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Comparative selective signature analysis and high-resolution GWAS reveal a new candidate gene controlling seed weight in soybean

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Abstract

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We detected a QTL qHSW-16 undergone strong selection associated with seed weight and identified a novel candidate gene controlling seed weight candidate gene for this major QTL by qRT-PCT.

Abstract

Soybean [Glycine max (L.) Merr.] provides more than half of the world’s oilseed production. To expand its germplasm resources useful for breeding increased yield and oil quality cultivars, it is necessary to resolve the diversity and evolutionary history of this crop. In this work, we resequenced 283 soybean accessions from China and obtained a large number of high-quality SNPs for investigation of the population genetics that underpin variation in seed weight and other agronomic traits. Selective signature analysis detected 78 (~ 25.0 Mb) and 39 (~ 22.60 Mb) novel putative selective signals that were selected during soybean domestication and improvement, respectively. Genome-wide association study (GWAS) identified five loci associated with seed weight. Among these QTLs, qHSW-16, overlapped with the improvement-selective region on chromosome 16, suggesting that this QTL may be underwent strong selection during soybean improvement. Of the 18 candidate genes in qHSW-16, only SoyZH13_16G122400 showed higher expression levels in a large seed variety compared to a small seed variety during seed development. These results identify SoyZH13_16G122400 as a novel candidate gene controlling seed weight and provide foundational insights into the molecular targets for breeding improvement of seed weight and potential seed yield in soybean.

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Acknowledgements

This work was supported by the National Key Research and Development Program of China (2018YFE0112200), the Key R&D project of Jiangsu Province (BE2019376).

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  1. Wei Zhang and Wenjing Xu have contributed equally to this work.

Authors and Affiliations

  1. Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China

    Wei Zhang, Hongmei Zhang, Xiaoqing Liu, Xiaoyan Cui, Songsong Li, Xin Chen & Huatao Chen

  2. College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China

    Wenjing Xu, Songsong Li & Yuelin Zhu

  3. Joint International Research Laboratory of Agriculture and Agri-Product Safety, Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, 225009, China

    Li Song

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  1. Wei Zhang
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Contributions

ZW, WX, HZ, and SL contributed to field design and phenotypic data collection; ZW and XC performed phenotypic analysis; WX, LS, XL, YZ, and CX assisted in revising the manuscript; ZW analyzed the experimental results; ZW and HT wrote the manuscript. All authors reviewed the manuscript and provided suggestions.

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Correspondence to Xin Chen or Huatao Chen.

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Zhang, W., Xu, W., Zhang, H. et al. Comparative selective signature analysis and high-resolution GWAS reveal a new candidate gene controlling seed weight in soybean. Theor Appl Genet 134, 1329–1341 (2021). https://doi.org/10.1007/s00122-021-03774-6

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