Natural variation in GmSW17 controls seed size in soybean

Shan Liang, Zongbiao Duan, Xuemei He, Xia Yang, Yaqin Yuan, Qianjin Liang, Yi Pan, Guoan Zhou, Min Zhang, Shulin Liu () and Zhixi Tian ()
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Shan Liang: Chinese Academy of Sciences
Zongbiao Duan: Yazhouwan National Laboratory
Xuemei He: Chinese Academy of Sciences
Xia Yang: Chinese Academy of Sciences
Yaqin Yuan: Chinese Academy of Sciences
Qianjin Liang: Chinese Academy of Sciences
Yi Pan: Chinese Academy of Sciences
Guoan Zhou: Chinese Academy of Sciences
Min Zhang: Chinese Academy of Sciences
Shulin Liu: Chinese Academy of Sciences
Zhixi Tian: Chinese Academy of Sciences

Nature Communications, 2024, vol. 15, issue 1, 1-14

Abstract: Abstract Seed size/weight plays an important role in determining crop yield, yet only few genes controlling seed size have been characterized in soybean. Here, we perform a genome-wide association study and identify a major quantitative trait locus (QTL), named GmSW17 (Seed Width 17), on chromosome 17 that determine soybean seed width/weight in natural population. GmSW17 encodes a ubiquitin-specific protease, an ortholog to UBP22, belonging to the ubiquitin-specific protease (USPs/UBPs) family. Further functional investigations reveal that GmSW17 interacts with GmSGF11 and GmENY2 to form a deubiquitinase (DUB) module, which influences H2Bub levels and negatively regulates the expression of GmDP-E2F-1, thereby inhibiting the G1-to-S transition. Population analysis demonstrates that GmSW17 undergo artificial selection during soybean domestication but has not been fixed in modern breeding. In summary, our study identifies a predominant gene related to soybean seed weight, providing potential advantages for high-yield breeding in soybean.

Date: 2024
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DOI: 10.1038/s41467-024-51798-5

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