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

Gunvant Patil, Tuyen Do, Tri D. Vuong, Babu Valliyodan, Jeong Dong Lee, Juhi Chaudhary, J. Grover Shannon, Henry T. Nguyen

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139 Scopus citations


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 (F 8) 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.

Original languageEnglish (US)
Article number19199
JournalScientific reports
StatePublished - Jan 19 2016

Bibliographical note

Funding Information:
The authors gratefully acknowledge the financial support for this study provided by United Soybean Board and Missouri Soybean Merchandising Council. The authors acknowledge Dr. Li Song, Cuilan Liu and Dennis Yungbluth, Division of Plant Sciences, University of Missouri, for their technical assistance. The authors also would like to thank Theresa A. Musket for editing the manuscript.


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