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Genome-wide association study (GWAS) of salt tolerance in worldwide soybean germplasm lines

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Abstract

Salt is a severe abiotic stress causing soybean yield loss in saline soils and irrigated fields. Marker-assisted selection (MAS) is a powerful genomic tool for improving the efficiency of breeding salt-tolerant soybean varieties. The objectives of this study were to uncover novel single-nucleotide polymorphisms (SNPs) and quantitative trait loci (QTLs) associated with salt tolerance and to confirm the previously identified genomic regions and SNPs for salt tolerance. A total of 283 diverse soybean plant introductions (PIs) were screened for salt tolerance in the greenhouse based on leaf chloride concentrations and leaf chlorophyll concentrations after 12–18 days of 120-mM NaCl treatment. A total of 33,009 SNPs across 283 genotypes from the Illumina Infinium SoySNP50K BeadChip database were employed in the association analysis with leaf chloride concentrations and leaf chlorophyll concentrations. Genome-wide association mapping showed that 45 SNPs representing nine genomic regions on chromosomes (Chr.) 2, 3, 7, 8, 10, 13, 14, 16, and 20 were significantly associated with both leaf chloride concentrations and leaf chlorophyll concentrations in 2014, 2015, and combined years. A total of 31 SNPs on Chr. 3 were mapped at or near the previously reported major salt tolerance QTL. The significant SNP on Chr. 2 was also in proximity to the previously reported SNP for salt tolerance. The other significant SNPs represent seven putative novel QTLs for salt tolerance. The significant SNP markers on Chr. 2, 3, 14, 16, and 20, which were identified in both general linear model and mixed linear model, were highly recommended for MAS in breeding salt-tolerant soybean varieties.

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Acknowledgements

This work was supported by Arkansas Soybean Promotion Board and United Soybean Board. I would also like to thank the team members in soybean breeding and genetics program at the University of Arkansas for helping me with the greenhouse experiments.

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Author notes

  1. P. Chen

    Present address: Fisher Delta Research Center, University of Missouri, 147 State Hwy T, Portageville, MO, 63873, USA

Authors and Affiliations

  1. Department of Crop, Soil, and Environmental Sciences, University of Arkansas, Fayetteville, AR, 72701, USA

    A. Zeng, P. Chen, A. Pereira, K. Brye & C. Wu

  2. Department of Plant Pathology, University of Arkansas, Fayetteville, AR, 72701, USA

    K. Korth

  3. Former Monsanto Soybean Breeder, 2711 Blacks Ferry Road, Pocahontas, AR, 72455, USA

    F. Hancock

  4. Department of Horticulture, University of Arkansas, Fayetteville, AR, 72701, USA

    A. Shi

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Correspondence to P. Chen.

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Zeng, A., Chen, P., Korth, K. et al. Genome-wide association study (GWAS) of salt tolerance in worldwide soybean germplasm lines. Mol Breeding 37, 30 (2017). https://doi.org/10.1007/s11032-017-0634-8

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