文献类型： 外文期刊

作者： Liu, Lei ¹ ; Yi, Guoqiang ¹ ; Yao, Yilong ¹ ; Liu, Yuwen ¹ ; Li, Jiang ⁵ ; Yang, Yalan ¹ ; Liu, Mei ⁶ ; Fang, Lingzhao ⁷ ; Mo, Delin ⁸ ; Zhang, Longchao ⁹ ; Liu, Yonggang ¹⁰ ; Niu, Yongchao ⁵ ; Wang, Liyuan ¹ ; Qu, Xiaolu ¹ ; Pan, Zhangyuan ⁹ ; Wang, Lei ¹ ; Chen, Muya ¹ ; Fan, Xinhao ¹ ; Chen, Yun ¹ ; Zhang, Yongsheng ¹ ; Li, Xingzheng ¹ ; Wang, Zhen ¹ ; Tang, Yijie ¹ ; Huang, Hetian ¹¹ ; Yuan, Pengxiang ¹ ; Liao, Yuying ¹² ; Li, Xinjian ¹¹ ; Yin, Zongjun ¹³ ; Liu, Di ¹⁴ ; Zhang, Dongjie ¹⁴ ; Zhou, Quanyong ¹⁵ ; Wu, Wangjun ¹⁶ ; Jiang, Jicai ¹⁷ ; Gao, Yahui ¹⁸ ; Liu, George E. ¹⁸ ; Wang, Lixian ⁹ ; Chen, Yaosheng ⁸ ; Li, Kui ¹ ; Groenen, Martien A. M. ¹⁹ ; Tang, Zhonglin ¹ ;

作者机构： 1.Agr Genom Inst, Guangdong Lab Lingnan Modern Agr, Shenzhen Branch, Key Lab Livestock & Poultry Multiom MARA, Shenzhen 518124, Peoples R China

2.Chinese Acad Agr Sci, Agr Genom Inst, Kunpeng Inst Modern Agr Foshan, Foshan, Peoples R China

3.Yazhouwan Natl Lab, Sanya, Peoples R China

4.Guangxi Engn Ctr Resource Dev Bama Xiang Pig, Bama, Peoples R China

5.Biozeron Shenzhen Inc, Shenzhen, Peoples R China

6.Hunan Agr Univ, Coll Anim Sci & Technol, Changsha, Peoples R China

7.Aarhus Univ, Ctr Quantitat Genet & Genom, Aarhus, Denmark

8.Sun Yat Sen Univ, Sch Life Sci, State Key Lab Biocontrol, Guangzhou, Peoples R China

9.Chinese Acad Agr Sci, Inst Anim Sci, Beijing, Peoples R China

10.Yunnan Agr Univ, Fac Anim Sci & Technol, Kunming, Yunnan, Peoples R China

11.Henan Agr Univ, Coll Anim Sci & Technol, Zhengzhou, Peoples R China

12.Guangxi Vet Res Inst, Nanning, Peoples R China

13.Anhui Agr Univ, Coll Anim Sci & Technol, Hefei, Peoples R China

14.Heilongjiang Acad Agr Sci, Inst Anim Husb, Harbin, Peoples R China

15.Jiangxi Acad Agr Sci, Inst Anim Husb & Vet Med, Nanchang, Jiangxi, Peoples R China

16.Nanjing Agr Univ, Dept Anim Genet Breeding & Reprod, Coll Anim Sci & Technol, Nanjing, Peoples R China

17.North Carolina State Univ, Dept Anim Sci, Raleigh, NC USA

18.USDA, Agr Res Serv, Henry Wallace Beltsville Agr Res Ctr, Anim Genom & Improvement Lab, Beltsville, MD USA

19.Wageningen Univ & Res, Anim Breeding & Genom Grp, POB 338, NL-6700 AH Wageningen, Netherlands

关键词： epigenetics; genomic variation; pan-genome; phenotype differentiation; pig; skeletal muscle development

期刊名称：IMETA （ 影响因子：33.2； 五年影响因子：33.2 ）

ISSN： 2770-5986

年卷期： 2024 年 3 卷 6 期

页码：

收录情况： SCI

摘要： The genetic basis of complex traits and phenotypic differentiation remains unclear in pigs. Using nine genomes-seven of which were newly generated, high-quality de novo assembled genomes-and 1081 resequencing genomes, we built a pan-genome and identified 134.24Mb nonredundant nonreference sequences, 1099 novel protein-coding genes, 187,927 structural variations (SVs) and 30,143,962 single-nucleotide polymorphisms (SNPs). Analysis of selective domestication revealed BRCA1 associated with enhanced adipocyte growth and fat deposition, and ABCA3 linked to an alleviated immune response and reduced lung injury. Integrating 162 transcriptomes and 162 methylomes of skeletal muscle across 27 developmental stages revealed the regulatory mechanism of phenotypic differentiation between Eastern and Western breeds. Artificial selection reshaped local DNA methylation status and imparted regulatory effects on the progression patterns of heterochronic genes such as GHSR and BDH1, particularly during embryonic development. Altogether, our work provides valuable resources for understanding molecular mechanisms behind phenotypic variations and enhancing the genetic improvement programs in pigs.