Integrated transcriptomics and metabolomics revealed the mechanism of flavonoid biosynthesis in response to sunlit stress in Amomum tsao-ko

Sunlit stress inhibits growth, development, and quality in shade-requiring plants, but the molecular responses of Amomum tsao-ko remain unclear. In this study, we investigated the adaptation of A. tsao-ko to nature sunlit stress and sunlit stress treatments. Sunlit stress led to higher glandular trichome density, elevated levels of total flavonoids and monomeric flavonoids, and decreased chlorophyll levels compared to the control. Analysis of leaf transcriptomes showed a significant enrichment of genes related to the flavonoid biosynthesis pathway under natural sunlit stress and controlled sunlit stress conditions. Pearson correlation analysis demonstrated a strong positive relationship between flavonoid levels and genes, indicating a significant link between flavonoid compounds and 6 structural genes along with 34 TFs. Transient expression assays demonstrated that a key module gene, chalcone synthase 1 (AmTCHS1), contributes to flavonoid biosynthesis, and that AmTCHS1 expression is regulated by the AmTbHLH1 and AmTMYB2. Together, these results clarify an adaptive mechanism by which A. tsao-ko responds to sunlit stress and provide a foundation for further studies on plant adaptation to sunlit environments.