2013 cornell's plant breeding and genetic seminar series

Current Topics on Cassava Genetics Research and

Future “Omics” Perspective

Becerra Lopez-Lavalle L.A., Duitama J., Perera C., Ovalle T., Castillo K., and J. Tohme

CIAT’s Annual Program Report – Cali14 August 2013

Current ResearchEnhancing Cassava productivity

through more targeted use of global genetic diversity

Functional Genetic for high quality cassava: pVA and Starch

synthase pathways

Whitefly control: a durable solution to cassava-disease pandemics (Africa and Asia)

Bemisia tabaci J N410741


Bemisia tabaci biotypeB KF059959 CIAT

Bemisia tabaci biotypeA KF059958 CIAT

Bemisia tabaci AY521259

Aleurolobus marlatti J Q340188

Siphoninus philyreae J Q340199

Aleurocanthus inceratus HM150621

Aleurocanthus spiniferus J Q340176

Crenidorsum micheliae J Q340190

Aleurotrachelus trachoides KF059957 CIAT

Aleurothrachelus socialis KF059953 CIAT

Aleurothrixus floccosus KF059956 CIAT

Aleuroclava sp J Q340187

Dialeuropora J Q340197

Dialeurodes citri J Q340193

Dialeurodes hongkongensis J Q340195

Trialeurodes variabilis KF059962 CIAT

Trialeurodes vaporiariorum KF192508 CIAT

Trialeurodes vaporariorum AY521265

Aleuronudus melzeri KF059955 CIAT

Aleurodicus dugessi AY521251

Lecanoideus floccissimus KF059960 CIAT

Aleurodicus dispersus KF059954 CIAT

Aleurodicus dispersus EU581838


Drosophila melanogaster ADW61439


Drosophila melanogaster AGE13862

100

100

75

99

46

95

99

99

99

81

100

99

88

99

89

98

93

98

97

96

73

68

45

30

0.000.050.100.150.20

Asia / Asia-Minor

New World

Ale

uro

dic

inae

Ale

yro

din

ae

A

B

C

D

E

F

G

H

I

New World

G-I

G-I

I

Asia

Asia

G-I

II

G-I

VG

-V

G-V

I

Asia

New World

New World

Asia

CMC-40

MEcu 72

A B

C D

Whitefly resistance

Whitefly molecular identification

Next-generation sequencing

α-carotene

PDS + Z-ISOZDS + CRTISO

LCYB

Phytoene

15µg

25 µg Total Carotenoid Content

Chromoplast

GGPPPSY

ζ-carotene

Lycopene

β-caroteneLCYB + LCYE

β+ε-OHase

Lutein

β-OHaseZeaxanthin

Metabolomic profiling

GBSSI

SSISSII

SSIIISBEI

SBEIIDE

ADP

ADPG

25% Amylose

75% Amylopectin

ATP PPi

G1P

Amyloplast

Starch Synthase Pathway

Carotenoid Synthase Pathway

Our goal

• Undertake world-ranking plant biology and cassava improvement research …

• To support small holder farmers, by expanding and diversifying the use of cassava as renewable sources of …

• High-value food, feed and industrial biomaterials (carbohydrate and fiber)

Global Cassava DiversityEnhancing Cassava productivity




5000 to 7000 AC(Piperno and Holst 1998; Rouse 1953

1800 AC to 1532 BCUgent et al. 1986

M. aesculifolia Rogers 1965; Rogers and Fleming 1973; Rogers and Appan 1973)

1,250 AC

NO DATEDAllem et al. 1994 Allem et al. 2001 and Allem 2002





AfricaAsia




Metabolomic profilingGWAS

1’000,000 bp = 50 to 100 genes

http://www.vasculairegeneeskunde.nl/ivg-2010-presentatie-4




Global Cassava Diversity: GenomicsEnhancing Cassava productivity




Strategy

Sampling

RAD-SEQBioinformatic

Pipeline

Pop. GENOMICS

Whole Genome Region/Window

SNP-KIT

Genotype validation/

Identification

•Selection of relevant breeding genotypes

•Geographic distribution

•Mapping to REF-GENOME

•Adequate data filtering

• Variant detection and genotyping (NGSEP)

•Pop. Structure

•Pop. diversity

•Differential and random matting estimates

•Nucleotide diversity

•Tajima’s D

•Kernell smoothed FSTs

• Identification of highly informative SNPs to discriminate among cassava accessions

Global Cassava Diversity: Historical DataEnhancing Cassava productivity




• 1,900 Experimental nurseries

• Nearly 15’000,000 data points

Global Cassava Diversity: CIAT’s breedingEnhancing Cassava productivity




• Identification of the 139 founders CIAT’s cassava breeding program

• Champion genotypes: MCol22, MCol1505, MCol1684, MBra12.

• Identification of 25 trait-specific genotypes to construct the Cassava-Basic Metabolome Profile

Genotypes

Fo

un

der

fre

q.

