Assessment of genetic diversity in pigeonpea using SSR markers

Pigeonpea [Cajanus cajan (L.) Millspaugh] is a very versatile legume with diversified uses as food, feed, fodder and fuel. With the objective of enhancing the utilization of germplasm in breeding and genomic research, a composite collection of 1000 accessions was developed and profiled using 20 SSR markers. Analysis of molecular data for 952 accessions detected 197 alleles, of which 115 were rare and 82 common. Gene diversity varied from 0.002 to 0.726. There were 60 group-specific unique alleles in wild types and 64 in cultivated. Among the cultivated accessions, 37 unique alleles were found in indeterminate (NDT) types. Geographically, 32 unique alleles were found in Asia 4 (Southern Indian provinces, Maldives, and Sri Lanka). Only two alleles differentiated Africa from other regions. Wild and cultivated types shared 73, DT (Determinate) and NDT shared 10, DT and wild shared 4, and the NDT and wild shared 20 alleles. Wild types as a group were genetically more diverse than cultivated types. NDT types were more diverse than the other two groups based on flowering pattern (DT and SDT: Semi-determinate). A reference set based on SSR data and consisting of 300 most diverse accessions, captured 187 (95%) of the 197 alleles of the composite collection. Another reference set based on qualitative traits captured 87% alleles of the composite set. The reference set consisting of 300 most diverse accessions will be profiled with additional markers and extensively phenotyped for traits of economic importance to identify accessions for beneficial traits for utilization in pigeonpea breeding and genomics