuehellip

Guijun Yan 2012

44

Applications of Genomic

tools in Super-Domestication

45

Genome Sequencing

Potential methods of sequencing

1 Clone by clone approach

2 Whole genome shotgun approach

3 Combination of the two methods

Till today no of cultivated plants completely sequenced -85

2016- Arachis duranensis

2015- Solanum cumersonii (Wild potato)

(Ref- NCBI)

46

GWAS

It is a study design in which many markers spread across a genome

are genotyped and test a statistical association with a phenotype are

performed locally along the genome

It is also an examination of many common genetic variants in different

individuals to see if any variant is associated with a trait

Used in successfully studying maize sorghum and barley

Method is efficient for large scale low cost genotyping (even with the

minimum number of SNPs)

Cannot be utilized generally because it needs large population size

GWAS identify rare alleles more precisely

If small population we can opt NAM

47

GWAS and whole genome prediction

Xuehui Huang and Bin Han 2014

48

Five high throuput genotyping methods

Xuehui Huang and Bin Han 2014

49

Role of NGS in domestication Capture of novel genes from wild species will be made easier by

understanding the molecular events associated with crop domestication

Re-sequencing of domesticated species can identify low diversity regions

resulting from selection during domestication

To identify gene-specific sequences to aid the cloning of homologues of key

domestication genes from wild relatives

Candidate genes from wild and domesticated plant populations can define

diversity of target genes in wild populations and lead to the discovery of key

genes for important traits by association analysis

NGS of amplicons of large numbers of candidate genes from wild and

domesticated plant populations can define diversity of target genes in

wild populations and lead to the discovery of key genes for important

traits by association analysis

50

NGS

supports the rapid domestication of new plant species and the efficient

identification and capture of novel genetic variation from related species

Allows whole-genome analysis to determine the genetic basis of

phenotypic differences

NGS allows rapid expansion of genomic analysis to investigation of non-

model species

Made rice study easy by related grass

cost-effective method for plant identification

useful strategy to analysis the chloroplast genome sequence from whole-

genome shot-gun sequencing

facilitates managing this diversity and any changes in crop performance

over time due to genetic drift

Patterns of gene expression have been evaluated in hybrids using NGS

51

Two Approaches to Finding Adaptive Genes

Ross-Ibarra et al2007

52

Techniques to re-wild the plants (transgene free)

1 Introgression

breeding

2 Specific

insertion of lost genes

3 Precision

mutagenesis

Palmgren et al2014

53

Process of rewilding

Palmgren et al2014

54

Synthetic biology projects(i) Modifying cereals including wheat to fix atmospheric nitrogen

(ii) Redesigning metabolic pathways to increase the yield of

secondary metabolites or to generate compounds with enhanced

properties

(iii) Transferring the C4 photosynthesis pathway to rice

(iv) Modifying the glycosylation pathway in plants to accommodate

production of therapeutic proteins

(v) Introducing synthetic signal transduction systems that respond to

external cues

55

Synthetic biology projects

Nicholas J Baltes et al 2015

56

Refactoring the N fixation gene cluster from Klebsiella

Karsten Temme et al 2012

34

DOMESTICATION RELATED TRAITS CONTROLLED BY ONLY FEW GENES

Trait Crops

Plant architecturegrowth habit Ricemaizemilletsbeantomato

Flowering timephotoperiod sensitivity Ricemaizesorghumbeantomato

Fruit size Tomato egg plant

Grain size Ricemaizesorghumbean

Seed dispersal Brassica rice

Inflorescence modification Brassica

Dormancy Bean

35

Genes Crop Moleular and phenotypic function Causative change

Genes identified as controlling domestication traits

tb1 Maize Transcriptional regulator (TCP) plant and

inflorescence structure

regulatory change

tga1 Maize Transcriptional regulator (SBP) seed casing amino acid change

qSH1 Rice Transcriptional regulator (homeodomain)

abscission layer formation shattering

regulatory change

Rc Rice Transcriptional regulator (bHLH) seed color disrupted coding

sequence

sh4 Rice Transcriptional regulator (Myb3) abscission

layer formation shattering

regulatoryamino

acid change

fw22 Tomato Cell signaling fruit weight regulatory change

Q Wheat Transcriptional regulator (AP2) inflorescence

structure

regulatoryamino

acid change

Vrs1 Barley Inflorescence structure Premature stop Amino acid change

Genes of interest in crop domestication and improvement

36

Genes Crop Moleular and phenotypic function Causative change

c1

r1

Maize Transcriptional regulator (MYB) kernel color and

Transcriptional regulator (bHLH) kernel color

regulatory change

sh2 Maize pyrophosphorylase supersweet sweet corn transposon

insertion

su1 Maize isoamylase sweet corn gene amino acid change

brix9-2-5 Tomato Invertase fruit soluble solid content amino acid change

ovate Tomato Unknown fruit shap early stop codon

R Pea Starch branching enzyme seed sugar content transposon

insertion

ehd1 Rice B-type response regulator flowering time amino acid change

hd1 Rice Transcriptional regulator (zinc finger) flowering

time

disrupted coding

sequence

waxy Rice Starch synthase sticky grains intron splicing

defect

rht Wheat Transcriptional regulator (SH2) plant height early stop codon

vrn1 Wheat Transcriptional regulator (MADS) vernalization regulatory change

vrn2 Wheat Transcriptional regulator (ZCCT) vernalization amino acid change

Genes Identified as Controlling Varietal Differences

37

Process of domestication over the yearshellip

Rachel S Meyer 2012

38

Genetic bottleneck

Cultivated crops undergone with narrowing of diversity problem

But this is not the case in weeds

Weeds are the major threats from the beginning of domestication till

today

Problem arose due to

1 Crop mimicry

2 Genetic assimilation

3 Genetic evolution

39

Super- Domestication Vaughn et al (2007) first used the term super-domestication

The processes that lead to a domesticate with dramatically

increased yield that could not be selected in natural environments

from naturally occurring variation without recourse to new

technologies

Super-domesticates can be constructed with knowledge led

approaches based on current needs using the range of new

technologies now available

Plants exploited for continuous selection introduction hybridization

etc which boosted the process of domestication but now the plant

genetic engineering approach is exploiting plants towards synthetic

biology

40

How to use diversitybull Cross two varieties

bull Genome manipulations

Cell fusion hybrids

bull Chromosome manipulation Backcross a new species

bull Generate recombinants Chromosome recombinations

bull Use a new species wild germplasm

Transgenic approach Modern mutagenesis synthetic gene

construction by utilizing green florescent protein genome editing

NGS GWAS sequencing etchelliphelliphelliphelliphellip

41

Reduce genetic bottlenecks through polyplodization

More vigour

SC

Buffering capacity

Heterotic advantage

Enhaced vegetative

charachers

Enhanced oil

Meiotic stability

42

Approach 1 Use one tetraploid and one diploid as parents (4X ndash 2X) followed by the

chromosome doubling of triploid hybrids (Chrom doubling)

a) Cross between B juncea (AjAjBjBj ) and B oleracea (CoCo) to produce hexaploids

(AjAjBjBjCoCo)

(b) Cross between B napus (AnAnCnCn) and B nigra (BniBni) to produce hexaploids

(AnAnBniBniCnCn)

(c) Cross between B carinata (BcaBcaCcaCca) and B rapa (ArAr) to produce hexaploids

(ArArBcaBcaCcaCca)

Approach 2 Use three tetraploids as parents

(a) Cross between B napus (AnAnCnCn) and B carinata (BcaBcaCcaCca) to produce unbalanced

allotetraploids (AnBcaCnCca ndash unreduced gametes gametes with the somatic chromosome

number and cross with B juncea (AjAjBjBj) to obtain allohexaploids (AnAjBcaBjCnCca

(b) Cross between B napus (AnAnCnCn) and B juncea (AjAjBjBj) to produce unbalanced

allotetraploids (AnAjBjCn ndash unreduced gametes) and cross with B carinata (BcaBcaCcaCca) to

obtain allohexaploids (AnAjBcaBjCnCca)

(c) Cross between B carinata (BcaBcaCcaCca) and B juncea (AjAjBjBj) to produce unbalanced

allotetraploids (AjBcaBjCca - ndash unreduced gametes) and cross with B napus (AnAnCnCn) to obtain

allohexaploids (AnAjBcaBjCnCca)

Approach 3 Use three diploids as parents (2X ndash 2X ndash 2X) Cross between B rapa (ArAr) B

nigra (BniBni) and B oleracea (CoCo) sequentially to obtain hexaploid hybrids (ArArBniBniCoCo)

43

Continuehellip

Guijun Yan 2012

44

Applications of Genomic

tools in Super-Domestication

45

Genome Sequencing

Potential methods of sequencing

1 Clone by clone approach

2 Whole genome shotgun approach

3 Combination of the two methods

Till today no of cultivated plants completely sequenced -85

2016- Arachis duranensis

2015- Solanum cumersonii (Wild potato)

(Ref- NCBI)

46

GWAS

It is a study design in which many markers spread across a genome

are genotyped and test a statistical association with a phenotype are

performed locally along the genome

It is also an examination of many common genetic variants in different

individuals to see if any variant is associated with a trait

Used in successfully studying maize sorghum and barley

Method is efficient for large scale low cost genotyping (even with the

minimum number of SNPs)

Cannot be utilized generally because it needs large population size

GWAS identify rare alleles more precisely

If small population we can opt NAM

47

GWAS and whole genome prediction

Xuehui Huang and Bin Han 2014

48

Five high throuput genotyping methods

Xuehui Huang and Bin Han 2014

49

Role of NGS in domestication Capture of novel genes from wild species will be made easier by

understanding the molecular events associated with crop domestication

Re-sequencing of domesticated species can identify low diversity regions

resulting from selection during domestication

To identify gene-specific sequences to aid the cloning of homologues of key

domestication genes from wild relatives

Candidate genes from wild and domesticated plant populations can define

diversity of target genes in wild populations and lead to the discovery of key

genes for important traits by association analysis

NGS of amplicons of large numbers of candidate genes from wild and

domesticated plant populations can define diversity of target genes in

wild populations and lead to the discovery of key genes for important

traits by association analysis

50

NGS

supports the rapid domestication of new plant species and the efficient

identification and capture of novel genetic variation from related species

Allows whole-genome analysis to determine the genetic basis of

phenotypic differences

NGS allows rapid expansion of genomic analysis to investigation of non-

model species

Made rice study easy by related grass

cost-effective method for plant identification

useful strategy to analysis the chloroplast genome sequence from whole-

genome shot-gun sequencing

facilitates managing this diversity and any changes in crop performance

over time due to genetic drift

Patterns of gene expression have been evaluated in hybrids using NGS

51

Two Approaches to Finding Adaptive Genes

Ross-Ibarra et al2007

52

Techniques to re-wild the plants (transgene free)

1 Introgression

breeding

2 Specific

insertion of lost genes

3 Precision

mutagenesis

Palmgren et al2014

53

Process of rewilding

Palmgren et al2014

54

Synthetic biology projects(i) Modifying cereals including wheat to fix atmospheric nitrogen

