Characterization of linkage disequilibrium and population structure in a mungbean diversity panel

Abstract

Mungbean (Vigna radiata (L.) R. Wilczek var. radiata) is an important grain legume globally, providing a high-quality plant protein source largely produced and consumed in South and East Asia. This study aimed to characterise a mungbean diversity panel consisting of 466 cultivated accessions and demonstrate its utility by conducting a pilot genome-wide association study of seed coat colour. In addition 16 wild accessions were genotyped for comparison and in total over 22,000 polymorphic genome-wide SNPs were identified and used to analyse the genetic diversity, population structure, linkage disequilibrium (LD) of mungbean. Polymorphism was lower in the cultivated accessions in comparison to the wild accessions, with average polymorphism information content (PIC) values 0.174, versus 0.305 in wild mungbean. LD decayed in ~100Kb in cultivated lines, a distance higher than the linkage decay of ~60 Kb estimated in wild mungbeanLD decayed at ~100kb in the cultivated lines was higher compared with the LD decay of ~60 kb in wild mungbean. Four distinct subgroups were identified within the cultivated lines, which broadly corresponded to geographic origin and seed characteristics. In a pilot GWAS study of seed coat colour, five genomic regions associated were identified, two of which were close to seed coat colour genes in other species. This mungbean diversity panel constitutes a valuable resource for genetic dissection of important agronomical traits to accelerate mungbean breeding.