Genome-Wide SNP Identification and Association Mapping for Seed Mineral Concentration in Mung Bean (Vigna radiata L.)

TLDR

Mung bean quality depends on seed composition, yet its micronutrient genetics are understudied and genomic resources are limited. The study aimed to develop a GBS‑based marker system, assess genetic diversity in US breeding germplasm, and conduct a GWAS for seven mineral concentrations using ICP spectroscopy. The authors genotyped 95 cultivated mung bean accessions from the USDA core collection representing 13 countries. They identified 6,486 high‑quality SNPs and 43 marker–trait associations across 35 genomic regions explaining an average of 22 % of variation in seed mineral content, providing candidate loci for breeding and marker‑assisted selection.

Abstract

Mung bean (Vigna radiata L.) quality is dependent on seed chemical composition, which in turn determines the benefits of its consumption for human health and nutrition. While mung bean is rich in a range of nutritional components, such as protein, carbohydrates and vitamins, it remains less well studied than other legume crops in terms of micronutrients. In addition, mung bean genomics and genetic resources are relatively sparse. The objectives of this research were three-fold, namely: to develop a genome-wide marker system for mung bean based on genotyping by sequencing (GBS), to evaluate diversity of mung beans available to breeders in the United States and finally, to perform a genome-wide association study (GWAS) for nutrient concentrations based on a seven mineral analysis using inductively coupled plasma (ICP) spectroscopy. All parts of our research were performed with 95 cultivated mung bean genotypes chosen from the USDA core collection representing accessions from 13 countries. Overall, we identified a total of 6,486 high quality single nucleotide polymorphisms (SNPs) from the GBS dataset and found 43 marker × trait associations (MTAs) with calcium, iron, potassium, manganese, phosphorous, sulfur or zinc concentrations in mung bean grain produced in either of two consecutive years' field experiments. The MTAs were scattered across 35 genomic regions explaining on average 22% of the variation for each seed nutrient in each year. Most of the gene regions provided valuable candidate loci to use in future breeding of new varieties of mung bean and further the understanding of genetic control of nutritional properties in the crop. Other SNPs identified in this study will serve as important resources to enable marker-assisted selection (MAS) for nutritional improvement in mung bean and to analyze cultivars of mung bean.