(ii) Redesigning metabolic pathways to increase the yield of

secondary metabolites or to generate compounds with enhanced

properties

(iii) Transferring the C4 photosynthesis pathway to rice

(iv) Modifying the glycosylation pathway in plants to accommodate

production of therapeutic proteins

(v) Introducing synthetic signal transduction systems that respond to

external cues

55

Synthetic biology projects

Nicholas J Baltes et al 2015

56

Refactoring the N fixation gene cluster from Klebsiella

Karsten Temme et al 2012

35

Genes Crop Moleular and phenotypic function Causative change

Genes identified as controlling domestication traits

tb1 Maize Transcriptional regulator (TCP) plant and

inflorescence structure

regulatory change

tga1 Maize Transcriptional regulator (SBP) seed casing amino acid change

qSH1 Rice Transcriptional regulator (homeodomain)

abscission layer formation shattering

regulatory change

Rc Rice Transcriptional regulator (bHLH) seed color disrupted coding

sequence

sh4 Rice Transcriptional regulator (Myb3) abscission

layer formation shattering

regulatoryamino

acid change

fw22 Tomato Cell signaling fruit weight regulatory change

Q Wheat Transcriptional regulator (AP2) inflorescence

structure

regulatoryamino

acid change

Vrs1 Barley Inflorescence structure Premature stop Amino acid change

Genes of interest in crop domestication and improvement

36

Genes Crop Moleular and phenotypic function Causative change

c1

r1

Maize Transcriptional regulator (MYB) kernel color and

Transcriptional regulator (bHLH) kernel color

regulatory change

sh2 Maize pyrophosphorylase supersweet sweet corn transposon

insertion

su1 Maize isoamylase sweet corn gene amino acid change

brix9-2-5 Tomato Invertase fruit soluble solid content amino acid change

ovate Tomato Unknown fruit shap early stop codon

R Pea Starch branching enzyme seed sugar content transposon

insertion

ehd1 Rice B-type response regulator flowering time amino acid change

hd1 Rice Transcriptional regulator (zinc finger) flowering

time

disrupted coding

sequence

waxy Rice Starch synthase sticky grains intron splicing

defect

rht Wheat Transcriptional regulator (SH2) plant height early stop codon

vrn1 Wheat Transcriptional regulator (MADS) vernalization regulatory change

vrn2 Wheat Transcriptional regulator (ZCCT) vernalization amino acid change

Genes Identified as Controlling Varietal Differences

37

Process of domestication over the yearshellip

Rachel S Meyer 2012

38

Genetic bottleneck

Cultivated crops undergone with narrowing of diversity problem

But this is not the case in weeds

Weeds are the major threats from the beginning of domestication till

today

Problem arose due to

1 Crop mimicry

2 Genetic assimilation

3 Genetic evolution

39

Super- Domestication Vaughn et al (2007) first used the term super-domestication

The processes that lead to a domesticate with dramatically

increased yield that could not be selected in natural environments

from naturally occurring variation without recourse to new

technologies

Super-domesticates can be constructed with knowledge led

approaches based on current needs using the range of new

technologies now available

Plants exploited for continuous selection introduction hybridization

etc which boosted the process of domestication but now the plant

genetic engineering approach is exploiting plants towards synthetic

biology

40

How to use diversitybull Cross two varieties

bull Genome manipulations

Cell fusion hybrids

bull Chromosome manipulation Backcross a new species

bull Generate recombinants Chromosome recombinations

bull Use a new species wild germplasm

Transgenic approach Modern mutagenesis synthetic gene

construction by utilizing green florescent protein genome editing

NGS GWAS sequencing etchelliphelliphelliphelliphellip

41

Reduce genetic bottlenecks through polyplodization

More vigour

SC

Buffering capacity

Heterotic advantage

Enhaced vegetative

charachers

Enhanced oil

Meiotic stability

42

Approach 1 Use one tetraploid and one diploid as parents (4X ndash 2X) followed by the

chromosome doubling of triploid hybrids (Chrom doubling)

a) Cross between B juncea (AjAjBjBj ) and B oleracea (CoCo) to produce hexaploids

(AjAjBjBjCoCo)

(b) Cross between B napus (AnAnCnCn) and B nigra (BniBni) to produce hexaploids

(AnAnBniBniCnCn)

(c) Cross between B carinata (BcaBcaCcaCca) and B rapa (ArAr) to produce hexaploids

(ArArBcaBcaCcaCca)

Approach 2 Use three tetraploids as parents

(a) Cross between B napus (AnAnCnCn) and B carinata (BcaBcaCcaCca) to produce unbalanced

allotetraploids (AnBcaCnCca ndash unreduced gametes gametes with the somatic chromosome

number and cross with B juncea (AjAjBjBj) to obtain allohexaploids (AnAjBcaBjCnCca

(b) Cross between B napus (AnAnCnCn) and B juncea (AjAjBjBj) to produce unbalanced

allotetraploids (AnAjBjCn ndash unreduced gametes) and cross with B carinata (BcaBcaCcaCca) to

obtain allohexaploids (AnAjBcaBjCnCca)

(c) Cross between B carinata (BcaBcaCcaCca) and B juncea (AjAjBjBj) to produce unbalanced

allotetraploids (AjBcaBjCca - ndash unreduced gametes) and cross with B napus (AnAnCnCn) to obtain

allohexaploids (AnAjBcaBjCnCca)

Approach 3 Use three diploids as parents (2X ndash 2X ndash 2X) Cross between B rapa (ArAr) B

nigra (BniBni) and B oleracea (CoCo) sequentially to obtain hexaploid hybrids (ArArBniBniCoCo)

43

Continuehellip

Guijun Yan 2012

44

Applications of Genomic

tools in Super-Domestication

45

Genome Sequencing

Potential methods of sequencing

1 Clone by clone approach

2 Whole genome shotgun approach

3 Combination of the two methods

Till today no of cultivated plants completely sequenced -85

2016- Arachis duranensis

2015- Solanum cumersonii (Wild potato)

(Ref- NCBI)

46

GWAS

It is a study design in which many markers spread across a genome

are genotyped and test a statistical association with a phenotype are

performed locally along the genome

It is also an examination of many common genetic variants in different

individuals to see if any variant is associated with a trait

Used in successfully studying maize sorghum and barley

Method is efficient for large scale low cost genotyping (even with the

minimum number of SNPs)

Cannot be utilized generally because it needs large population size

GWAS identify rare alleles more precisely

If small population we can opt NAM

47

GWAS and whole genome prediction

Xuehui Huang and Bin Han 2014

48

Five high throuput genotyping methods

Xuehui Huang and Bin Han 2014

49

Role of NGS in domestication Capture of novel genes from wild species will be made easier by

understanding the molecular events associated with crop domestication

Re-sequencing of domesticated species can identify low diversity regions

resulting from selection during domestication

To identify gene-specific sequences to aid the cloning of homologues of key

domestication genes from wild relatives

Candidate genes from wild and domesticated plant populations can define

diversity of target genes in wild populations and lead to the discovery of key

genes for important traits by association analysis

NGS of amplicons of large numbers of candidate genes from wild and

domesticated plant populations can define diversity of target genes in

wild populations and lead to the discovery of key genes for important

traits by association analysis

50

NGS

supports the rapid domestication of new plant species and the efficient

identification and capture of novel genetic variation from related species

Allows whole-genome analysis to determine the genetic basis of

phenotypic differences

NGS allows rapid expansion of genomic analysis to investigation of non-

model species

Made rice study easy by related grass

cost-effective method for plant identification

useful strategy to analysis the chloroplast genome sequence from whole-

genome shot-gun sequencing

facilitates managing this diversity and any changes in crop performance

over time due to genetic drift

Patterns of gene expression have been evaluated in hybrids using NGS

51

Two Approaches to Finding Adaptive Genes

Ross-Ibarra et al2007

52

Techniques to re-wild the plants (transgene free)

1 Introgression

breeding

2 Specific

insertion of lost genes

3 Precision

mutagenesis

Palmgren et al2014

53

Process of rewilding

Palmgren et al2014

54

Synthetic biology projects(i) Modifying cereals including wheat to fix atmospheric nitrogen

(ii) Redesigning metabolic pathways to increase the yield of

secondary metabolites or to generate compounds with enhanced

properties

(iii) Transferring the C4 photosynthesis pathway to rice

(iv) Modifying the glycosylation pathway in plants to accommodate

production of therapeutic proteins

(v) Introducing synthetic signal transduction systems that respond to

external cues

55

Synthetic biology projects

Nicholas J Baltes et al 2015

56

Refactoring the N fixation gene cluster from Klebsiella

Karsten Temme et al 2012

36

Genes Crop Moleular and phenotypic function Causative change

c1

r1

Maize Transcriptional regulator (MYB) kernel color and

Transcriptional regulator (bHLH) kernel color

regulatory change

sh2 Maize pyrophosphorylase supersweet sweet corn transposon

insertion

su1 Maize isoamylase sweet corn gene amino acid change

brix9-2-5 Tomato Invertase fruit soluble solid content amino acid change

ovate Tomato Unknown fruit shap early stop codon

R Pea Starch branching enzyme seed sugar content transposon

insertion

ehd1 Rice B-type response regulator flowering time amino acid change

hd1 Rice Transcriptional regulator (zinc finger) flowering

time

disrupted coding

sequence

waxy Rice Starch synthase sticky grains intron splicing

defect

rht Wheat Transcriptional regulator (SH2) plant height early stop codon

vrn1 Wheat Transcriptional regulator (MADS) vernalization regulatory change

vrn2 Wheat Transcriptional regulator (ZCCT) vernalization amino acid change

Genes Identified as Controlling Varietal Differences

37

Process of domestication over the yearshellip

Rachel S Meyer 2012

38

Genetic bottleneck

Cultivated crops undergone with narrowing of diversity problem

But this is not the case in weeds

Weeds are the major threats from the beginning of domestication till

today

Problem arose due to

1 Crop mimicry

2 Genetic assimilation

3 Genetic evolution

39

Super- Domestication Vaughn et al (2007) first used the term super-domestication

The processes that lead to a domesticate with dramatically

increased yield that could not be selected in natural environments

from naturally occurring variation without recourse to new

technologies

Super-domesticates can be constructed with knowledge led

approaches based on current needs using the range of new

technologies now available

Plants exploited for continuous selection introduction hybridization

etc which boosted the process of domestication but now the plant

genetic engineering approach is exploiting plants towards synthetic

biology

40

How to use diversitybull Cross two varieties

bull Genome manipulations

Cell fusion hybrids

bull Chromosome manipulation Backcross a new species

bull Generate recombinants Chromosome recombinations

bull Use a new species wild germplasm

Transgenic approach Modern mutagenesis synthetic gene

construction by utilizing green florescent protein genome editing

NGS GWAS sequencing etchelliphelliphelliphelliphellip

41

Reduce genetic bottlenecks through polyplodization

More vigour

SC

Buffering capacity

Heterotic advantage

Enhaced vegetative

charachers

Enhanced oil

Meiotic stability

42

Approach 1 Use one tetraploid and one diploid as parents (4X ndash 2X) followed by the

chromosome doubling of triploid hybrids (Chrom doubling)

a) Cross between B juncea (AjAjBjBj ) and B oleracea (CoCo) to produce hexaploids

(AjAjBjBjCoCo)

(b) Cross between B napus (AnAnCnCn) and B nigra (BniBni) to produce hexaploids

(AnAnBniBniCnCn)

(c) Cross between B carinata (BcaBcaCcaCca) and B rapa (ArAr) to produce hexaploids

(ArArBcaBcaCcaCca)

Approach 2 Use three tetraploids as parents

(a) Cross between B napus (AnAnCnCn) and B carinata (BcaBcaCcaCca) to produce unbalanced

allotetraploids (AnBcaCnCca ndash unreduced gametes gametes with the somatic chromosome

number and cross with B juncea (AjAjBjBj) to obtain allohexaploids (AnAjBcaBjCnCca

(b) Cross between B napus (AnAnCnCn) and B juncea (AjAjBjBj) to produce unbalanced

allotetraploids (AnAjBjCn ndash unreduced gametes) and cross with B carinata (BcaBcaCcaCca) to

obtain allohexaploids (AnAjBcaBjCnCca)

(c) Cross between B carinata (BcaBcaCcaCca) and B juncea (AjAjBjBj) to produce unbalanced

allotetraploids (AjBcaBjCca - ndash unreduced gametes) and cross with B napus (AnAnCnCn) to obtain

allohexaploids (AnAjBcaBjCnCca)

Approach 3 Use three diploids as parents (2X ndash 2X ndash 2X) Cross between B rapa (ArAr) B

nigra (BniBni) and B oleracea (CoCo) sequentially to obtain hexaploid hybrids (ArArBniBniCoCo)

