iMeta (Dec 2024)
Multiomics analysis reveals signatures of selection and loci associated with complex traits in pigs
- Lei Liu,
- Guoqiang Yi,
- Yilong Yao,
- Yuwen Liu,
- Jiang Li,
- Yalan Yang,
- Mei Liu,
- Lingzhao Fang,
- Delin Mo,
- Longchao Zhang,
- Yonggang Liu,
- Yongchao Niu,
- Liyuan Wang,
- Xiaolu Qu,
- Zhangyuan Pan,
- Lei Wang,
- Muya Chen,
- Xinhao Fan,
- Yun Chen,
- Yongsheng Zhang,
- Xingzheng Li,
- Zhen Wang,
- Yijie Tang,
- Hetian Huang,
- Pengxiang Yuan,
- Yuying Liao,
- Xinjian Li,
- Zongjun Yin,
- Di Liu,
- Dongjie Zhang,
- Quanyong Zhou,
- Wangjun Wu,
- Jicai Jiang,
- Yahui Gao,
- George E. Liu,
- Lixian Wang,
- Yaosheng Chen,
- Kui Li,
- Martien A. M. Groenen,
- Zhonglin Tang
Affiliations
- Lei Liu
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi‐omics of MARA, Agricultural Genomics Institute at Shenzhen Chinese Academy of Agricultural Sciences Shenzhen China
- Guoqiang Yi
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi‐omics of MARA, Agricultural Genomics Institute at Shenzhen Chinese Academy of Agricultural Sciences Shenzhen China
- Yilong Yao
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi‐omics of MARA, Agricultural Genomics Institute at Shenzhen Chinese Academy of Agricultural Sciences Shenzhen China
- Yuwen Liu
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi‐omics of MARA, Agricultural Genomics Institute at Shenzhen Chinese Academy of Agricultural Sciences Shenzhen China
- Jiang Li
- Biozeron Shenzhen, Inc. Shenzhen China
- Yalan Yang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi‐omics of MARA, Agricultural Genomics Institute at Shenzhen Chinese Academy of Agricultural Sciences Shenzhen China
- Mei Liu
- College of Animal Science and Technology Hunan Agricultural University Changsha China
- Lingzhao Fang
- Center for Quantitative Genetics and Genomics Aarhus University Aarhus Denmark
- Delin Mo
- State Key Laboratory of Biocontrol, School of Life Sciences Sun Yat‐sen University Guangzhou China
- Longchao Zhang
- Institute of Animal Sciences Chinese Academy of Agricultural Sciences Beijing China
- Yonggang Liu
- Faculty of Animal Science and Technology Yunnan Agricultural University Kunming China
- Yongchao Niu
- Biozeron Shenzhen, Inc. Shenzhen China
- Liyuan Wang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi‐omics of MARA, Agricultural Genomics Institute at Shenzhen Chinese Academy of Agricultural Sciences Shenzhen China
- Xiaolu Qu
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi‐omics of MARA, Agricultural Genomics Institute at Shenzhen Chinese Academy of Agricultural Sciences Shenzhen China
- Zhangyuan Pan
- Institute of Animal Sciences Chinese Academy of Agricultural Sciences Beijing China
- Lei Wang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi‐omics of MARA, Agricultural Genomics Institute at Shenzhen Chinese Academy of Agricultural Sciences Shenzhen China
- Muya Chen
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi‐omics of MARA, Agricultural Genomics Institute at Shenzhen Chinese Academy of Agricultural Sciences Shenzhen China
- Xinhao Fan
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi‐omics of MARA, Agricultural Genomics Institute at Shenzhen Chinese Academy of Agricultural Sciences Shenzhen China
- Yun Chen
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi‐omics of MARA, Agricultural Genomics Institute at Shenzhen Chinese Academy of Agricultural Sciences Shenzhen China
- Yongsheng Zhang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi‐omics of MARA, Agricultural Genomics Institute at Shenzhen Chinese Academy of Agricultural Sciences Shenzhen China
- Xingzheng Li
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi‐omics of MARA, Agricultural Genomics Institute at Shenzhen Chinese Academy of Agricultural Sciences Shenzhen China
- Zhen Wang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi‐omics of MARA, Agricultural Genomics Institute at Shenzhen Chinese Academy of Agricultural Sciences Shenzhen China
- Yijie Tang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi‐omics of MARA, Agricultural Genomics Institute at Shenzhen Chinese Academy of Agricultural Sciences Shenzhen China
- Hetian Huang
- College of Animal Sciences and Technology Henan Agricultural University Zhengzhou China
- Pengxiang Yuan
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi‐omics of MARA, Agricultural Genomics Institute at Shenzhen Chinese Academy of Agricultural Sciences Shenzhen China
- Yuying Liao
- Guangxi Veterinary Research Institute Nanning China
- Xinjian Li
- College of Animal Sciences and Technology Henan Agricultural University Zhengzhou China
- Zongjun Yin
- College of Animal Science and Technology Anhui Agricultural University Hefei China
- Di Liu
- Institute of Animal Husbandry Heilongjiang Academy of Agricultural Sciences Haerbin China
- Dongjie Zhang
- Institute of Animal Husbandry Heilongjiang Academy of Agricultural Sciences Haerbin China
- Quanyong Zhou
- Institute of Animal Husbandry and Veterinary Medicine Jiangxi Academy of Agricultural Sciences Nanchang China
- Wangjun Wu
- Department of Animal Genetics, Breeding and Reproduction College of Animal Science and Technology Nanjing Agricultural University Nanjing China
- Jicai Jiang
- Department of Animal Science North Carolina State University Raleigh North Carolina USA
- Yahui Gao
- Animal Genomics and Improvement Laboratory, Henry A. Wallace Beltsville Agricultural Research Center, Agricultural Research Service, USDA Beltsville Maryland USA
- George E. Liu
- Animal Genomics and Improvement Laboratory, Henry A. Wallace Beltsville Agricultural Research Center, Agricultural Research Service, USDA Beltsville Maryland USA
- Lixian Wang
- Institute of Animal Sciences Chinese Academy of Agricultural Sciences Beijing China
- Yaosheng Chen
- State Key Laboratory of Biocontrol, School of Life Sciences Sun Yat‐sen University Guangzhou China
- Kui Li
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi‐omics of MARA, Agricultural Genomics Institute at Shenzhen Chinese Academy of Agricultural Sciences Shenzhen China
- Martien A. M. Groenen
- Animal Breeding and Genomics Group Wageningen University & Research Wageningen The Netherlands
- Zhonglin Tang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi‐omics of MARA, Agricultural Genomics Institute at Shenzhen Chinese Academy of Agricultural Sciences Shenzhen China
- DOI
- https://doi.org/10.1002/imt2.250
- Journal volume & issue
-
Vol. 3,
no. 6
pp. n/a – n/a
Abstract
Abstract 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 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.
Keywords
