ABSTRACT: Seasonal temperature variation poses a major physiological challenge for cold-water aquaculture species, yet the molecular mechanisms underlying seasonal adaptation in large-sized triploid rainbow trout (Oncorhynchus mykiss) remain largely unexplored. Here, we integrated liver transcriptomics and LC-MS-based untargeted metabolomics across four seasons (February, May, August, November) to investigate this process. Seasonal comparisons revealed pronounced molecular reprogramming, with February versus August showing the largest transcriptomic shift (13,359 differentially expressed genes) and May versus November the greatest metabolic divergence (1,036 differentially accumulated metabolites). Pathway enrichment analysis identified significant seasonal regulation of oxidative phosphorylation, ribosome, proteasome, and TCA cycle pathways at the transcript level, alongside altered amino acid biosynthesis, fatty acid biosynthesis, arachidonic acid metabolism, and linoleic acid metabolism at the metabolome level. Integrated network analysis further pinpointed key gene–metabolite correlations. In β-alanine metabolism, amb, aco1, aco3 and ahr91a showed strong positive correlations with carnosine, histidine, and spermine, and negative correlations with aspartate and pantothenate (|r| > 0.8). In fatty acid biosynthesis, accta and acs59z correlated positively with palmitic acid and negatively with palmitoleic acid. In the pentose phosphate pathway, g6pdh and 6pgdh correlated positively with ribose-1-phosphate and negatively with erythrose-4-phosphate. These data indicate that large-sized triploid rainbow trout mount a coordinated adaptive response to seasonal temperature changes: during warm months (August), enhanced TCA cycle and oxidative phosphorylation support increased energy demands, accompanied by accumulation of protective antioxidants such as carnosine and spermine; during cold months (February, November), protein synthesis and ribosome pathways predominate. Collectively, this study reveals the molecular architecture of seasonal adaptation in triploid rainbow trout and provides a foundation for improving stress resilience and aquaculture management.