43

Continuehellip

Guijun Yan 2012

44

Applications of Genomic

tools in Super-Domestication

45

Genome Sequencing

Potential methods of sequencing

1 Clone by clone approach

2 Whole genome shotgun approach

3 Combination of the two methods

Till today no of cultivated plants completely sequenced -85

2016- Arachis duranensis

2015- Solanum cumersonii (Wild potato)

(Ref- NCBI)

46

GWAS

It is a study design in which many markers spread across a genome

are genotyped and test a statistical association with a phenotype are

performed locally along the genome

It is also an examination of many common genetic variants in different

individuals to see if any variant is associated with a trait

Used in successfully studying maize sorghum and barley

Method is efficient for large scale low cost genotyping (even with the

minimum number of SNPs)

Cannot be utilized generally because it needs large population size

GWAS identify rare alleles more precisely

If small population we can opt NAM

47

GWAS and whole genome prediction

Xuehui Huang and Bin Han 2014

48

Five high throuput genotyping methods

Xuehui Huang and Bin Han 2014

49

Role of NGS in domestication Capture of novel genes from wild species will be made easier by

understanding the molecular events associated with crop domestication

Re-sequencing of domesticated species can identify low diversity regions

resulting from selection during domestication

To identify gene-specific sequences to aid the cloning of homologues of key

domestication genes from wild relatives

Candidate genes from wild and domesticated plant populations can define

diversity of target genes in wild populations and lead to the discovery of key

genes for important traits by association analysis

NGS of amplicons of large numbers of candidate genes from wild and

domesticated plant populations can define diversity of target genes in

wild populations and lead to the discovery of key genes for important

traits by association analysis

50

NGS

supports the rapid domestication of new plant species and the efficient

identification and capture of novel genetic variation from related species

Allows whole-genome analysis to determine the genetic basis of

phenotypic differences

NGS allows rapid expansion of genomic analysis to investigation of non-

model species

Made rice study easy by related grass

cost-effective method for plant identification

useful strategy to analysis the chloroplast genome sequence from whole-

genome shot-gun sequencing

facilitates managing this diversity and any changes in crop performance

over time due to genetic drift

Patterns of gene expression have been evaluated in hybrids using NGS

51

Two Approaches to Finding Adaptive Genes

Ross-Ibarra et al2007

52

Techniques to re-wild the plants (transgene free)

1 Introgression

breeding

2 Specific

insertion of lost genes

3 Precision

mutagenesis

Palmgren et al2014

53

Process of rewilding

Palmgren et al2014

54

Synthetic biology projects(i) Modifying cereals including wheat to fix atmospheric nitrogen

(ii) Redesigning metabolic pathways to increase the yield of

secondary metabolites or to generate compounds with enhanced

properties

(iii) Transferring the C4 photosynthesis pathway to rice

(iv) Modifying the glycosylation pathway in plants to accommodate

production of therapeutic proteins

(v) Introducing synthetic signal transduction systems that respond to

external cues

55

Synthetic biology projects

Nicholas J Baltes et al 2015

56

Refactoring the N fixation gene cluster from Klebsiella

Karsten Temme et al 2012

37

Process of domestication over the yearshellip

Rachel S Meyer 2012

38

Genetic bottleneck

Cultivated crops undergone with narrowing of diversity problem

But this is not the case in weeds

Weeds are the major threats from the beginning of domestication till

today

Problem arose due to

1 Crop mimicry

2 Genetic assimilation

3 Genetic evolution

39

Super- Domestication Vaughn et al (2007) first used the term super-domestication

The processes that lead to a domesticate with dramatically

increased yield that could not be selected in natural environments

from naturally occurring variation without recourse to new

technologies

Super-domesticates can be constructed with knowledge led

approaches based on current needs using the range of new

technologies now available

Plants exploited for continuous selection introduction hybridization

etc which boosted the process of domestication but now the plant

genetic engineering approach is exploiting plants towards synthetic

biology

40

How to use diversitybull Cross two varieties

bull Genome manipulations

Cell fusion hybrids

bull Chromosome manipulation Backcross a new species

bull Generate recombinants Chromosome recombinations

bull Use a new species wild germplasm

Transgenic approach Modern mutagenesis synthetic gene

construction by utilizing green florescent protein genome editing

NGS GWAS sequencing etchelliphelliphelliphelliphellip

41

Reduce genetic bottlenecks through polyplodization

More vigour

SC

Buffering capacity

Heterotic advantage

Enhaced vegetative

charachers

Enhanced oil

Meiotic stability

42

Approach 1 Use one tetraploid and one diploid as parents (4X ndash 2X) followed by the

chromosome doubling of triploid hybrids (Chrom doubling)

a) Cross between B juncea (AjAjBjBj ) and B oleracea (CoCo) to produce hexaploids

(AjAjBjBjCoCo)

(b) Cross between B napus (AnAnCnCn) and B nigra (BniBni) to produce hexaploids

(AnAnBniBniCnCn)

(c) Cross between B carinata (BcaBcaCcaCca) and B rapa (ArAr) to produce hexaploids

(ArArBcaBcaCcaCca)

Approach 2 Use three tetraploids as parents

(a) Cross between B napus (AnAnCnCn) and B carinata (BcaBcaCcaCca) to produce unbalanced

allotetraploids (AnBcaCnCca ndash unreduced gametes gametes with the somatic chromosome

number and cross with B juncea (AjAjBjBj) to obtain allohexaploids (AnAjBcaBjCnCca

(b) Cross between B napus (AnAnCnCn) and B juncea (AjAjBjBj) to produce unbalanced

allotetraploids (AnAjBjCn ndash unreduced gametes) and cross with B carinata (BcaBcaCcaCca) to

obtain allohexaploids (AnAjBcaBjCnCca)

(c) Cross between B carinata (BcaBcaCcaCca) and B juncea (AjAjBjBj) to produce unbalanced

allotetraploids (AjBcaBjCca - ndash unreduced gametes) and cross with B napus (AnAnCnCn) to obtain

allohexaploids (AnAjBcaBjCnCca)

Approach 3 Use three diploids as parents (2X ndash 2X ndash 2X) Cross between B rapa (ArAr) B

nigra (BniBni) and B oleracea (CoCo) sequentially to obtain hexaploid hybrids (ArArBniBniCoCo)

43

Continuehellip

Guijun Yan 2012

44

Applications of Genomic

tools in Super-Domestication

45

Genome Sequencing

Potential methods of sequencing

1 Clone by clone approach

2 Whole genome shotgun approach

3 Combination of the two methods

Till today no of cultivated plants completely sequenced -85

2016- Arachis duranensis

2015- Solanum cumersonii (Wild potato)

(Ref- NCBI)

46

GWAS

It is a study design in which many markers spread across a genome

are genotyped and test a statistical association with a phenotype are

performed locally along the genome

It is also an examination of many common genetic variants in different

individuals to see if any variant is associated with a trait

Used in successfully studying maize sorghum and barley

Method is efficient for large scale low cost genotyping (even with the

minimum number of SNPs)

Cannot be utilized generally because it needs large population size

GWAS identify rare alleles more precisely

If small population we can opt NAM

47

GWAS and whole genome prediction

Xuehui Huang and Bin Han 2014

48

Five high throuput genotyping methods

Xuehui Huang and Bin Han 2014

49

Role of NGS in domestication Capture of novel genes from wild species will be made easier by

understanding the molecular events associated with crop domestication

Re-sequencing of domesticated species can identify low diversity regions

resulting from selection during domestication

To identify gene-specific sequences to aid the cloning of homologues of key

domestication genes from wild relatives

Candidate genes from wild and domesticated plant populations can define

diversity of target genes in wild populations and lead to the discovery of key

genes for important traits by association analysis

NGS of amplicons of large numbers of candidate genes from wild and

domesticated plant populations can define diversity of target genes in

wild populations and lead to the discovery of key genes for important

traits by association analysis

50

NGS

supports the rapid domestication of new plant species and the efficient

identification and capture of novel genetic variation from related species

Allows whole-genome analysis to determine the genetic basis of

phenotypic differences

NGS allows rapid expansion of genomic analysis to investigation of non-

model species

Made rice study easy by related grass

cost-effective method for plant identification

useful strategy to analysis the chloroplast genome sequence from whole-

genome shot-gun sequencing

facilitates managing this diversity and any changes in crop performance

over time due to genetic drift

Patterns of gene expression have been evaluated in hybrids using NGS

51

Two Approaches to Finding Adaptive Genes

Ross-Ibarra et al2007

52

Techniques to re-wild the plants (transgene free)

1 Introgression

breeding

2 Specific

insertion of lost genes

3 Precision

mutagenesis

Palmgren et al2014

53

Process of rewilding

Palmgren et al2014

54

Synthetic biology projects(i) Modifying cereals including wheat to fix atmospheric nitrogen

(ii) Redesigning metabolic pathways to increase the yield of

secondary metabolites or to generate compounds with enhanced

properties

(iii) Transferring the C4 photosynthesis pathway to rice

(iv) Modifying the glycosylation pathway in plants to accommodate

production of therapeutic proteins

(v) Introducing synthetic signal transduction systems that respond to

external cues

55

Synthetic biology projects

Nicholas J Baltes et al 2015

56

Refactoring the N fixation gene cluster from Klebsiella

Karsten Temme et al 2012

38

Genetic bottleneck

Cultivated crops undergone with narrowing of diversity problem

But this is not the case in weeds

Weeds are the major threats from the beginning of domestication till

today

Problem arose due to

1 Crop mimicry

2 Genetic assimilation

3 Genetic evolution

39

Super- Domestication Vaughn et al (2007) first used the term super-domestication

The processes that lead to a domesticate with dramatically

increased yield that could not be selected in natural environments

from naturally occurring variation without recourse to new

technologies

Super-domesticates can be constructed with knowledge led

approaches based on current needs using the range of new

technologies now available

Plants exploited for continuous selection introduction hybridization

etc which boosted the process of domestication but now the plant

genetic engineering approach is exploiting plants towards synthetic

biology

40

How to use diversitybull Cross two varieties

bull Genome manipulations

Cell fusion hybrids

bull Chromosome manipulation Backcross a new species

bull Generate recombinants Chromosome recombinations

bull Use a new species wild germplasm

Transgenic approach Modern mutagenesis synthetic gene

construction by utilizing green florescent protein genome editing

NGS GWAS sequencing etchelliphelliphelliphelliphellip

41

Reduce genetic bottlenecks through polyplodization

More vigour

SC

Buffering capacity

Heterotic advantage

Enhaced vegetative

charachers

Enhanced oil

Meiotic stability

42

Approach 1 Use one tetraploid and one diploid as parents (4X ndash 2X) followed by the

chromosome doubling of triploid hybrids (Chrom doubling)

a) Cross between B juncea (AjAjBjBj ) and B oleracea (CoCo) to produce hexaploids

(AjAjBjBjCoCo)

(b) Cross between B napus (AnAnCnCn) and B nigra (BniBni) to produce hexaploids

(AnAnBniBniCnCn)

(c) Cross between B carinata (BcaBcaCcaCca) and B rapa (ArAr) to produce hexaploids

(ArArBcaBcaCcaCca)

Approach 2 Use three tetraploids as parents

(a) Cross between B napus (AnAnCnCn) and B carinata (BcaBcaCcaCca) to produce unbalanced

allotetraploids (AnBcaCnCca ndash unreduced gametes gametes with the somatic chromosome

number and cross with B juncea (AjAjBjBj) to obtain allohexaploids (AnAjBcaBjCnCca

(b) Cross between B napus (AnAnCnCn) and B juncea (AjAjBjBj) to produce unbalanced

allotetraploids (AnAjBjCn ndash unreduced gametes) and cross with B carinata (BcaBcaCcaCca) to

obtain allohexaploids (AnAjBcaBjCnCca)

