Integrative analysis of metabolome and transcriptome reveals the mechanism of color formation in white root (Salvia miltiorrhiza).

• The root color of Salvia miltiorrhiza determined by the content of tanshinone. • The simultaneous downregulation of the expression of several key genes leading to the decrease of tanshinone content in Salvia miltiorrhiza root. • Identified several candidate cytochrome P450 genes for tanshinone synthesis. • 22 transcription factors that may be involved in the regulation of tanshinone synthesis. Tanshinones are a class of bioactive components and pigments found in the traditional Chinese herb Salvia miltiorrhiza (S. miltiorrhiza). To clarify the biosynthesis of tanshinones in S. miltiorrhiza roots, the metabolome and transcriptome were compared among three S. miltiorrhiza lines (two red root lines: HG and CK, one white root line: BG). In this study, 18 tanshinones showed markedly lower abundances in BG lines than in other lines and 15 significant differentially accumulated metabolites (DAMs) were chosen as potential marker compounds. Meanwhile, the expression of 5 tanshinone biosynthesis genes in BG was significantly downregulated, which affected the metabolic flow of tanshinones. We speculated that this was the reason BG exhibited white roots. Moreover, 49 cytochrome P450 genes and 22 transcription factors were identified as candidate genes for tanshinone synthesis and regulation. Our results not only explain the formation of root color in S. miltiorrhiza , but also provide an effective solution to explore the biosynthetic pathway of tanshinones. [ABSTRACT FROM AUTHOR]