Assessment of Simple Sequence Repeat (SSR) Markers Derived from Whole-Genome Sequence (WGS) of Mungbean (Vigna radiata L. Wilczek): Cross-Species Transferability and Population Genetic Studies in Vigna Species

Abstract

The genus Vigna is pan-tropical, having more than 200 species with many desirable economically important traits. This study aimed to validate the in silico polymorphism of whole-genome-sequence-developed mungbean-specific SSR markers and their transferability among different Vigna species. The present study utilized a set of 200 SSR markers developed from the whole-genome sequence of mungbean and validated them using a diversity panel of 25 accessions that belong to 13 Vigna species. Out of 200 SSR markers, 130 markers (65%) were polymorphic across the various Vigna species, and the number of alleles amplified varied from 7 to 24. The SSR markers showed more than 90 percent transferability across the different Vigna species accessions. Utilizing allelic data, the 25 Vigna accessions were clustered into three groups using the unweighted pair group method with arithmetic mean (UPGMA). The two integral coalitions explained 50.79 and 15.42% of the total variance. The principal coordinate analysis (PCA) biplot graph and UPGMA-based neighbor-joining clustering diagram showed a similar pattern of Vigna accession distribution. A population structure assessment grouped the cultivated and wild species accessions into two sub-populations based upon a maximum delta K value of 144.79, which drew a sharp peak at K = 2. The estimated marker parameters, such as the polymorphic information content (0.09–0.84), marker index (0.091–3.342), and effective multiplex ratio (1.0–4.0), suggested their adequacy for several genetic studies, such as parental selection, hybrid testing, genetic mapping, and marker-aided breeding programs, for the genetic enhancement of species belonging to the Vigna genus.