Abstract
DNA methylation is a crucial epigenetic modification involved in diverse biological processes. There is significant phenotypic variance between Chinese indigenous and western pig breeds. Here, we surveyed the genome-wide DNA methylation profiles of blood leukocytes from three pig breeds (Tongcheng, Landrace, and Wuzhishan) by methylated DNA immunoprecipitation sequencing. The results showed that DNA methylation was enriched in gene body regions and repetitive sequences. LINE/L1 and SINE/tRNA-Glu were the predominant methylated repeats in pigs. The methylation level in the gene body regions was higher than in the 5′ and 3′ flanking regions of genes. About 15% of CpG islands were methylated in the pig genomes. Additionally, 2,807, 2,969, and 5,547 differentially methylated genes (DMGs) were identified in the Tongcheng vs. Landrace, Tongcheng vs. Wuzhishan, and Landrace vs. Wuzhishan comparisons, respectively. A total of 868 DMGs were shared by the three contrasts. The DMGs were significantly enriched in development- and metabolism-related biological processes and pathways. Finally, we identified 32 candidate DMGs associated with phenotype variance in pigs. Our research provides a DNA methylome resource for pigs and furthers understanding of epigenetically regulated phenotype variance in mammals.
Highlights
The domestic pig (Sus scrofa) is an economically important food source and an attractive disease model because of anatomical, physiological, pathological, and genomic similarities to humans[1,2,3]
representation bisulfite sequencing (RRBS) studies of the pig genome have been conducted using different types of tissue[36,37], whereas aging skeletal muscle[38] has been assessed using MeDIP-seq; these results indicate that pigs are an ideal model organism for biomedical studies related to aging
We carried out genome-wide DNA methylation profiling using MeDIP-seq
Summary
The domestic pig (Sus scrofa) is an economically important food source and an attractive disease model because of anatomical, physiological, pathological, and genomic similarities to humans[1,2,3]. RRBS studies of the pig genome have been conducted using different types of tissue[36,37], whereas aging skeletal muscle[38] has been assessed using MeDIP-seq; these results indicate that pigs are an ideal model organism for biomedical studies related to aging. Another RRBS analysis reported differences in prenatal and postnatal DNA methylation in intestinal tissue[39]. We used MeDIP-seq to carry out genome-wide DNA methylation analysis of blood leukocytes from three pig breeds with substantial phenotype differences in body size, growth rate, and fat content: Tongcheng, Landrace, and Wuzhishan. We obtained comprehensive DNA methylation profiles for these pig breeds and identified differentially methylated genes (DMGs) related to development and metabolism that might contribute to phenotypic variance among pig breeds
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