Amplification of chickpea-specific SSR primers in Cajanus species and their validity in diversity analysis

Abstract

Paucity of polymorphic molecular markers in pigeonpea, Cajanus cajan (L.) Millsp., has been a major limiting factor in application of molecular tools for its genetic improvement. As the development of microsatellite markers requires considerable time, expertise and research infrastructure, transfer of markers from other related genera offers an alternative option to increase the number of available markers. Since microsatellite sequences are conserved across Fabaceae taxa, transferability of 100 chickpea (Cicer arietinum L.)-specific SSR markers was studied in two genotypes each of five wild and one cultivated species of Cajanus. The results revealed a significant transferability (46%) of chickpea microsatellites to Cajanus. In cultivated pigeonpea, chickpea-specific SSRs showed 38–39% transferability, while among wild Cajanus species, it ranged from 26% in Cajanus sericeus ICP 15760 to 40% in C. sericeus ICP 15761. The transferable primers exhibited extensive polymorphism in Cajanus with an average number of 4.11 alleles per marker. High level of polymorphism exhibited by chickpea microsatellite markers in the present study indicates their usefulness in diversity analysis, mapping agronomically important traits and marker-assisted breeding in pigeonpea.