Metabolismics and Transcriptomics Combined with Confocal Laser Scanning Microscopy Analyzes the Purple and Green Characterization of Salvia miltiorrhiza

Introduction: Salvia miltiorrhiza is an important model medicinal plant for secondary metabolism research. There is a leaf color variation (purple) in the aboveground part of S. miltiorrhiza in the process of growth and development, which is mostly caused by the loss or variation of structural genes regulating a certain pigment. Objectives In order to screen the key genes related to purple traits and explore the differences of their metabolites. In addition to further explore the synthesis, accumulation and transport pathway of flavonoids secondary metabolites in aboveground of S. miltiorrhiza . Methods The above ground tissues were analyzed by metabolomics and transcriptomics. And tissue localization and quantitative analysis of flavonoids secondary metabolites were carried out by laser scanning confocal microscope (LSCM). Results The results showed PAL、CYP73A/C4H、4CL、ANS、DFR、3AT、HCT and MYB、bHLH、WADS、WRKY transcription families involved in anthocyanin synthesis were highly differentially expressed. In addition, six GST genes, nine ABC transporters, twenty-two MATE genes and three SNARE genes were detected to play a key role in metabolite transport. A variety of flavonoids and glycosidic carbohydrates were found in the metabolites. Finally, tissue localization and quantitative analysis showed that flavonoids were mainly distributed in epidermis, cortex and collenchyma. Conclusion The dynamic accumulation model of flavonoids biosynthesis pathway was established, and the biological transport pathway of flavonoids was explored. These findings provide insights into the changes of purple phenotype during the development of S. miltiorrhiza , and provide valuable resources for the study of metabolic regulatory networks.