Integrated multi-omics and functional characterization reveal that COL6-mediated flavonoid metabolism contributes to drought tolerance in Juniperus sabina.
Drought stress significantly constrains plant productivity in arid and semi-arid habitats. Understanding the molecular pathways of drought tolerance is essential for germplasm enhancement and ecological restoration. This study investigated the drought adaptation mechanisms of Juniperus sabina L., an ecologically vital evergreen shrub, using integrated physiological, transcriptomic, and metabolomic analyses. Under extreme drought stress, the drought-tolerant provenance (DBD) demonstrated superior photosynthetic stability and robust antioxidant capacity compared to the drought-sensitive provenance (WDH). WDH exhibited significant photosystem impairment and membrane degradation, indicated by elevated relative electrical conductivity and malondialdehyde levels. Integrated analysis identified phenylpropanoid and flavonoid biosynthesis as critical pathways for adaptation. Notably, the DBD provenance utilized a specific metabolic reprogramming strategy, potentially mediated by the transcription factor CONSTANS-LIKE 6 (COL6). This regulatory mechanism involved down-regulating upstream biosynthetic genes (e.g., 4CL, CHS) while activating downstream modification genes (e.g., UGT, COMT-2). This shift redirected metabolic flux toward the accumulation of specific antioxidant flavonoids, such as syringetin, while maintaining cellular structural integrity. Our findings reveal a COL6-mediated regulatory network that coordinates metabolic flux redistribution and stress adaptation in J. sabina. Furthermore, transient overexpression of JsCOL6 in Nicotiana benthamiana confirmed its nuclear localization and demonstrated that it significantly enhanced drought tolerance. JsCOL6-overexpressing plants exhibited robust antioxidant capacity under PEG-induced drought stress, which was molecularly coupled with the transcriptional up-regulation of the downstream peroxidase gene (NbPER-1) and elevated activities of antioxidant enzymes. These results highlight promising molecular targets for breeding drought-resistant conifers and optimizing secondary metabolite production in marginal environments.