Muscle proteomics reveals biomarkers of stress and meat quality in organic versus conventional broiler chickens

Animal welfare is a crucial factor in animal production, given its impact on ethics, consumer choices, and meat quality. Stress markedly influences poultry physiology and meat quality by affecting muscle biochemistry and key attributes such as tenderness, flavor, and color. This study employed a label-free quantitative (LFQ) proteomics approach using nLC-ESI-MS/MS combined with bioinformatics to compare muscle protein expression in broiler chickens raised under organic versus conventional production systems. A total of 722 proteins were identified, with 165 significantly upregulated and 162 downregulated in organic chickens. STRING analysis indicated that proteins upregulated in the organic group were primarily associated with oxygen transport, oxygen/metal binding, and muscle structure, suggesting improved oxygen metabolism and muscle development under enhanced welfare conditions. In contrast, proteins involved in ribosomal activity, structural molecule function, RNA binding, and translation regulation were more abundant in conventionally raised chickens, suggesting stress-related alterations in protein synthesis. KEGG pathway enrichment analysis revealed increased activity in carbon metabolism, amino acid biosynthesis, nitrogen metabolism, and the tricarboxylic acid cycle in organic chickens, while glycolysis, gluconeogenesis, and ribosomal pathways were downregulated. Key differentially expressed proteins included PGM1, AMPD1, LDHA, ENO3, VDAC1, HSPB8, and PKLR (downregulated), and COL1A1, COL1A2, TTN, TPM2, CA3, MB, HSPB1, ACO2, ACAA2, GPX1, PRDX1, and TF (upregulated) in the organic group. These proteins, related to muscle structure and energy metabolism, may serve as potential biomarkers to differentiate meat quality based on production system. These findings enhance the understanding of stress-associated proteomic responses in poultry and support welfare-oriented production strategies. In this context, the results not only offert insight into the molecular mechanisms underlying meat quality, but also identify potential markers for its objective evaluation, offering valuable tools for both research and practical applications.