Genomic-assisted haplotype analysis and the development of high-throughput SNP markers for salinity tolerance in soybean

Scientific Reports
Gunvant PatilHenry T Nguyen

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-...Continue Reading

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Datasets Mentioned

BETA
KF879911.1

Methods Mentioned

BETA
genotyping
salt treatment
transgenic
PCR
PCA

Software Mentioned

BAM
NTSYS
FLAPJACK
KASPar
MEGA
GenomeBrowse
SAM
SNPviz
pc
BioEdit

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