Multiomics analysis reveals signatures of selection and loci associated with complex traits in pigs
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 134.24 Mb 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 <i>BRCA1</i> associated with enhanced adipocyte growth and fat deposition, and <i>ABCA3</i> 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 <i>GHSR</i> and <i>BDH1</i>, 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.
Authors
- Mei Liu (ORCID: https://orcid.org/0000-0001-6057-3028)
- Lingzhao Fang (ORCID: https://orcid.org/0000-0003-1103-3679)
- Longchao Zhang (ORCID: https://orcid.org/0000-0002-4520-3165)
- Muya Chen
- Delin Mo (ORCID: https://orcid.org/0000-0002-8738-4486)
- Zhangyuan Pan (ORCID: https://orcid.org/0000-0001-5394-3203)
- Yonggang Liu (ORCID: https://orcid.org/0000-0001-9768-328X)
- Guoqiang Yi (ORCID: https://orcid.org/0000-0001-8248-9126)
- Martien A. M. Groenen (ORCID: https://orcid.org/0000-0003-0484-4545)
- Xinhao Fan (ORCID: https://orcid.org/0009-0004-2208-0133)
- X Li (ORCID: https://orcid.org/0000-0003-4756-4068)
- Yuying Liao (ORCID: https://orcid.org/0000-0001-6230-7436)
- Yaosheng Chen (ORCID: https://orcid.org/0000-0002-3871-7651)
- Yijie Tang (ORCID: https://orcid.org/0000-0003-2628-6230)
- Jicai Jiang (ORCID: https://orcid.org/0000-0001-6890-7539)
- Wangjun Wu (ORCID: https://orcid.org/0000-0003-3775-2663)
- Yalan Yang (ORCID: https://orcid.org/0000-0003-4912-1869)
- Yun Chen (ORCID: https://orcid.org/0000-0002-5663-2352)
- George E. Liu (ORCID: https://orcid.org/0000-0003-0192-6705)
- Yilong Yao (ORCID: https://orcid.org/0000-0003-3525-1152)
- Yongchao Niu (ORCID: https://orcid.org/0000-0002-9774-5417)
- Zhonglin Tang (ORCID: https://orcid.org/0000-0002-4538-4349)
- Lei Liu (ORCID: https://orcid.org/0000-0002-0839-0678)
- Jiang Li (ORCID: https://orcid.org/0000-0003-2099-8165)
- Kui Li (ORCID: https://orcid.org/0000-0002-5686-3898)
- Zhen Wang (ORCID: https://orcid.org/0000-0002-1695-4517)
- Xinjian Li (ORCID: https://orcid.org/0000-0002-7685-3806)
- Zongjun Yin (ORCID: https://orcid.org/0000-0001-9893-743X)
- Yahui Gao (ORCID: https://orcid.org/0000-0003-0602-4823)
- Di Liu (ORCID: https://orcid.org/0000-0003-3241-1421)
- Lei Wang (ORCID: https://orcid.org/0000-0002-4912-5387)
- Dongjie Zhang
- Lixian Wang (ORCID: https://orcid.org/0000-0001-8943-4697)
- Yuwen Liu
- Pengxiang Yuan
- Hetian Huang
- Xiaolu Qu (ORCID: https://orcid.org/0000-0002-1166-2021)
- Yongsheng Zhang (ORCID: https://orcid.org/0000-0003-0135-4997)
- Quanyong Zhou
- Liyuan Wang (ORCID: https://orcid.org/0000-0003-0223-4751)
Institutions
- Nanjing Agricultural University (CN)
- Agricultural Research Service (US)
- North Carolina State University (US)
- Anhui Agricultural University (CN)
- Sun Yat-sen University (CN)
- Yunnan Agricultural University (CN)
- Aarhus University (DK)
- Agricultural Genomics Institute at Shenzhen (CN)
- Animal Science Research Institute (CN)
- Beltsville Agricultural Research Center (US)
- Guangxi Veterinary Research Institute (CN)
- Chinese Academy of Agricultural Sciences (CN)
- Institute of Animal Sciences (CN)
- Environmental Development Centre (CN)
- Jiangxi Academy of Agricultural Sciences (CN)
- Henan Agricultural University (CN)
- Hunan Agricultural University (CN)
- Wageningen University & Research (NL)
Publication Details
- Journal
- iMeta
- Published
- 2024-12-01
- DOI
- https://doi.org/10.1002/imt2.250
- Citations
- 11
- Primary Topic
- Genetic Mapping and Diversity in Plants and Animals
- Type
- article
- Field-Weighted Citation Impact
- 6.05
Funders
- National Natural Science Foundation of China
- Zhejiang University
- Chinese Academy of Agricultural Sciences
- Agricultural Science and Technology Innovation Program