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

Xingbo Wu,Jerzy Mierzwa,Matthew W Blair,Naransa Limpot,Lucas Mackasmiel,Andrés J Cortés,A S M Faridul Islam

doi:10.3389/fgene.2020.00656

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.

Highlights

Mung bean (Vigna radiata) is an important pulse crop for most of the highly populated countries of Asia, such as Bangladesh, China, India, Indonesia, Laos, Malaysia, Myanmar, Pakistan, Thailand and Vietnam with growing presence in other parts of the world too (Nair et al, 2013)
Given the benefits of using genotyping by sequencing (GBS) in our study, we expect this technology to become widely adopted in mung bean research for marker discovery and application in markerassisted breeding
Association of genotypic and phenotypic data in our genome-wide association study (GWAS) models and based on our GBS dataset, identified a total of 43 single nucleotide polymorphisms (SNPs) markers that were found to be highly associated with mineral concentration

Summary

Introduction

Mung bean (Vigna radiata) is an important pulse crop for most of the highly populated countries of Asia, such as Bangladesh, China, India, Indonesia, Laos, Malaysia, Myanmar, Pakistan, Thailand and Vietnam with growing presence in other parts of the world too (Nair et al, 2013). High nitrogen fixation gives mung bean a vital role in intercropping with corn or millet in East Asia or for crop rotation with cereals, such as rice or wheat in South and Southeast Asia (Blair et al, 2016c). Production of mung bean usually increases soil fertility for subsequent cereal crop yields through symbiotic Nitrogen fixation. High market demands make mung bean a profitable crop for export from Australia, Europe, and United States to East Asia (Pandey et al, 2018). Mung bean is the third most important legume in China after soybean and common bean (Li et al, 2017)

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