Comparative Analysis of mRNA and miRNA Related to Lipid Metabolism in Skeletal Muscle of New Zealand White Rabbit and...

Meat quality is a complex trait affected by genetic and environmental factors. Intramuscular fat (IMF) is one of the most important factors affecting meat quality. However, there is little research focusing on IMF deposition in rabbits. In this study, we compared the meat quality and nutritional composition of New Zealand White rabbits (NZWRs) and Yufeng Yellow rabbits (YFYRs). The results showed that the drip loss of longissimus dorsi muscle (LD muscle) of YFYR was significantly lower than that of NZWR (p < 0.05), and the pH₄₅ of YFYR was significantly higher than that of NZWR (p < 0.001). Compared with NZWR, the content of IMF, C22:6 n3, C16:0, C20:3 n3, and n-3 PUFA in the LD muscle of YFYR was significantly increased (p < 0.05), while the content of C15:0 was significantly decreased (p < 0.05). RNA-Seq and miRNA-Seq of the LD muscle tissue were performed to measure the mRNA and miRNA expressions of both NZWR and YFYR. A total of 1175 differentially expressed genes (DEGs) were identified between the two rabbit species, including 340 upregulated and 835 downregulated mRNAs in NZWR. A total of 138 differentially expressed miRNAs (DE-miRNAs) were identified, including 31 upregulated and 107 downregulated miRNAs in NZWR. Functional enrichment analysis revealed that the target genes of differential genes and miRNAs were enriched in lipid binding, long-chain fatty acid binding, lipid metabolic process, and fatty acid metabolism, as well as the PPAR signaling pathway, glycerol phospholipid metabolism, and other pathways related to lipid deposition. MiR-973-y, ocu-miR-124-3p, ocu-miR-2355-5p, miR-197-y, and ocu-miR-301b-3p are key miRNAs regulating IMF deposition, and GPX7, GPD2, BDH1, PCYT1B, and ACER2 are key target genes related to lipid deposition and metabolism. In addition, correlation analysis suggested that the IMF content was positively correlated with PAFAH2 and HSD11B2 genes (p < 0.05), while negatively correlated with PRKAG2 (p < 0.01). Taken together, this study suggests that YFYR has relatively better meat quality and nutritional value relative to NZWR; the identified DEGs and target miRNAs provide strong evidence for further studying the regulatory mechanism of IMF deposition in rabbits.