Dynamic polyphenolic profiling of soybean seeds and leaves during developmental stages

Soybean (Glycine max L.) is a globally important crop recognized for its high protein content and bioactive compounds, such as flavonoids and isoflavones, which contribute to its nutritional and health benefits. However, the metabolic profiles of soybean leaves at various growth stages remain underexplored. We investigated the polyphenolic (flavonoid and isoflavone) metabolite profiles in 10 genetically diverse soybean varieties across 6 leaf developmental stages and seeds. Sixteen flavonoids and isoflavones were identified through ultra-performance liquid chromatography-mass spectrometry. Data analysis, including principal component analysis, revealed metabolic differences among seed profiles. Partial least squares discriminant analysis (PLS-DA) explored metabolite changes across stages, while orthogonal PLS-DA separated vegetative and reproductive stages. Variable importance in projection scores highlighted naringenin, genistin, and kaempferol as key discriminative metabolites. Heatmap analysis showed flavonoids, particularly kaempferol glycosides, were abundant in the leaves, whereas isoflavones such as daidzin and genistin dominated seeds. Cultivars Hoseo, Sohwang, and Kwangan had the highest kaempferol glycoside levels. Correlating these metabolites with six key polyphenolic biosynthesis genes, chalcone synthase, chalcone isomerase, flavonol synthase, 2-hydroxyisoflavanone dehydratase, isoflavone 7-o-methyl transferase, and isoflavone synthase, revealed variety-specific regulation. This study provides key insights into developmental metabolite dynamics in soybeans and supports strategies to enhance soybean nutritional quality.