Understanding molecular divergence and population structure of parental lines of CMS hybrids in pigeonpea

Pigeonpea is an important food legume crop providing significant protein and nutrients to the human diet in less-developed regions of Asia and Africa. CMS-based hybrid technology has been established in pigeonpea to impart yield stability and resilience in pigeonpea. Understanding the genetic relationships between parental lines is a key to find the cross combinations that offer increased level of heterosis. In the present study, we used 35 simple sequence repeat (SSR) markers to screen 75 pigeonpea genotypes including A, B and R lines, and inferred genetic diversity and population structure. Phylogenetic analysis suggested strong convergent pattern of evolution among the lines. Our results indicate presence of moderate genetic diversity in the panel. Population structure and principal coordinate analysis (PCoA) confirmed existence of two distinct subpopulations. Furthermore, analysis of molecular variance (AMOVA) accounted for 4% variance among and 96% variance within subpopulations, implying towards a high rate of gene exchange (or low genetic differentiation) between the two subpopulations. These undings provide a preliminary molecular framework to enable discovery of optimal hybrid combinations to enable improved hybrid vigour in pigeonpea.