Diversity Analysis in Chickpea Germplasm Using SNP and DArT markers

To estimate genetic diversity within or between 10 Cicer species (94 accessions) covering the primary, secondary and tertiary gene pool were analyzed with 5257 DArT markers and 651 KASPar SNP markers. However, allelic data for only 2763 DArT and 624 SNP markers polymorphic between accessions of primary and tertiary genepools were analyzed further to tackle ascertainment bias. STRUCTURE analyses showed 3 populations (kabuli, desi and pea shaped) in the cultivated material, while two populations were observed among the wild species using DArT markers. Analysis of molecular variance (AMOVA) was used to partition variance among hierarchical sets of landraces and wild species at either geographical level or species level. 61% of the variation was found between species, and 39% within species. Molecular variance among the wild species was high (39%) as compared to cultivated (10%). We found widespread variation in linkage disequilibrium (LD) across the genome, with variation in patterns between the relatively homogenous domesticated and more diverse wild germplasm. Observed heterozygosity was higher in wild than cultivated for each linkage group. Our results confirm the Fertile Crescent both as the center of domestication and diversification of chickpea. Although the collection used in the present study has limitations for inferences about wild diversity, it still has higher diversity in the Fertile Crescent. Shared alleles between different gene pools suggest the possibility of gene flow among these species or incomplete lineage sorting and could indicate complicated patterns of divergence and fusion of wild chickpea taxa during the Pleistocene.