Metabolomics in chickens: Bridging the gap between genotypes and phenotypes

Chickens are the most widely raised and economically valuable poultry species worldwide. Traditional breeding methods, along with genomics, transcriptomics, and proteomics, have been unable to fully elucidate the complex regulatory mechanisms linking genotypes and phenotypes. In contrast, metabolomics allows the direct detection of small-molecule metabolites and accurately reflects physiological states, thus serving as a vital bridge connecting genotypes and phenotypes. This review systematically covers the latest research advances in economic traits, including growth, meat quality, stress resistance, and disease resistance, based on metabolomic platforms. Current evidence indicates that amino acid metabolism, lipid metabolism and energy metabolism are central to trait regulation. For meat quality, metabolites such as triglycerides, gallic acid, γ-linolenic acid, and bile acids are associated with intramuscular fat content in chicken meat, whereas histidine dipeptides (e.g., anserine and carnosine) influence antioxidant capacity and flavor. Branched-chain amino acids, such as valine and isoleucine, correlate with meat color, whereas creatine and glucose are associated with drip loss via modulating postmortem muscle energy metabolism. Under heat stress and during growth and development, energy metabolism intermediates such as lactate, pyruvate, 3-hydroxybutyrate, and l-carnitine have been identified as key biomarkers. For disease resistance, metabolomic studies reveal amino acid and lipid metabolic reprogramming during immune responses, thereby providing potential biomarkers for disease-resistant breeding. This review outlines future research directions, including the development of chicken-specific metabolic databases, spatial and single-cell metabolomics, and genome-wide metabolomics association studies. It aims to comprehensively assess the application of metabolomics in the poultry sector and provide a theoretical foundation for chicken genetic breeding, nutritional regulation, and optimized farming practices.