Abstract
Soil salinity is a limiting factor of crop yield. The soybean is sensitive to soil salinity, and a dominant gene, Glyma03g32900 is primarily responsible for salt-tolerance. The identification of high throughput and robust markers as well as the deployment of salt-tolerant cultivars are effective approaches to minimize yield loss under saline conditions. We utilized high quality (15x) whole-genome resequencing (WGRS) on 106 diverse soybean lines and identified three major structural variants and allelic variation in the promoter and genic regions of the GmCHX1 gene. The discovery of single nucleotide polymorphisms (SNPs) associated with structural variants facilitated the design of six KASPar assays. Additionally, haplotype analysis and pedigree tracking of 93 U.S. ancestral lines were performed using publically available WGRS datasets. Identified SNP markers were validated, and a strong correlation was observed between the genotype and salt treatment phenotype (leaf scorch, chlorophyll content and Na+ accumulation) using a panel of 104 soybean lines and, an interspecific bi-parental population (F8) from PI483463 x Hutcheson. These markers precisely identified salt-tolerant/sensitive genotypes (>91%), and different structural-variants (>98%). These SNP assays, supported by accurate phenotyping, haplotype analyses and pedigree tracking information, will accelerate marker-assisted selection programs to enhance the development of salt-tolerant soybean cultivars.
Highlights
Been proposed that salts outside of roots had an immediate effect on cell growth and associated metabolism and that salt slowly accumulates inside plants before affecting overall plant function[12]
A great effort has been made to understand the mechanism of salt reaction[39] and to precisely identify gene(s) underlying salt tolerance quantitative trait loci (QTL) in soybeans[24,25]
Previous studies have shown that a QTL on Chr. 3 is the major genomic region determining salinity tolerance in soybean
Summary
Been proposed that salts outside of roots had an immediate effect on cell growth and associated metabolism and that salt slowly accumulates inside plants before affecting overall plant function[12]. SNP markers have gained significant importance in plant genetics and molecular breeding due to their suitability for genetic diversity analysis, abundance in genomes, evolutionary relationships and association with complex phenotypic traits[29]. Their detection and related assays are amenable to automation and are useful for high throughput genotyping. We evaluated a salt-tolerance locus to verify the allelic variation in 106 soybean resequencing lines and identified SNPs in the promoter as well as exonic and intronic regions for the development of a panel of breeder-friendly KASPar assays
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