X





Sampling

CASSAVA (N=139)

MEX (7)CUB (6)PTR(5)RDOM (2)GUA (13)CR (10)PAN (5)COL (29)VEN (9)ECU (6)BRA (5)PER (9)BOL (3)PAR (2)ARG (7)CH (2)TAI (3)MAL (4)IND (2)AFR(4)BREED (4)

WILD (N=24)

FLAV (3) - M. flabellifolia ALT- M. alutaceaBLO- M. brachyloba CTH- M. carthaginensis GUT- M. guaranitica PIL- M. pilosa S1WPD - M. walkereae TST - M. tristisPNT - M. PentaphyllaORB - M. orbicularisPEL - M. peltata





Bioinformatic’s Pipeline

Global Cassava Diversity: Genomics

Bioinformatics' Pipeline

• Align reads to reference

• Sort alignments

• Bowtie2-2.1.0-beta7

• Piccard’s Tools

• Calling SNPs

• Calling Genotypes

• NGSEP – CIAT’s

• Allele and genotypes counts / Frequencies

• Statistics & Annotations using GFF from Phytozome

• Java customized programs

• Comparing genotypes across populations.

• Statistics & Annotations using GFF from Phytozome

• Structure

• Power Marker

• TASSEL

• CIAT costumed programs





Population Structure

• STRUCTURE v.2.3.4 (Pritchard, Stephens, & Donnelly, 2000).

Admixture model with correlated of allele frequencies.

Number of populations (K) from 1 to 10.

Burn-in period on 10000 and MCMC Reps 20000.

• ΔK method (Evanno 2005) implemented in the software STRUCTURE HARVESTER (Earl et al., 2012) to ascertain the most likely value of K.

• Membership coefficients (Q scores) >= 0.9 used to assign individuals to clusters.

• With and without sampling locations as a prior (Country of origin)





Population Genomics

• PowerMarker v.3.25 (Liu and Muse 2005)

• Unbiased estimate of gene diversity (He) (Nei’s 1983)

• F-statistics to quantify genetic differentiation and random mating within and between hierarchical levels (Wright 1983)

• Frequency matrix and genetic distance followed by cluster analysis with the weighted neighbor-joining (NJ) algorithm.

• Relationships among groups were visualized in a dendogram edited in MEGA Vs.5.1, and colored by structure clusters.

FST (coancestry coefficient or fixation index) proportion of the total genetic variance contained in a subpopulation.

FIS (Inbreeding coeffficient) proportion of the genetic variance of the subpopulation contained in a individual

FST = 1 - (HS / HT)

FIS = 1 - (HI / HS)


Sliding Windows approachTEST of departures from Neutral Equilibrium:

• Genes critical to cassava domestication can be identified from their wild relatives.

• Genomic regions with increased or decreased differentiation across populations

• diversifying or stabilizing natural selection

• identify candidate genes, pathways and alleles for targeted functional analysis

Genomic regions can be identified as outliers in a genome scan increasing the power to detect selection in natural populations

Continuous distribution across the genome

• Nucleotide Diversity (π)

• Heterozygosity

• Kernell – Smoothed FST

• Tajima’s D

• ROD= Reduction of diversity

Lev

el o

f P

oly

mo

rph

ism

Chromosomal position


Sliding Windows approach

Genomic regions can be identified as outliers in a genome scan

increasing the power to detect selection in natural populations

Limited software to perform genome windows analysis across the genome

STACKS ???

• Only accept data organized by chromosomes

• Don’t allow for populations comparison

• Do not calculate divergence estimates: FST

TASSEL


High Quality SNPs

SNPs shared between WGS and RAD-seq

Filters:Repetitive regions and CNVs

Quality Score: Higher than 40

DEVELOPING A CORE SET OF SNPs FOR VALIDATION AND IDENTIFICATION OF CASSAVA ACCESSIONS


VARIATION IN THE RESTRICTION SITES UNDERESTIMATE HETEROZYGOSITY IN RAD SEQUENCING

IGB vs.7.03


• Higher diversity in Wild (0.33) than in Cassava (0.12)

• Most wild Cassava relatives highly differentiated for cultivated Cassava (Fst=0,65 W-C and 0,96 K between clusters).

• More similar wild relatives: FLA, ALT, TST

• More distant wild relatives: S1WPD1

• Fis higher in Wild Manihot species (0.98).

Segregating SNPs34 M. tristis1342 M. guaranitica 1700 M. walkereae

Genetic distance and Structure betweenCassava and wild relatives

Global Cassava Diversity: 3rd OutputEnhancing Cassava productivity




Gu

ate

ma

la

Gu

ate

ma

la –

Co

sta

Ric

a

Co

lom

bia

–V

en

ezu

ela

Cu

ba

-P

an

am

a

Co

lom

bia

–E

cu

ad

or

-P

eru

• 700 LAC + 300 Africa towards the global goal.

• Designed 180 SNPs for variety identification and pedigree reconstruction (underway).

