Multi-omics analysis of the formation mechanism of dark-cutting beef in Xinjiang brown beef cattle

Introduction The Xinjiang Brown beef cattle, an emerging Chinese breed prized for its superior meat quality, is susceptible to dark-cutting beef (DFD), which causes substantial economic losses, necessitating systematic elucidation of its formation mechanism to support molecular breeding strategies for its mitigation. Methods For this study, twelve Xinjiang Brown beef cattle were selected, and an integrated approach combining phenotypic analysis, transcriptomics, and non-targeted metabolomics was employed to comprehensively investigate the molecular and metabolic basis of DFD in this breed. Results DFD meat was characterized by significantly darker color (reduced L*, a*, b*) and lower cooking loss. Consistently, transcriptomic analysis identified 1,516 differentially expressedgenes, comprising 752 up-regulated and 764 down-regulated genes, among which key glycolytic genes were significantly down-regulated. Metabolomic analysis identified a total of 98 differential metabolites, comprising 33 upregulated and 65 down-regulated metabolites. Notably, depletion of glycolytic intermediates and accumulation ofoxidative stress-related metabolites were observed. Multi-omics integration highlighted a coordinated mechanism linking glycolytic suppression to oxidative stress. Discussion In summary, this study systematically elucidates the genetic and metabolic basis of DFD meat formation in Xinjiang Brown beef cattle, demonstrating that post-mortem energy metabolism dysfunction is central to high ultimate pH and abnormal coloration. These findings offer a mechanistic basis for mitigating DFD through targeted genetic selection and improved pre-slaughter management.