Multi-omics elucidation of temporal patterns in tanshinone accumulation in Salvia miltiorrhiza

Salvia miltiorrhiza is valued for tanshinones, but the dynamics and regulatory mechanisms of tanshinone accumulation from root expansion to harvest are unclear. This study investigated temporal changes in tanshinone content and their molecular basis in five germplasms. Tanshinone levels were monitored from June 2024 to January 2025. Phenotypic correlation, integrated transcriptomic and metabolomic analyses, Weighted Gene Co-expression Network Analysis (WGCNA), and RT-qPCR validation were applied. Tanshinone content initially decreased then stabilized. Root branch number positively correlated with Tanshinone IIA (Tan IIA) and (Tan I) content, while root diameter negatively correlated with tanshinone IIA. Downregulation of key biosynthetic genes (SmHMGR3, SmMK, SmDXS1, SmDXS2, SmCYP76AK1) from late August was linked to reduced tanshinone accumulation. WGCNA identified a transcript-metabolite network with bHLH transcription factors as potential regulators. The temporal progression of tanshinone accumulation is associated with specific root morphological traits and coordinated downregulation of biosynthetic genes. These findings provide a theoretical basis for selecting high-yielding genotypes and optimizing harvest timing.