Transcriptomic and metabolomic analyses reveal moderate topping is favor of flavonoid accumulation in Scutellaria baicalensis Georgi

Scutellaria baicalensi s Georgi is a traditional Chinese herbal medicine, in which the main active ingredients are flavonoids. Pharmacological uses of this herb include anti-oxidation, -cancer, -inflammatory, and -cell-proliferation activities. Topping enhances plant yield and quality, but how it regulates flavonoid biosynthesis at transcriptional and metabolic levels is unclear. We investigate how topping affects flavonoid synthesis in S. baicalensis by integrating transcriptome and metabolome analyses. Topping significantly increases accumulation of flavonoids in root tissues. Transcriptome analysis identified 2924, 4191, and 3316 differentially expressed genes (DEGs) in root, stem, and leaf tissues, respectively, between topping and control groups. DEGs included members of transcription factor families associated with stress responses (e.g., AP2/ERF, WRKY, bHLH ). Ten DEGs involved in the flavonoid skeleton biosynthesis pathway are identified. Metabolomic analysis screened 217, 400, and 436 significantly different metabolites in root, stem, and leaf tissues, respectively. Co-expression network analysis revealed a synergistic regulatory relationship between DEGs and DEMs. Key gene (Chalcone isomerase, Phenylalanine Ammonia-Lyase, Flavonol synthase) expression was upregulated, and flavonoid metabolite accumulation increased. This response likely activated the plant’s antioxidant enzyme system, enhancing defense against oxidative stress induced by topping. Elevated expressions of flavonoid biosynthesis-related genes (e.g., CHI, PAL, FLS ) promoted synthesis and accumulation of specific flavonoid components. By determining how topping regulates flavonoid biosynthesis in S. baicalensis from a multi-omics perspective, we provide a framework for understanding the physiological regulation of topping in rhizome medicinal plants, and the functional characterization of genes related to reproductive growth.