An Epigenome-Wide DNA Methylation Map of Testis in Pigs for Study of Complex Traits

Conclusion This is the first study to report catalog of adult pig testis epigenome by developing a genome-wide DNA methylation map with the use of RRBS technology. We found that the methylation rates were lowest in promoters (0.15) and highest in introns (0.55). Cytosines binding to CpG islands showed different methylation patterns between intron and exon regions. Methylation levels of CpG islands were lower than CpG island shores in different genic features. We detected 12,738 DMCs in total. They distributions of DMCs within CpG islands, CpG island shores and other regions were 36.86, 21.65, and 41.49%, respectively. The distributions of DMCs were 0.33, 1.71, 5.95, and 92.01% in promoter, exon, intron and intergenic regions, respectively. Fifteen genes with DMCs were associated with human fertility (ACACA, CYP21A2, CYP27A1, HSD17B2, LHB, PARVG, and SERPINC1), pig reproduction (DICER1, PCK1, SS18, and TGFB3) and boar taint traits (CAPN10, FTO, HSD17B2, IGF2, and SALL4). These findings on genome-wide epigenetic signatures will be useful to understand testis-related trait inheritance in pigs (e.g., male fertility, semen quality, boar taint) for pig production and welfare. This study, based on sequence-level resolution of epigenetic changes, also contributes to understanding and capturing part of the genetic variation that are considered missing (“missing heritability”) in genome-wide genomic prediction studies. Since pigs are useful as an animal model for human r...
Source: Frontiers in Genetics - Category: Genetics & Stem Cells Source Type: research