Abstract
Rainbow trout (Oncorhynchus mykiss) is an economically important fish species, in which the muscle nutritional composition of market-size fish can vary significantly due to differences in genetic background and breeding environments. This study employed a metabolomics approach to conduct an in-depth comparative analysis of muscle samples from our independently bred new variety "All-Female No. 1", as well as Spanish and Danish all-female strains. A total of 2198 metabolites were identified. Following screening with PCA and PLS-DA, 228 differential metabolites were obtained. These were most abundantly enriched in the categories of organic acids and derivatives, benzene and substituted derivatives, and amino acids and metabolites. KEGG pathway enrichment analysis revealed that the differential metabolites had the most significant impact on the phenylalanine, tyrosine, and tryptophan biosynthesis pathway. Further targeted quantification of amino acid metabolites identified 11 differentially expressed amino acids, which also exerted the strongest influence on this key pathway. Consequently, L-tyrosine, tryptamine, and L-phenylalanine were determined to be the key metabolites affecting the phenylalanine, tyrosine, and tryptophan biosynthesis pathway in the muscle of rainbow trout from different germplasms. This study provides a comprehensive evaluation of the nutritional value, particularly regarding amino acid profiles, of rainbow trout from different genetic sources, offering critical data and a scientific basis for subsequent related research.