Insight into Molecular Mechanism of Phenotype Variance in Skeletal Muscle Based on DNA Methylation, mRNA and microRNA Profiling in Different Pig Breeds

In order to understand molecular mechanism of the phenotype difference, we carried out the genome-wide DNA methylation, mRNA and microRNA profiling based on the adult skeletal muscle in three breeds, including Landrace (lean-type), Tongcheng (obese-type) and Wuzhishan (mini-pig) pigs. The MeDIP analysis showed that three breed pigs have analogous patterns of DNA methylation. There was higher methylation density in the intron than in the UTR and exon regions. Reads in the repeat elements mainly concentrated in the SINE/tRNA-Glu and LINE/L1 elements, accounted for 79% of the total repeat element reads. 8.35%,10.06% and 8.79% islands were kept in methylated states in skeletal muscle at Tongcheng, Landrace and Wuzhishan pigs, respectively. We identified 2203 genes differentially methylated between three pig breeds. We identified 43, 92 and 145 mRNAs differently expressed in Tongcheng VS. Landrace, Tongcheng VS. Wuzhishan and Landrace VS. Wuzhishan pigs, respectively. Clustering analysis of mRNA showed that Tongcheng and Landrace pigs had a more similar expression pattern than Wuzhishan pigs. The GO (Gene Ontology) and KEGG pathway analysis indicated that the DEGs (Different Expressed Genes) significantly enriched in muscle development and fatty acid metabolism-related biological processes and pathways. The miRNA profiling revealed that 106, 151 and 156 miRNAs were differently expressed in Tongcheng VS. Landrace, Tongcheng VS. Wuzhishan and Landrace VS. Wuzhishan pigs, respectively. Combining mRNA and microRNA with DNA methylation data, we constructed the miRNA-mRNA regulatory networks of skeletal muscle in these three breeds.