200 genotypes

Global Cassava Diversity: MetabolomicsEnhancing Cassava productivity




Genotype Trait Clones1 BRA488 High Cianide Content 62 DOM2 High Dry Matter Content 63 COL2017 High Sugar Content 64 PAR36 High Amilose Content 65 MPER183 High PPD Tolerance/Frog Skin disease/Low Carotene 66 MCOL2436 High Carotene/Trips Susceptible 67 MECU72 WF Resistance/Bacteriosis Susceptible 68 MCUB74 High Culinary Quality/Z06 adaptation 69 CUB23 Waxi Potential 6

10 PAN139 Trips Resistance 611 TMS604444 Transformacion 612 TME3 CMD 613 TMS305555 CMD 614 BRA1A High carotene 615 MCOL1505 Z01 nd Z04 adaptation 616 MCOL1522 Z05 adaptation 617 GUA35 Low Sugar Content 618 CUB25 Low Amilose Content 619 MVEN25 Low Culinary Quality 620 MCOL22 PPD susceptible 621 MGUA85 Adaptation Z02 622 MVEN77 Drought tolerance 623 MCOL113 Adaptation Z06 624 MCOL638 Bacteriosis resistance 625 MCOL1684 Z03 adaptation 6

150

Materials for Metabolomic profiling

pVA and Starch: WhyFunctional Genetic for high

quality cassava: pVA and Starch synthase pathways

α-carotene


LCYB

Phytoene

15µg


Chromoplast

GGPPPSY

ζ-carotene

Lycopene


β+ε-OHase

Lutein

β-OHaseZeaxanthin

GBSSI

SSISSII

SSIIISBEI

SBEIIDE

ADP

ADPG

25% Amylose

75% Amylopectin

ATP PPi

G1P

Amyloplast



Amyloplast vs. Chromoplast

α-carotene


LCYB

Phytoene

15µg


Chromoplast

GGPP

PSY

ζ-carotene

Lycopene


β+ε-OHase

Lutein

β-OHaseZeaxanthin

α-carotene


LCYB

Phytoene

15µg


Chromoplast

GGPP

PSY

ζ-carotene

Lycopene


β+ε-OHase

Lutein

β-OHaseZeaxanthin

α-carotene


LCYB

Phytoene

15µg


Chromoplast

GGPP

PSY

ζ-carotene

Lycopene


β+ε-OHase

Lutein

β-OHaseZeaxanthin

α-carotene


LCYB

Phytoene

15µg


Chromoplast

GGPP

PSY

ζ-carotene

Lycopene


β+ε-OHase

Lutein

β-OHaseZeaxanthin

α-carotene


LCYB

Phytoene

15µg


Chromoplast

GGPP

PSY

ζ-carotene

Lycopene


β+ε-OHase

Lutein

β-OHaseZeaxanthin

α-carotene


LCYB

Phytoene

15µg


Chromoplast

GGPP

PSY

ζ-carotene

Lycopene


β+ε-OHase

Lutein

β-OHaseZeaxanthin

α-carotene


LCYB

Phytoene

15µg


Chromoplast

GGPP

PSY

ζ-carotene

Lycopene


β+ε-OHase

Lutein

β-OHaseZeaxanthin

α-carotene


LCYB

Phytoene

15µg


Chromoplast

GGPP

PSY

ζ-carotene

Lycopene


β+ε-OHase

Lutein

β-OHaseZeaxanthin

α-carotene


LCYB

Phytoene

15µg


Chromoplast

GGPP

PSY

ζ-carotene

Lycopene


β+ε-OHase

Lutein

β-OHaseZeaxanthin

α-carotene


LCYB

Phytoene

15µg


Chromoplast

GGPP

PSY

ζ-carotene

Lycopene


β+ε-OHase

Lutein

β-OHaseZeaxanthin

α-carotene


LCYB

Phytoene

15µg


Chromoplast

GGPP

PSY

ζ-carotene

Lycopene


β+ε-OHase

Lutein

β-OHaseZeaxanthin

α-carotene


LCYB

Phytoene

15µg


Chromoplast

GGPP

PSY

ζ-carotene

Lycopene


β+ε-OHase

Lutein

β-OHaseZeaxanthin

α-carotene


LCYB

Phytoene

15µg


Chromoplast

GGPP

PSY

ζ-carotene

Lycopene


β+ε-OHase

Lutein

β-OHaseZeaxanthin

α-carotene


LCYB

Phytoene

15µg


