Enhancing the Value of Legume Genetic Resources Using Core
Enhancing the Value of Legume Genetic Resources Using Core
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ABSTRACT
Grain legumes are rich resource of dietary proteins, minerals, and vitamins; however,
productivity remains low, narrow genetic base of the cultivars being one of the several reasons to low
productivity.
Legumes genomics resources in the past lagged behind cereals. However, situation dramatically
changed with emergence of Medicago truncatula, Lotus japonicus, and Glycine max as models for
comparative genomics within legume family. Several genomic resources including markers, maps,
transcriptomics, proteomics, metabolomics, and bioinformatics resources have been developed. These
resources in model plants will not only allow investigation of basic processes important to legumes, but
also open the possibility to transfer those processes to- or locate them in other crop species including
several legumes. Several genomic projects are developing tools for less-studied legumes which are
economically important in Africa and Asia.
These genetic and genomic resources represent major milestones in the history of legumes
research, which will help understand the evolutionary events that shaped legume genomes, and provide
avenues for genetic enhancement for sustainable agriculture.
I. Introduction:
Legumes represent the second largest family of higher plants after cereals. Leguminasae
consists of about 20,000 species across 700 genera, traditionally divided into three subfamilies:
Caesalpinoideae, Mimosoideae and Papilionoideae (Doyle and Luckow 2003). The two major groups of
cultivated species in the Papilionoideae are the tropical or 'phaseoloid' legumes (Phaseolus, Vigna,
Glycine, and Cajanus) and the temperate or 'galegoid' legumes (Melilo/us, Trifolium, Me dicago ,
Pisum, Vicia, Lotus, Cicer, Lens, and Lathyrus). Groundnut is somewhat distinct from the phaseoloid
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Figure 1. Phylogenetic rewtionship between the model legumes and major temperate and tropical legumes
(Crouch and Dwivedi 2005)
The use of plant genetic resources in crop improvement is one of the most sustainable ways to
conserve valuable genetic resources for the future, and simultaneously to increase agricultural
production and food security. Key to successful crop improvement is a continued supply of genetic
diversity in the breeding programs, including new or improved variability for target traits. Collectively,
the CGIAR centers possesses about 600,000 samples, of which, grain legumes represents about 30%,
second only after cereals (65%). The Patancheru-based ICRISAT genebank in India contains 49,344
germplasm accessions of its three legume crops (chickpea, groundnut and pigeonpea), of which, 48,004
belong to cultivated and 1,340 wild species accessions.
The genetic base of legumes is narrow. In addition to bottlenecks associated with the origin and
do~estication events of these crops there has been limited use of germ plasm in breeding programs in
spite of the relatively large collections maintained in the genebanks, and because of the repeated use of
the few germplasmladvanced lines for the development of new cultivars (reviewed in Upadhyaya et al.
2009). The reasons for the underutilization of germplasm include i) lack of accurate and precise large
II. Core and mini core collection: Crop germplasm collections held in genebanks are the best
genetic resources for detailed characterization of important traits such as tolerance to biotic and abiotic
stresses, yield, nutrition, and grain quality. However, the size of most crop-related global germ plasm
collections is simply too vast for systematic evaluation in replicated multilocational trials. The
development of core collections (Brown 1989) has been shown to be a particularly powerful strategy
for providing crop breeding programs with a systematic yet manageable entry point into global
germplasm resources. Using passport, characterization and agronomic evaluation data, the core is
constituted from the 10% of the entire germplasm collection, representing over 70% of the collections
variability in that collection. Core collections are a cost-effective means of identifying accessions with
desirable agronomic traits as well new sources of disease and pest resistance or abiotic stress tolerance.
