Multi-Omics Revealed Breed Dominates over Plumage Color in Regulating Pigeon Meat Quality and Flavor

Both breed and plumage color are considered potential genetic factors influencing meat quality in pigeons, yet their independent effects remain poorly distinguished. This study aimed to disentangle the regulatory roles of breed and plumage color on meat quality, nutritional composition, and flavor-related metabolites in meat pigeons. White-feathered (SQB) and grey-feathered (SQH) Shiqi pigeons were compared with European Mimas white pigeons (MMS) under identical rearing conditions. Slaughter performance, meat quality traits, and flavor profiles were assessed, followed by untargeted metabolomics and transcriptomics sequencing of pectoral muscle tissues. The results demonstrated that breed exerted a significant influence on carcass traits, water-holding capacity, collagen content, as well as the composition of fatty acids and free amino acids. In contrast, no notable disparity in meat quality was observed between the white- and gray-feathered varieties within the same Shiqi pigeon breed. A total of 114 and 205 differentially expressed metabolites (DEMs), and 11 and 327 differentially expressed genes (DEGs) were identified in plumage color and breed comparisons, respectively. Key flavor-associated metabolites, including glutathione, L-histidine, L-carnosine, and cytidine-5′-monophosphate, were identified as candidate biomarkers for breed-specific flavor differentiation. Breed is the dominant genetic factor determining meat quality and flavor in meat pigeons, while plumage color variation within breed has a limited impact. The identified pathways and regulatory networks provide actionable targets for the precision breeding and flavor enhancement of local pigeon breeds.