Discerning genetic diversity among super early pigeonpea germplasm using microsatellite markers

In the present study genetic diversity studies have been carried out using twenty four polymorphic SSR markers in a set of thirty five super early pigeonpea germplasm. The primers amplified a total of 69 alleles with 24 primers having highest PIC of 0.74. The SSR markers grouped the germplasm into four clusters based on jaccard’s similarity coefficient. To test the goodness of fit of a clustering to a set of SSR data, cophenetic correlation coefficient or cophenetic value was estimated using the COPH and MXCOMP options in NTSYS-pc program. The cophenetic value of 0.94 obtained using the SSR data indicated a very good fit. The polymorphic SSR primers could clearly distinguish the determinate germplasm and non-determinate germplasm. PCA revealed that phenotypic variation explained by the SSRs with first four PCs accounted to 65.4% of total variation. Analysis of molecular variance of pigeonpea germplasm has shown that approximately 1.2% of genetic diversity was within super early germplasm, 71% among germplasm, and 27% among determinate and indeterminate types.