DNA methylation patterns and gene expression associated with litter size in Berkshire pig placenta.

Tae Wan Kim,Il-Suk Kim,Seulgi Kwon,Sang Mi An,Ramona Natacha Pena I Subirà,Chul Wook Kim,Jung Hye Hwang,Deok Gyeong Kang,Go Eun Yu,Hwa Chun Park,Jeongim Ha,Da Hye Park

doi:10.1371/journal.pone.0184539

Tae Wan Kim, Il-Suk Kim + Show 10 more

Open Access

https://doi.org/10.1371/journal.pone.0184539

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Abstract

Increasing litter size is of great interest to the pig industry. DNA methylation is an important epigenetic modification that regulates gene expression, resulting in livestock phenotypes such as disease resistance, milk production, and reproduction. We classified Berkshire pigs into two groups according to litter size and estimated breeding value: smaller (SLG) and larger (LLG) litter size groups. Genome-wide DNA methylation and gene expression were analyzed using placenta genomic DNA and RNA to identify differentially methylated regions (DMRs) and differentially expressed genes (DEGs) associated with litter size. The methylation levels of CpG dinucleotides in different genomic regions were noticeably different between the groups, while global methylation pattern was similar, and excluding intergenic regions they were found the most frequently in gene body regions. Next, we analyzed RNA-Seq data to identify DEGs between the SLG and LLG groups. A total of 1591 DEGs were identified: 567 were downregulated and 1024 were upregulated in LLG compared to SLG. To identify genes that simultaneously exhibited changes in DNA methylation and mRNA expression, we integrated and analyzed the data from bisulfite-Seq and RNA-Seq. Nine DEGs positioned in DMRs were found. The expression of only three of these genes (PRKG2, CLCA4, and PCK1) was verified by RT-qPCR. Furthermore, we observed the same methylation patterns in blood samples as in the placental tissues by PCR-based methylation analysis. Together, these results provide useful data regarding potential epigenetic markers for selecting hyperprolific sows.

Highlights

Litter size is an economically important trait in the pig industry [1] and a great deal of effort has been devoted to improving this trait
To identify differentially expressed genes (DEGs) positioned in differentially methylated regions (DMRs), we first selected the differentially methylated genes (DMGs) by a difference rate of methylation level > 30% between SLG and LLG
To generate DNA methylation profiles associated with litter size, we assayed genomic DNA from the placental tissues of the Berkshire pigs using bisulfite sequencing

Summary

Introduction

Litter size is an economically important trait in the pig industry [1] and a great deal of effort has been devoted to improving this trait. A number of factors, including physiological components as well as environment, diet, and strain, have been shown to affect litter size. DNA methylation and gene expression with litter size in Berkshire pig. From Gyeongnam National University of Science and Technology Grant 2016. The Dasan Pig Breeding Co. provided support in the form of a salary for author HCP, but did not have any additional role in the study design, data collection and analysis, decision to publish, or preparation of the manuscript. The specific role of this author is articulated in the ‘author contributions’ section

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