Multi-omics reveals stage-specific mechanisms of Ginseng response to protopanaxadiol-type ginsenosides stress

BACKGROUND: Panax ginseng faces continuous cropping obstacles due to autotoxicity from protopanaxadiol-type ginsenosides. Despite studies on individual ginsenosides being reported, the integrated impact of these compounds across different growth stages requires further investigation. METHODS: We employed multi-omics approaches to elucidate stage-specific molecular mechanisms in ginseng under protopanaxadiol-type ginsenosides stress. Plants were treated with varying concentrations (10-150 mg/L) of protopanaxadiol-type ginsenosides across four growth stages, followed by integrated transcriptomics, extensively targeted metabolomics, and phytohormone-targeted metabolomics analyses with morphological and physiological assessments. RESULTS: Ginseng plants treated with 100 mg/L protopanaxadiol-type ginsenosides showed stage-specific stress responses. Transcriptomics analysis revealed over 20,000 differentially expressed genes across developmental stages (P < 0.05). Significant alterations were observed in pathways related to flavonoids biosynthesis, leading to the identification of 31 key differentially abundant metabolites and 22 critical enzyme genes. Furthermore, 47 differentially expressed genes involved in zeatin biosynthesis and phytohormone signal transduction pathways were identified, potentially regulating the differential accumulation of 8 phytohormones (abscisic acid, jasmonic acid, jasmonoyl-L-isoleucine, salicylic acid, and cytokinins). These molecular responses were putatively associated with enhanced resistance and adaptation to protopanaxadiol-type ginsenosides component stress in ginseng plants. WGCNA identified co-expression modules associated with flavonoid metabolites and phytohormones, providing network-level support for the coordinated regulation between these pathways. Strong correlations were observed between differentially expressed genes and differentially abundant metabolites, suggesting stage-dependent coordinated regulatory networks. CONCLUSION: Protopanaxadiol-type ginsenosides triggered stage-specific regulatory networks in ginseng, especially during the flowering period stage. Parallel activation of flavonoid biosynthesis and phytohormone signaling pathways contributed to the adaptive response to autotoxicity. These findings provided preliminary insights for solving continuous cropping obstacle of ginseng and provided a research strategy for investigating stress response mechanisms of plants.