EST-SSRs reveal genetic distinction between lac and grain yielding genotypes of pigeonpea

Pigeonpea, an important legume crop is a good host plant for lac cultivation in North East India. In the present study, sixty-three polymorphic EST microsatellite markers were screened across the twenty-seven pigeonpea genotypes collected from different parts of India. The markers used in the study amplified a total of 352 alleles with an average high polymorphic information content of 0.75. The number of alleles per locus varied from 1 to 16 with an average of 5.58, indicating a greater magnitude of diversity among the genotypes. From the Nei’s analysis it was found that maximum diversity exists between the genotypes RCMP 3 and Pant Arhar-291. AMOVA showed a significant amount of variability (63.37%) among the genotypes compared to individuals within the groups or genotypes (36.63%). Mean Shannon information index was 1.15 demonstrating high rate of genetic variability. The neutrality of each marker tested by Ewens–Watterson test for neutrality suggested that all the microsatellite loci except ASSR-70, ASSR-228, ASSR-230 and ASSR-1432 were neutral. According to the dendrogram based on Nei′s analysis the whole population was divided into two major clusters. The first cluster comprised of sixteen local germplasm responsible for high broodlac yield and the second cluster contained eleven high grain yielding varieties. Molecular markers can be effectively used for the selection of elite germplasm of pigeonpea for lac cultivation and high yield of pulses, and consequently benefit farmers and consumers of this important pulse crop of India and the semi-arid regions of the world.