Selection of differential methylation genes of longissimus dorsi muscle during different developmental stages in Huainan pig breed

CHEN Junfeng; WANG Jing; JIN Wei; CHAI Jin; ZHANG Jiaqing; REN Qiaoling; XING Baosong

doi:10.13300/j.cnki.hnlkxb.2025.01.020

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Selection of differential methylation genes of longissimus dorsi muscle during different developmental stages in Huainan pig breed

Animal science·Veterinary medicine | 更新时间：2026-11-05

- Selection of differential methylation genes of longissimus dorsi muscle during different developmental stages in Huainan pig breed
- Journal of Huazhong Agricultural University Vol. 44, Issue 1, Pages: 183-190(2025)
- 作者机构：
  
  1.河南省畜禽繁育及营养调控重点实验室/河南省农业科学院畜牧兽医研究所，郑州 450002
  2.农业农村部猪遗传育种重点开放实验室/农业动物遗传育种与繁殖教育部重点实验室/ 华中农业大学动物科技学院，武汉 430070
- 作者简介：
- 基金信息：
- DOI：10.13300/j.cnki.hnlkxb.2025.01.020
  CLC： S828
- Received：06 May 2023，
  
  Published：15 January 2025
- 稿件说明：
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陈俊峰，王璟，靳玮，等.淮南猪肌肉组织不同发育阶段的甲基化差异基因筛选［J］.华中农业大学学报，2025，44（1）：183‐190.

CHEN Junfeng,WANG Jing,JIN Wei,et al.Selection of differential methylation genes of longissimus dorsi muscle during different developmental stages in Huainan pig breed[J].Journal of Huazhong Agricultural University,2025,44(01):183-190.
陈俊峰，王璟，靳玮，等.淮南猪肌肉组织不同发育阶段的甲基化差异基因筛选［J］.华中农业大学学报，2025，44（1）：183‐190. DOI： 10.13300/j.cnki.hnlkxb.2025.01.020.

CHEN Junfeng,WANG Jing,JIN Wei,et al.Selection of differential methylation genes of longissimus dorsi muscle during different developmental stages in Huainan pig breed[J].Journal of Huazhong Agricultural University,2025,44(01):183-190. DOI： 10.13300/j.cnki.hnlkxb.2025.01.020.

摘要

为进一步开展淮南猪分子选育，提升其生长速度和瘦肉率等经济性状，选取淮南猪胚胎期（days post coitus， dpc）第38、58、78天和出生后第21天4个发育阶段的淮南公猪背最长肌，开展全基因组甲基化测序并通过信号通路富集分析筛选调控肌肉发育的甲基化差异的候选基因。结果显示，基因主体的CpG甲基化程度高于基因上下游2 kb序列的CpG甲基化，基因组元件中内含子、3' UTR和重复序列等甲基化程度最高。随着发育时间的增加，基因主体的CpG甲基化水平逐渐下降，上下游2 kb则是下降-上升-下降趋势。基因组元件中内含子区、3' UTR区和重复序列的甲基化水平都逐渐下降，启动子区则为下降-上升-下降趋势。信号通路富集分析显示，在淮南猪相邻的发育阶段38~58 dpc、58~78 dpc、78 dpc~21 d三者间的差异化均达到极显著水平，黏着斑信号通路存在CpG甲基化差异基因，且达到极显著水平（

值分别为0.000 9、0.000 4、0.000 1），细胞黏附连接信号通路存在CHH甲基化差异基因，且分别达到显著或极显著水平（

值分别为0.013 2、0.012 8、0.000 5），生物信息学分析结果显示，在2个信号通路中筛选到辅肌动蛋白Α4基因（actinin-4，

ACTN4

）和成纤维细胞生长因子受体（fibroblast growth factor receptor，

FGFR1

）基因。

ACTN4

基因调节肌动蛋白结合过程，在4个发育阶段的甲基化水平分别为55.75%、11.18%、10.18%、59.75%，

FGFR1

基因和肌肉细胞分化相关，在4个发育阶段的甲基化水平分别为0.81%、0.78%、7.52%、0.44%。以上结果表明，在淮南猪肌肉组织不同发育阶段筛选到的2个甲基化差异基因

ACTN4

和

FGFR1

可作为淮南猪肌肉发育候选基因进行分子育种。

Abstract

To further enhance the growth rate and lean meat percentage traits in Huainan pigs through molecular breeding， we performed whole genome methylation sequencing and screened for candidate muscle-regulating genes with differential methylation levels through pathway enrichment analyses using the longissimus dorsi muscle of Huainan boars at 38， 58， and 78 days post coitus （dpc） and at 21 postnatal days. The results showed that the methylation level of mCpG in gene body regions was higher than that in the upstream 2 kb and downstream 2 kb regions of the gene， and the highest methylation levels were observed in introns， 3’UTRs and repeat sequences. During development， the methylation levels in the gene body regions decreased， while those in the upstream 2 kb and downst

ream 2 kb of the gene regions exhibited a trend of down-up-down. The methylation levels of introns， 3’UTRs and repeat sequences gradually decreased， while the methylation levels of promoter regions exhibited a pattern of down-up-down. Pathway enrichment analyses were conducted， revealing significant differences in CpG methylation of focal adhesion （

=0.000 9，

=0.000 4，

=0.000 1） and CHH methylation of adherents junctions （

=0.013 2，

=0.012 8，

=0.000 5） during the adjacent developmental stages of 38~58 dpc， 58~78 dpc， 78 dpc~21 d of Huainan pigs. Through bioinformatics analyses，

ACTN4

and

FGFR1

were identified as candidate genes involved in muscle development from these pathways.

ACTN4

plays a role in regulating actin binding， and the methylation levels at different developmental stages were found to be 55.75%， 11.18%， 10.18%， and 59.75%.

FGFR1

is associated with muscle cell differentiation， and the methylation levels were 0.81%， 0.78%， 7.52%， and 0.44% at different developmental stages. In conclusion， two differentially methylated genes can be selected as candidate genes affecting muscle development to facilitate molecular breeding of Huainan pigs.

关键词

Keywords

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