|Epigenome-wide DNA methylation analysis reveals differentially methylation patterns in skeletal muscle between Chinese Chenghua and Qingyu pigs
|WANG Kai1*, WU Ping-xian1, 5*, WANG Shu-jie1, JI Xiang1, CHEN Dong1, JIANG An-an1, XIAO Wei-hang1, JIANG Yan-zhi2, ZHU Li1, ZENG Yang-shuang3, XU Xu3, QIU Xiao-tian4, LI Ming-zhou1, LI Xue-wei1, TANG Guo-qing1
|1 Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, P.R.China
2 College of Life Science, Sichuan Agricultural University, Yaan 625014, P.R.China
3 Sichuan Animal Husbandry Station, Chengdu 610041, P.R.China
4 National Animal Husbandry Service, Beijing 100125, P.R.China
5 Chongqing Academy of Animal Science, Chongqing 402460, P.R.China
Abstract Chenghua (CH) pig and Qingyu (QY) pig are typical Chinese native fatty breeds. CH pig is mainly distributed in Chengdu Plain, while QY pig is widely distributed throughout the mountain areas around the Sichuan Basin. There are significant differences in their phenotypic traits, including body image, growth performance, and meat quality. This study compared several meat quality traits of CH and QY pigs and conducted a genome-wide DNA methylation analysis using reduced representation bisulfite sequencing (RRBS). It was observed that the pH at 45 min (pH45min, P=5.22e–13), lightness at 45 min (L*45min, P=4.85e–5), and lightness at 24 h (L*24h, P=3.57e–5) of CH pigs were higher than those of QY pigs. We detected 10 699 differentially methylated cytosines (DMCs) and 2 760 differentially methylated genes (DMGs) associated with these DMCs. Functional analysis showed that these DMGs were mainly enriched in the AMPK signaling pathway, Type II diabetes mellitus, Insulin signaling pathway, mTOR signaling pathway, and Insulin resistance. Furthermore, 15 DMGs were associated with fat metabolism (ACACA, CAB39, CRADD, CRTC2, FASN, and GCK), muscle development (HK2, IKBKB, MTOR, PIK3CD, PPARGC1A, and RPTOR), or meat quality traits (PCK1, PRKAG2, and SLC2A4). The findings may help to understand further the epigenetic regulation mechanisms of meat quality traits in pigs and provide new basic data for the study of local pigs.
Received: 14 January 2021
Accepted: 05 August 2021
|Fund: The study was supported by the grants from the Sichuan Science and Technology Program, China (2020YFN0024), the China Agriculture Research System of MOF and MARA (CARS-35-01A), the National Key R&D Program of China (2018YFD0501204), the National Natural Science Foundation of China (C170102), and the Sichuan Innovation Team of Pig, China (sccxtd-2021-08). This study supported by the High-performance Computing Platform of Sichuan Agricultural University, China.
|About author: WANG Kai, E-mail: firstname.lastname@example.org; Correspondence TANG Guo-qing, E-mail: email@example.com
* These authors contributed equally to this study.
Cite this article:
WANG Kai, WU Ping-xian, WANG Shu-jie, JI Xiang, CHEN Dong, JIANG An-an, XIAO Wei-hang, JIANG Yan-zhi, ZHU Li, ZENG Yang-shuang, XU Xu, QIU Xiao-tian, LI Ming-zhou, LI Xue-wei, TANG Guo-qing.
Epigenome-wide DNA methylation analysis reveals differentially methylation patterns in skeletal muscle between Chinese Chenghua and Qingyu pigs. Journal of Integrative Agriculture, 21(6): 1731-1739.
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