1. Crop Plants Genetic and Genomic
Resources - Two Sides of the Same Coin
Arun Prabhu Dhanapal
[Fritschi Lab]

2. 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

3. 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

4. Plant Genetic Resources (PGR)
• 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.

5. 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.

7. Genetic erosion
• 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.

8. 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

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

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

11. Svalbard Global Seed Vault in Norway

12. 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.

13. • 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.

14. • 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).

15. 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.

16. • 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.

17. Genomic Resources
• 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

18. Application of Genomics for 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.

19. Genomic Resources
Name of crop plants References
Arabidopsis thaliana and The Arabidopsis Genome Initiative, 2000;
Arabidopsis lyrata 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

20. Update in 2013
Name of Crop Plants References
Tomato(Solanum lycopersicum) The Tomato Genome Consortium 2012
Water Melon (Citrullus lanatus) Guo et al 2013
Peach (Prunus persica) Ahmad et al 2012 and Jun et al 2012
Cotton (Gossypium raimonddi Wang et al 2012
Barley (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.

21. 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.

22. 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.

23. Quick transition of Equipment's
HiSeq2000
ABI 3130 Genome Analyzer IIx
Genetic Analyser Miseq
Genome Analyzer IIx HiSeq2000 Miseq
Output (Gb) 95 600 >1
Yield 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 50 ng with Nextra 50 ng with Nextra
100ng-1 ug with TrueSeq 100ng-1 ug with 100ng-1 ug with TrueSeq
TrueSeq
Read length 2 x 150 bp 2 x 100 bp 2 x 150 bp
Applications supported Genome, epigenome, Genome, epigenome, Amplicon, small genome,
transcriptome transcriptome clone checking

24. 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.

26. 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)

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

28. 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)
51
BBC S+EX
IG48766-1 Le banon
IG46812-3 Turke y Aegilops speltoides (BB)
97
80 IG46811-2 Turke y
89
IG46597-5 Syria
69
IG46593-4 Syria
100
DDC S+EX
AE525-1 Iran
AE526-2 Iran Aegilops taushcii (DD)
98
AE527-3 Iran
AE541-4 Iran
71
AE1068-5 Syria
100
AAC S+EX
IG45475-1 Le banon
IG115817-2 Jordan
Triticum uratu (AA)
98
IG44831-3 Syria
IG45108-4 Turke y
IG45477-5 Iran

30. 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