Integrated transcriptomic and metabolomic profiling deciphers breed-, age-, and rearing system-dependent regulation of muscle development and meat quality in chickens

and lipids. Free-range rearing increased precursors of flavor, including glutamine and malvidin-3-glucoside, by activating glycolysis and fatty acid metabolism pathways. In Yandang chickens, leg muscle exhibited greater concentrations of flavor metabolites like serine and proline, along with elevated expression of lipid-related genes such as APOA1, compared to AA broilers. With age, BM accumulated oleic acid, while LM showed increases in polyunsaturated fatty acids (PUFAs) like docosapentaenoic acid. PPAR signaling was identified as a key pathway integrating metabolic responses with rearing conditions. These results improve our understanding of meat quality development and can inform breeding and management practices.