Meat quality characteristics are important economic traits of ducks. To identify the molecular bases of these traits, we performed an integrated multi-omics analysis (metabolomics, transcriptomics, and miRNAomics) that compared the breast muscle of 300-day-old Liancheng white duck (LD), which is a lean-type breed prized for its soup flavor, and traditional meat duck Cherry Valley duck (CD), which is a fast-growing fat-type breed used for roasting. The results show that LD had higher levels of amino and bile acids, while CD had higher levels of carbohydrates. Integration analysis revealed key breed-specific molecular signatures. In LD, upregulation of the amino acid transporters SLC7A6 and SLC6A9 related to amino acid transport was consistent with elevated intramuscular amino acids. For carbohydrate metabolism, SOCS3-a well-established negative regulator of glucose uptake in mammalian skeletal muscle-was significantly upregulated in LD, consistent with their lower intramuscular carbohydrate levels. SLC6A9 and SOCS3 were predicted to be negatively regulated by oan-miR-1386. In LD, upregulation of the bile acid biosynthesis gene CH25H paralleled the higher bile acid content, suggesting complex, tissue-specific regulation of these pathways. This integrated analysis provides a resource for candidate genes, miRNAs, and metabolic pathways underlying breed-specific meat quality traits in ducks. The findings generate testable hypotheses for future functional studies and offer potential molecular targets for breeding strategies aimed at improving poultry meat quality.
Keywords: amino acids; breast muscle; carbohydrates; duck; metabonomics; miRNA.