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Journal of Integrative Agriculture  2022, Vol. 21 Issue (6): 1731-1739    DOI: 10.1016/S2095-3119(21)63814-5
Special Issue: 动物科学合辑Animal Science
Animal Science · Veterinary Medicine Advanced Online Publication | Current Issue | Archive | Adv Search |
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
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本研究基于20头成华猪和30头青裕猪的简化代表性甲基化测序数据使用全基因组分析的方法识别成华猪和青裕猪差异甲基化位点。当甲基化位点的甲基化差异大于0.25以及q值小于0.01时,把该位点识别为差异甲基化位点,然后基于差异甲基化位点搜索对应的差异甲基化基因。结果发现成华猪的几个肉质性状,包括45分钟的pH值 (pH45min),45分钟的肉色亮度值(L45min)以及24小时的肉色亮度值(L24h),均显著高于青裕猪。然后我们检测到10699个差异甲基化位点,并基于这些位点搜索到2760个差异甲基化基因。通过基因功能分析我们发现这些差异甲基化基因主要涉及AMPK信号通路,II型糖尿病,胰岛素信号通路,mTOR信号通路以及胰岛素抵抗等。此外,通过相关文献和研究资料,发现一些差异甲基化基因与脂质代谢,肌肉发育以及肉质性状相关。本研究结果表明成华猪和青裕猪有着不同的甲基化模式,这些甲基化模式的差异反映了二者表型性状的差异。本研究基于简化甲基化测序数据对成华猪和青裕猪进行全基因组甲基化差异分析,研究结果系统解析了成华猪和青裕猪的DNA甲基化模式和表观遗传调控机制

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.
Keywords:  DNA methylation        reduced representation bisulfite sequencing (RRBS)        Chenghua pig        Qingyu pig  
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:; Correspondence TANG Guo-qing, E-mail: * 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. 2022. 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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