Genome-wide DNA methylation analysis reveals candidate epigenetic biomarkers of boar taint in pigs

Breeding pigs with genetic or epigenetic factors in order to reduce levels of boar taint (BT) compounds such as androstenone and skatol can avoid surgical castration – an animal welfare concern. This study conducted Reduced representation bisulfite sequencing (RRBS) of DNA methylation in high versus low BT pigs and identified candidate epigenetic biomarkers associated with BT that could be used in selective breeding. Nine samples of three different BT levels were analyzed using RRBS data. Filtering and quality control by Trimmomatic software removed RRBS adapters and transcripts with low read counts. Clean reads were mapped to pig reference genome (Sscrofa11.1/susScr11) by Bismark Bisulfite Mapper. Methylation levels of cytosine were analyzed by R package methylKit. Differentially methylated cytosine (DMC) was defined with regard to CpG islands, CpG islands shores and the proximity to nearest transcription start site (TSS) using R package genomation. Gene ontology (GO) enrichment and pathway terms were analyzed by GenCLiP 2.0 software. Interactive gene networks were visualized in Cytoscape Web. The rate of uniquely mapped clean read pairs was 48.7%. The mean distribution of cytosine methylation rate in CpG, CHG and CHH sites were 49.0%, 0.9% and 0.7%, respectively. The distribution of DMC annotation within CpG islands, CpG islands shores and other regions were 57.2%, 14.7% and 28.1%, as well as 5.30%, 1.22%, 3.79% and 89.7% in promoter, exon, intron and intergenic regions, respectively. Co-analysis of differentially expressed (DE) genes and significant DMCs found 32 significant co-identified genes. Joint analysis of GO terms, pathways and gene networks revealed that DMAP1, EGFR and PEMT were very important in regulating gene expression underlying BT, especially PEMT might be positive to estrogen and BT status. To our knowledge, we are the first to report epigenetic mechanisms and epigenetic markers using genome-wide DNA methylation profiles for BT in pigs. Results could be used in biotechnology and breeding industries.