Integrated transcriptomic and metabolomic analyses reveal light-quality-dependent regulation of specialized metabolism in Pseudostellaria heterophylla

Pseudostellaria heterophylla is a medicinal and edible plant whose tuberous roots accumulate diverse bioactive metabolites. Light quality is a key environmental signal regulating plant metabolism, but its role in P. heterophylla remains unclear. Here, we integrated transcriptomic and widely targeted metabolomic analyses of in vitro–grown tuberous roots exposed to red, blue, and white light. Distinct light-dependent transcriptional and metabolic patterns were detected. Red light mainly enhanced primary metabolism, particularly amino acid-related pathways, while suppressing several specialized metabolites. In contrast, blue light strongly promoted phenylpropanoid- and flavonoid-related metabolites, whereas white light yielded a more balanced metabolic profile. Integrated pathway enrichment and correlation analyses identified the phenylpropanoid and flavonoid network as a central hub of spectral regulation. Overall, these results provide a systems-level view of light-quality-driven metabolic reprogramming in P. heterophylla and a mechanistic basis for optimizing LED spectral strategies in tissue culture and controlled cultivation systems.