Integrated transcriptomic and metabolomic analyses reveal the molecular mechanisms underlying the improvement of muscle quality in grass carp (Ctenopharyngodon idellus) following 30-week nano-selenium supplementation.

Grass carp (Ctenopharyngodon idellus) holds significant economic and nutritional value in China. However, its intensive cultivation can decrease muscle antioxidant capacity and deteriorate textural properties. Nano-selenium (NSe) represents a novel and efficient source of selenium for regulating fish muscle quality. In this study, a 30-week feeding experiment was conducted to systematically evaluate the effects of long-term NSe supplementation on the muscle quality of grass carp and to reveal the underlying changes in gene expression and metabolites based on transcriptomic and metabolomic analyses. Transcriptome analysis revealed 681 differentially expressed genes (239 upregulated and 442 downregulated), with key genes such as the collagen gene col1a1a/1a2 and the cell cycle regulation gene cdc20 showing particularly significant expression changes. These genes were primarily enriched in signaling pathways such as extracellular matrix organization, cell cycle regulation, and glycolysis/gluconeogenesis, indicating that NSe may improve the textural properties and physiological basis of muscle by promoting muscle structural remodeling and energy metabolism reprogramming. Metabolomics revealed 290 differential metabolites (129 upregulated and 161 downregulated), primarily glycerophospholipids and amino acid derivatives. These were implicated in lipid, amino acid, and nucleotide metabolism, as well as antioxidant response. In conclusion, NSe may synergistically improve muscle tissue structure and functional characteristics through multiple pathways, such as regulating protein anabolism and optimizing the lipid metabolism network. These findings provide a theoretical basis for the application of NSe as a green and efficient feed additive in the healthy aquaculture of high-quality grass carp.