(c) Cross between B carinata (BcaBcaCcaCca) and B juncea (AjAjBjBj) to produce unbalanced

allotetraploids (AjBcaBjCca - ndash unreduced gametes) and cross with B napus (AnAnCnCn) to obtain

allohexaploids (AnAjBcaBjCnCca)

Approach 3 Use three diploids as parents (2X ndash 2X ndash 2X) Cross between B rapa (ArAr) B

nigra (BniBni) and B oleracea (CoCo) sequentially to obtain hexaploid hybrids (ArArBniBniCoCo)

43

Continuehellip

Guijun Yan 2012

44

Applications of Genomic

tools in Super-Domestication

45

Genome Sequencing

Potential methods of sequencing

1 Clone by clone approach

2 Whole genome shotgun approach

3 Combination of the two methods

Till today no of cultivated plants completely sequenced -85

2016- Arachis duranensis

2015- Solanum cumersonii (Wild potato)

(Ref- NCBI)

46

GWAS

It is a study design in which many markers spread across a genome

are genotyped and test a statistical association with a phenotype are

performed locally along the genome

It is also an examination of many common genetic variants in different

individuals to see if any variant is associated with a trait

Used in successfully studying maize sorghum and barley

Method is efficient for large scale low cost genotyping (even with the

minimum number of SNPs)

Cannot be utilized generally because it needs large population size

GWAS identify rare alleles more precisely

If small population we can opt NAM

47

GWAS and whole genome prediction

Xuehui Huang and Bin Han 2014

48

Five high throuput genotyping methods

Xuehui Huang and Bin Han 2014

49

Role of NGS in domestication Capture of novel genes from wild species will be made easier by

understanding the molecular events associated with crop domestication

Re-sequencing of domesticated species can identify low diversity regions

resulting from selection during domestication

To identify gene-specific sequences to aid the cloning of homologues of key

domestication genes from wild relatives

Candidate genes from wild and domesticated plant populations can define

diversity of target genes in wild populations and lead to the discovery of key

genes for important traits by association analysis

NGS of amplicons of large numbers of candidate genes from wild and

domesticated plant populations can define diversity of target genes in

wild populations and lead to the discovery of key genes for important

traits by association analysis

50

NGS

supports the rapid domestication of new plant species and the efficient

identification and capture of novel genetic variation from related species

Allows whole-genome analysis to determine the genetic basis of

phenotypic differences

NGS allows rapid expansion of genomic analysis to investigation of non-

model species

Made rice study easy by related grass

cost-effective method for plant identification

useful strategy to analysis the chloroplast genome sequence from whole-

genome shot-gun sequencing

facilitates managing this diversity and any changes in crop performance

over time due to genetic drift

Patterns of gene expression have been evaluated in hybrids using NGS

51

Two Approaches to Finding Adaptive Genes

Ross-Ibarra et al2007

52

Techniques to re-wild the plants (transgene free)

1 Introgression

breeding

2 Specific

insertion of lost genes

3 Precision

mutagenesis

Palmgren et al2014

53

Process of rewilding

Palmgren et al2014

54

Synthetic biology projects(i) Modifying cereals including wheat to fix atmospheric nitrogen

(ii) Redesigning metabolic pathways to increase the yield of

secondary metabolites or to generate compounds with enhanced

properties

(iii) Transferring the C4 photosynthesis pathway to rice

(iv) Modifying the glycosylation pathway in plants to accommodate

production of therapeutic proteins

(v) Introducing synthetic signal transduction systems that respond to

external cues

55

Synthetic biology projects

Nicholas J Baltes et al 2015

56

Refactoring the N fixation gene cluster from Klebsiella

Karsten Temme et al 2012

39

Super- Domestication Vaughn et al (2007) first used the term super-domestication

The processes that lead to a domesticate with dramatically

increased yield that could not be selected in natural environments

from naturally occurring variation without recourse to new

technologies

Super-domesticates can be constructed with knowledge led

approaches based on current needs using the range of new

technologies now available

Plants exploited for continuous selection introduction hybridization

etc which boosted the process of domestication but now the plant

genetic engineering approach is exploiting plants towards synthetic

biology

40

How to use diversitybull Cross two varieties

bull Genome manipulations

Cell fusion hybrids

bull Chromosome manipulation Backcross a new species

bull Generate recombinants Chromosome recombinations

bull Use a new species wild germplasm

Transgenic approach Modern mutagenesis synthetic gene

construction by utilizing green florescent protein genome editing

NGS GWAS sequencing etchelliphelliphelliphelliphellip

41

Reduce genetic bottlenecks through polyplodization

More vigour

SC

Buffering capacity

Heterotic advantage

Enhaced vegetative

charachers

Enhanced oil

Meiotic stability

42

Approach 1 Use one tetraploid and one diploid as parents (4X ndash 2X) followed by the

chromosome doubling of triploid hybrids (Chrom doubling)

a) Cross between B juncea (AjAjBjBj ) and B oleracea (CoCo) to produce hexaploids

(AjAjBjBjCoCo)

(b) Cross between B napus (AnAnCnCn) and B nigra (BniBni) to produce hexaploids

(AnAnBniBniCnCn)

(c) Cross between B carinata (BcaBcaCcaCca) and B rapa (ArAr) to produce hexaploids

(ArArBcaBcaCcaCca)

Approach 2 Use three tetraploids as parents

(a) Cross between B napus (AnAnCnCn) and B carinata (BcaBcaCcaCca) to produce unbalanced

allotetraploids (AnBcaCnCca ndash unreduced gametes gametes with the somatic chromosome

number and cross with B juncea (AjAjBjBj) to obtain allohexaploids (AnAjBcaBjCnCca

(b) Cross between B napus (AnAnCnCn) and B juncea (AjAjBjBj) to produce unbalanced

allotetraploids (AnAjBjCn ndash unreduced gametes) and cross with B carinata (BcaBcaCcaCca) to

obtain allohexaploids (AnAjBcaBjCnCca)

(c) Cross between B carinata (BcaBcaCcaCca) and B juncea (AjAjBjBj) to produce unbalanced

allotetraploids (AjBcaBjCca - ndash unreduced gametes) and cross with B napus (AnAnCnCn) to obtain

allohexaploids (AnAjBcaBjCnCca)

Approach 3 Use three diploids as parents (2X ndash 2X ndash 2X) Cross between B rapa (ArAr) B

nigra (BniBni) and B oleracea (CoCo) sequentially to obtain hexaploid hybrids (ArArBniBniCoCo)

43

Continuehellip

Guijun Yan 2012

44

Applications of Genomic

tools in Super-Domestication

45

Genome Sequencing

Potential methods of sequencing

1 Clone by clone approach

2 Whole genome shotgun approach

3 Combination of the two methods

Till today no of cultivated plants completely sequenced -85

2016- Arachis duranensis

2015- Solanum cumersonii (Wild potato)

(Ref- NCBI)

46

GWAS

It is a study design in which many markers spread across a genome

are genotyped and test a statistical association with a phenotype are

performed locally along the genome

It is also an examination of many common genetic variants in different

individuals to see if any variant is associated with a trait

Used in successfully studying maize sorghum and barley

Method is efficient for large scale low cost genotyping (even with the

minimum number of SNPs)

Cannot be utilized generally because it needs large population size

GWAS identify rare alleles more precisely

If small population we can opt NAM

47

GWAS and whole genome prediction

Xuehui Huang and Bin Han 2014

48

Five high throuput genotyping methods

Xuehui Huang and Bin Han 2014

49

Role of NGS in domestication Capture of novel genes from wild species will be made easier by

understanding the molecular events associated with crop domestication

Re-sequencing of domesticated species can identify low diversity regions

resulting from selection during domestication

To identify gene-specific sequences to aid the cloning of homologues of key

domestication genes from wild relatives

Candidate genes from wild and domesticated plant populations can define

diversity of target genes in wild populations and lead to the discovery of key

genes for important traits by association analysis

NGS of amplicons of large numbers of candidate genes from wild and

domesticated plant populations can define diversity of target genes in

wild populations and lead to the discovery of key genes for important

traits by association analysis

50

NGS

supports the rapid domestication of new plant species and the efficient

identification and capture of novel genetic variation from related species

Allows whole-genome analysis to determine the genetic basis of

phenotypic differences

NGS allows rapid expansion of genomic analysis to investigation of non-

model species

Made rice study easy by related grass

cost-effective method for plant identification

useful strategy to analysis the chloroplast genome sequence from whole-

genome shot-gun sequencing

facilitates managing this diversity and any changes in crop performance

over time due to genetic drift

Patterns of gene expression have been evaluated in hybrids using NGS

51

Two Approaches to Finding Adaptive Genes

Ross-Ibarra et al2007

52

Techniques to re-wild the plants (transgene free)

1 Introgression

breeding

2 Specific

insertion of lost genes

3 Precision

mutagenesis

Palmgren et al2014

53

Process of rewilding

Palmgren et al2014

54

Synthetic biology projects(i) Modifying cereals including wheat to fix atmospheric nitrogen

(ii) Redesigning metabolic pathways to increase the yield of

secondary metabolites or to generate compounds with enhanced

properties

(iii) Transferring the C4 photosynthesis pathway to rice

(iv) Modifying the glycosylation pathway in plants to accommodate

production of therapeutic proteins

(v) Introducing synthetic signal transduction systems that respond to

external cues

55

Synthetic biology projects

Nicholas J Baltes et al 2015

56

Refactoring the N fixation gene cluster from Klebsiella

Karsten Temme et al 2012

40

How to use diversitybull Cross two varieties

bull Genome manipulations

Cell fusion hybrids

bull Chromosome manipulation Backcross a new species

bull Generate recombinants Chromosome recombinations

bull Use a new species wild germplasm

Transgenic approach Modern mutagenesis synthetic gene

construction by utilizing green florescent protein genome editing

NGS GWAS sequencing etchelliphelliphelliphelliphellip

41

Reduce genetic bottlenecks through polyplodization

More vigour

SC

Buffering capacity

Heterotic advantage

Enhaced vegetative

charachers

Enhanced oil

Meiotic stability

42

Approach 1 Use one tetraploid and one diploid as parents (4X ndash 2X) followed by the

chromosome doubling of triploid hybrids (Chrom doubling)

a) Cross between B juncea (AjAjBjBj ) and B oleracea (CoCo) to produce hexaploids

(AjAjBjBjCoCo)

(b) Cross between B napus (AnAnCnCn) and B nigra (BniBni) to produce hexaploids

(AnAnBniBniCnCn)

(c) Cross between B carinata (BcaBcaCcaCca) and B rapa (ArAr) to produce hexaploids

(ArArBcaBcaCcaCca)

Approach 2 Use three tetraploids as parents

(a) Cross between B napus (AnAnCnCn) and B carinata (BcaBcaCcaCca) to produce unbalanced

allotetraploids (AnBcaCnCca ndash unreduced gametes gametes with the somatic chromosome

number and cross with B juncea (AjAjBjBj) to obtain allohexaploids (AnAjBcaBjCnCca

(b) Cross between B napus (AnAnCnCn) and B juncea (AjAjBjBj) to produce unbalanced

allotetraploids (AnAjBjCn ndash unreduced gametes) and cross with B carinata (BcaBcaCcaCca) to

obtain allohexaploids (AnAjBcaBjCnCca)

(c) Cross between B carinata (BcaBcaCcaCca) and B juncea (AjAjBjBj) to produce unbalanced

allotetraploids (AjBcaBjCca - ndash unreduced gametes) and cross with B napus (AnAnCnCn) to obtain

allohexaploids (AnAjBcaBjCnCca)

Approach 3 Use three diploids as parents (2X ndash 2X ndash 2X) Cross between B rapa (ArAr) B

nigra (BniBni) and B oleracea (CoCo) sequentially to obtain hexaploid hybrids (ArArBniBniCoCo)

