title: Genomic-assisted haplotype analysis and the development of high-throughput SNP markers for salinity tolerance in soybean.
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.
authors.affiliation: National Center for Soybean Biotechnology and Division of Plant Sciences, University of Missouri, Columbia, 65211, MO, USA.
authors.forename: Gunvant
authors.initials: G
authors.lastname: Patil
authors.affiliation: National Center for Soybean Biotechnology and Division of Plant Sciences, University of Missouri, Columbia, 65211, MO, USA.
authors.forename: Tuyen
authors.initials: T
authors.lastname: Do
authors.affiliation: National Center for Soybean Biotechnology and Division of Plant Sciences, University of Missouri, Columbia, 65211, MO, USA.
authors.forename: Tri D
authors.initials: TD
authors.lastname: Vuong
authors.affiliation: National Center for Soybean Biotechnology and Division of Plant Sciences, University of Missouri, Columbia, 65211, MO, USA.
authors.forename: Babu
authors.initials: B
authors.lastname: Valliyodan
authors.affiliation: School of Applied Biosciences, Kyungpook National University, Daegu, 41566, Republic of Korea.
authors.forename: Jeong-Dong
authors.initials: JD
authors.lastname: Lee
authors.affiliation: National Center for Soybean Biotechnology and Division of Plant Sciences, University of Missouri, Columbia, 65211, MO, USA.
authors.forename: Juhi
authors.initials: J
authors.lastname: Chaudhary
authors.affiliation: National Center for Soybean Biotechnology and Division of Plant Sciences, University of Missouri, Columbia, 65211, MO, USA.
authors.forename: J Grover
authors.initials: JG
authors.lastname: Shannon
authors.affiliation: National Center for Soybean Biotechnology and Division of Plant Sciences, University of Missouri, Columbia, 65211, MO, USA.
authors.forename: Henry T
authors.initials: HT
authors.lastname: Nguyen
mesh_terms: D000483:Alleles; D002874:Chromosome Mapping; D018745:Genome, Plant; D023281:Genomics; D005838:Genotype; D006239:Haplotypes; D010641:Phenotype; D020641:Polymorphism, Single Nucleotide; D040641:Quantitative Trait Loci / Q000235:genetics*; D055049:Salt Tolerance / Q000235:genetics*; D012965:Sodium Chloride / Q000633:toxicity; D013025:Glycine max / Q000235:genetics* / Q000502:physiology
chemical_list: D012965:Sodium Chloride