Color variations in the seed coat and other organs of the soybean emerged during the domestication process. Most of the known genes involved in the pigmentation of each organ are involved in flavonoid synthesis. In this study, we investigated the coloration in each organ of soybean using the FUKUSHIMAPanel of 333 soybean varieties. We analyzed the expression of genes involved in flavonoid biosynthesis pathways in each organ and found that the activities of specific branches of the flavonoid pathway differ among organs, explaining the organ-specific differences in color determination. Combinations of four known color-related genes (I, R, W1, and T) altered functional pathways and seed coat pigmentation in the seed coat, resulting in diverse seed coat colors. In this context, we found that the reddish seed coat pigment is a pelargonidin-3-glucoside (Pg3G) anthocyanin, and its causative gene is a combination of non-functional haplotypes of W1 and T, previously unidentified. Finally, the process of colorlessness in domestication and breeding was investigated. The i i or I locus was selected in the domestication and early breeding process. In contrast, a combination of non-functional R and T haplotypes was selected in the modern breeding process to completely inactivate the flavonoid biosynthesis pathway to produce seeds with good appearance. • Organ-specific flavonoid pathways determine soybean tissue coloration. • Four major pigment genes regulate pathways to generate diversity in the color of the seed coat. • A novel reddish seed coat pigment and its causal genes combinations were identified. • Complete loss of coloration resulted from stepwise selection during domestication and breeding.
Suganami et al. (2026) studied this question.