Genetic structure, diversity, and allelic richness in composite collection and reference set in chickpea (Cicer arietinum L.)

Background Plant genetic resources (PGR) are the basic raw materials for future genetic progress and an insurance against unforeseen threats to agricultural production. An extensive characterization of PGR provides an opportunity to dissect structure, mine allelic variations, and identify diverse accessions for crop improvement. The Generation Challenge Program http://www.generationcp.org conceptualized the development of "composite collections" and extraction of "reference sets" from these for more efficient tapping of global crop-related genetic resources. In this study, we report the genetic structure, diversity and allelic richness in a composite collection of chickpea using SSR markers, and formation of a reference set of 300 accessions. Results The 48 SSR markers detected 1683 alleles in 2915 accessions, of which, 935 were considered rare, 720 common and 28 most frequent. The alleles per locus ranged from 14 to 67, averaged 35, and the polymorphic information content was from 0.467 to 0.974, averaged 0.854. Marker polymorphism varied between groups of accessions in the composite collection and reference set. A number of group-specific alleles were detected: 104 in Kabuli, 297 in desi, and 69 in wild Cicer; 114 each in Mediterranean and West Asia (WA), 117 in South and South East Asia (SSEA), and 10 in African region accessions. Desi and kabuli shared 436 alleles, while wild Cicer shared 17 and 16 alleles with desi and kabuli, respectively. The accessions from SSEA and WA shared 74 alleles, while those from Mediterranean 38 and 33 alleles with WA and SSEA, respectively. Desi chickpea contained a higher proportion of rare alleles (53%) than kabuli (46%), while wild Cicer accessions were devoid of rare alleles. A genotype-based reference set captured 1315 (78%) of the 1683 composite collection alleles of which 463 were rare, 826 common, and 26 the most frequent alleles. The neighbour-joining tree diagram of this reference set represents diversity from all directions of the tree diagram of the composite collection. Conclusion The genotype-based reference set, reported here, is an ideal set of germplasm for allele mining, association genetics, mapping and cloning gene(s), and in applied breeding for the development of broad-based elite breeding lines/cultivars with superior yield and enhanced adaptation to diverse environments

Allelic richness and diversity in global composite collection and reference sets in chickpea (Cicer arietinum L.)

Chickpea is the fourth largest grain legume crop globally. A composite collection of 3000 accessions was formed and genotyped using 50 SSR markers. The accessions were also field evaluated for seven qualitative traits. Analysis of 48 SSR markers data on 2915 accessions detected 1683 alleles, of which 935 were rare and 748 common. Gene diversity varied from 0.533 to 0.975. Kabuli chickpea as a group were genetically more diverse than other seed types. Several group-specific unique alleles were detected: 104 in Kabuli, 297 in desi, and 69 in wild Cicer; 114 each in West Asia and Mediterranean, 117 in South and South East Asia, and 10 in African region accessions. A genotype-based reference set captured 1315 alleles compared to 1237 alleles in the reference set based on qualitative traits or 1354 alleles based on SSRs and qualitative traits data. The relative usefulness of these reference sets in chickpea breeding and genomics studies are being further investigated

Mining allelic diversity associated with drought and salinity tolerance in reference subset of chickpea germplasm collections

Drought, salinity, and extreme variations in temperature are the major abiotic constraints to chickpea production worldwide. With support from GCP, we developed a global composite collection (3,000 accessions), profiled its structure and diversity using SSRs (50), and a reference set of 300 accessions (211 chickpea mini core + 89 additional diverse accessions) identified using DARwin-5.0. This reference set captured 78% (1403 alleles) of the 1791 alleles of the composite collection. Currently, we are saturating this reference set with additional SSRs and have plans to survey this reference set using DArT markers once the DArT technology is established at ICRISAT. Techniques for screening for drought (root traits) and salinity tolerance have been standardized. Published studies revealed genetic variability for traits associated with drought and salinity tolerance among chickpea mini core germplasm accessions. We plan to extensively evaluate this reference set (300 accessions) for drought and salinity tolerance besides agronomic and quality traits and associate this variation with allelic diversity present in the reference subset. The genetically diverse accessions with contrasting response to drought and salinity will be identified for diverse uses in chickpea genomics and breeding