Chromoplast

GGPP

PSY

ζ-carotene

Lycopene


β+ε-OHase

Lutein

β-OHaseZeaxanthin

α-carotene


LCYB

Phytoene

15µg


Chromoplast

GGPP

PSY

ζ-carotene

Lycopene


β+ε-OHase

Lutein

β-OHaseZeaxanthin

α-carotene


LCYB

Phytoene

15µg


Chromoplast

GGPP

PSY

ζ-carotene

Lycopene


β+ε-OHase

Lutein

β-OHaseZeaxanthin

α-carotene


LCYB

Phytoene

15µg


Chromoplast

GGPP

PSY

ζ-carotene

Lycopene


β+ε-OHase

Lutein

β-OHaseZeaxanthin

α-carotene


LCYB

Phytoene

15µg


Chromoplast

GGPP

PSY

ζ-carotene

Lycopene


β+ε-OHase

Lutein

β-OHaseZeaxanthin

α-carotene


LCYB

Phytoene

15µg


Chromoplast

GGPP

PSY

ζ-carotene

Lycopene


β+ε-OHase

Lutein

β-OHaseZeaxanthin

α-carotene


LCYB

Phytoene

15µg


Chromoplast

GGPP

PSY

ζ-carotene

Lycopene


β+ε-OHase

Lutein

β-OHaseZeaxanthin

GBSSI

SSISSII

SSIIISBEI

SBEIIDE

ADP

ADPG

25% Amylose

75% Amylopectin

ATP PPi

G1P

Amyloplast

α-carotene


LCYB

Phytoene

15µg


Chromoplast

GGPP

PSY

ζ-carotene

Lycopene


β+ε-OHase

Lutein

β-OHaseZeaxanthin

α-carotene


LCYB

Phytoene

15µg


Chromoplast

GGPP

PSY

ζ-carotene

Lycopene


β+ε-OHase

Lutein

β-OHaseZeaxanthin

α-carotene


LCYB

Phytoene

15µg


Chromoplast

GGPP

PSY

ζ-carotene

Lycopene


β+ε-OHase

Lutein

β-OHaseZeaxanthin

α-carotene


LCYB

Phytoene

15µg


Chromoplast

GGPP

PSY

ζ-carotene

Lycopene


β+ε-OHase

Lutein

β-OHaseZeaxanthin

α-carotene


LCYB

Phytoene

15µg


Chromoplast

GGPP

PSY

ζ-carotene

Lycopene


β+ε-OHase

Lutein

β-OHaseZeaxanthin

α-carotene


LCYB

Phytoene

15µg


Chromoplast

GGPP

PSY

ζ-carotene

Lycopene


β+ε-OHase

Lutein

β-OHaseZeaxanthin

α-carotene


LCYB

Phytoene

15µg


Chromoplast

GGPP

PSY

ζ-carotene

Lycopene


β+ε-OHase

Lutein

β-OHaseZeaxanthin

α-carotene


LCYB

Phytoene

15µg


Chromoplast

GGPP

PSY

ζ-carotene

Lycopene


β+ε-OHase

Lutein

β-OHaseZeaxanthin

α-carotene


LCYB

Phytoene

15µg


Chromoplast

GGPP

PSY

ζ-carotene

Lycopene


β+ε-OHase

Lutein

β-OHaseZeaxanthin

α-carotene


LCYB

Phytoene

15µg


Chromoplast

GGPP

PSY

ζ-carotene

Lycopene


β+ε-OHase

Lutein

β-OHaseZeaxanthin

α-carotene


LCYB

Phytoene

15µg


Chromoplast

GGPP

PSY

ζ-carotene

Lycopene


β+ε-OHase

Lutein

β-OHaseZeaxanthin

α-carotene


LCYB

Phytoene

15µg


Chromoplast

GGPP

PSY

ζ-carotene

Lycopene


β+ε-OHase

Lutein

β-OHaseZeaxanthin

GBSSI

SSISSII

SSIIISBEI

SBEIIDE

ADP

ADPG

25% Amylose

75% Amylopectin

ATP PPi

G1P

Amyloplast

GBSSI

SSISSII

SSIIISBEI

SBEIIDE

ADP

ADPG

25% Amylose

75% Amylopectin

ATP PPi

G1P

Amyloplast

GBSSI

SSISSII

SSIIISBEI

SBEIIDE

ADP

ADPG

25% Amylose

75% Amylopectin

ATP PPi

G1P

Amyloplast

GBSSI

SSISSII

SSIIISBEI

SBEIIDE

ADP

ADPG

25% Amylose

75% Amylopectin

ATP PPi

G1P

Amyloplast

GBSSI

SSISSII

SSIIISBEI

SBEIIDE

ADP

ADPG

25% Amylose

75% Amylopectin

ATP PPi

G1P

Amyloplast

GBSSI

SSISSII

