Metabolic Basis of Breast Muscle Flavor in Houdan Chicken Crossbreeds Revealed by GC/LC-MS Metabolomics

The quality and flavor of chicken meat are fundamentally determined by muscle metabolite composition, which reflects the regulatory effects of genetic background on metabolic pathways and muscle development. In this study, we profiled the meat quality of breast muscle across 3 crossbreeding combinations (D×HD, HD×D, and D×LD) between the Yunong D line and Houdan chickens to elucidate the metabolic mechanisms underlying flavor variation. Eighteen representative breast muscle samples were analyzed using common physicochemical indexes, untargeted metabolomics based on Gas Chromatography-Time-of-Flight Mass Spectrometry (GC-TOF-MS) and Ultra-High-Performance Liquid Chromatography coupled with Quadrupole Exactive Mass Spectrometry (UHPLC-QE-MS). Differential metabolites were identified through Orthogonal Partial Least Squares Discriminant Analysis (OPLS-DA). Multivariate analysis revealed distinct metabolic signatures among crossbreeding combinations, with HD×D exhibiting the most favorable tenderness, color, and water-holding capacity. A total of nine differential metabolites (5 upregulated and 4 downregulated) were identified between D×HD and HD×D, and thirty-eight metabolites (18 upregulated and 27 downregulated) between D×HD and D×LD. The identified metabolites were predominantly associated with amino acid metabolism, lipid biosynthesis, nucleotide turnover, and energy metabolism. Among these, arachidonic acid, taurine, L-alanine, and citric acid exhibited marked intergroup differences. Enrichment analysis based on the Kyoto Encyclopedia of Genes and Genomes (KEGG) indicated significant involvement of pathways such as amino acid biosynthesis, taurine and hypotaurine metabolism, and ABC transporters in flavor formation. Hierarchical clustering and Pearson correlation analyses further delineated synergistic or antagonistic interactions among key metabolites, suggesting the existence of intricate regulatory mechanisms. These findings reveal critical metabolites and metabolic pathways associated with flavor attributes, offering both a theoretical framework and potential molecular targets for enhancing poultry meat quality through breeding strategies.