Natural variation in GmSW6 regulates seed weight and quality in soybean

Introduction Seed weight and nutritional composition (protein and oil content) are critical agronomic traits that collectively determine the yield and quality in soybean. However, the genetic architecture and regulatory mechanisms governing these traits remain poorly understood. Objectives This study aimed to identify the key genes and molecular mechanisms governing 100-seed weight and nutritional quality in soybean, providing a theoretical framework for the dual-enhancement of seed weight and protein content. Methods A genome-wide association study (GWAS) was conducted using 1,702 diverse soybean cultivars to identify candidate loci associated with seed weight. Functional characterization was conducted through CRISPR-mediated knockout and overexpression analyses. Population genomic analyses were further performed to elucidate the evolutionary history and selection signals of the candidate gene. Results We identified GmSW6 ( Seed Weight 6 ), encoding a 2-oxoglutarate Fe(II)-dependent dioxygenase (2OGD), as a master regulator of 100-seed weight. Knockout of GmSW6 markedly enhanced seed weight and protein content while simultaneously reducing oil content. Mechanistically, we demonstrated that the transcription factor GmSW13 directly activates GmSW6 expression. This GmSW13-GmSW6 module, in turn, upregulates GmOLEO1 to coordinately modulate both seed weight and quality. Population genomic analysis revealed that the elite allele, GmSW6 G , is significantly associated with increased seed weight and has undergone intense positive selection during soybean domestication and modern improvement. Conclusion Our findings elucidate a hierarchical genetic pathway governing soybean seed development and provide potent molecular targets for simultaneous improvement of seed weight and protein content in future ’designer’ varieties.