Multi-omics reveals the biosynthesis and pharmacological targets of antioxidant polyphenols in Polygonatum cyrtonema

Polygonatum cyrtonema Hua is a crucial medicinal and edible plant whose antioxidant activity is primarily attributed to its phenolic constituents. Evaluating samples from five geographical origins revealed that the Fuzhou (FZ) ecotype exhibited the strongest antioxidant capacity, significantly correlating with total phenolic content (TPC). Integrated metabolomics and co-expression network analyses identified 32 key polyphenols (flavonoids, lignans, and phenolic acids) as central contributors to this antioxidant capacity. Furthermore, network pharmacology and molecular docking predicted that 10 key polyphenols stably interact with core oxidative damage-related proteins, including prostaglandin-endoperoxide synthase 2 (PTGS2), matrix metallopeptidase 9 (MMP9), and epidermal growth factor receptor (EGFR). Transcriptomic profiling highlighted the enrichment of phenylpropanoid and flavonoid biosynthesis pathways across origins. Integrative analysis identified 14 structural genes driving polyphenol biosynthesis, with RT-qPCR confirming the upregulation of 4-coumarate : CoA ligase ( 4CL ), Chalcone synthase ( CHS ), Shikimic acid/Quinic acid hydroxycinnamoyl transferase ( HCT ), and Dirigent protein ( DIR ) in the FZ samples. Ultimately, this study elucidates the gene-metabolite basis of geographical variations in P. cyrtonema antioxidant capacity, providing valuable pharmacological insights and genetic resources for breeding superior, high-polyphenol cultivars.