Proteiomics Analysis Indicated that Mitochondrial Energy Metabolism in Skeletal Muscle Tissue was Negatively Correlated with Feed Efficiency in Pigs

Feed efficiency (FE) is a highly important economic trait in pig production. Investigating the molecular mechanism of FE is essential for trait improvement. In this study, we firstly measured the FE trait of 236 Large White pigs. Then, transcriptome and proteinomics of skeletal muscle tissue of three pigs with extremely high FE and three pigs with extremely low FE were investigated using RNA-seq and iTRAQ approaches, respectively. According to the RNA-seq results, 99 differentially expressed genes were identified between high- and low-FE pigs. In high-FE pigs, the down-regulated genes were mainly involved in mitochondrial energy metabolism and the up-regulated genes were mainly involved in myogensis. We also identified 15 differentially expressed miRNAs between high- and low-FE pigs. Functional study indicated that these miRNAs could participate energy metabolism through targeting the differentially expressed genes. For iTRAQ assay, 1,780 proteins were identified in the muscle tissue. Among them, 74 proteins were up-regulated and 50 proteins were down-regulated in the high-FE pigs. Functional annotation also indicated that mitochondrial energy metabolism was highly important for FE pigs. All 25 differentially expressed proteins located in the mitochondria were down-regulated in high-FE pigs. Moreover, we deduced that glucose utilization was more efficient in the muscle tissue of high-FE pigs based on differentially expressed proteins. Pathway analysis indicated that AMPK-PGC-1αand glucose–pyruvate–TCA–oxidative phosphorylation energy metabolism signal pathways were participated into regulation of FE in pigs. Therefore, we concluded that mitochondrial energy metabolism in the muscle tissue was negatively correlated with FE in pigs.