Natural allelic variation in SW14 determines seed weight and quality in soybean

Seed weight and oil/protein content are critical agronomic traits that determine soybean yield and quality. However, the key genes controlling these traits and the underlying regulatory mechanisms remain poorly understood. Here, we performed a combination of genome-wide association study and quantitative trait loci (QTL) mapping with seed weight variations, and identified a Nuclear Factor-YA (NF-YA) gene on chromosome 14 that positively regulates seed weight and protein content while negatively regulating oil content without affecting other agronomic traits, designated as Seed Weight 14 (SW14). SW14 physically interacts with GmLEC1a/b, the soybean orthologs of the central regulator of plant seed development, Leafy Cotyledon1 (LEC1), to disrupt the formation of a non-canonical NF-Y complex comprising GmLEC1, GmNF-YC2, and GmbZIP67, thereby inhibiting the GmLEC1-mediated transcriptional activation involved in seed development process. Natural allelic variations in SW14 affect the stability of the SW14 protein, which in turn confers varied seed weight and oil/protein content in soybean. Further analysis demonstrates that the elite SW14^H3 allele has undergone artificial selection during domestication and holds potential for improving yield in soybean. Collectively, our findings provide insights into the molecular basis that specifically regulates seed weight and quality, offering a potential strategy for overcoming tradeoff effects and facilitating high-yield breeding in soybean.