Isoflavones profiling of soybean [Glycine max (L.) Merrill] germplasms and their correlations with metabolic pathways

•Isoflavone diversity (44 varieties) of the soybean seeds were examined by HPLC.•Multivariate analyses were performed to classify genetic varieties.•Metabolic profiling could be used as a tool for identifying metabolic links. The isoflavone diversity (44 varieties) of the soybean, Glycine max (L.) Merrill, from China, Japan, and Korea was examined by high-performance liquid chromatography. The profiles of 12 isoflavones identified from the grains were subjected to data-mining processes, including partial least-squares discriminant analysis (PLS-DA), Pearson’s correlation analysis, and hierarchical clustering analysis (HCA). Although PLS-DA did not reveal significant differences among extracts of soybean from 3 countries, the results clearly show that the variation between varieties was low. The CS02554 variety was separate from the others in the first 2 principal components of PLS-DA. HCA of these phytochemicals resulted in clusters derived from closely related biochemical pathways. Daidzin, genistin, and glycitin contents were significantly correlated with their respective malonyl glycoside contents. Daidzein content correlated positively with genistein content (r=0.8189, P