GSE129385
Genome-wide DNA methylation analysis using next generation sequencing to reveal candidate genes responsible for boar taint in pigs
Boar taint (BT) is an offensive flavor observed in non-castrated male pigs that reduces the carcass price. Surgical castration effectively avoids the taint but is associated with animal welfare concerns. The functional annotation of farm animal genomes (FAANG) for understanding the biology of complex traits and diseases can be used in the selection of breeding animals to achieve favorable phenotypic outcomes. The characterization of pig epigenomes/methylation changes between animals with high and low BT and genome-wide epigenetic markers that can predict BT are lacking. Reduced representation bisulfite sequencing (RRBS) of DNA methylation patterns based on next generation sequencing (NGS) is an efficient technology to identify candidate epigenetic biomarkers associated with BT. Three different BT levels were analyzed using RRBS data to calculate the methylation levels of cytosine. The co-analysis of differentially methylated cytosines (DMCs) identified by this study and differentially expressed (DE) genes identified by previous study found 32 significant co-located genes. The joint analysis of GO terms and pathways revealed that methylation and gene expression of seven candidate genes were associated with BT; in particular, FASN plays a key role in fatty acid biosynthesis, and PEMT might be involved in estrogen regulation and the development of BT. This study is the first to report the genome-wide DNA methylation profiles of BT in pigs using NGS and summarize candidate genes associated with epigenetic markers of BT, which could contribute to the understanding of functional biology of BT traits and selective breeding of pigs against BT based on epigenetic biomarkers. Overall design: Reduced representation bisulfite sequencing (RRBS) of DNA methylation by Illumina HiSeq 2500 for testis of 9 Danish Landrace pigs with 3 groups (Low, Medium and High genetic merit) of boar taint (BT).