Crop Plants Genetic and Genomic Resources - Two Sides of the Same

Coin

Arun Prabhu Dhanapal

[Fritschi Lab]

Outline of today’s talk • Plant Genetic Resources• Genetic Diversity • Genetic Erosion • Conservation of PGR• Value of CGR• Genomic Resources• Genomic Tools• Sequencing Technologies• Comparative and Translational Genomics• Promoter study in PDI gene

Total Number of Plants

Name of Plant Species Purpose

250,000-400,000 Identified as higher plant species

7000 Cultivated plant species

150 Grown commercially

30 Feeding the world

12 75% of food

4 50 % of food we eat

The Guardian, 2010; FAO, 2007

• The PGR include primitive forms of cultivated plant species and landraces, modern cultivars, obsolete cultivars, breeding lines and genetic stocks, weedy types and related wild species

(FAO, 1983; IPGRI, 1993).

• Crop genetic resources are used by breeders to develop new and improved varieties for farmers.

• Genetic resources are constantly required as inputs into the continuing process of enhancement through selective breeding.

Plant Genetic Resources (PGR)

Genetic Diversity

• Genetic diversity is defined as variations in the genetic composition of individuals within or among species.

• Diversity of genes within species increases its ability to adapt to adverse environmental conditions. When varieties or populations of these species are destroyed, the genetic diversity within the species is diminished.

• Conservation of crop genetic resources is needed, given their critical role in agricultural production.

 

• The loss of genetic diversity in a species is called as genetic erosion, and reason for this decline in diversity has been the loss of landraces and wild relatives of cultivated crops.

• In many cases, habitat destruction has narrowed the genetic variability of species lowering the ability to adapt to changed environmental conditions.

• The use of land to preserve habitats for wild relatives remains undervalued compared with alternative uses such as clearing for agricultural or urban use.

Genetic erosion

Conservation of genetic resources

• Agriculture is becoming more and more intensified and location specific, crop improvement objectives are also becoming more and more complex.

• All aspects related to genetic resources (collection, conservation, evaluation, management and utilization) are however needed and to be done eminently.

1) Ex situ conservation – Off-site conservation Germplasm in a gene bank

2) In situ conservation - On-site conservation Nature or biosphere reserves and national parks

Seed storage chamber (-4ºC) for the active seed collection. CRF, Madrid (Spain)

Seed storage chamber (-18ºC) for the base seed collection. CRF, Madrid (Spain)

Svalbard Global Seed Vault in Norway

Value of Crop Genetic Resources

• Conserved genetic resources may also have economic value even if the resources are not currently being used.

• For example, we may not currently need to use a particular species of potato occurring naturally in the Andes. However, information about that species (for example, that it has genes adapted for high altitudes) may be of value to agricultural producers in the future.

• Widespread adoption of genetically uniform crop varieties makes the crop population more susceptible to a widespread disease or pest infestation. Genetic uniformity itself, mean that a variety is more vulnerable to pest and diseases.

• The introgression of genes that reduced plant height and increased disease resistance in wheat provided the foundation for the ‘‘Green Revolution’’ and demonstrated the tremendous impact that genetic resources on crop production.

• ‘‘Norin 10,’’ a cultivar from Japan, provided two very important genes, Rht1 and Rht2, that resulted in the reduced height (or dwarf) of wheats.

• The incorporation of the Sr2 (Fontana) and Lr34 (Hope) genes from genetic resources into cultivated wheat varieties represent milestones in the grain’s genetic advancement. > 50% of the wheat varieties has stable resistance.

• In USA (1970) the uniformity of the maize crop enabled a Southern leaf blight to destroy almost US $1,000 million of maize and reduced yields by as much as 50 percent.

• Resistance to the blight was finally found in the genes of an African maize variety called Mayorbella (National Research Council, 1972).

• National Research Council (1993) determined that genetic uniformity of rice, beans, and many minor crops is still a major concern.

• > 85 percent of wheat production is susceptible to Ug99 and its variants (CIMMYT & BGRI).

Consultative Group of International Agricultural Research (CGIAR)

• CIAT - Centro Internacional de Agricultura Tropical, Cali, Colombia. Founded in 1967 to focus on crop improvement in Latin American lowland tropical agriculture. Research covers rice, beans, cassava, forages and pasture.

• CIMMYT - Centro Internacional de Mejoramiento de Maíz y Trigo, Mexico D.F., Mexico. Founded 1966. Focus on crop improvement in maize, wheat, barley and triticale.

• CIP - Centro Internacional de la Papa, Lima, Peru. Founded 1971. Focus on potato and sweet potato improvement with special attention to the ecology of specific mountain regions.

