Floral‑specific activation of the phenylpropanoid‑flavonoid pathway is associated with enhanced antioxidant capacity in Dendrobium flexicaule

Plant secondary metabolites are essential for stress resilience and environmental adaptation; however, how their accumulation is differentially regulated across organs remains poorly understood. Reproductive organs such as flowers often experience greater oxidative challenges than vegetative tissues, potentially necessitating enhanced antioxidant defences. This study aimed to elucidate these organ-specific mechanisms in Dendrobium flexicaule ( D. flexicaule ) by integrating multi-omics to investigate whether flowers exhibit superior antioxidant capacity and explore the associated metabolic and transcriptional features. Ethanolic extracts from flowers, stems, leaves and roots were evaluated for antioxidant activity using 2,2-Diphenyl-1-picrylhydrazyl radical (DPPH), 2,2'-Azinobis-(3-ethylbenzothiazoline-6-sulphonic acid) radical cation (ABTS• + ), hydroxyl radical (•OH), and ferric reducing antioxidant power (FRAP) assays; untargeted metabolomics and transcriptomics were integrated to identify differentially accumulated metabolites (DAMs) and differentially expressed genes (DEGs), followed by pathway analysis and qRT-PCR validation. Flowers exhibited the highest comprehensive antioxidant capacity. Spearman correlation analysis with stringent statistics thresholds (|ρ|> 0.85, FDR < 0.05) identified 9 flower‑enriched metabolites significantly associated with antioxidant activity, including ferulic acid, keracyanin, avicularin, nystose and bilobalide. Transcriptomic analysis revealed upregulated expression of phenylpropanoid–flavonoid pathway genes in flowers, including coordinated expression of structural genes ( PAL , CYP73A , 4CL , CHS , CHI , CYP75A , CYP75B ) and transcription factors (MADS‑box, MYB, bHLH, AP2/ERF-ERF and NAC). Additionally, co‑expression networks involving lipid/terpenoid and carbohydrate/energy metabolism were associated with non‑flavonoid antioxidant accumulation. In conclusion, the superior antioxidant capacity of D. flexicaule flowers is correlated with the coordinated activation of the phenylpropanoid–flavonoid pathway, orchestrated by a multi‑transcription‑factor network and complemented by auxiliary lipid/terpenoid and carbohydrate/energy metabolism. Together, these findings establish a correlative framework for organ‑specific secondary metabolism and provide a basis for future functional validation of the candidate genes and metabolites involved.