Integrated Multi-Omic Analyses Reveal Gender-Specific Molecular Mechanisms Regulating Growth and Muscle Development in Zhongshan Partridge Ducks

Zhongshan Partridge duck is a unique indigenous dual-purpose waterfowl native to China’s Pearl River Delta. This once endangered breed has been restored through conserved breeding. Its slow growth and low breast muscle yield limit industrial application, and obvious sexual dimorphism in pectoral muscle growth and metabolism lacks systematic molecular explanation. Herein, we combined GWAS, pectoral RNA-seq and untargeted metabolome to dissect regulatory networks of growth and carcass traits using 365 standardized ducks. Ten growth and carcass phenotypes were collected, and the Gompertz model fitted growth trajectories with mean R2 > 0.98. Critical trait-related genes, including FTO, ACVR2B and IGFBP3, were identified by GWAS. We detected 313 differentially expressed genes (DEGs) showed differentially expressed pattern between high- and low-breast-weight groups in males and 309 DEGs in females. Distinct sex-specific metabolic patterns were observed: males depended on pentose phosphate and glycine–serine–threonine pathways for muscle protein deposition, whereas females utilized fatty acid β-oxidation for energy and lipid control. Lipid gene ECHS1 and growth factor PRDM16 were identified as candidate regulators mediating sexually dimorphic breast muscle development. Joint enrichment of DEGs and differentially expressed metabolites (DEMs) pinpointed key pathways for myogenesis. This study elucidates multi-level sexual dimorphism in duck pectoral development, supplies molecular markers for indigenous duck conservation and breeding, and advances our understanding of poultry growth regulation.