Unraveling the molecular mechanisms of flavonoid biosynthesis in Panax notoginseng flowers across planting patterns and developmental stages using integrated metabolomics and transcriptomics analyses

The simulative habitat cultivation of Panax notoginseng (Sanqi) under pine forests using organic management (OM) enhances the quality of Sanqi roots. However, the impact of the OM on the quality of Sanqi flowers remains unknown. The Sanqi flowers cultivated under OM compared with those cultivated under CM (conventional management) exhibited higher levels of flavonoids, saponins, and polysaccharides, as well as dry/fresh weight. Principal component analysis demonstrated that metabolites were predominantly influenced by the cultivation patterns followed by the flowering stage. Several of the differentially abundant metabolites and expressed genes were upregulated in Sanqi flowers cultivated under OM. The flavonoid biosynthesis pathway was highly affected by the cultivation systems and flowering stages, mediated by the essential genes C4H, HCT, C3′H, DFR, and FLS. Flavonoid levels peaked at full bloom, indicating that this is the optimum stage for harvesting Sanqi flowers. Our findings are of great value for developing optimal cultivation and harvest practices.