Seed maturity differentially mediates metabolic responses in black soybean

•Changes in pigmentation on black soybean seeds corresponded with the water soluble extracts.•Metabolic responses differentially responded to seed maturity.•Isoflavones, raffinose, stachyose and total oil were highly associated with seed maturity.•Estimated levels of each targeted metabolite were differentially mediated with seed maturation in black soybean seeds. The soybean seed is placed in the middle of the morphological and developmental alterations, such as changes in seed size, weight, and colour, and alteration of the composition and contents of metabolites during maturation. In this study, we used black soybean seeds to investigate the effect of maturity on metabolite levels at different maturity stages. Seeds were sorted into five maturity categories, from M1 to M5, based on seed size and external pigmentation. Maturity stages M1, M3, and M5 are equivalent to R6, R7, and R8 on the soybean reproductive growth stage scale, indicating full seed, beginning maturity, and full maturity, respectively. As seed maturation progressed, the seed size decreased and the water soluble extract changed, indicating that a change of seed pigmentation occurred. At the same time, numerous metabolites responded differentially to seed maturation. The partial least squares (PLS) scores plot indicated that the metabolic alteration during maturation was clearly visible. Furthermore, isoflavones were highly associated with seed maturity on the PLS loading plot while fatty acids, glucose, fructose, and sucrose were less linked with seed maturity, indicating that those metabolites responded less to seed maturation. Overall, the results indicate that each category of metabolites is mediated differentially during maturation in black soybean seeds.