Transcriptome and Metabolome-Based Analysis Reveals the Molecular Mechanisms Underlying the Differences in Tanshinone...

Background/Objectives: Salvia miltiorrhiza (Danshen) is a well-known medicinal herb in traditional Chinese medicine. It produces tanshinones and salvianolic acids as key bioactive constituents in its roots, yet the molecular basis for their tissue-specific accumulation is still poorly understood. This study aims to identify candidate functional genes involved in the biosynthesis of tanshinones and salvianolic acids, and to reveal the molecular basis underlying their tissue-specific accumulation in S. miltiorrhiza. Methods: For this purpose, we compared transcriptomic and metabolomic differences between the roots and leaves, and further measured a set of physiological parameters, including the POD, SOD, CAT and PAL activities, as well as the total phenols and flavones contents. Results: Metabolomic analysis identified 6805 metabolites, of which 241 were differentially accumulated between roots and leaves, with 172 upregulated in roots. The elevated metabolites included gibberellin, cryptotanshinone, decursinol angelate, chalcone, and psoralenol. Transcriptome analysis identified 32,700 annotated genes, with 9895 showing differential expression between roots and leaves, including 4199 upregulated in roots. Roots exhibited higher levels of phenols and flavones, as well as significantly greater POD, SOD, CAT, and PAL activities. Conclusions: Integrated omics analysis identified putative candidate genes including CPS, KS, and P450s as potential contributors for tanshinone and salvianolic acid biosynthesis. The identified genes provide valuable resources for molecular breeding, offering opportunities to improve the medicinal quality of S. miltiorrhiza.