A natural allele of PC08 lost in domestication contributes to soybean seed storage protein accumulation

Soybean serves as a critical source of plant-based protein for both livestock and human nutrition, making seed protein content a key agronomic trait. However, modern soybean cultivars exhibit reduced seed protein content compared to their wild relatives, as a consequence of domestication and historical selection that favored yield over nutritional quality. Thus, genetic improvement of seed protein is highly desired in soybean breeding, while numerous genetic loci associated with this trait remain uncharacterized. Here, we report Protein Contributor 08 ( PC08 ), identified through a genome-wide association study, as a key regulator of seed storage protein accumulation. PC08 encodes a homolog of the 9-cis-epoxycarotenoid dioxygenase 5 enzyme, a rate-limiting enzyme in abscisic acid (ABA) biosynthesis, and is highly expressed during seed development. A nucleic acid T and A (TA)-rich insertion within the PC08 promoter region (designated as PC08 Ins ) enhances transcriptional activity, leading to elevated PC08 expression. Transgenic evidence confirmed its positive regulatory role in seed protein accumulation, mechanistically linked to increased ABA biosynthesis in developing seeds. ABA upregulation activates downstream pathways that promote storage protein synthesis. Population genetic analyses revealed that the PC08 Ins , which confers high protein content, exclusively exists in wild soybean populations and was entirely absent after domestication. Introgression of PC08 Ins into the elite cultivar Hei Nong 35 significantly increased seed protein content. These findings highlight a domestication-eroded allele with untapped potential for modern breeding, offering a valuable genetic target to enhance soybean nutritional quality.