Genome-wide DNA methylation and transcriptome analysis reveal epigenetic features associated with subcutaneous fat deposition in Kele pigs

To investigate the role of genome-wide DNA methylation in adipose tissue morphology, Kele pigs were divided into two groups (H_IBH, n = 3; L_IBH, n = 3) according to the morphological index of subcutaneous adipose tissue. Genome-wide DNA methylation and transcriptome analyses were performed using subcutaneous adipose tissue to identify differentially methylated regions (DMRs) and differentially expressed genes (DEGs) related to fat deposition. The results showed that CG sites exhibited significantly higher methylation levels than CHG and CHH sites. Among genomic regions, intronic regions showed the highest methylation levels, followed by CGI-shore and 3′UTR regions. A total of 19,701 DMRs were identified under the CG context, and BSP validation demonstrated high concordance with WGBS data. KEGG analysis indicated that differentially methylated genes (DMGs) were significantly enriched in lipid metabolism pathways, including glycerolipid metabolism. RNA-seq analysis identified 353 DEGs, including 218 downregulated and 135 upregulated genes in the H_IBH group. Integrated analysis identified 63 overlapping genes between DMGs and DEGs, and RT-qPCR validated the expression of APOA1, MEOX1, SMOC1, KLF2, and PPARD. Additionally, SNPs within the DMRs of MEOX1 and SMOC1 were analyzed in 37 Kele pigs using PCR amplification and Sanger sequencing. Furthermore, two SNPs were identified in the MEOX1 gene: g.860 G>A (exon 1) and g.1058 G>A (intron 1). The polymorphism information content values of the two single nucleotide polymorphisms (SNPs) were 0.2597 and 0.2710, respectively. Overall, this study provides novel insights into the epigenetic mechanisms underlying fat deposition in Kele pigs.