Integrated multi-omics analysis reveals breed-specific molecular and metabolic architectures of breast muscle in Cherry Valley, Muscovy, and mule ducks.

Integrated transcriptomic and metabolomic analyses of pectoralis major muscle were used to characterize molecular differences among Cherry Valley duck (CVD), Muscovy duck (MD), and their mule hybrid (MU). Birds were reared under identical conditions and evaluated for carcass traits, free amino acids, fatty acids, untargeted metabolomics, and transcriptomics (n = 8 per genotype for phenotypic and metabolomic analyses; CVD = 4, MD = 3, and MU = 4 for transcriptomics). The highest transcriptional difference occurred between the parental lines, with 6,041 differentially expressed genes (DEGs), compared with 2,758 DEGs between CVD and MU and 2,986 between MD and MU. CVD had higher expression of proteasome subunit genes than MD and MU, including genes encoding the 20S core, 19S regulatory particle, and PA28 and PA200 activators. Genes associated with mTOR signalling were also more highly expressed in CVD, accompanied by enrichment of ribosome biogenesis gene sets. Collagen and extracellular matrix genes showed the inverse pattern, with lower expression in CVD and similar expression in MD and MU. MU formed a distinct transcriptional profile from both parental lines. Most DEGs in the parent-hybrid comparisons were more abundant in MU, and oxidative phosphorylation gene sets were more highly expressed in MU than in MD. Free arginine was approximately twice as abundant in MU as in either parent, while total free amino acids did not differ among genotypes. MD had the highest glutamine, asparagine, serine, glycine, and lysine concentrations, while CVD had the highest thrombogenic index and ω-6/ω-3 ratio. These results identify distinct molecular and compositional profiles among the three genotypes, with specific patterns associated with the parental backgrounds and hybridisation.