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Association mapping of soybean seed germination under salt stress

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Abstract

Soil salinity is a serious threat to agriculture sustainability worldwide. Seed germination is a critical phase that ensures the successful establishment and productivity of soybeans in saline soils. However, little information is available regarding soybean salt tolerance at the germination stage. The objective of this study was to identify the genetic mechanisms of soybean seed germination under salt stress. One natural population consisting of 191 soybean landraces was used in this study. Soybean seeds produced in four environments were used to evaluate the salt tolerance at their germination stage. Using 1142 single-nucleotide polymorphisms (SNPs), the molecular markers associated with salt tolerance were detected by genome-wide association analysis. Eight SNP-trait associations and 13 suggestive SNP-trait associations were identified using a mixed linear model and the TASSEL 4.0 software. Eight SNPs or suggestive SNPs were co-associated with two salt tolerance indices, namely (1) the ratio of the germination index under salt conditions to the germination index under no-salt conditions (ST-GI) and (2) the ratio of the germination rate under salt conditions to the germination rate under no-salt conditions (ST-GR). One SNP (BARC-021347-04042) was significantly associated with these two traits (ST-GI and ST-GR). In addition, nine possible candidate genes were located in or near the genetic region where the above markers were mapped. Of these, five genes, Glyma08g12400.1, Glyma08g09730.1, Glyma18g47140.1, Glyma09g00460.1, and Glyma09g00490.3, were verified in response to salt stress at the germination stage. The SNPs detected could facilitate a better understanding of the genetic basis of soybean salt tolerance at the germination stage, and the marker BARC-021347-04042 could contribute to future breeding for soybean salt tolerance by marker-assisted selection.

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Acknowledgments

This study was funded by the National Natural Science Foundation of China (31301341), the Fundamental Research Funds for the Central Universities (KJQN201421), and Jiangsu Collaborative Innovation Center for Modern Crop Production (JCIC-MCP).

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The authors declare that they have no conflict of interest.

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This article does not contain any studies with human participants or animals performed by any of the authors.

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Authors and Affiliations

  1. National Center for Soybean Improvement/National Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China

    Guizhen Kan, Wei Zhang, Wenming Yang, Deyuan Ma, Zhenbin Hu & Deyue Yu

  2. Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China

    Dan Zhang

  3. Jiangsu Yanjiang Institute of Agricultural Sciences, Nantong, 226541, China

    Derong Hao

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  1. Guizhen Kan
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  2. Wei Zhang
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  3. Wenming Yang
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  4. Deyuan Ma
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  5. Dan Zhang
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  7. Zhenbin Hu
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Correspondence to Deyue Yu.

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Communicated by L. Xiong.

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Kan, G., Zhang, W., Yang, W. et al. Association mapping of soybean seed germination under salt stress. Mol Genet Genomics 290, 2147–2162 (2015). https://doi.org/10.1007/s00438-015-1066-y

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