Integrated Transcriptome and Metabolome Analysis of Meat Quality Differences in Longissimus Dorsi Muscle Between New Zealand White Rabbits and Rex Rabbits

ABSTRACT

Rabbit meat is widely recognized for its favorable nutritional properties, while the molecular mechanisms underlying differences in meat quality between New Zealand White rabbits and Rex rabbits are essential for rabbit production. In this study, a total of 120 healthy 13‐week‐old rabbits (60 per group) were used to evaluate meat quality traits. The longissimus dorsi muscle (LDM) was then collected for transcriptomic and metabolomic analyses. The results showed that New Zealand White rabbits exhibited significantly higher live weight before slaughter, eviscerated weight, semi‐eviscerated weight, and pH ₂₄ ( p  < 0.01), whereas Rex rabbits displayed higher cooking loss ( p  < 0.01) and intramuscular fat content ( p  < 0.05). Metabolomic profiling identified 218 differential metabolites (DMs), which were mainly enriched in amino acid biosynthesis and the pentose phosphate pathway, including key metabolites such as DL‐arginine, gallic acid, and lipid‐related compounds. Transcriptomic analysis identified 227 differentially expressed genes (DEGs) enriched in pathways associated with muscle development and meat quality, including oxidative phosphorylation, FoxO, and MAPK signaling pathways. Key DEGs, such as MYH13 , HOXA13 , and PDK4 , were associated with muscle fiber formation and fat deposition. Integrated analysis revealed that 34 DEGs and 24 DMs were co‐enriched in 26 pathways, with strong correlations observed between oxidative phosphorylation‐related genes and energy metabolites, as well as between collagen‐associated genes and amino acids. These findings establish a gene–metabolite regulatory network underlying breed‐specific differences in meat quality and identify potential molecular markers to improve rabbit meat quality and to better understand muscle metabolism across different rabbit breeds.