Identification of new loci for salt tolerance in soybean by high-resolution genome-wide association mapping

Tuyen D. Do,Pengyin Chen,Michael Clubb,David Dunn,Babu Valliyodan,Tri D. Vuong,Gunvant Patil,J. Grover Shannon,Henry T. Nguyen,Dong Xu

doi:10.1186/s12864-019-5662-9

Tuyen D. Do, Pengyin Chen + Show 8 more

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https://doi.org/10.1186/s12864-019-5662-9

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Abstract

BackgroundSalinity is an abiotic stress that negatively affects soybean [Glycine max (L.) Merr.] seed yield. Although a major gene for salt tolerance was identified and consistently mapped to chromosome (Chr.) 3 by linkage mapping studies, it does not fully explain genetic variability for tolerance in soybean germplasm. In this study, a genome-wide association study (GWAS) was performed to map genomic regions for salt tolerance in a diverse panel of 305 soybean accessions using a single nucleotide polymorphism (SNP) dataset derived from the SoySNP50K iSelect BeadChip. A second GWAS was also conducted in a subset of 234 accessions using another 3.7 M SNP dataset derived from a whole-genome resequencing (WGRS) study. In addition, three gene-based markers (GBM) of the known gene, Glyma03g32900, on Chr. 3 were also integrated into the two datasets. Salt tolerance among soybean lines was evaluated by leaf scorch score (LSS), chlorophyll content ratio (CCR), leaf sodium content (LSC), and leaf chloride content (LCC).ResultsFor both association studies, a major locus for salt tolerance on Chr. 3 was confirmed by a number of significant SNPs, of which three gene-based SNP markers, Salt-20, Salt14056 and Salt11655, had the highest association with all four traits studied. Also, additional genomic regions on Chrs. 1, 8, and 18 were found to be associated with various traits measured in the second GWAS using the WGRS-derived SNP dataset.ConclusionsA region identified on Chr. 8 was identified to be associated with all four traits and predicted as a new minor locus for salt tolerance in soybean. The candidate genes harbored in this minor locus may help reveal the molecular mechanism involved in salt tolerance and to improve tolerance in soybean cultivars. The significant SNPs will be useful for marker-assisted selection for salt tolerance in soybean breeding programs.

Highlights

Salinity is an abiotic stress that negatively affects soybean [Glycine max (L.) Merr.] seed yield
The phenotypic variation among 305 soybean lines was statistically significant for all traits studied, including leaf scorch score (LSS), chlorophyll content ratio (CCR), leaf sodium content (LSC) and leaf chloride content (LCC), ranging from 1 to 5, 0.3–1.2, 0.03–1.7 (g kg− 1) and 2.7–18.2 (g kg− 1), respectively (Table 1)
These results indicate that all four measurements are valid and representative of salt tolerance and can be used in screening and selection for salt tolerance

Summary

Introduction

Salinity is an abiotic stress that negatively affects soybean [Glycine max (L.) Merr.] seed yield. A major gene for salt tolerance was identified and consistently mapped to chromosome (Chr.) 3 by linkage mapping studies, it does not fully explain genetic variability for tolerance in soybean germplasm. Three gene-based markers (GBM) of the known gene, Glyma03g32900, on Chr. 3 were integrated into the two datasets. In the worldwide crop agriculture, salinity is considered a major abiotic stress. Near-isogenic lines carrying the salt tolerant gene were selected using molecular markers and showed high yield under saline field conditions [21, 22]. Gene-based makers (GBM) were developed for marker-assisted selection (MAS) and for identifying new tolerance genes [20, 23]. The major limitations of bi-parental linkage mapping can detect alleles from parents only and a few recombination events occur in mapping populations [26]

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