Integrative physiology, transcriptomic, and metabolomic analysis reveals key genes and pathways underlying chilling tolerance in Bougainvillea

Bougainvillea is widely grown ornamental and medicinal plant whose cultivation faces major constraints from chilling stress. However, the gene regulatory networks and molecular basis of chilling tolerance remain largely unexplored. Here, we elucidated cold tolerance mechanisms of Bougainvillea by examining two species with contrasting levels of cold tolerance: Bougainvillea glabra “Brasiliensis” (cold-tolerant) and B. spectabilis “Auratus” (cold-sensitive). Morphological, physiological, biochemical, transcriptomic, and metabolomic analyses revealed that chilling stress significantly inhibited growth, reducing leaf length, leaf width, leaf area, fresh weight, and dry weight in both cultivars. H₂O₂ and malondialdehyde accumulation was higher in Auratus than in Brasiliensis, and chloroplast damage was also more severe in Auratus. In contrast, Brasiliensis showed higher osmolyte accumulation and antioxidant enzyme activities, with less damage to chlorophyll and photosystem II efficiency. Transcriptomic analysis revealed key roles for carbohydrate and amino acid metabolism as well as hormone signaling in Bougainvillea cold responses. Weighted gene co-expression network analysis identified 10 core hub genes associated with chilling tolerance, including Bou_113215 (xylan synthesis-related gene), Bou_98583 (proline transporter gene), and Bou_44133 (NAC8 gene), which are critical in maintaining cell wall integrity, osmotic balance, and transcriptional control under chilling stress. Integrated transcriptomic and metabolomic profiling highlighted the pivotal role of carbohydrate metabolism in enhancing chilling tolerance. Brasiliensis successfully responded to chilling stress by boosting carbohydrate metabolism, antioxidant enzyme activities, osmolyte accumulation, and modulating hormone levels. These results offer valuable insights into the molecular basis of chilling tolerance in Bougainvillea and present candidate genes and pathways for breeding cold-tolerant cultivars.