Integration of transcriptome and metabolome analyses reveals the mechanism of high-quality formation in Salvia miltiorrhiza

Salvia miltiorrhiza is an important medicinal plant, and its medicinal value is largely associated with specialized metabolites such as tanshinones and salvianolic acids. However, systematic evaluation of high-performing candidate germplasms and the molecular features associated with favorable quality-related traits remains limited. Here, we established an integrated quality–efficiency evaluation framework to assess S. miltiorrhiza germplasms and explore transcriptome–metabolome associations potentially related to metabolite accumulation. Five cultivars (Danza No.1, Danza No.2, Jidan No.4, Danza No.5, and Anguo S. miltiorrhiza ) were evaluated by integrating phenotypic traits, quantitative determination of major active components, preliminary comparative enzyme-inhibition data, and non-targeted metabolite profiling. UHPLC–Q-Orbitrap-MS/MS annotated 95 constituents, and JD4 exhibited the most distinct metabolomic profile and the best overall performance in the integrated quality–efficiency evaluation, indicating it as a high-performing candidate germplasm. Comparative transcriptome analysis identified 2,851 differentially expressed genes (DEGs) in JD4, which were significantly enriched in plant hormone signaling, MAPK signaling, and plant–pathogen interaction pathways. Integrated metabolome–transcriptome analysis identified significant associations between tanshinone-related metabolites and defense- or hormone-responsive genes. In particular, cryptotanshinone was negatively associated with the calcium signaling component CML, whereas tanshinone IIA showed positive associations with the transcription factors PIF4 and ABF, suggesting that defense- and hormone-related regulatory pathways may contribute to tanshinone accumulation in JD4. This study provides a multi-dimensional framework for evaluating S. miltiorrhiza germplasms by integrating anatomical traits, chemical composition, preliminary bioactivity screening, metabolomics, and transcriptomics. The results highlight JD4 as a promising candidate germplasm that warrants further field and functional validation under the present experimental conditions, and provide candidate metabolites, genes, and pathways for future functional validation and molecular breeding of S. miltiorrhiza .