Whole-Genome Bisulfite Sequencing of Early Porcine Embryonic Muscle Reveals Distinct DNA Methylation Profiles Between Landrace and Wuzhishan Miniature Pig

DNA methylation is a crucial epigenetic modification in muscle development. Here, we performed the first whole-genome bisulfite sequencing of Landrace (LR) and Wuzhishan (WZS) pig longissimus dorsi muscle during early embryonic development. We provided a genome-wide landscape of DNA methylomes and their relationship with gene expression. LR showed higher methylation level across chromosomes especially in chromosome 16, 18 and X. CG methylation pattern of WZS and LR can be separated by cluster analysis. WZS showed lower methylation level in first exon and downstream elements at 18 and 28 dpc, while no significant difference was found at 21 dpc. Moreover, WZS and LR showed significant differences in CHG and CHH methylation level at all stages. From 18-21 dpc, the number of down-methylated genes increased and the number of up-methylated genes decreased. From 21-28 dpc, the number of up and down-methylated genes were all decreased. Few common genes were found in up and down-stream region between breeds. In genebody region, more common genes were found in upmethylated genes with less GO enrichment of biological processes. By comparing RNA-seq and qPCR with WBS data, most muscle related genes showed negative relation between mRNA expression and DNA methylation, while some expression level of genes such and MYOD1 show no strong relationship with DNA methylation. The integrated analysis provided valuable data for future epigenetic and transcriptomic studies of early porcine embryonic muscle development that may help uncover the molecular basis underling muscle development distinctions between breeds.