Abstract
Rosa rugosa is an economically significant ornamental species with limited understanding of its molecular cold adaptation mechanisms. This study utilized transcriptome sequencing to elucidate the temporal dynamics and organ-specific regulatory mechanisms underlying cold stress (4°C) responses in the leaves and one-year-old stem of R. rugosa. Differential gene expression analysis revealed distinct organ-specific and time-dependent transcriptional reprogramming. A core set of 1,479 and 1,872 genes were consistently differentially expressed from early to late stages (4-24 h) in leaves and stems, respectively. Intersection analysis identified 1,550 conserved early cold-responsive genes shared between two R. rugosa cultivars. These genes were significantly enriched in the MAPK signaling pathway, plant hormone signal transduction, cytoskeleton-related processes, and metabolic reprogramming. Weighted gene co-expression network analysis (WGCNA) pinpointed RrCBFs as central hubs. Genome-wide characterization identifies five RrCBF genes in R. rugosa as cold-inducible central regulators, universally upregulated under cold stress despite divergent cis-elements. Heterologous overexpression of RrCBF1/RrCBF5 in Arabidopsis enhanced freezing tolerance through reduced oxidative damage, improved osmoprotection, and stabilized photosystem function. Critically, transgenic lines exhibited pleiotropic developmental alterations: dwarfism, delayed flowering, and suppressed vegetative-reproductive transition, indicating trade-offs between growth and stress adaptation. Our results delineate a CBF-centric regulatory module coordinating antioxidant defense, photosynthetic protection, and developmental plasticity in R. rugosa cold adaptation, providing targets for cold-tolerance breeding.