Metabolite-based two germplasms, transplant time and seed color development codes in Psoralea corylifolia L.: insights from untargeted metabolomics

Psoralea corylifolia L. (PCL) is a high-value medicinal legume widely cultivated in tropical and subtropical regions for its diverse bioactive compounds. The plant exhibits significant metabolic plasticity, which is influenced by germplasm resources, cultivation practices, and ontogenetic maturation. However, the precise metabolic shifts driven by the interplay between flower color variants, transplantation timing, and seed development remain largely unexplored. This study aimed to systematically profile the metabolic variations in PCL to optimize cultivation and breeding strategies. Using non-targeted metabolomics, we analyzed seed metabolites across two germplasms (purple vs. white corolla), four transplantation windows (April to July), and three maturation stages (green, yellow, and black seeds). 2156 metabolites were identified through comparison with reference standards and public databases. Among them, significant fluctuations were observed among key bioactive coumarins and flavonoids, including 8-AHC, psoralen, bakuchiol, isobavachin, carpachromene, licoflavone B, corylin, and 8-prenylnaringenin. Pathway enrichment analysis revealed that flavone, flavonol, and isoflavone biosynthesis are the primary metabolic pathways responding to transplantation timing and seed maturation. Notably, isoflavone levels were significantly higher in late-maturity groups (P < 0.001), indicating that seed maturity is a critical determinant of pharmacological potency. This study elucidates the complex metabolic shifts occurring during PCL seed ontogeny and identifies specific environmental and genetic factors that govern metabolite accumulation. Our findings provide a scientific foundation for molecular breeding and the optimization of cultivation protocols to maximize the yield of therapeutic compounds. Furthermore, these results offer a theoretical framework for the comprehensive utilization of PCL resources and provide strategic guidance for future efforts aimed at the metabolic engineering of flavone and isoflavone biosynthesis.