43

Continuehellip

Guijun Yan 2012

44

Applications of Genomic

tools in Super-Domestication

45

Genome Sequencing

Potential methods of sequencing

1 Clone by clone approach

2 Whole genome shotgun approach

3 Combination of the two methods

Till today no of cultivated plants completely sequenced -85

2016- Arachis duranensis

2015- Solanum cumersonii (Wild potato)

(Ref- NCBI)

46

GWAS

It is a study design in which many markers spread across a genome

are genotyped and test a statistical association with a phenotype are

performed locally along the genome

It is also an examination of many common genetic variants in different

individuals to see if any variant is associated with a trait

Used in successfully studying maize sorghum and barley

Method is efficient for large scale low cost genotyping (even with the

minimum number of SNPs)

Cannot be utilized generally because it needs large population size

GWAS identify rare alleles more precisely

If small population we can opt NAM

47

GWAS and whole genome prediction

Xuehui Huang and Bin Han 2014

48

Five high throuput genotyping methods

Xuehui Huang and Bin Han 2014

49

Role of NGS in domestication Capture of novel genes from wild species will be made easier by

understanding the molecular events associated with crop domestication

Re-sequencing of domesticated species can identify low diversity regions

resulting from selection during domestication

To identify gene-specific sequences to aid the cloning of homologues of key

domestication genes from wild relatives

Candidate genes from wild and domesticated plant populations can define

diversity of target genes in wild populations and lead to the discovery of key

genes for important traits by association analysis

NGS of amplicons of large numbers of candidate genes from wild and

domesticated plant populations can define diversity of target genes in

wild populations and lead to the discovery of key genes for important

traits by association analysis

50

NGS

supports the rapid domestication of new plant species and the efficient

identification and capture of novel genetic variation from related species

Allows whole-genome analysis to determine the genetic basis of

phenotypic differences

NGS allows rapid expansion of genomic analysis to investigation of non-

model species

Made rice study easy by related grass

cost-effective method for plant identification

useful strategy to analysis the chloroplast genome sequence from whole-

genome shot-gun sequencing

facilitates managing this diversity and any changes in crop performance

over time due to genetic drift

Patterns of gene expression have been evaluated in hybrids using NGS

51

Two Approaches to Finding Adaptive Genes

Ross-Ibarra et al2007

52

Techniques to re-wild the plants (transgene free)

1 Introgression

breeding

2 Specific

insertion of lost genes

3 Precision

mutagenesis

Palmgren et al2014

53

Process of rewilding

Palmgren et al2014

54

Synthetic biology projects(i) Modifying cereals including wheat to fix atmospheric nitrogen

(ii) Redesigning metabolic pathways to increase the yield of

secondary metabolites or to generate compounds with enhanced

properties

(iii) Transferring the C4 photosynthesis pathway to rice

(iv) Modifying the glycosylation pathway in plants to accommodate

production of therapeutic proteins

(v) Introducing synthetic signal transduction systems that respond to

external cues

55

Synthetic biology projects

Nicholas J Baltes et al 2015

56

Refactoring the N fixation gene cluster from Klebsiella

Karsten Temme et al 2012

41

Reduce genetic bottlenecks through polyplodization

More vigour

SC

Buffering capacity

Heterotic advantage

Enhaced vegetative

charachers

Enhanced oil

Meiotic stability

42

Approach 1 Use one tetraploid and one diploid as parents (4X ndash 2X) followed by the

chromosome doubling of triploid hybrids (Chrom doubling)

a) Cross between B juncea (AjAjBjBj ) and B oleracea (CoCo) to produce hexaploids

(AjAjBjBjCoCo)

(b) Cross between B napus (AnAnCnCn) and B nigra (BniBni) to produce hexaploids

(AnAnBniBniCnCn)

(c) Cross between B carinata (BcaBcaCcaCca) and B rapa (ArAr) to produce hexaploids

(ArArBcaBcaCcaCca)

Approach 2 Use three tetraploids as parents

(a) Cross between B napus (AnAnCnCn) and B carinata (BcaBcaCcaCca) to produce unbalanced

allotetraploids (AnBcaCnCca ndash unreduced gametes gametes with the somatic chromosome

number and cross with B juncea (AjAjBjBj) to obtain allohexaploids (AnAjBcaBjCnCca

(b) Cross between B napus (AnAnCnCn) and B juncea (AjAjBjBj) to produce unbalanced

allotetraploids (AnAjBjCn ndash unreduced gametes) and cross with B carinata (BcaBcaCcaCca) to

obtain allohexaploids (AnAjBcaBjCnCca)

(c) Cross between B carinata (BcaBcaCcaCca) and B juncea (AjAjBjBj) to produce unbalanced

allotetraploids (AjBcaBjCca - ndash unreduced gametes) and cross with B napus (AnAnCnCn) to obtain

allohexaploids (AnAjBcaBjCnCca)

Approach 3 Use three diploids as parents (2X ndash 2X ndash 2X) Cross between B rapa (ArAr) B

nigra (BniBni) and B oleracea (CoCo) sequentially to obtain hexaploid hybrids (ArArBniBniCoCo)

43

Continuehellip

Guijun Yan 2012

44

Applications of Genomic

tools in Super-Domestication

45

Genome Sequencing

Potential methods of sequencing

1 Clone by clone approach

2 Whole genome shotgun approach

3 Combination of the two methods

Till today no of cultivated plants completely sequenced -85

2016- Arachis duranensis

2015- Solanum cumersonii (Wild potato)

(Ref- NCBI)

46

GWAS

It is a study design in which many markers spread across a genome

are genotyped and test a statistical association with a phenotype are

performed locally along the genome

It is also an examination of many common genetic variants in different

individuals to see if any variant is associated with a trait

Used in successfully studying maize sorghum and barley

Method is efficient for large scale low cost genotyping (even with the

minimum number of SNPs)

Cannot be utilized generally because it needs large population size

GWAS identify rare alleles more precisely

If small population we can opt NAM

47

GWAS and whole genome prediction

Xuehui Huang and Bin Han 2014

48

Five high throuput genotyping methods

Xuehui Huang and Bin Han 2014

49

Role of NGS in domestication Capture of novel genes from wild species will be made easier by

understanding the molecular events associated with crop domestication

Re-sequencing of domesticated species can identify low diversity regions

resulting from selection during domestication

To identify gene-specific sequences to aid the cloning of homologues of key

domestication genes from wild relatives

Candidate genes from wild and domesticated plant populations can define

diversity of target genes in wild populations and lead to the discovery of key

genes for important traits by association analysis

NGS of amplicons of large numbers of candidate genes from wild and

domesticated plant populations can define diversity of target genes in

wild populations and lead to the discovery of key genes for important

traits by association analysis

50

NGS

supports the rapid domestication of new plant species and the efficient

identification and capture of novel genetic variation from related species

Allows whole-genome analysis to determine the genetic basis of

phenotypic differences

NGS allows rapid expansion of genomic analysis to investigation of non-

model species

Made rice study easy by related grass

cost-effective method for plant identification

useful strategy to analysis the chloroplast genome sequence from whole-

genome shot-gun sequencing

facilitates managing this diversity and any changes in crop performance

over time due to genetic drift

Patterns of gene expression have been evaluated in hybrids using NGS

51

Two Approaches to Finding Adaptive Genes

Ross-Ibarra et al2007

52

Techniques to re-wild the plants (transgene free)

1 Introgression

breeding

2 Specific

insertion of lost genes

3 Precision

mutagenesis

Palmgren et al2014

53

Process of rewilding

Palmgren et al2014

54

Synthetic biology projects(i) Modifying cereals including wheat to fix atmospheric nitrogen

(ii) Redesigning metabolic pathways to increase the yield of

secondary metabolites or to generate compounds with enhanced

properties

(iii) Transferring the C4 photosynthesis pathway to rice

(iv) Modifying the glycosylation pathway in plants to accommodate

production of therapeutic proteins

(v) Introducing synthetic signal transduction systems that respond to

external cues

55

Synthetic biology projects

Nicholas J Baltes et al 2015

56

Refactoring the N fixation gene cluster from Klebsiella

Karsten Temme et al 2012

42

Approach 1 Use one tetraploid and one diploid as parents (4X ndash 2X) followed by the

chromosome doubling of triploid hybrids (Chrom doubling)

a) Cross between B juncea (AjAjBjBj ) and B oleracea (CoCo) to produce hexaploids

(AjAjBjBjCoCo)

(b) Cross between B napus (AnAnCnCn) and B nigra (BniBni) to produce hexaploids

(AnAnBniBniCnCn)

(c) Cross between B carinata (BcaBcaCcaCca) and B rapa (ArAr) to produce hexaploids

(ArArBcaBcaCcaCca)

Approach 2 Use three tetraploids as parents

(a) Cross between B napus (AnAnCnCn) and B carinata (BcaBcaCcaCca) to produce unbalanced

allotetraploids (AnBcaCnCca ndash unreduced gametes gametes with the somatic chromosome

number and cross with B juncea (AjAjBjBj) to obtain allohexaploids (AnAjBcaBjCnCca

(b) Cross between B napus (AnAnCnCn) and B juncea (AjAjBjBj) to produce unbalanced

allotetraploids (AnAjBjCn ndash unreduced gametes) and cross with B carinata (BcaBcaCcaCca) to

obtain allohexaploids (AnAjBcaBjCnCca)

(c) Cross between B carinata (BcaBcaCcaCca) and B juncea (AjAjBjBj) to produce unbalanced

allotetraploids (AjBcaBjCca - ndash unreduced gametes) and cross with B napus (AnAnCnCn) to obtain

allohexaploids (AnAjBcaBjCnCca)

Approach 3 Use three diploids as parents (2X ndash 2X ndash 2X) Cross between B rapa (ArAr) B

nigra (BniBni) and B oleracea (CoCo) sequentially to obtain hexaploid hybrids (ArArBniBniCoCo)

43

Continuehellip

Guijun Yan 2012

44

Applications of Genomic

tools in Super-Domestication

45

Genome Sequencing

Potential methods of sequencing

1 Clone by clone approach

2 Whole genome shotgun approach

3 Combination of the two methods

Till today no of cultivated plants completely sequenced -85

2016- Arachis duranensis

2015- Solanum cumersonii (Wild potato)

(Ref- NCBI)

46

GWAS

It is a study design in which many markers spread across a genome

are genotyped and test a statistical association with a phenotype are

performed locally along the genome

It is also an examination of many common genetic variants in different

individuals to see if any variant is associated with a trait

Used in successfully studying maize sorghum and barley

Method is efficient for large scale low cost genotyping (even with the

minimum number of SNPs)

Cannot be utilized generally because it needs large population size

GWAS identify rare alleles more precisely

If small population we can opt NAM

47

GWAS and whole genome prediction

Xuehui Huang and Bin Han 2014

48

Five high throuput genotyping methods

Xuehui Huang and Bin Han 2014

49

Role of NGS in domestication Capture of novel genes from wild species will be made easier by

understanding the molecular events associated with crop domestication

Re-sequencing of domesticated species can identify low diversity regions

resulting from selection during domestication

To identify gene-specific sequences to aid the cloning of homologues of key

domestication genes from wild relatives

Candidate genes from wild and domesticated plant populations can define

diversity of target genes in wild populations and lead to the discovery of key

genes for important traits by association analysis

NGS of amplicons of large numbers of candidate genes from wild and

domesticated plant populations can define diversity of target genes in

wild populations and lead to the discovery of key genes for important

traits by association analysis

50

NGS

supports the rapid domestication of new plant species and the efficient

identification and capture of novel genetic variation from related species

Allows whole-genome analysis to determine the genetic basis of

phenotypic differences

NGS allows rapid expansion of genomic analysis to investigation of non-

model species

Made rice study easy by related grass

cost-effective method for plant identification

useful strategy to analysis the chloroplast genome sequence from whole-

genome shot-gun sequencing

facilitates managing this diversity and any changes in crop performance

over time due to genetic drift

Patterns of gene expression have been evaluated in hybrids using NGS

51

Two Approaches to Finding Adaptive Genes

Ross-Ibarra et al2007

52

Techniques to re-wild the plants (transgene free)

