Integrated multi-omics analysis reveals the effects of cage and floor rearing systems on meat quality in Chengkou Mountain chickens

As potential substitutes of traditional floor rearing system (FRS) and cage-rearing system (CRS) are currently predominant dryland rearing systems for chickens. However, the influence of these two rearing systems on chicken meat quality are poorly understood. In the present study, a comprehensive comparison of lipidomic, metabolomic, and transcriptome profiles was conducted on the breast muscles of Chengkou mountain chicken (CMC) between CRS (n = 18) and FRS (n = 18) at 120 d of age, which exhibit significant variations in meat quality. Phenotypically, the breast muscle weight and thickness were significantly higher in chicken under FRS (p < 0.05). Metabolomic analysis of breast muscle revealed differential regulation of glycerophospholipid metabolism and linoleic acid metabolism between CRS and FRS. Lipidomic analysis indicated a higher abundance of saturated fatty acids (SFA) and polyunsaturated fatty acids (PUFA) in FRS. Transcriptomic analysis showed that differentially expressed genes (DEGs) were significantly enriched in the oxidative phosphorylation pathway and glycerophospholipid pathway. Integrative lipidomics, metabolomics, and transcriptomics analysis revealed that the improved meat quality of the breast muscle in the FRS chicken is mainly associated with oxidative phosphorylation and glycerophospholipid metabolism. This comprehensive analysis provides valuable insights into the distinct meat quality of rearing system.