SSIIISBEI

SBEIIDE

ADP

ADPG

25% Amylose

75% Amylopectin

ATP PPi

G1P

Amyloplast

GBSSI

SSISSII

SSIIISBEI

SBEIIDE

ADP

ADPG

25% Amylose

75% Amylopectin

ATP PPi

G1P

Amyloplast

GBSSI

SSISSII

SSIIISBEI

SBEIIDE

ADP

ADPG

25% Amylose

75% Amylopectin

ATP PPi

G1P

Amyloplast

GBSSI

SSISSII

SSIIISBEI

SBEIIDE

ADP

ADPG

25% Amylose

75% Amylopectin

ATP PPi

G1P

Amyloplast

GBSSI

SSISSII

SSIIISBEI

SBEIIDE

ADP

ADPG

25% Amylose

75% Amylopectin

ATP PPi

G1P

Amyloplast

GBSSI

SSISSII

SSIIISBEI

SBEIIDE

ADP

ADPG

25% Amylose

75% Amylopectin

ATP PPi

G1P

Amyloplast

GBSSI

SSISSII

SSIIISBEI

SBEIIDE

ADP

ADPG

25% Amylose

75% Amylopectin

ATP PPi

G1P

Amyloplast

GBSSI

SSISSII

SSIIISBEI

SBEIIDE

ADP

ADPG

25% Amylose

75% Amylopectin

ATP PPi

G1P

Amyloplast

GBSSI

SSISSII

SSIIISBEI

SBEIIDE

ADP

ADPG

25% Amylose

75% Amylopectin

ATP PPi

G1P

Amyloplast

GBSSI

SSISSII

SSIIISBEI

SBEIIDE

ADP

ADPG

25% Amylose

75% Amylopectin

ATP PPi

G1P

Amyloplast

GBSSI

SSISSII

SSIIISBEI

SBEIIDE

ADP

ADPG

25% Amylose

75% Amylopectin

ATP PPi

G1P

Amyloplast

GBSSI

SSISSII

SSIIISBEI

SBEIIDE

ADP

ADPG

25% Amylose

75% Amylopectin

ATP PPi

G1P

Amyloplast

GBSSI

SSISSII

SSIIISBEI

SBEIIDE

ADP

ADPG

25% Amylose

75% Amylopectin

ATP PPi

G1P

Amyloplast

GBSSI

SSISSII

SSIIISBEI

SBEIIDE

ADP

ADPG

25% Amylose

75% Amylopectin

ATP PPi

G1P

Amyloplast

GBSSI

SSISSII

SSIIISBEI

SBEIIDE

ADP

ADPG

25% Amylose

75% Amylopectin

ATP PPi

G1P

Amyloplast

GBSSI

SSISSII

SSIIISBEI

SBEIIDE

ADP

ADPG

25% Amylose

75% Amylopectin

ATP PPi

G1P

Amyloplast

GBSSI

SSISSII

SSIIISBEI

SBEIIDE

ADP

ADPG

25% Amylose

75% Amylopectin

ATP PPi

G1P

Amyloplast

GBSSI

SSISSII

SSIIISBEI

SBEIIDE

ADP

ADPG

25% Amylose

75% Amylopectin

ATP PPi

G1P

Amyloplast

GBSSI

SSISSII

SSIIISBEI

SBEIIDE

ADP

ADPG

25% Amylose

75% Amylopectin

ATP PPi

G1P

Amyloplast

GBSSI

SSISSII

SSIIISBEI

SBEIIDE

ADP

ADPG

25% Amylose

75% Amylopectin

ATP PPi

G1P

Amyloplast

GBSSI

SSISSII

SSIIISBEI

SBEIIDE

ADP

ADPG

25% Amylose

75% Amylopectin

ATP PPi

G1P

Amyloplast

GBSSI

SSISSII

SSIIISBEI

SBEIIDE

ADP

ADPG

25% Amylose

75% Amylopectin

ATP PPi

G1P

Amyloplast

pVA and Starch: Data integrityFunctional Genetic for high


α-carotene


LCYB

Phytoene

15µg


Chromoplast

GGPPPSY

ζ-carotene

Lycopene


β+ε-OHase

Lutein

β-OHaseZeaxanthin


Three years evaluation 2011, 2012 and 2013

y = 1.0899x - 0.0065R² = 0.8194

0

2

4

6

8

10

12

14

16

0 2 4 6 8 10 12 14

2012

2011

β-carotene content (HPLC method)

b-carotene content (HPLC method) Linear (b-carotene content (HPLC method))

y = 1.0007x + 1.7402R² = 0.821

0

5

10

15

20

25

30

0 5 10 15 20 25

2012

2011

Total Carotenoid Content(HPLC method)

Total Carotenoid Content (HPLC method) Linear (Total Carotenoid Content (HPLC method))

