Altered expression of metabolic pathways and immune-related genes revealed by RNA sequencing and metabolomic analysis in meat-type chickens with different growth rates

Differences in growth rates among broiler chickens within a single commercial genetic line have important economic implications; however, their molecular basis remains incompletely understood. This study analyzed male Ross 308 broilers classified into early- and late-growth lines based on weight gain from 1 to 5 days of age. We integrated RNA sequencing, metabolomics based on gas chromatography–mass spectrometry, and exploratory SNP analysis of pectoralis major muscle tissue collected at 35 days of age. Our integrative analysis revealed contrasting energy utilization programs. Slow early-growth phenotype chickens showed a Warburg-like metabolic profile characterized by glycolytic reliance, lactate fermentation, ketone metabolism, and enhanced proteolysis, accompanied by a bottleneck in mitochondrial oxidative phosphorylation. In contrast, fast early-growth phenotype chickens displayed enhanced oxidative phosphorylation, elevated glycerol-3-phosphate levels, and coordinated activation of pathways related to mitochondrial function and immune responses. Notably, reduced CARNS1 expression in the fast early-growth group suggested a potential trade-off with muscle quality, consistent with the role of carnosine in pH buffering and maintaining redox balance. Multi-omics integrated analysis revealed coordinated changes in metabolites and gene expression within glycolysis, lipid metabolism, and mitochondrial pathways. These findings indicate that the weight gain phenotype during early growth is associated with specific transcriptional and metabolic states during later development.