1 Introgression

breeding

2 Specific

insertion of lost genes

3 Precision

mutagenesis

Palmgren et al2014

53

Process of rewilding

Palmgren et al2014

54

Synthetic biology projects(i) Modifying cereals including wheat to fix atmospheric nitrogen

(ii) Redesigning metabolic pathways to increase the yield of

secondary metabolites or to generate compounds with enhanced

properties

(iii) Transferring the C4 photosynthesis pathway to rice

(iv) Modifying the glycosylation pathway in plants to accommodate

production of therapeutic proteins

(v) Introducing synthetic signal transduction systems that respond to

external cues

55

Synthetic biology projects

Nicholas J Baltes et al 2015

56

Refactoring the N fixation gene cluster from Klebsiella

Karsten Temme et al 2012

43

Continuehellip

Guijun Yan 2012

44

Applications of Genomic

tools in Super-Domestication

45

Genome Sequencing

Potential methods of sequencing

1 Clone by clone approach

2 Whole genome shotgun approach

3 Combination of the two methods

Till today no of cultivated plants completely sequenced -85

2016- Arachis duranensis

2015- Solanum cumersonii (Wild potato)

(Ref- NCBI)

46

GWAS

It is a study design in which many markers spread across a genome

are genotyped and test a statistical association with a phenotype are

performed locally along the genome

It is also an examination of many common genetic variants in different

individuals to see if any variant is associated with a trait

Used in successfully studying maize sorghum and barley

Method is efficient for large scale low cost genotyping (even with the

minimum number of SNPs)

Cannot be utilized generally because it needs large population size

GWAS identify rare alleles more precisely

If small population we can opt NAM

47

GWAS and whole genome prediction

Xuehui Huang and Bin Han 2014

48

Five high throuput genotyping methods

Xuehui Huang and Bin Han 2014

49

Role of NGS in domestication Capture of novel genes from wild species will be made easier by

understanding the molecular events associated with crop domestication

Re-sequencing of domesticated species can identify low diversity regions

resulting from selection during domestication

To identify gene-specific sequences to aid the cloning of homologues of key

domestication genes from wild relatives

Candidate genes from wild and domesticated plant populations can define

diversity of target genes in wild populations and lead to the discovery of key

genes for important traits by association analysis

NGS of amplicons of large numbers of candidate genes from wild and

domesticated plant populations can define diversity of target genes in

wild populations and lead to the discovery of key genes for important

traits by association analysis

50

NGS

supports the rapid domestication of new plant species and the efficient

identification and capture of novel genetic variation from related species

Allows whole-genome analysis to determine the genetic basis of

phenotypic differences

NGS allows rapid expansion of genomic analysis to investigation of non-

model species

Made rice study easy by related grass

cost-effective method for plant identification

useful strategy to analysis the chloroplast genome sequence from whole-

genome shot-gun sequencing

facilitates managing this diversity and any changes in crop performance

over time due to genetic drift

Patterns of gene expression have been evaluated in hybrids using NGS

51

Two Approaches to Finding Adaptive Genes

Ross-Ibarra et al2007

52

Techniques to re-wild the plants (transgene free)

1 Introgression

breeding

2 Specific

insertion of lost genes

3 Precision

mutagenesis

Palmgren et al2014

53

Process of rewilding

Palmgren et al2014

54

Synthetic biology projects(i) Modifying cereals including wheat to fix atmospheric nitrogen

(ii) Redesigning metabolic pathways to increase the yield of

secondary metabolites or to generate compounds with enhanced

properties

(iii) Transferring the C4 photosynthesis pathway to rice

(iv) Modifying the glycosylation pathway in plants to accommodate

production of therapeutic proteins

(v) Introducing synthetic signal transduction systems that respond to

external cues

55

Synthetic biology projects

Nicholas J Baltes et al 2015

56

Refactoring the N fixation gene cluster from Klebsiella

Karsten Temme et al 2012

44

Applications of Genomic

tools in Super-Domestication

45

Genome Sequencing

Potential methods of sequencing

1 Clone by clone approach

2 Whole genome shotgun approach

3 Combination of the two methods

Till today no of cultivated plants completely sequenced -85

2016- Arachis duranensis

2015- Solanum cumersonii (Wild potato)

(Ref- NCBI)

46

GWAS

It is a study design in which many markers spread across a genome

are genotyped and test a statistical association with a phenotype are

performed locally along the genome

It is also an examination of many common genetic variants in different

individuals to see if any variant is associated with a trait

Used in successfully studying maize sorghum and barley

Method is efficient for large scale low cost genotyping (even with the

minimum number of SNPs)

Cannot be utilized generally because it needs large population size

GWAS identify rare alleles more precisely

If small population we can opt NAM

47

GWAS and whole genome prediction

Xuehui Huang and Bin Han 2014

48

Five high throuput genotyping methods

Xuehui Huang and Bin Han 2014

49

Role of NGS in domestication Capture of novel genes from wild species will be made easier by

understanding the molecular events associated with crop domestication

Re-sequencing of domesticated species can identify low diversity regions

resulting from selection during domestication

To identify gene-specific sequences to aid the cloning of homologues of key

domestication genes from wild relatives

Candidate genes from wild and domesticated plant populations can define

diversity of target genes in wild populations and lead to the discovery of key

genes for important traits by association analysis

NGS of amplicons of large numbers of candidate genes from wild and

domesticated plant populations can define diversity of target genes in

wild populations and lead to the discovery of key genes for important

traits by association analysis

50

NGS

supports the rapid domestication of new plant species and the efficient

identification and capture of novel genetic variation from related species

Allows whole-genome analysis to determine the genetic basis of

phenotypic differences

NGS allows rapid expansion of genomic analysis to investigation of non-

model species

Made rice study easy by related grass

cost-effective method for plant identification

useful strategy to analysis the chloroplast genome sequence from whole-

genome shot-gun sequencing

facilitates managing this diversity and any changes in crop performance

over time due to genetic drift

Patterns of gene expression have been evaluated in hybrids using NGS

51

Two Approaches to Finding Adaptive Genes

Ross-Ibarra et al2007

52

Techniques to re-wild the plants (transgene free)

1 Introgression

breeding

2 Specific

insertion of lost genes

3 Precision

mutagenesis

Palmgren et al2014

53

Process of rewilding

Palmgren et al2014

54

Synthetic biology projects(i) Modifying cereals including wheat to fix atmospheric nitrogen

(ii) Redesigning metabolic pathways to increase the yield of

secondary metabolites or to generate compounds with enhanced

properties

(iii) Transferring the C4 photosynthesis pathway to rice

(iv) Modifying the glycosylation pathway in plants to accommodate

production of therapeutic proteins

(v) Introducing synthetic signal transduction systems that respond to

external cues

55

Synthetic biology projects

Nicholas J Baltes et al 2015

56

Refactoring the N fixation gene cluster from Klebsiella

Karsten Temme et al 2012

45

Genome Sequencing

Potential methods of sequencing

1 Clone by clone approach

2 Whole genome shotgun approach

3 Combination of the two methods

Till today no of cultivated plants completely sequenced -85

2016- Arachis duranensis

2015- Solanum cumersonii (Wild potato)

(Ref- NCBI)

46

GWAS

It is a study design in which many markers spread across a genome

are genotyped and test a statistical association with a phenotype are

performed locally along the genome

It is also an examination of many common genetic variants in different

individuals to see if any variant is associated with a trait

Used in successfully studying maize sorghum and barley

Method is efficient for large scale low cost genotyping (even with the

minimum number of SNPs)

Cannot be utilized generally because it needs large population size

GWAS identify rare alleles more precisely

If small population we can opt NAM

47

GWAS and whole genome prediction

Xuehui Huang and Bin Han 2014

48

Five high throuput genotyping methods

Xuehui Huang and Bin Han 2014

49

Role of NGS in domestication Capture of novel genes from wild species will be made easier by

understanding the molecular events associated with crop domestication

Re-sequencing of domesticated species can identify low diversity regions

resulting from selection during domestication

To identify gene-specific sequences to aid the cloning of homologues of key

domestication genes from wild relatives

Candidate genes from wild and domesticated plant populations can define

diversity of target genes in wild populations and lead to the discovery of key

genes for important traits by association analysis

NGS of amplicons of large numbers of candidate genes from wild and

domesticated plant populations can define diversity of target genes in

wild populations and lead to the discovery of key genes for important

traits by association analysis

50

NGS

supports the rapid domestication of new plant species and the efficient

identification and capture of novel genetic variation from related species

Allows whole-genome analysis to determine the genetic basis of

phenotypic differences

NGS allows rapid expansion of genomic analysis to investigation of non-

model species

Made rice study easy by related grass

cost-effective method for plant identification

useful strategy to analysis the chloroplast genome sequence from whole-

genome shot-gun sequencing

facilitates managing this diversity and any changes in crop performance

over time due to genetic drift

Patterns of gene expression have been evaluated in hybrids using NGS

51

Two Approaches to Finding Adaptive Genes

Ross-Ibarra et al2007

52

Techniques to re-wild the plants (transgene free)

1 Introgression

breeding

2 Specific

insertion of lost genes

3 Precision

mutagenesis

Palmgren et al2014

53

Process of rewilding

Palmgren et al2014

54

Synthetic biology projects(i) Modifying cereals including wheat to fix atmospheric nitrogen

(ii) Redesigning metabolic pathways to increase the yield of

secondary metabolites or to generate compounds with enhanced

properties

(iii) Transferring the C4 photosynthesis pathway to rice

(iv) Modifying the glycosylation pathway in plants to accommodate

production of therapeutic proteins

(v) Introducing synthetic signal transduction systems that respond to

external cues

55

Synthetic biology projects

Nicholas J Baltes et al 2015

56

Refactoring the N fixation gene cluster from Klebsiella

Karsten Temme et al 2012

46

GWAS

It is a study design in which many markers spread across a genome

are genotyped and test a statistical association with a phenotype are

performed locally along the genome

It is also an examination of many common genetic variants in different

individuals to see if any variant is associated with a trait

Used in successfully studying maize sorghum and barley

Method is efficient for large scale low cost genotyping (even with the

minimum number of SNPs)

Cannot be utilized generally because it needs large population size

GWAS identify rare alleles more precisely

If small population we can opt NAM

47

GWAS and whole genome prediction

Xuehui Huang and Bin Han 2014

48

Five high throuput genotyping methods

Xuehui Huang and Bin Han 2014

49

Role of NGS in domestication Capture of novel genes from wild species will be made easier by

understanding the molecular events associated with crop domestication

Re-sequencing of domesticated species can identify low diversity regions

resulting from selection during domestication

To identify gene-specific sequences to aid the cloning of homologues of key

domestication genes from wild relatives

Candidate genes from wild and domesticated plant populations can define

diversity of target genes in wild populations and lead to the discovery of key

genes for important traits by association analysis

NGS of amplicons of large numbers of candidate genes from wild and

domesticated plant populations can define diversity of target genes in

wild populations and lead to the discovery of key genes for important

traits by association analysis

50

NGS

supports the rapid domestication of new plant species and the efficient

identification and capture of novel genetic variation from related species

Allows whole-genome analysis to determine the genetic basis of

phenotypic differences

NGS allows rapid expansion of genomic analysis to investigation of non-

model species

Made rice study easy by related grass

cost-effective method for plant identification

useful strategy to analysis the chloroplast genome sequence from whole-

genome shot-gun sequencing

facilitates managing this diversity and any changes in crop performance

over time due to genetic drift

Patterns of gene expression have been evaluated in hybrids using NGS

51

Two Approaches to Finding Adaptive Genes

Ross-Ibarra et al2007

52

Techniques to re-wild the plants (transgene free)