pVA and Starch: The potentialFunctional Genetic for high


α-carotene


LCYB

Phytoene

15µg


Chromoplast

GGPPPSY

ζ-carotene

Lycopene


β+ε-OHase

Lutein

β-OHaseZeaxanthin



0

5

10

15

20

25

30

35

40

45

GM

3732

-28

GM

3736

-78

GM

3736

-84

GM

3736

-29

GM

3732

-19

GM

3732

-22

GM

3736

-75

GM

3736

-40

GM

3736

-56

GM

3736

-26

GM

3736

-45

GM

3736

-37

GM

3736

-34

GM

3732

-02

GM

3732

-05

GM

3732

-34

GM

3736

-17

GM

3736

-16

GM

3732

-17

GM

905-

57G

M37

36-3

2G

M37

36-1

5G

M37

32-1

8G

M37

36-5

8G

M37

36-5

9G

M37

32-1

1G

M37

32-0

8G

M37

36-7

7G

M37

36-2

0G

M37

36-6

9G

M90

5-60

GM

3732

-29

GM

3732

-30

GM

3736

-66

GM

3736

-38

GM

3736

-36

GM

3732

-01

GM

3736

-76

GM

3732

-21

GM

3736

-51

GM

3736

-43

GM

3732

-16

GM

3736

-18

GM

3736

-85

GM

3736

-12

GM

3736

-44

GM

3732

-37

GM

3732

-13

GM

3736

-13

GM

3736

-02

GM

3736

-06

GM

3736

-48

GM

3736

-53

GM

3736

-54

GM

3736

-74

GM

3732

-23

GM

3732

-36

GM

3736

-72

GM

3732

-31

GM

3736

-57

GM

905-

52G

M37

36-5

2G

M37

36-0

3G

M37

36-0

8G

M37

32-2

5G

M37

36-1

9G

M37

36-1

1G

M37

32-2

7G

M37

36-2

3G

M37

36-8

0G

M37

32-1

2G

M37

32-3

5G

M37

36-0

5G

M37

36-7

9G

M37

32-1

4G

M37

32-0

4G

M37

36-6

3G

M37

32-2

0G

M37

32-3

2G

M37

32-0

9G

M37

36-2

4G

M37

36-2

5G

M37

36-4

1G

M37

32-3

3G

M37

36-7

3G

M37

32-0

3G

M37

36-1

0G

M37

32-0

6G

M37

36-2

2G

M37

36-6

1G

M37

36-3

5G

M37

36-4

7G

M37

36-2

1G

M37

36-3

0G

M37

36-2

7G

M37

36-7

0G

M37

32-0

7G

M37

36-3

9G

M37

32-1

5G

M37

36-4

9G

M37

36-8

1G

M37

32-1

0G

M37

36-0

9G

M37

36-3

3G

M37

36-5

0G

M37

32-2

4G

M37

36-2

8G

M37

36-7

1G

M37

36-6

4G

M37

36-1

4G

M37

36-5

5G

M37

36-8

2G

M37

36-4

2G

M37

36-4

6G

M37

36-6

2G

M37

36-6

7G

M37

36-0

1G

M37

36-8

3

PTFN 2012

PTH 2012

TCH 2012

Car

ote

no

id

Gai

ne

dC

aro

ten

oid

P

ote

nti

al

IPP

Geranylgeranyl diphosphate

Phytoene

Lycopene

-carotene(vitamin A precursor)

