Integrated transcriptome and metabolome analysis of the regulation of flavonoid biosynthesis in Potentilla anserina L. under different abiotic stress

The tuberous root of Potentilla anserina L., a treasured medicinal and edible plant in Tibetan medicine, contains flavonoids with demonstrated antioxidant and hypoglycemic activities. This study investigates the impact of low-temperature and drought stresses on flavonoid biosynthesis in P. anserina amid frequent extreme climate events. Using an integrated transcriptomic and metabolomic analysis, we identified 10 key gene families in the downstream flavonoid pathway and characterized their expression profiles under stress. Both stresses significantly modulated the expression of flavonoid biosynthetic genes and key transcription factors, such as MYB and WRKY . The expression of most flavonoid biosynthesis-related genes was suppressed by low-temperature stress in the leaves and tuberous roots. However, under drought stress, their expression was suppressed in the roots but induced in the leaves. Metabolomic analysis further revealed stress-induced alterations of flavonoid accumulation in the tuberous roots. Notably, dihydrokaempferol content decreased under both stresses, whereas dihydromyricetin accumulated under drought. This study provides crucial genetic insights into the flavonoid biosynthesis pathway in P. anserina and lays a theoretical foundation for future quality improvement through genetic engineering and advanced ethnomedical applications. • Transcriptome map of flavonoid pathway in P. anserina under cold/drought stress. • Cold suppresses and drought activates the flavonoid pathway in leaves. • Key FLS ( Pan1G00187 ) and TF networks were detected for molecular breeding targets. • Key flavonoid metabolites correlate with gene expression under stress. • Stress–gene–metabolite model connects flavonoid regulation to quality traits.