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Genome-wide association study of soybean seed germination under drought stress

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Abstract

Drought stress, which is increasing with climate change, is a serious threat to agricultural sustainability worldwide. Seed germination is an essential growth phase that ensures the successful establishment and productivity of soybean, which can lose substantial productivity in soils with water deficits. However, only limited genetic information is available about how germinating soybean seeds may exert drought tolerance. In this study, we examined the germinating seed drought-tolerance phenotypes and genotypes of a panel of 259 released Chinese soybean cultivars panel. Based on 4616 Single-Nucleotide Polymorphisms (SNPs), we conducted a mixed-linear model GWAS that identified a total of 15 SNPs associated with at least one drought-tolerance index. Notably, three of these SNPs were commonly associated with two drought-tolerance indices. Two of these SNPs are positioned upstream of genes, and 11 of them are located in or near regions where QTLs have been previously mapped by linkage analysis, five of which are drought-related. The SNPs detected in this study can both drive hypothesis-driven research to deepen our understanding of genetic basis of soybean drought tolerance at the germination stage and provide useful genetic resources that can facilitate the selection of drought stress traits via genomic-assisted selection.

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Acknowledgements

This work was supported by the National Key R & D Program for Crop Breeding (Grant No. 2016YFD0100304), the Development of Novel Elite Soybean Cultivars and Lines with High Oil Content (Grant No. Z161100000916005-06), the Crop Germplasm Resources Protection (Grant No. 2017NWB036-5), the Platform of National Crop Germplasm Resources of China (Grant Nos. 2018-004 and 2017-004), the Agricultural Science and Technology Innovation Program of the Chinese Academy of Agricultural Sciences (CAAS), and the Improvement of Soybean Abiotic Stress Tolerance to Address the Climate Change (Grant No. PJ0121092018).

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  1. Zhangxiong Liu, Huihui Li, and Zuowang Gou have contributed equally to this work.

Authors and Affiliations

  1. National Key Facility for Gene Resources and Genetic Improvement/Key Laboratory of Crop Germplasm Utilization, Ministry of Agriculture/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China

    Zhangxiong Liu, Huihui Li, Yinghui Li, Lili Yu, Huawei Gao & Lijuan Qiu

  2. Institute of Crop Sciences, Gansu Academy of Agricultural Sciences, Lanzhou, 730070, China

    Zuowang Gou, Yanjun Zhang, Xingrong Wang & Xusheng Qi

  3. Maize Research Institute, Heilongjiang Academy of Agricultural Sciences, Harbin, 150086, China

    Honglei Ren

  4. Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, 48824, USA

    Zixiang Wen & Dechun Wang

  5. Upland Crop Breeding Research Division, Department of Southern Area Crop Science, National Institute of Crop Science, Miryang, 52402, Korea

    Beom-Kyu Kang

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  1. Zhangxiong Liu
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Contributions

ZL, XQ, and LQ conceived and designed the experiments. ZL, ZG, YZ, XW, and HR performed the experiments. ZL, HL, ZW, BKW, YL, LY, HG, DW, XQ, and LQ analyzed data and wrote the manuscript. All authors read and approved the manuscript.

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Correspondence to Lijuan Qiu.

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Liu, Z., Li, H., Gou, Z. et al. Genome-wide association study of soybean seed germination under drought stress. Mol Genet Genomics 295, 661–673 (2020). https://doi.org/10.1007/s00438-020-01646-0

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