• IPGRI - International Plant Genetic Resources Institute, Rome.

Founded 1974. Conservation of gene pools for crops and forages.

• ICARDA - International Center for Agricultural Researach in the Dry Areas. Aleppo, Syria. Founded 1977. Focus on improving farming systems for North Africa and West Asia. Research covers wheat, barley, chickpea, lentils, pasture legumes and small ruminants.

• ICRISAT - International Crops Research Institute for the Semi-Arid Tropics, Patancheru, Andhra Pradesh, India. Founded 1972. Focus on crop improvement, cropping systems in sorghum, millet, chickpea, pigeonpea and groundnut.

• IITA - International Institute of Tropical Agriculture, Ibadan, Nigeria. Founded 1967. Focus on crop improvement and land management in humid and sub-humid tropics, farming systems in maize, cassava, cowpea, plantain, soybean, rice and yam.

• IRRI - International Rice Research Institute, Manila, The Philippines. Founded 1960. Research on global rice improvement.

• WARDA - West Africa Rice Development Association, Bouake, Côte

d'Ivoire. Founded 1970. Focus on rice improvement in West Africa, with research on rice in mangrove and inland swamps, upland conditions, irrigated conditions.

• Crop Plant genome sequences and related data presently with us are valuable Genomic resources.

• Genomics is a discipline in genetics that applies recombinant DNA, DNA sequencing methods, and bioinformatics to sequence, assemble, and analyze the function and structure of genomes (the complete set of DNA within a single cell of an organism).

• Crop Genomics potentially carries the strength to shape the future of agriculture and its sustainability

• The better prediction of the phenotype that a particular genotype will produce is a primary goal of genomics based breeding

Genomic Resources

• Mapping the genome of an crop/plant

• Sequencing a single individual or several individuals from a given species

• Studying genetic variability within species

• Studying genetic similarities across species

• Discovering gene function, and the relationship between gene structure, protein synthesis, and metabolic pathways

• Studying gene regulation, including gene activation and gene silencing

• Studying gene interaction and phenomena dependent on many genes.

Application of Genomics for Genomic Resources

Name of crop plants References Arabidopsis thaliana and

Arabidopsis lyrata The Arabidopsis Genome Initiative, 2000;

Cao et al. 2011; Hu et al. 2011 Oryza sativa ssp indica and japonica Yu et al. 2002; Goff et al. 2002

Poplar (Populus trichocarpa) Tuskan et al. 2006 Grape (Vitis vinifera) Jaillon et al. 2007

Mosses (Physcomitrella patens) Rensing et al. 2007 Lotus (Lotus japonicas) Sato et al. 2008 Papaya (Carica papaya) Ming et al. 2008

Maize (Zea mays) Schnable et al. 2009 Sorghum (Sorghum bicolor) Paterson et al. 2009 Cucumber (Cucumis sativus) Huang et al. 2009 Potato (Solanum tuberosum) The Potato Genome Sequencing Consortium, 2011 Rape seed (Brassica napus) Wang et al. 2011 Cucumber (Cucumis sativus) Wóycicki et al. 2011

Crucifer (Thellungiella parvula) Dassanayake et al. 2011 Cacao (Theobroma cacao) Argout et al. 2011

Castor bean (Ricinus communis) Chan et al. 2011 Apple (Malus domestica) Velasco et al. 2010

Cannabis (Cannabis sativa) van Bakel et al. 2011 Strawberry (Fragaria vesca) Shulaev et al. 2011

Soybeans (Glycine max) Schmutz et al. 2010 Pigeon pea (Cajanaus cajan) Varshney et al. 2011

Alfalfa (Medicago sativa), Young et al. 2011 Date palm (Phoenix dactylifera) Al-Dous et al. 2011

Model Grass (Brachypodium distachyon)

International Brachypodium Initiative, 2011

Spike mosses (Selaginella moellendorffii)

Banks et al. 2011

Genomic Resources

Update in 2013

Name of Crop Plants ReferencesTomato(Solanum lycopersicum) The Tomato Genome Consortium 2012Water Melon (Citrullus lanatus) Guo et al 2013Peach (Prunus persica) Ahmad et al 2012 and Jun et al 2012Cotton (Gossypium raimonddi Wang et al 2012Barley (Hordeum vulgare) The International Barley Genome Sequencing

Consortium (2012)Foxtail Millet (Setaria italica) Zheng G et al. (2012) Bennetzen J et al.