However, in crop species with several thousands of germ plasm accessions, even a core collection
would be unwieldy for evaluation by the breeders in the multi-location replicated trials. To overcome
this, Upadhyaya and Ortiz (2001) suggested mini-core collection approach which is a core of core
(10% of core or 1% of entire collection) representing the species diversity. Mini-core is established
after evaluating the core subset for various morphological, agronomic, and seed quality traits, and
selecting about 10% accessions from the core subset. At both stages in selection of core and mini-core
-
collections, standard clustering procedures are used to separate groups of similar accessions combined
with various statistical tests to identify the best representatives. Conventional core and mini core
collections have been developed in chickpea (Upadhyaya et al. 2001; Upadhyaya and Ortiz 2001),
groundnut (Holbrook et al. 1993; Upadhyaya et al. 2002, 2003; Holbrook and Dong 2005; Dwivedi et
al. 2008a), and pigeonpea (Reddy et al. 2005; Upadhyaya et al. 2006). Core collections have also been
reported in pea, lentil, common bean, and soybean (Dwivedi et al. 2005). More recently,
genotype-based reference sets have also been developed in some legumes including chickpea,
groundnut and pigeonpea (http://www.generationcp.org). Availability of these genetic resources sets
offers immense opportunities to identify new sources of variation for use in crop breeding.
III. New sources of variation: Evaluation of core and mini-core collections has been suggested
as the most efficient and reliable means of carrying out an initial search of germplasm collections for
desirable traits. Such efforts have led to the identification of diverse germplasm with desirable
agronomic traits inchding resistance to biotic and abioitc stresses in chickpea, ground nut, and
pigeonpea (Table 1; ICRISA T Project 2 Archival Report 2008). New sources of variation have also
been reported for agronomic traits including resistance to diseases and pests in pea, lentil, and common
bean (Dwivedi et al. 2005).
A. Model legumes: Medicago truncatula and Lotusjaponiclis have emerged as models for plant
genomic research in legumes, relatively with compact genomes of approximately 470 Mbp. Scientists
now study these species to investigate a range of questions from disease resistance to environmental
tolerance and from bacterial and fungal symbiosis to complex secondary metabolism. However, both
belong to temperate legume. For tropical legumes, soybean has emerged as a model genome. M
truncatula (http://www.medicago.org/genoIl1:e/), L. japoniclis (http://www.kazusa.or.jp/lotus/) and
soybean (http://www.phytozome.net/soybean) genomes are currently the subject of independent
large-scale sequencing projects. In addition, large-scale transcriptomics, proteomics, metabolomics,
phenomics, and bioinformatics resources and reverse genetic tools have been developed. The
characterization of these three legume genomes will undoubtedly enhance ongoing comparative
genomic analyses (Szczyglowski and Stougaard 2008; Cannon et al. 2006; Ane et al. 2008; Rose 2008).
The value of model systems will be enhanced by the ability to connect model systems to crops at
structural and functional genome levels, for example, synteny between model and crop species should
Table 1. New sources of variation identified after evaluating core/mini core subsets in chickpea,
groundnut, and pigeonpea
Trait Chickpea Groundnut Pigeonpea . -
Diseases FW-67 GRD- 3 SM -·28
AB-3 ELS-1 F"W - 4
BGM -55 BW -14 PB -78
DRR- 5 Aflatoxin - 5 Multiple resistance -2
Drought 18 18
parS alinity 12 12 16
High temperature 5
Low temperature 158
Early maturity 28 21 20
Seed size 16 7
Grain yield 39 60 54
Protein content 5 5
Table 2. Genomic resources in chickpea, common bean, cowpea, groundnut and pigeonpea
(Source: Modified from Varshney et al. 2009)
Genomic resource Cowpea Chickpea Groundnut Pigeonpea Common
bean
Ploidy 2n= 22 2n = 16 4n= 40 2n= 22 2n = 22
Genome size (Mbp) 620 740 2890 858 637
SSR 768 -2000 -2700 -3200 -500
BAC 6-l7X 3.8 - lOX 4X -7.4X llX 10-20X
BAC-end sequences 50,120 46,270 41,856 85,785 89,017
(36.7Mhp) (33.2Mbp) (28.6 Mbp) (56.5 Mbp) (62Mbp)
Genetic maps (bc) ++ ++ AA (2X) No ++
genome: ++
Genetic maps (nc) + + BB (2X) No +
genome: ++
AABB (4X): +
Physical map Yes No In progress No Yes
(AAgenome)
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