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, Zhixi Tian
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. Seed size plays an important role in determining soybean yield. Here, the authors report GmSW17, encoding a homolog of Arabidopsis UBP22 that plays a role in deubiquitination, as a positive regulator of soybean seed width and seed weight through inhibition of the G1-to-S transition by interacting with GmSGF11 and GmENY2.