Multiomics analysis reveals flavonoid accumulation and biosynthesis across different cultivation years and localities of

Background: The dried root of Methods: This study investigated differences in flavonoid accumulation and transcriptional regulation in Dai-Bai-Jie cultivated for one, two, and three years at high altitudes, and three years at low altitudes. Transcriptome and widely targeted metabolome analyses were conducted. A total of 1,495 metabolites were identified using ultra-performance liquid chromatography coupled with tandem mass spectrometry (UPLC-MS/MS), with 943 showing differential accumulation across the four groups. All flavonoids were classified into six clusters using k-means clustering. Flavonoid levels were generally higher in plants cultivated for two and three years, with total metabolite content also more abundant in these groups. Two-year cultivation was recommended as the optimal harvesting strategy. Results: A regulatory relationship was observed between genes such as phenylalanine ammonia-lyase, CYP73A, 4-coumarate: coenzyme A ligase, and flavonol synthase, and the flavonoid components in Dai-Bai-Jie. No significant differences were found in Shannon, Chao1, or abundance coverage estimator (ACE) indices of rhizosphere microorganisms across different cultivation years and locations. Conclusions: This study elucidates the mechanisms of flavonoid accumulation and supports the scientific rationale for optimal harvesting years of Dai-Bai-Jie. The findings provide a valuable foundation for guiding large-scale cultivation and reducing reliance on wild resources.