GmGASA12 coordinates hormonal dynamics to enhance soybean water-soluble protein accumulation and seed size

Water-soluble protein (WSP) content determines soybean nutritional value and processing efficiency, yet its genetic and molecular regulation remains poorly understood. Here, we identified Glycine max gibberellic acid-stimulated Arabidopsis 12 (GmGASA12), encoding a gibberellin-regulated protein, as a major quantitative trait locus (QTL) governing WSP, through genome-wide association studies across five environments. Knockout of GmGASA12 resulted in 28.7% higher WSP content, 27.6% enlarged seed cells, and 20% yield increase, while overexpression suppressed these traits. Hormonal profiling revealed that GmGASA12 knockout elevates gibberellin, auxin, and abscisic acid but reduces cytokinin, driving cell expansion and protein body accumulation. GmGASA12 cooperatively regulates the biosynthesis of β-conglycinin and glycinin, the core storage proteins in soybean seeds, through its interaction with GmCG-6. Transcriptomics linked GmGASA12 to nitrogen metabolism and hormone signaling, with knockout upregulating amino acid transporters (GmAAP3/6/27) and storage protein genes (GmCG-1-6). Evolutionary analyses demonstrated strong selection for elite GmGASA12 haplotypes during domestication, with 94% of cultivars harboring favorable alleles. Our findings establish GmGASA12 as a molecular hub integrating hormonal dynamics and protein interaction to enhance soybean quality and yield, offering a pivotal target for breeding nutrient-dense varieties.