Integrated miRNAs, Transcriptome, and Metabolome Uncover Underlying Mechanisms for Breast Muscle Metabolic Regulation in Liancheng White and Cherry Valley Ducks

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 <i>SLC7A6</i> and <i>SLC6A9</i> related to amino acid transport was consistent with elevated intramuscular amino acids. For carbohydrate metabolism, <i>SOCS3</i>-a well-established negative regulator of glucose uptake in mammalian skeletal muscle-was significantly upregulated in LD, consistent with their lower intramuscular carbohydrate levels. <i>SLC6A9</i> and <i>SOCS3</i> were predicted to be negatively regulated by oan-miR-1386. In LD, upregulation of the bile acid biosynthesis gene <i>CH25H</i> 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.