(2012)Banana (Musa acuminate) D'Hont et al (2012)

• These genomes reveals numerous species-specific details, including genome size, gene number, patterns of sequence duplication, a catalog of transposable elements, and syntenic relationships.

• To understand the complex instructions contained in all these raw sequence information of the plant genome, large-scale functional genomics projects are required.

Genomic Tools• Marker Assisted Selection (MAS)• Quantitative Trait Loci Mapping (QTL Mapping and e QTL

Mapping)• Candidate Gene Mapping & Allele mining• Targeting induced Local Lesions In Genomes (TILLING) & Eco

TILLING• Association Mapping (GWAS) • Nested Association Mapping (NAM)• Multiparental advanced generation intercross (MAGIC)• Recombinant inbred advanced intercross lines (RIAIL)

• Development in crop genomics play key role in crop improvement in two general ways.

• A better understanding of the biological mechanisms can lead to new or improved screening methods for selecting superior genotypes more efficiently.

• New knowledge can improve the decision-making process for more efficient breeding strategies.

Sequencing Technologies

• Sanger dideoxy sequencing and its modifications dominated the DNA sequencing field for nearly 30 years.

• In the past 10 years sequence reads has increased from 450 bases to more than 1 kb in the length of Sanger sequencing.

Varshney, 2009

• The term NGS is used to collectively describe technologies other than Sanger sequencing that have the potential to sequence the human and plant genome.

• Sequencing machine are constantly increasing sequence output in terms of number of reads (bp-base pair), in-creasing read length, as well as working to improve read quality.

  Genome Analyzer IIx

HiSeq2000 Miseq

Output (Gb) 95 600 >1Yield of error-free data (Gb)

67 400-480 >0.8

Single-end reads 320 Million 2.5 -3 Billion 3.4 Million Paired-end reads 640 Million 5-6 Billion 6.8 Million Required input 50 ng with Nextra

100ng-1 ug with TrueSeq

50 ng with Nextra100ng-1 ug with TrueSeq

50 ng with Nextra100ng-1 ug with TrueSeq

Read length 2 x 150 bp 2 x 100 bp 2 x 150 bpApplications supported Genome, epigenome,

transcriptomeGenome, epigenome, transcriptome

Amplicon, small genome, clone checking

ABI 3130 Genetic Analyser

Genome Analyzer IIx

HiSeq2000

Miseq

Quick transition of Equipment's

Comparative Genomics• It is the study of the relationship of genome structure

and function across different species.

• It has advantage in providing information of signatures of selection to understand the function and evolutionary processes that act on genomes.

Translational Genomics • Implies the translation of gene functions from a model

species (Arabidopsis) to a cultivated crop species.

• Genes with a proven or predicted function in a “model” species (functional candidate genes) or genes that are co-localized with a trait-locus (positional candidate genes) could control a similar function or trait in an target crop of interest.

Promoter Study in Classical / Typical PDI Gene

• The Protein Disulfide Isomerase (PDI) gene family encodes several PDI and PDI-like proteins containing thioredoxin domains and controlling diversified metabolic functions, including disulfide bond formation and isomerisation during protein folding.

• Study of variability in partial promoter region of 700 bp (Comprising 600 bp of 5’ upstream putative promoter

region and 100 bp of the first exon of the typical PDI gene.)

• Five accessions, eight plants per accession. • Triticum uratu (AA)• Aegilops speltoides (BB)• Aegilops tauschii (DD)

• Total Number of Sequences =

(3×5×8=120)

Accession numbers and geographical origin of the wheat samples used in this study

Phylogenetic tree of PDI gene sequences (partial promoter and partial part of first exon) of Triticum uratu (AA), Aegilops speltoides (BB) and Aegilpos taushcii (DD)

BBCS+EX

IG48766-1 Lebanon

IG46812-3 Turkey

IG46811-2 Turkey

IG46597-5 Syria

IG46593-4 Syria

DDCS+EX

AE525-1 Iran

AE526-2 Iran

AE527-3 Iran

AE541-4 Iran

AE1068-5 Syria

AACS+EX

IG45475-1 Lebanon

IG115817-2 Jordan

IG44831-3 Syria

IG45108-4 Turkey

IG45477-5 Iran

51

9780

89

69

100

98

71

100

98

Aegilops speltoides (BB)

Aegilops taushcii (DD)

Triticum uratu (AA)

Take Home Message !!

• Present day crop cultivars has led to increased productivity of crop species, but at the same time has narrowed their genetic basis.

• Fortunately, wild relatives of crop plants exhibit vast genetic diversity for adaptation to stressful environments such as frost, drought and high salt and metal etc..

THANK YOU