Molecular Insight into the Genetic structure and Banding pattern Analysis of Bambara groundnut (Vigna subterranea L.) with Random Amplified Microsatellites (RAMs)

Abstract

Abstract Background A set of 44 selected Bambara groundnut (Vigna subterranea L. Verdc.) accessions was sampled from 11 distinct populations of four geographical zones to assess the genetic drift, population structure, phylogenetic relationship, and genetic differentiation linked with ISSR primers. In Malaysia, this is an exotic legume introduced from Africa and having tremendous nutritional values and diverse usages. Methods and Results The amplification of genomic DNA with 32 ISSR markers detected an average of 97.64% polymorphism while 35.15% and 51.08% polymorphism per population and geographical zone, respectively. Genetic diversity estimated by Shannon’s information index (I) = 0.177 (average) and populations under Gombe showed maximum diversity (I = 0.271) with 90.98% polymorphism. Analysis of molecular variance revealed significant variation within population 75% and between population 25% whereas within region 84% and between region 16%. The study also divulged total genetic variation Ht = 0.1781 closer to within population diversity (Hs = 0.1155). Among the population, Cancaraki revealed 40.39% polymorphism while the average polymorphism was 35.15%. The Bidillali exposed greater number of locally common band i.e., NLCB (≤ 25%) = 25 and NLCB (≤ 50%) = 115 were shown by Cancaraki while the lowest was recorded as NLCB (≤ 25%) = 6 and NLCB (≤ 50%) = 72 for Roko and Maibergo, accordingly. The highest PhiPT value was noted between Roko and Katawa (0.405*) whereas Nei’s genetic distance was maximum between Roko and Karu (0.124). The genetic differentiation among population Gst = 0.3514 (35.14%) leaving 65.86% of genetic variation leads to within-population with gene flow of Nm = 0.9229. Based on Nei’s genetic distance, a radial phylogenetic tree was constructed that assembled the entire accessions into 3 major clusters for further confirmation unrooted NJ vs NNet split tree analysis based on uncorrected P distance exposed the similar result. Principal coordinate analysis showed variation as PC1 (15.04%) > PC2 (5.81%). Mantel test exposed a significant correlation among genetic and geographic distance of accessions. STRUCTURE analysis (Bayesian) grouped the accessions into 3 major genetic components based on best ΔK = 3 and admixture population. Conclusions The current study leads to prompting the genetic improvement and future breeding program by maximum utilization and better conservation of existing V. subterranea accessions in this subtropical environment.