Identifying key DNA methylation sites and their cis-methylation quantitative loci for intramuscular fatty acid traits using genome and methylome data in Yorkshire pigs

Single-nucleotide polymorphisms (SNPs) that are located near CpG sites have the potential to influence DNA methylation levels, leading to distinct patterns of DNA methylation. These methylation quantitative trait loci (meQTLs) can influence methylation levels across the entire genome, thereby impacting phenotypic traits. In this study, we utilised reduced representation bisulphite sequencing (RRBS) to analyse DNA methylation in muscle tissue samples collected from 140 Yorkshire pigs. Additionally, we assessed SNPs using the Porcine 50K chip, examined 17 fatty acid traits, and conducted epigenome-wide association studies (EWAS) and genome-wide association studies (GWAS). Our investigation revealed numerous associations between DNA methylation and fatty acid traits, including C16:0, C18:0, C20:3n-3, and C22:6n-3. Notably, a substantial portion of these associations was specifically identified by EWAS and not GWAS. Subsequently, we performed GWAS to identify meQTLs using methylation levels of significant CpGs from the EWAS as traits. The results revealed the predominance of trans-meQTLs; however, we also discovered a cis-meQTL on SSC12. Finally, we reported a crucial CpG site (SSC12:3735523) and its cis-meQTL on SSC12, which are located in close proximity to the FASN gene. Our findings contribute to the identification of CpG sites and their cis-meQTLs associated with fatty acid traits, utilising comprehensive genome and methylome data. Moreover, our study provides novel insights into the molecular mechanisms underlying fatty acid traits in pigs.

Automated summary

In this study, DNA methylation in muscle tissue samples from 140 Yorkshire pigs was analyzed using RRBS. Associations between DNA methylation and fatty acid traits were found, with some associations specifically identified by EWAS. GWAS was performed to identify meQTLs using significantly methylated CpGs from EWAS, revealing the predominance of trans-meQTLs and a cis-meQTL on SSC12. A crucial CpG site and its cis-meQTL on SSC12, located near the FASN gene, were reported. These findings contribute to the understanding of the molecular mechanisms underlying fatty acid traits in pigs.