1 Introgression

breeding

2 Specific

insertion of lost genes

3 Precision

mutagenesis

Palmgren et al2014

53

Process of rewilding

Palmgren et al2014

54

Synthetic biology projects(i) Modifying cereals including wheat to fix atmospheric nitrogen

(ii) Redesigning metabolic pathways to increase the yield of

secondary metabolites or to generate compounds with enhanced

properties

(iii) Transferring the C4 photosynthesis pathway to rice

(iv) Modifying the glycosylation pathway in plants to accommodate

production of therapeutic proteins

(v) Introducing synthetic signal transduction systems that respond to

external cues

55

Synthetic biology projects

Nicholas J Baltes et al 2015

56

Refactoring the N fixation gene cluster from Klebsiella

Karsten Temme et al 2012

47

GWAS and whole genome prediction

Xuehui Huang and Bin Han 2014

48

Five high throuput genotyping methods

Xuehui Huang and Bin Han 2014

49

Role of NGS in domestication Capture of novel genes from wild species will be made easier by

understanding the molecular events associated with crop domestication

Re-sequencing of domesticated species can identify low diversity regions

resulting from selection during domestication

To identify gene-specific sequences to aid the cloning of homologues of key

domestication genes from wild relatives

Candidate genes from wild and domesticated plant populations can define

diversity of target genes in wild populations and lead to the discovery of key

genes for important traits by association analysis

NGS of amplicons of large numbers of candidate genes from wild and

domesticated plant populations can define diversity of target genes in

wild populations and lead to the discovery of key genes for important

traits by association analysis

50

NGS

supports the rapid domestication of new plant species and the efficient

identification and capture of novel genetic variation from related species

Allows whole-genome analysis to determine the genetic basis of

phenotypic differences

NGS allows rapid expansion of genomic analysis to investigation of non-

model species

Made rice study easy by related grass

cost-effective method for plant identification

useful strategy to analysis the chloroplast genome sequence from whole-

genome shot-gun sequencing

facilitates managing this diversity and any changes in crop performance

over time due to genetic drift

Patterns of gene expression have been evaluated in hybrids using NGS

51

Two Approaches to Finding Adaptive Genes

Ross-Ibarra et al2007

52

Techniques to re-wild the plants (transgene free)

1 Introgression

breeding

2 Specific

insertion of lost genes

3 Precision

mutagenesis

Palmgren et al2014

53

Process of rewilding

Palmgren et al2014

54

Synthetic biology projects(i) Modifying cereals including wheat to fix atmospheric nitrogen

(ii) Redesigning metabolic pathways to increase the yield of

secondary metabolites or to generate compounds with enhanced

properties

(iii) Transferring the C4 photosynthesis pathway to rice

(iv) Modifying the glycosylation pathway in plants to accommodate

production of therapeutic proteins

(v) Introducing synthetic signal transduction systems that respond to

external cues

55

Synthetic biology projects

Nicholas J Baltes et al 2015

56

Refactoring the N fixation gene cluster from Klebsiella

Karsten Temme et al 2012

48

Five high throuput genotyping methods

Xuehui Huang and Bin Han 2014

49

Role of NGS in domestication Capture of novel genes from wild species will be made easier by

understanding the molecular events associated with crop domestication

Re-sequencing of domesticated species can identify low diversity regions

resulting from selection during domestication

To identify gene-specific sequences to aid the cloning of homologues of key

domestication genes from wild relatives

Candidate genes from wild and domesticated plant populations can define

diversity of target genes in wild populations and lead to the discovery of key

genes for important traits by association analysis

NGS of amplicons of large numbers of candidate genes from wild and

domesticated plant populations can define diversity of target genes in

wild populations and lead to the discovery of key genes for important

traits by association analysis

50

NGS

supports the rapid domestication of new plant species and the efficient

identification and capture of novel genetic variation from related species

Allows whole-genome analysis to determine the genetic basis of

phenotypic differences

NGS allows rapid expansion of genomic analysis to investigation of non-

model species

Made rice study easy by related grass

cost-effective method for plant identification

useful strategy to analysis the chloroplast genome sequence from whole-

genome shot-gun sequencing

facilitates managing this diversity and any changes in crop performance

over time due to genetic drift

Patterns of gene expression have been evaluated in hybrids using NGS

51

Two Approaches to Finding Adaptive Genes

Ross-Ibarra et al2007

52

Techniques to re-wild the plants (transgene free)

1 Introgression

breeding

2 Specific

insertion of lost genes

3 Precision

mutagenesis

Palmgren et al2014

53

Process of rewilding

Palmgren et al2014

54

Synthetic biology projects(i) Modifying cereals including wheat to fix atmospheric nitrogen

(ii) Redesigning metabolic pathways to increase the yield of

secondary metabolites or to generate compounds with enhanced

properties

(iii) Transferring the C4 photosynthesis pathway to rice

(iv) Modifying the glycosylation pathway in plants to accommodate

production of therapeutic proteins

(v) Introducing synthetic signal transduction systems that respond to

external cues

55

Synthetic biology projects

Nicholas J Baltes et al 2015

56

Refactoring the N fixation gene cluster from Klebsiella

Karsten Temme et al 2012

49

Role of NGS in domestication Capture of novel genes from wild species will be made easier by

understanding the molecular events associated with crop domestication

Re-sequencing of domesticated species can identify low diversity regions

resulting from selection during domestication

To identify gene-specific sequences to aid the cloning of homologues of key

domestication genes from wild relatives

Candidate genes from wild and domesticated plant populations can define

diversity of target genes in wild populations and lead to the discovery of key

genes for important traits by association analysis

NGS of amplicons of large numbers of candidate genes from wild and

domesticated plant populations can define diversity of target genes in

wild populations and lead to the discovery of key genes for important

traits by association analysis

50

NGS

supports the rapid domestication of new plant species and the efficient

identification and capture of novel genetic variation from related species

Allows whole-genome analysis to determine the genetic basis of

phenotypic differences

NGS allows rapid expansion of genomic analysis to investigation of non-

model species

Made rice study easy by related grass

cost-effective method for plant identification

useful strategy to analysis the chloroplast genome sequence from whole-

genome shot-gun sequencing

facilitates managing this diversity and any changes in crop performance

over time due to genetic drift

Patterns of gene expression have been evaluated in hybrids using NGS

51

Two Approaches to Finding Adaptive Genes

Ross-Ibarra et al2007

52

Techniques to re-wild the plants (transgene free)

1 Introgression

breeding

2 Specific

insertion of lost genes

3 Precision

mutagenesis

Palmgren et al2014

53

Process of rewilding

Palmgren et al2014

54

Synthetic biology projects(i) Modifying cereals including wheat to fix atmospheric nitrogen

(ii) Redesigning metabolic pathways to increase the yield of

secondary metabolites or to generate compounds with enhanced

properties

(iii) Transferring the C4 photosynthesis pathway to rice

(iv) Modifying the glycosylation pathway in plants to accommodate

production of therapeutic proteins

(v) Introducing synthetic signal transduction systems that respond to

external cues

55

Synthetic biology projects

Nicholas J Baltes et al 2015

56

Refactoring the N fixation gene cluster from Klebsiella

Karsten Temme et al 2012

50

NGS

supports the rapid domestication of new plant species and the efficient

identification and capture of novel genetic variation from related species

Allows whole-genome analysis to determine the genetic basis of

phenotypic differences

NGS allows rapid expansion of genomic analysis to investigation of non-

model species

Made rice study easy by related grass

cost-effective method for plant identification

useful strategy to analysis the chloroplast genome sequence from whole-

genome shot-gun sequencing

facilitates managing this diversity and any changes in crop performance

over time due to genetic drift

Patterns of gene expression have been evaluated in hybrids using NGS

51

Two Approaches to Finding Adaptive Genes

Ross-Ibarra et al2007

52

Techniques to re-wild the plants (transgene free)

1 Introgression

breeding

2 Specific

insertion of lost genes

3 Precision

mutagenesis

Palmgren et al2014

53

Process of rewilding

Palmgren et al2014

54

Synthetic biology projects(i) Modifying cereals including wheat to fix atmospheric nitrogen

(ii) Redesigning metabolic pathways to increase the yield of

secondary metabolites or to generate compounds with enhanced

properties

(iii) Transferring the C4 photosynthesis pathway to rice

(iv) Modifying the glycosylation pathway in plants to accommodate

production of therapeutic proteins

(v) Introducing synthetic signal transduction systems that respond to

external cues

55

Synthetic biology projects

Nicholas J Baltes et al 2015

56

Refactoring the N fixation gene cluster from Klebsiella

Karsten Temme et al 2012

51

Two Approaches to Finding Adaptive Genes

Ross-Ibarra et al2007

52

Techniques to re-wild the plants (transgene free)

1 Introgression

breeding

2 Specific

insertion of lost genes

3 Precision

mutagenesis

Palmgren et al2014

53

Process of rewilding

Palmgren et al2014

54

Synthetic biology projects(i) Modifying cereals including wheat to fix atmospheric nitrogen

(ii) Redesigning metabolic pathways to increase the yield of

secondary metabolites or to generate compounds with enhanced

properties

(iii) Transferring the C4 photosynthesis pathway to rice

(iv) Modifying the glycosylation pathway in plants to accommodate

production of therapeutic proteins

(v) Introducing synthetic signal transduction systems that respond to

external cues

55

Synthetic biology projects

Nicholas J Baltes et al 2015

56

Refactoring the N fixation gene cluster from Klebsiella

Karsten Temme et al 2012

52

Techniques to re-wild the plants (transgene free)

1 Introgression

breeding

2 Specific

insertion of lost genes

3 Precision

mutagenesis

Palmgren et al2014

53

Process of rewilding

Palmgren et al2014

54

Synthetic biology projects(i) Modifying cereals including wheat to fix atmospheric nitrogen

(ii) Redesigning metabolic pathways to increase the yield of

secondary metabolites or to generate compounds with enhanced

properties

(iii) Transferring the C4 photosynthesis pathway to rice

(iv) Modifying the glycosylation pathway in plants to accommodate

production of therapeutic proteins

(v) Introducing synthetic signal transduction systems that respond to

external cues

55

Synthetic biology projects

Nicholas J Baltes et al 2015

56

Refactoring the N fixation gene cluster from Klebsiella

Karsten Temme et al 2012

53

Process of rewilding

Palmgren et al2014

54

Synthetic biology projects(i) Modifying cereals including wheat to fix atmospheric nitrogen

(ii) Redesigning metabolic pathways to increase the yield of

secondary metabolites or to generate compounds with enhanced

properties

(iii) Transferring the C4 photosynthesis pathway to rice

(iv) Modifying the glycosylation pathway in plants to accommodate

production of therapeutic proteins

(v) Introducing synthetic signal transduction systems that respond to

external cues

55

Synthetic biology projects

Nicholas J Baltes et al 2015

56

Refactoring the N fixation gene cluster from Klebsiella

Karsten Temme et al 2012

54

Synthetic biology projects(i) Modifying cereals including wheat to fix atmospheric nitrogen