Phytoene synthase

Phytoene desaturase

Lycopene-beta-cyclase

ξ-carotene desaturase

pVA and Starch: No Lycopene Functional Genetic for high


α-carotene


LCYB

Phytoene

15µg


Chromoplast

GGPPPSY

ζ-carotene

Lycopene


β+ε-OHase

Lutein

β-OHaseZeaxanthin



Car

ote

no

id

Gai

ne

dC

aro

ten

oid

P

ote

nti

al

0

5

10

15

20

25

30

35

40

45

GM

3732

-28

GM

3736

-78

GM

3736

-84

GM

3736

-29

GM

3732

-19

GM

3732

-22

GM

3736

-75

GM

3736

-40

GM

3736

-56

GM

3736

-26

GM

3736

-45

GM

3736

-37

GM

3736

-34

GM

3732

-02

GM

3732

-05

GM

3732

-34

GM

3736

-17

GM

3736

-16

GM

3732

-17

GM

905-

57G

M37

36-3

2G

M37

36-1

5G

M37

32-1

8G

M37

36-5

8G

M37

36-5

9G

M37

32-1

1G

M37

32-0

8G

M37

36-7

7G

M37

36-2

0G

M37

36-6

9G

M90

5-60

GM

3732

-29

GM

3732

-30

GM

3736

-66

GM

3736

-38

GM

3736

-36

GM

3732

-01

GM

3736

-76

GM

3732

-21

GM

3736

-51

GM

3736

-43

GM

3732

-16

GM

3736

-18

GM

3736

-85

GM

3736

-12

GM

3736

-44

GM

3732

-37

GM

3732

-13

GM

3736

-13

GM

3736

-02

GM

3736

-06

GM

3736

-48

GM

3736

-53

GM

3736

-54

GM

3736

-74

GM

3732

-23

GM

3732

-36

GM

3736

-72

GM

3732

-31

GM

3736

-57

GM

905-

52G

M37

36-5

2G

M37

36-0

3G

M37

36-0

8G

M37

32-2

5G

M37

36-1

9G

M37

36-1

1G

M37

32-2

7G

M37

36-2

3G

M37

36-8

0G

M37

32-1

2G

M37

32-3

5G

M37

36-0

5G

M37

36-7

9G

M37

32-1

4G

M37

32-0

4G

M37

36-6

3G

M37

32-2

0G

M37

32-3

2G

M37

32-0

9G

M37

36-2

4G

M37

36-2

5G

M37

36-4

1G

M37

32-3

3G

M37

36-7

3G

M37

32-0

3G

M37

36-1

0G

M37

32-0

6G

M37

36-2

2G

M37

36-6

1G

M37

36-3

5G

M37

36-4

7G

M37

36-2

1G

M37

36-3

0G

M37

36-2

7G

M37

36-7

0G

M37

32-0

7G

M37

36-3

9G

M37

32-1

5G

M37

36-4

9G

M37

36-8

1G

M37

32-1

0G

M37

36-0

9G

M37

36-3

3G

M37

36-5

0G

M37

32-2

4G

M37

36-2

8G

M37

36-7

1G

M37

36-6

4G

M37

36-1

4G

M37

36-5

5G

M37

36-8

2G

M37

36-4

2G

M37

36-4

6G

M37

36-6

2G

M37

36-6

7G

M37

36-0

1G

M37

36-8

3

PTFN 2012

PTH 2012

TCH 2012

IPP


Phytoene

Lycopene


Phytoene synthase

Phytoene desaturase



pVA and Starch: Unknown carotenoidsFunctional Genetic for high


α-carotene


LCYB

Phytoene

15µg


Chromoplast

GGPPPSY

ζ-carotene

Lycopene


β+ε-OHase

Lutein

β-OHaseZeaxanthin



Car

ote

no

id

Gai

ne

dC

aro

ten

oid

P

ote

nti

al

0

5

10

15

20

25

30

35

40

45

GM

3732

-28

GM

3736

-78

GM

3736

-84

GM

3736

-29

GM

3732

-19

GM

3732

-22

GM

3736

-75

GM

3736

-40

GM

3736

-56

GM

3736

-26

GM

3736

-45

GM

3736

-37

GM

3736

-34

GM

3732

-02

GM

3732

-05

GM

3732

-34

GM

3736

-17

GM

3736

-16

GM

3732

-17

GM

905-

57G

M37

36-3

2G

M37

36-1

5G

M37

32-1

8G

M37

36-5

8G

M37

36-5

9G

M37

32-1

1G

M37

32-0

8G

M37

36-7

7G

M37

36-2

0G

M37

36-6

9G

M90

5-60

GM

3732

-29

GM

3732

-30

GM

3736

-66

GM

3736

-38

GM

3736

-36

GM

3732

-01

GM

3736

-76

GM

3732

-21

GM

3736

-51

GM

3736

-43

GM

3732

-16

GM

3736

-18

GM

3736

-85

GM

3736

-12

GM

3736

-44

GM

3732

-37

GM

3732

-13

GM

3736

-13

GM

3736

-02

GM

3736

-06

GM

3736

-48

GM

3736

-53

GM

3736

-54

GM

3736

-74

GM

3732

-23

GM

3732

-36

GM

3736

-72

GM

3732

-31

GM

3736

-57

GM

905-

52G

M37

36-5

2G

M37

36-0

3G

M37

36-0

8G

M37

32-2

5G

M37

36-1

9G

M37

36-1

1G

M37

32-2

7G

M37

36-2

3G

M37

36-8

0G

M37

32-1

2G

M37

32-3

5G

M37

36-0

5G

M37

36-7

9G

M37

32-1

4G

M37

32-0

4G

M37

36-6

3G

M37

32-2

0G

M37

32-3

2G

M37

32-0

9G

M37

36-2

4G

M37

36-2

5G

M37

36-4

1G

M37

32-3

3G

M37

36-7

3G

M37

32-0

3G

M37

36-1

0G

M37

32-0

6G

M37

36-2

2G

M37

36-6

1G

M37

36-3

5G

M37

36-4

7G

M37

36-2

1G

M37

36-3

0G

M37

36-2

7G

M37

36-7

0G

M37

32-0

7G

M37

36-3

9G

M37

32-1

5G

M37

36-4

9G

M37

36-8

1G

M37

32-1

0G

M37

36-0

9G

M37

36-3

3G

M37

36-5

0G

M37

32-2

4G

M37

36-2

8G

M37

36-7

1G

M37

36-6

4G

M37

36-1

4G

M37

36-5

5G

M37

36-8

2G

M37

36-4

2G

M37

36-4

6G

M37

36-6

2G

M37

36-6

7G

M37

36-0

1G

M37

36-8

3

PTFN 2012

PTH 2012

TCH 2012

IPP


Phytoene

Lycopene


Phytoene synthase

Phytoene desaturase



Unknown Carotenoids

pVA and Starch: DMC do not matterFunctional Genetic for high


α-carotene


LCYB

Phytoene

15µg


Chromoplast

GGPPPSY

ζ-carotene

Lycopene


β+ε-OHase

Lutein

β-OHaseZeaxanthin


Carotenoids vs Dry Matter Content (DMC)

