A SNP-Based Genome-Wide Association Study to Mine Genetic Loci Associated to Salinity Tolerance in Mungbean (Vigna radiata L.).

Caleb Manamik Breria,Ching-Hsiang Hsieh,Jo-Yi Yen,Roland Schafleitner,Thomas J Noble,Tsair-Bor Yen

doi:10.3390/genes11070759

Abstract

Mungbean (Vigna radiata (L.) R. Wilzeck var. radiata) is a protein-rich short-duration legume that fits well as a rotation crop into major cereal production systems of East and South-East Asia. Salinity stress in arid areas affects mungbean, being more of a glycophyte than cereals. A significant portion of the global arable land is either salt or sodium affected. Thus, studies to understand and improve salt-stress tolerance are imminent. Here, we conducted a genome-wide association study (GWAS) to mine genomic loci underlying salt-stress tolerance during seed germination of mungbean. The World Vegetable Center (WorldVeg) mungbean minicore collection representing the diversity of mungbean germplasm was utilized as the study panel and variation for salt stress tolerance was found in this germplasm collection. The germplasm panel was classed into two agro-climatic groups and showed significant differences in their germination abilities under salt stress. A total of 5288 SNP markers obtained through genotyping-by-sequencing (GBS) were used to mine alleles associated with salt stress tolerance. Associated SNPs were identified on chromosomes 7 and 9. The associated region at chromosome 7 (position 2,696,072 to 2,809,200 bp) contains the gene Vradi07g01630, which was annotated as the ammonium transport protein (AMT). The associated region in chromosome 9 (position 19,390,227 bp to 20,321,817 bp) contained the genes Vradi09g09510 and Vradi09g09600, annotated as OsGrx_S16-glutaredoxin subgroup II and dnaJ domain proteins respectively. These proteins were reported to have functions related to salt-stress tolerance.

Highlights

A significant portion of the world’s land area is either salt- or sodium-affected
The results indicated that genotypes originating from tropical/subtropical areas displayed higher variability in their tolerance as compared to genotypes originating from arid/semiarid areas
The findings suggested that ammonium transport mitigates ammonia toxicity caused by salt stress

Summary

Introduction

A significant portion of the world’s land area is either salt- or sodium-affected. Soil salinity can be due to natural processes, or due to human intervention, such as extensive fertilization or wrong irrigation practices [1]. Plants encounter osmotic imbalances and toxicity effects once the salt concentration is higher than the optimum concentration. High salt concentrations of the growing medium impede water absorption via the roots (osmotic effect); and high ionic concentrations (most common Na+ , and other ions) within plant tissues are toxic to the plant metabolism (toxicity effect) [3]. The osmotic stress phase begins immediately when the salt concentration outside the roots increases above the optimum level. The ionic phase of the salinity response begins when ions accumulate in plant tissues. When the loss of old leaves exceeds the production of new ones, the photosynthetic capacity of the plant is impeded, resulting in limited carbohydrate production, the growth of young developing leaves is stunted

Methods

Discussion

Conclusion