Multi-omics analysis reveals tissue-specific patterns of chicken growth driven by metabolic reorganization

Abstract Genetic variation in growth rate is associated with substantial metabolic differences in poultry, but its tissue-specific effects remain insufficiently characterized. Using an F2 population derived from Russian Snow White and White Cornish chickens, we profiled liver, leg muscle, and breast muscle from fast-growing (FG) and slow-growing (SG) birds using NMR metabolomics and CAGE-seq transcriptomics. These data were integrated into a refined genome-scale metabolic model using a Differential Pathway Flux Analysis (DPFA) framework. Across tissues, FG birds showed coordinated but tissue-specific metabolic changes. Oxidative phosphorylation was reduced in both breast muscle and liver. Breast muscle exhibited selective redistribution within amino acid metabolism alongside suppressed folate pathways, while liver showed markedly elevated central carbon metabolism with concurrent suppression of amino acid and folate catabolism. In contrast, leg muscle demonstrated enhanced TCA cycle activity and nitrogen disposal, with reduced folate metabolism and broadly suppressed amino acid catabolism. Transcriptomic analysis identified enrichment of hypoxia-related pathways and Wnt signaling in muscle tissues, along with coordinated downregulation of cell cycle-associated transcriptional programs, consistent with a shift toward hypertrophic growth. These results were consistent across flux predictions, metabolomics, and transcriptomics, and provide a systems-level characterization of metabolic differences associated with growth rate in poultry.