Diversity Assessment in Cajanus Germplasm using Single-Nucleotide Polymorphisms (SNPs)

This study was undertaken to estimate the genetic variability both within and between diverse set of Cajanus lines including 56 breeding lines, 21 land races and 107 accessions from 18 wild species by using 1,616 single nucleotide polymorphism (SNPs) on KASPar assays. The results revealed 75.8% SNPs polymorphic, and more than 95% of these assays could be transferred to wild species. Genetic polymorphism was highest in the wild species (73.76%) followed by landrace (13%) and breeding lines (8.29%). Analysis of Molecular Variance (AMOVA) and STRUCTURE were used to partition variance among hierarchical sets of landraces and wild species at either continental scale or within India. STRUCTURE separated most of the domesticated germplasm from wild species, and separates Australian and Asian wild species. At the continental scale, 69% of the variation was found between landraces and wild species, and 31% within continents, with no variation among continents.  Among Indian regions and states within regions, 36% of the variation was found between regions, and 64% within landraces or wild species within states and highest diversity was found in Andhra Pradesh (AP). These results indicate AP being the center of domestication, and potentially a center of diversification of pigeonpea, though sample sizes analyzed in this study were inadequate to have complete confidence in this conclusion. In addition to enhancing understanding about domestication and diversification of pigeonpea, this study also provides diverse lines and highly informative markers for their use in breeding programmes.