Genome-wide DNA Methylation Analysis in Chinese Chenghua and Yorkshire Pigs

Overview

Journal BMC Genom Data

Publisher Biomed Central

Specialty Genetics

Date 2021 Jun 17

PMID 34134626

Citations 5

Authors

Kai Wang

Pingxian Wu

Shujie Wang

Xiang Ji

Dong Chen

Anan Jiang

Weihang Xiao

Yiren Gu

Yanzhi Jiang

Yangshuang Zeng

Xu Xu

Xuewei Li

Guoqing Tang

Affiliations

Soon will be listed here.

Abstract

Background: The Chinese Chenghua pig (CHP) is a typical Chinese domestic fatty pig breed with superior meat quality characteristics, while the Yorkshire pig (YP) has the characteristics of fast growth and a high rate of lean meat. Long term natural selection and artificial selection resulted in great phenotypic differences between the two breeds, including growth, development, production performance, meat quality, and coat color. However, genome-wide DNA methylation differences between CHP and YP remain unclear.

Results: DNA methylation data were generated for muscle tissues of CHP and YP using reduced representation bisulfite sequencing (RRBS). In this study, a total of 2,416,211 CpG sites were identified. Besides, the genome-wide DNA methylation analysis revealed 722 differentially methylated regions (DMRs) and 466 differentially methylated genes (DMGs) in pairwise CHP vs. YP comparison. Six key genomic regions (Sus scrofa chromosome (SSC)1:253.47-274.23 Mb, SSC6:148.71-169.49 Mb, SSC7:0.25-9.86 Mb, SSC12:43.06-61.49 Mb, SSC14:126.43-140.95 Mb, and SSC18:49.17-54.54 Mb) containing multiple DMRs were identified, and differences of methylation patterns in these regions may be related to phenotypic differences between CHP and YP. Based on the functional analysis of DMGs, 8 DMGs (ADCY1, AGBL4, EXOC2, FUBP3, PAPPA2, PIK3R1, MGMT and MYH8) were considered as important candidate genes associated with muscle development and meat quality traits in pigs.

Conclusions: This study explored the difference in meat quality between CHP and YP from the epigenetic point of view, which has important reference significance for the local pork industry and pork food processing.

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