Combined Analysis of Transcriptome and Metabolome of Large-Size Triploid Rainbow Trout in Different Seasons

Seasonal temperature variation poses a significant physiological challenge for cold-water aquaculture species; however, the molecular mechanisms underlying seasonal adaptation in large-sized triploid rainbow trout (Oncorhynchus mykiss) remain largely unexplored. In this study, we integrated liver transcriptomics and LC-MS-based untargeted metabolomics across four seasons (February, May, August, November) to investigate this phenomenon. Seasonal comparisons revealed pronounced molecular reprogramming, with the comparison between May and August showing the largest transcriptomic shift (13,359 differentially expressed genes), while the comparison between May and November exhibited the greatest metabolic divergence (1036 differentially accumulated metabolites). Pathway enrichment analysis identified significant seasonal regulation of oxidative phosphorylation, ribosome, proteasome, and TCA cycle pathways at the transcript level, alongside alterations in amino acid biosynthesis, fatty acid biosynthesis, arachidonic acid metabolism, and linoleic acid metabolism at the metabolomic level. Integrated network analysis further elucidated key gene–metabolite correlations. Integrated network analysis identified season-specific regulatory hubs: Ferroptosis (L-cystine/L-cysteine correlations) dominated the LLF-to-LLM transition; the TCA cycle (citric, fumaric, malic, succinic, and α-ketoglutaric acids) was most responsive from LLF to LLA; Arachidonic acid metabolism linked prostaglandins/thromboxane B2 with PC-class phospholipids from LLM to LLN; and the pentose phosphate pathway (rbks, g6pd, and rpe positively correlated with ribose-1-phosphate) characterized the LLA-to-LLN transition. These findings suggest that large-sized triploid rainbow trout mount a coordinated adaptive response to seasonal temperature fluctuations: during warm months (August), enhanced TCA cycle activity and oxidative phosphorylation meet increased energy demands, accompanied by the accumulation of protective antioxidants such as carnosine and spermine; during cold months (February and November), protein synthesis and ribosomal pathways predominate. Collectively, this study elucidates the molecular architecture of seasonal adaptation in triploid rainbow trout and provides a foundation for enhancing stress resilience and optimizing aquaculture management.