Introduction: Arnebia euchroma (Royle) Johnst., a perennial herb in the Boraginaceae family, is valued for its medicinal properties. The harvesting period is crucial for ensuring both the quality and yield of this medicinal material. However, gaps in the knowledge of its optimal harvesting period impede the establishment of standardized cultivation and quality control protocols. This study aims to analyze the quality variations and their dynamic patterns in A. euchroma across different growth years, to provide evidence for determining its optimal harvesting time. Methods: This study used roots from 2- to 7-year-old A. euchroma as the research material. Fresh and dry root weights across multiple growth stages were compared, and key marker compounds were quantified using Ultraviolet–visible(UV) spectrophotometry and High Performance Liquid Chromatography(HPLC). At the same time, metabolite accumulation patterns were profiled via Ultra High Performance Liquid Chromatography-Tandem Mass Spectrometry(UHPLC-MS) untargeted metabolomics. We also applied network pharmacology to identify potential bioactive constituents, and their in vitro antioxidant activity was evaluated using 2,2’-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid) (ABTS), 2,2-diphenyl-1-picrylhydrazyl (DPPH), and ferric ion reducing antioxidant potential (FRAP) assays. Results: This study demonstrated that the fresh and dry weights of A. euchroma roots increased steadily and consistently with increasing growth years. Total hydroxynaphthoquinone pigments followed a “rise-decline-rise” trend, The content ranged from 1.73% to 4.44%. The concentration of β,β′-dimethylacrylshikonin increased steadily from 0.11% in 2-year-old plants to 0.52% in 7-year-old plants. Untargeted metabolomic analysis identified 1,058 metabolites, including 355 differentially accumulated metabolites (DAMs). K-means clustering of DAMs revealed distinct accumulation patterns: flavonoids, phenolic acids, polyketides, phenylpropanoids, and fatty acids peaked in 4-year-old plants. Network pharmacology analysis identified 14 potential bioactive compounds, with notably high expression levels in 4- and 7-year-old plants. In vitro antioxidant testing revealed that antioxidant activity peaked in 4-year-old plants under DPPH and FRAP assays, whereas ABTS scavenging ability was most pronounced in 6-year-old plants. Discussion: These findings elucidate the quality variations and seasonal dynamics of A. euchroma . Across growth years, a comprehensive evaluation identifies the 4-year growth period as the optimal harvest timing for A. euchroma , providing a reference for the development of standardized harvesting and quality control protocols.

Backgroud/Objectives: Ferula spp. is an essential crop in Central Asia with pronounced economic benefits governed by its flowering process. However, the mechanisms of the flowering phenotype remain unclear. Methods: In this study, using F. sinkiangensis as a model plant, we integrated transcriptome, proteome, and metabolome analyses to compare the multilayer differences in leaves and roots of plants with flowering and unflowering phenotypes. Results: We found that several variations in the transcriptome, proteome, and metabolome were closely associated with flowering. The Photosynthesis and Phenylpropanoid biosynthesis pathways in plants with the flowering phenotype were more active. Additionally, three flowering genes, named FL2–FL4, were upregulated in the leaves of flowering plants. Notably, six transcription factors were potentially responsible for regulating the expression of FL2–FL4 in the leaves to mediate flowering process of F. sinkiangensis. Moreover, genes relevant to Photosynthesis and Phenylpropanoid biosynthesis were also involved in regulating the expression of FL2–FL4 in flowering plants. Conclusions: The active regulation network together with Photosynthesis and Phenylpropanoid biosynthesis were essential for inducing the expression of flowering-related genes in leaves to promote the flowering process of F. sinkiangensis.