Characterization of Global DNA Methylation in Different Gene Regions Reveals Candidate Biomarkers in Pigs with High and Low Levels of Boar Taint

Abstract

DNA methylation of different gene components, including different exons and introns, or different lengths of exons and introns is associated with differences in gene expression. To investigate the methylation of porcine gene components associated with the boar taint (BT) trait, this study used reduced representation bisulfite sequencing (RRBS) data from nine porcine testis samples in three BT groups (low, medium and high BT). The results showed that the methylation levels of the first exons and first introns were lower than those of the other exons and introns. The first exons/introns of CpG island regions had even lower levels of methylation. A total of 123 differentially methylated promoters (DMPs), 194 differentially methylated exons (DMEs) and 402 differentially methylated introns (DMIs) were identified, of which 80 DMPs (DMP-CpGis), 112 DMEs (DME-CpGis) and 166 DMIs (DMI-CpGis) were discovered in CpG islands. Importantly, GPX1 contained one each of DMP, DME, DMI, DMP-CpGi, DME-CpGi and DMI-CpGi. Gene-GO term relationships and pathways analysis showed DMP-CpGi-related genes are mainly involved in methylation-related biological functions. In addition, gene–gene interaction networks consisted of nodes that were hypo-methylated GPX1, hypo-methylated APP, hypo-methylated ATOX1, hyper-methylated ADRB2, hyper-methylated RPS6KA1 and hyper-methylated PNMT. They could be used as candidate biomarkers for reducing boar taint in pigs, after further validation in large cohorts.

Putative Epigenetic Biomarkers of Stress in Red Blood Cells of Chickens Reared Across Different Biomes

“…Epigenetic research has permeated several fields of biological research, from molecular to evolutionary biology ( Richard and Stein, 2012 ). However, despite the importance of epigenetic mechanisms in biology in general, epigenetic studies in production animals are incipient, with some studies performed in chickens ( Pértille et al, 2017a , 2019 ; Bélteky et al, 2018 ; Guerrero-Bosagna et al, 2020 ), in cattle ( Su et al, 2014 ; Fang et al, 2017 ; Zhou et al, 2018 ; Sevane et al, 2019 ), in sheep ( Cao et al, 2017 ; Capra et al, 2017 ; Zhang X. et al, 2017 ; Zhang Y. et al, 2017 ), and pigs ( Gao et al, 2014 ; Choi et al, 2015 ; Yuan et al, 2017 ; Wang and Kadarmideen, 2019 , 2020 ). Among production animals, chickens have recently emerged as a promising model for epigenetic studies ( Frésard et al, 2013 ) following their historical use as a model for translational research with implications for human health and physiology ( Kain et al, 2014 ).…”

Genome-wide DNA methylation analysis in Chinese Chenghua and Yorkshire pigs

“…Thus, RRBS was used in this study because of its high coverage, small data requirement, low cost, and simple operation. Compared to other studies in pigs [ 16 , 17 , 19 ], this study used a larger population size. Therefore, RRBS is suitable for detecting DNA methylation differences among breeds in this study.…”

How Epigenetics Can Enhance Pig Welfare?

“…An important role of epigenetics in gene expression of productive [ 15 , 16 , 96 , 97 , 98 ] and reproductive traits of pigs [ 99 , 100 , 101 ] has been demonstrated. Moreover, recent work has demonstrated the impact of several factors on the epigenome of the domestic pig such as the influence of nutrition on the pregnant sow epigenome [ 93 , 94 , 102 ], the impact of exposure of pregnant sows to chemicals on its offspring’s epigenome [ 89 , 91 ], and the influence of the year´s season on the epigenome of the boars’ ejaculate and its fertility [ 95 , 103 , 104 , 105 ].…”