Assessment of molecular genetic diversity of 384 chickpea genotypes and development of core set of 192 genotypes for chickpea improvement programs

Cicer arietinum L. (chickpea) is one of the most significant legume crops domesticated in the Fertile Crescent. This study was aimed to characterize a diverse composite set of 384 Cicer genotypes using unlinked simple sequence repeat (SSR) markers. The genotypes grown under the temperate conditions of Western-Himalayas included cultivated and wild relatives from primary (Cicer reticulatum Ladiz.), secondary (Cicer echinospermum P.H. Davis) and tertiary (Cicer microphyllum Benth.) gene pools. The analysis of genotypic data of eight SSR markers from eight linkage groups led to the identification of 63 alleles, ranging from 2 to 6 with an average value of 3.7 alleles per locus. The polymorphic information content of SSR markers ranged from 0.46 to 0.79 with an average value of 0.77 and the gene diversity ranged from 0.47 to 0.79 with an average of 0.64. The clustering of genotypes in the form of dendrogram discriminated all 384 genotypes into four major clusters. The wild genotypes belonging to different gene pools got clustered uniformly in different clusters along with cultivated chickpea genotypes. The analysis of data also led to the selection of core set of 192 genotypes. The core set was found to possess same diversity (63 alleles; average alleles per locus: 3.7; gene diversity: 0.65) as that of composite set of 384 genotypes. The development of core set in chickpea shall prove useful in gene discovery for variety of traits through genome-wide association studies. The results also provide an insight into gene/allele diversity available in our chickpea germplasm collection grown under agro-climatic conditions of the North Western-Himalayas.

Automated summary

The study characterized 384 Cicer genotypes using SSR markers, identified 63 alleles, formed four major clusters, and selected a core set of 192 genotypes with the same diversity as the composite set. The core set development in chickpea will be useful for gene discovery through genome-wide association studies. The results provide insights into gene/allele diversity in chickpea germplasm grown under agro-climatic conditions of the North Western-Himalayas.