Epigenome-wide association studies of meat traits in Chinese Yorkshire pigs highlights several DNA methylation loci and genes

Abstract Background: DNA methylation is a key epigenetic mechanism. Most of epigenetic studies of pigs to date have focused on differential methylation analysis. However, few studies have conducted association study between DNA methylation and phenotypic traits. Thus, it is critical to link DNA methylation and phenotypic traits in order to understand the molecular mechanism on epigenomes. In this study, we aimed to identified CpG sites at which DNA methylation levels are associated with meat quality traits in 140 Yorkshire pigs, including pH at 45min (pH45min), pH at 24h (pH24h), drip loss (DL), meat redness value (a*), yellowness (b*) and lightness (L*).Results: Genome-wide methylation levels were measured in muscular tissue using reduced representation bisulfite sequencing (RRBS). Associations between DNA methylation levels and meat quality traits were examined using linear mixed-effect models that were adjusted for gender, year, month and body weight. A Bonferroni-corrected P value lower than was considered statistically significant threshold. Eight CpG sites were associated with DL, including CpG sites annotated to RBM14 gene (cpg301054, cpg301055, cpg301058, cpg301059, cpg301066, cpg301072 and cpg301073) and NCAM1 gene (cpg1802985). Two CpG sites were associated with b*, including RNFT1 and MED13 (cpg2272837) and TRIM37 gene (cpg2270611). Five CpG sites were associated with L*, including GSDMA and LRRC3C gene (cpg2252750) and ENSSSCG00000043539 and IRX1 gene (cpg2820178, cpg2820179, cpg2820181 and cpg2820182). No significant associations were observed with pH45min, pH24h or a*.Conclusion: We reported associations of meat quality traits with DNA methylation and identified some candidate genes associated with these traits, such as NCAM1, MED13 and TRIM37 gene. These results provide new insight into the epigenetic molecular mechanisms of meat quality traits in pigs.