Car

ote

no

id

Gai

ne

dC

aro

ten

oid

P

ote

nti

al

IPP


Phytoene

Lycopene


Phytoene synthase

Phytoene desaturase



0

5

10

15

20

25

30

35

40

45

50

GM

3732

-28

GM

3736

-78

GM

3736

-84

GM

3736

-29

GM

3732

-19

GM

3732

-22

GM

3736

-75

GM

3736

-40

GM

3736

-56

GM

3736

-26

GM

3736

-45

GM

3736

-37

GM

3736

-34

GM

3732

-02

GM

3732

-05

GM

3732

-34

GM

3736

-17

GM

3736

-16

GM

3732

-17

GM

905-

57G

M37

36-3

2G

M37

36-1

5G

M37

32-1

8G

M37

36-5

8G

M37

36-5

9G

M37

32-1

1G

M37

32-0

8G

M37

36-7

7G

M37

36-2

0G

M37

36-6

9G

M90

5-60

GM

3732

-29

GM

3732

-30

GM

3736

-66

GM

3736

-38

GM

3736

-36

GM

3732

-01

GM

3736

-76

GM

3732

-21

GM

3736

-51

GM

3736

-43

GM

3732

-16

GM

3736

-18

GM

3736

-85

GM

3736

-12

GM

3736

-44

GM

3732

-37

GM

3732

-13

GM

3736

-13

GM

3736

-02

GM

3736

-06

GM

3736

-48

GM

3736

-53

GM

3736

-54

GM

3736

-74

GM

3732

-23

GM

3732

-36

GM

3736

-72

GM

3732

-31

GM

3736

-57

GM

905-

52G

M37

36-5

2G

M37

36-0

3G

M37

36-0

8G

M37

32-2

5G

M37

36-1

9G

M37

36-1

1G

M37

32-2

7G

M37

36-2

3G

M37

36-8

0G

M37

32-1

2G

M37

32-3

5G

M37

36-0

5G

M37

36-7

9G

M37

32-1

4G

M37

32-0

4G

M37

36-6

3G

M37

32-2

0G

M37

32-3

2G

M37

32-0

9G

M37

36-2

4G

M37

36-2

5G

M37

36-4

1G

M37

32-3

3G

M37

36-7

3G

M37

32-0

3G

M37

36-1

0G

M37

32-0

6G

M37

36-2

2G

M37

36-6

1G

M37

36-3

5G

M37

36-4

7G

M37

36-2

1G

M37

36-3

0G

M37

36-2

7G

M37

36-7

0G

M37

32-0

7G

M37

36-3

9G

M37

32-1

5G

M37

36-4

9G

M37

36-8

1G

M37

32-1

0G

M37

36-0

9G

M37

36-3

3G

M37

36-5

0G

M37

32-2

4G

M37

36-2

8G

M37

36-7

1G

M37

36-6

4G

M37

36-1

4G

M37

36-5

5G

M37

36-8

2G

M37

36-4

2G

M37

36-4

6G

M37

36-6

2G

M37

36-6

7G

M37

36-0

1G

M37

36-8

3

Dry Matter Content (2012)

High β-carotene has no penalty on DMC

Gains from 2010/12 to 2013From 25ug to 29ug in TCCFrom 15ug to 22ug in TBC

pVA and Starch: Novel starchesFunctional Genetic for high


GBSSI

SSISSII

SSIIISBEI

SBEIIDE

ADP

ADPG

25% Amylose

75% Amylopectin

ATP PPi

G1P

Amyloplast


Waxy and small-granule cassava

GBSSI

SSISSII

SSIIISBEI

SBEIIDE

ADP

ADPG

25% Amylose

75% Amylopectin

ATP PPi

G1P

Amyloplast

X

Easy hydrolysis good for bioethanol and bioplastic production

pVA and Starch: Novel starchesFunctional Genetic for high


GBSSI

SSISSII

SSIIISBEI

SBEIIDE

ADP

ADPG

25% Amylose

75% Amylopectin

ATP PPi

G1P

Amyloplast



GBSSI

SSISSII

SSIIISBEI

SBEIIDE

ADP

ADPG

25% Amylose

75% Amylopectin

ATP PPi

G1P

Amyloplast

X

pVA and Starch: Novel starches WAXYFunctional Genetic for high


GBSSI

SSISSII

SSIIISBEI

SBEIIDE

ADP

ADPG

25% Amylose

75% Amylopectin

ATP PPi

G1P

Amyloplast



• GBSSI in cassava is ~3400 bp• 2 to 3 allelic versions• Among 7 different sources of the

mutation span 126 SNPs• 3 are diagnostic of the trait

pVA and Starch: Team and FounderFunctional Genetic for high


α-carotene


LCYB

Phytoene

15µg


Chromoplast

GGPPPSY

ζ-carotene

Lycopene


β+ε-OHase

Lutein

β-OHaseZeaxanthin

GBSSI

SSISSII

SSIIISBEI

SBEIIDE

ADP

ADPG

25% Amylose

75% Amylopectin

ATP PPi

G1P

Amyloplast



Whitefly researchWhitefly control: a durable

solution to cassava-disease pandemics (Africa and Asia)






























100

100

75

99

46

95

99

99

99

81

100

99

88

99

89

98

93

98

97

96

73

68

45

30

0.000.050.100.150.20

Asia / Asia-Minor

New World

Ale

uro

dic

inae

Ale

yro

din

ae

A

B

C

D

E

F

G

H

I

New World

G-I

G-I

I

Asia

Asia

G-I

II

G-I

VG

-V

G-V

I

Asia

New World

New World

Asia

CMC-40

MEcu 72

A B

C D

Whitefly resistance































100

100

75

99

46

95

99

99

99

81

100

99

88

99

89

98

93

98

97

96

73

68

45

30

0.000.050.100.150.20

Asia / Asia-Minor

New World

Ale

uro

dic

inae

Ale

yro

din

ae

A

B

C

D

E

F

G

H

I

New World

G-I

G-I

I

Asia

Asia

G-I

II

G-I

VG

-V

G-V

I

Asia

New World

New World

Asia

Whitefly DNA barcoding

6 new species molecular identification

Whitefly researchWhitefly control: a durable

solution to cassava-disease pandemics (Africa and Asia)






























100

100

75

99

46

95

99

99

99

81

100

99

88

99

89

98

93

98

97

96

73

68

45

30

0.000.050.100.150.20

Asia / Asia-Minor

New World

Ale

uro

dic

inae

Ale

yro

din

ae

A

B

C

D

E

F

G

H

I

New World

G-I

G-I

I

Asia

Asia

G-I

II

G-I

VG

-V

G-V

I

Asia

New World

New World

Asia

CMC-40

MEcu 72

A B

C D

Whitefly resistance


Whitefly DNA species identification assay

Partner reach

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