(ii) Redesigning metabolic pathways to increase the yield of

secondary metabolites or to generate compounds with enhanced

properties

(iii) Transferring the C4 photosynthesis pathway to rice

(iv) Modifying the glycosylation pathway in plants to accommodate

production of therapeutic proteins

(v) Introducing synthetic signal transduction systems that respond to

external cues

55

Synthetic biology projects

Nicholas J Baltes et al 2015

56

Refactoring the N fixation gene cluster from Klebsiella

Karsten Temme et al 2012

55

Synthetic biology projects

Nicholas J Baltes et al 2015

56

Refactoring the N fixation gene cluster from Klebsiella

Karsten Temme et al 2012

56

Refactoring the N fixation gene cluster from Klebsiella

Karsten Temme et al 2012

57

Continuehellip

Karsten Temme et al 2012

58

Genome editing

Sequence specific nucleases

1 Meganucleases

2 ZFMs ndashZink finger motifs

3 TALENs- Transcription activator like effector nuclease

4 CRISPR CAS-9 ndash Clustered interspaced short palindromic

repeats

qmp4

59Khaoula Belhaj et al 2015

60

Genome modifications achieved in plants using sequence specific nucleases

Type of DNA

modification

Nuclease Delivery

methods

Plants Targets

Trait stacking Megnucleases Bombardment Cotton Intergenic sequence

ZFN Bombardment Maize Transgene

Rewriting host

DNA

Megnucleases Stable integration Maize Intergenic sequence

ZFN Stable integration Soybean Transgene

TALEN Stable integration Barley PAPhy_a

TALEN Agrobacterium

T-DNA (transient)

Oryza sativa SWEET14

TALEN No Protoplasts Arabidopsis

Tobacco

AtTT4 AtADH NbSurB

TALEN Bombardment Wheat MLO

TALEN Protoplasts

Stable integration

Maize PDS IPK1A IPK MRP4

CRISPRCas Protoplasts

Agrobacterium

T-DNA (transient)

Tobacco

Arabidopsis

Sorghum Oryza

OsSWEET14 transgene

61

Type of DNA

modification

Nuclease Delivery

methods

Plants Targets

Rewriting host

DNA large

deletion

Zinc-finger

nuclease

Stable

integration

Tobacco Transgene

CRISPRCas Protoplasts

Stable

integration

Rice Labdane-related

diterpenoid gene

clusters

on Chr 2 4 and 6

Zinc-finger

nuclease

Agrobacterium

T-DNA

(transient)

Tobacco CHN50 transgene

Zinc-finger

nuclease

Whiskers Maize IPK1

CRISPRCas Protoplasts Rice PDS

Controlling gene

expression

TALE repressor

(SRDX)

Stable

integration

Arabidopsis RD29A transgene

Zinc-finger

activator (VP16)

Stable

integration

Brassica

napus

KasII

Continue

62

Application of genome editing1 Introduction of precise and predictable modifications directly in an elite

background

2 multiple traits can be modified simultaneously

3 NHEJ enables gene knockout and targeted modifications

4 Introduction of transgenes at defined loci that promote high-level

transcription and do not interfere with the activity of endogenous genes

5 Site-specific nucleases also allow targeted molecular trait stacking -low

risk of segregation

6 CRISPR Cas is a transgene free approach ndash No regulatory burdens

7 frequency of off-target mutations is well below that caused by chemical

and physical mutagenesis techniques

8 In future can be utilized for metabolic engineering and molecular farming

63

Six-way Venn diagram showing the distribution of shared genefamilies (sequence clusters) among M acuminata P dactyliferaArabidopsis thaliana Oryza sativa Sorghum bicolor and Brachypodiumdistachyon genomes

A DrsquoHont et al Nature 2012 doi101038nature11241

64

Achieving super-DomesticationINTROGRESS-RECREATE-CREATE-DOMESTICATEREDOMESTICATE

bull Mobilizing left out genetic

variation still available in

land races and wild and

weedy species

bull Replaying the evolutionary

tape( resynthesis in

polyploids)

bull Domesticateredomesticate

65

We can admire and emulate how indigenous people still domesticateplants create biodiversity and manage it to sustain their future Thereis no equivalently dynamic or flexible crop breeding in modernagriculture to promote biodiversity we still have much to learn from

traditional knowledge Jan Salick 2012

60

Genome modifications achieved in plants using sequence specific nucleases

Type of DNA

modification

Nuclease Delivery

methods

Plants Targets

Trait stacking Megnucleases Bombardment Cotton Intergenic sequence

ZFN Bombardment Maize Transgene

Rewriting host

DNA

Megnucleases Stable integration Maize Intergenic sequence

ZFN Stable integration Soybean Transgene

TALEN Stable integration Barley PAPhy_a

TALEN Agrobacterium

T-DNA (transient)

Oryza sativa SWEET14

TALEN No Protoplasts Arabidopsis

Tobacco

AtTT4 AtADH NbSurB

TALEN Bombardment Wheat MLO

TALEN Protoplasts

Stable integration

Maize PDS IPK1A IPK MRP4

CRISPRCas Protoplasts

Agrobacterium

T-DNA (transient)

Tobacco

Arabidopsis

Sorghum Oryza

OsSWEET14 transgene

61

Type of DNA

modification

Nuclease Delivery

methods

Plants Targets

Rewriting host

DNA large

deletion

Zinc-finger

nuclease

Stable

integration

Tobacco Transgene

CRISPRCas Protoplasts

Stable

integration

Rice Labdane-related

diterpenoid gene

clusters

on Chr 2 4 and 6

Zinc-finger

nuclease

Agrobacterium

T-DNA

(transient)

Tobacco CHN50 transgene

Zinc-finger

nuclease

Whiskers Maize IPK1

CRISPRCas Protoplasts Rice PDS

Controlling gene

expression

TALE repressor

(SRDX)

Stable

integration

Arabidopsis RD29A transgene

Zinc-finger

activator (VP16)

Stable

integration

Brassica

napus

KasII

Continue

62

Application of genome editing1 Introduction of precise and predictable modifications directly in an elite

background

2 multiple traits can be modified simultaneously

3 NHEJ enables gene knockout and targeted modifications

4 Introduction of transgenes at defined loci that promote high-level

transcription and do not interfere with the activity of endogenous genes

5 Site-specific nucleases also allow targeted molecular trait stacking -low

risk of segregation

6 CRISPR Cas is a transgene free approach ndash No regulatory burdens

7 frequency of off-target mutations is well below that caused by chemical

and physical mutagenesis techniques

8 In future can be utilized for metabolic engineering and molecular farming

63

Six-way Venn diagram showing the distribution of shared genefamilies (sequence clusters) among M acuminata P dactyliferaArabidopsis thaliana Oryza sativa Sorghum bicolor and Brachypodiumdistachyon genomes

A DrsquoHont et al Nature 2012 doi101038nature11241

64

Achieving super-DomesticationINTROGRESS-RECREATE-CREATE-DOMESTICATEREDOMESTICATE

bull Mobilizing left out genetic

variation still available in

land races and wild and

weedy species

bull Replaying the evolutionary

tape( resynthesis in

polyploids)

bull Domesticateredomesticate

65

We can admire and emulate how indigenous people still domesticateplants create biodiversity and manage it to sustain their future Thereis no equivalently dynamic or flexible crop breeding in modernagriculture to promote biodiversity we still have much to learn from

traditional knowledge Jan Salick 2012

61

Type of DNA

modification

Nuclease Delivery

methods

Plants Targets

Rewriting host

DNA large

deletion

Zinc-finger

nuclease

Stable

integration

Tobacco Transgene

CRISPRCas Protoplasts

Stable

integration

Rice Labdane-related

diterpenoid gene

clusters

on Chr 2 4 and 6

Zinc-finger

nuclease

Agrobacterium

T-DNA

(transient)

Tobacco CHN50 transgene

Zinc-finger

nuclease

Whiskers Maize IPK1

CRISPRCas Protoplasts Rice PDS

Controlling gene

expression

TALE repressor

(SRDX)

Stable

integration

Arabidopsis RD29A transgene

Zinc-finger

activator (VP16)

Stable

integration

Brassica

napus

KasII

Continue

62

Application of genome editing1 Introduction of precise and predictable modifications directly in an elite

background

2 multiple traits can be modified simultaneously

3 NHEJ enables gene knockout and targeted modifications

4 Introduction of transgenes at defined loci that promote high-level

transcription and do not interfere with the activity of endogenous genes

5 Site-specific nucleases also allow targeted molecular trait stacking -low

risk of segregation

6 CRISPR Cas is a transgene free approach ndash No regulatory burdens

7 frequency of off-target mutations is well below that caused by chemical

and physical mutagenesis techniques

8 In future can be utilized for metabolic engineering and molecular farming

63

Six-way Venn diagram showing the distribution of shared genefamilies (sequence clusters) among M acuminata P dactyliferaArabidopsis thaliana Oryza sativa Sorghum bicolor and Brachypodiumdistachyon genomes

A DrsquoHont et al Nature 2012 doi101038nature11241

64

Achieving super-DomesticationINTROGRESS-RECREATE-CREATE-DOMESTICATEREDOMESTICATE

bull Mobilizing left out genetic

variation still available in

land races and wild and

weedy species

bull Replaying the evolutionary

tape( resynthesis in

polyploids)

bull Domesticateredomesticate

65

We can admire and emulate how indigenous people still domesticateplants create biodiversity and manage it to sustain their future Thereis no equivalently dynamic or flexible crop breeding in modernagriculture to promote biodiversity we still have much to learn from

traditional knowledge Jan Salick 2012

62

Application of genome editing1 Introduction of precise and predictable modifications directly in an elite

background

2 multiple traits can be modified simultaneously

3 NHEJ enables gene knockout and targeted modifications

4 Introduction of transgenes at defined loci that promote high-level

transcription and do not interfere with the activity of endogenous genes

5 Site-specific nucleases also allow targeted molecular trait stacking -low

risk of segregation

6 CRISPR Cas is a transgene free approach ndash No regulatory burdens

7 frequency of off-target mutations is well below that caused by chemical

and physical mutagenesis techniques

8 In future can be utilized for metabolic engineering and molecular farming

63

Six-way Venn diagram showing the distribution of shared genefamilies (sequence clusters) among M acuminata P dactyliferaArabidopsis thaliana Oryza sativa Sorghum bicolor and Brachypodiumdistachyon genomes

A DrsquoHont et al Nature 2012 doi101038nature11241

64

Achieving super-DomesticationINTROGRESS-RECREATE-CREATE-DOMESTICATEREDOMESTICATE

bull Mobilizing left out genetic

variation still available in

land races and wild and

weedy species

bull Replaying the evolutionary

tape( resynthesis in

polyploids)

bull Domesticateredomesticate

65

We can admire and emulate how indigenous people still domesticateplants create biodiversity and manage it to sustain their future Thereis no equivalently dynamic or flexible crop breeding in modernagriculture to promote biodiversity we still have much to learn from

traditional knowledge Jan Salick 2012

63

Six-way Venn diagram showing the distribution of shared genefamilies (sequence clusters) among M acuminata P dactyliferaArabidopsis thaliana Oryza sativa Sorghum bicolor and Brachypodiumdistachyon genomes

A DrsquoHont et al Nature 2012 doi101038nature11241

64

Achieving super-DomesticationINTROGRESS-RECREATE-CREATE-DOMESTICATEREDOMESTICATE

bull Mobilizing left out genetic

variation still available in

land races and wild and

weedy species

bull Replaying the evolutionary

tape( resynthesis in

polyploids)

bull Domesticateredomesticate

65

We can admire and emulate how indigenous people still domesticateplants create biodiversity and manage it to sustain their future Thereis no equivalently dynamic or flexible crop breeding in modernagriculture to promote biodiversity we still have much to learn from

traditional knowledge Jan Salick 2012

64

Achieving super-DomesticationINTROGRESS-RECREATE-CREATE-DOMESTICATEREDOMESTICATE

bull Mobilizing left out genetic

variation still available in

land races and wild and

weedy species

bull Replaying the evolutionary

tape( resynthesis in

polyploids)

bull Domesticateredomesticate

65

We can admire and emulate how indigenous people still domesticateplants create biodiversity and manage it to sustain their future Thereis no equivalently dynamic or flexible crop breeding in modernagriculture to promote biodiversity we still have much to learn from

traditional knowledge Jan Salick 2012

65

We can admire and emulate how indigenous people still domesticateplants create biodiversity and manage it to sustain their future Thereis no equivalently dynamic or flexible crop breeding in modernagriculture to promote biodiversity we still have much to learn from

traditional knowledge Jan Salick 2012