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Quan J, Yang M, Wang X, Cai G, Ding R, Zhuang Z, Zhou S, Tan S, Ruan D, Wu J, Zheng E, Zhang Z, Liu L, Meng F, Wu J, Xu C, Qiu Y, Wang S, Lin M, Li S, Ye Y, Zhou F, Lin D, Li X, Deng S, Zhang Y, Yao Z, Gao X, Yang Y, Liu Y, Zhan Y, Liu Z, Zhang J, Ma F, Yang J, Chen Q, Yang J, Ye J, Dong L, Gu T, Huang S, Xu Z, Li Z, Yang J, Huang W, Wu Z. Multi-omic characterization of allele-specific regulatory variation in hybrid pigs. Nat Commun 2024; 15:5587. [PMID: 38961076 PMCID: PMC11222378 DOI: 10.1038/s41467-024-49923-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Accepted: 06/25/2024] [Indexed: 07/05/2024] Open
Abstract
Hybrid mapping is a powerful approach to efficiently identify and characterize genes regulated through mechanisms in cis. In this study, using reciprocal crosses of the phenotypically divergent Duroc and Lulai pig breeds, we perform a comprehensive multi-omic characterization of regulatory variation across the brain, liver, muscle, and placenta through four developmental stages. We produce one of the largest multi-omic datasets in pigs to date, including 16 whole genome sequenced individuals, as well as 48 whole genome bisulfite sequencing, 168 ATAC-Seq and 168 RNA-Seq samples. We develop a read count-based method to reliably assess allele-specific methylation, chromatin accessibility, and RNA expression. We show that tissue specificity was much stronger than developmental stage specificity in all of DNA methylation, chromatin accessibility, and gene expression. We identify 573 genes showing allele specific expression, including those influenced by parent-of-origin as well as allele genotype effects. We integrate methylation, chromatin accessibility, and gene expression data to show that allele specific expression can be explained in great part by allele specific methylation and/or chromatin accessibility. This study provides a comprehensive characterization of regulatory variation across multiple tissues and developmental stages in pigs.
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Affiliation(s)
- Jianping Quan
- State Key Laboratory of Swine and Poultry Breeding Industry, National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong, China
- Department of Animal Science, Michigan State University, East Lansing, MI, USA
- State Regional Livestock and Poultry Genebank, Guangdong Genebank of Livestock and Poultry, South China Agricultural University, Guangzhou, Guangdong, China
- Guangdong Zhongxin Breeding Technology Co., Ltd, Guangzhou, Guangdong, China
| | - Ming Yang
- College of Animal Science and Technology, Zhongkai University of Agriculture and Engineering, Guangzhou, Guangdong, China
- Yunfu Subcenter of Guangdong Laboratory for Lingnan Modern Agriculture, Yunfu, Guangdong, China
| | - Xingwang Wang
- State Key Laboratory of Swine and Poultry Breeding Industry, National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong, China
- Guangdong Provincial Key Laboratory of Agro-animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou, Guangdong, China
| | - Gengyuan Cai
- State Key Laboratory of Swine and Poultry Breeding Industry, National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong, China
- State Regional Livestock and Poultry Genebank, Guangdong Genebank of Livestock and Poultry, South China Agricultural University, Guangzhou, Guangdong, China
- Guangdong Provincial Key Laboratory of Agro-animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou, Guangdong, China
| | - Rongrong Ding
- State Key Laboratory of Swine and Poultry Breeding Industry, National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong, China
- Department of Animal Science, Michigan State University, East Lansing, MI, USA
- Guangdong Zhongxin Breeding Technology Co., Ltd, Guangzhou, Guangdong, China
- Yunfu Subcenter of Guangdong Laboratory for Lingnan Modern Agriculture, Yunfu, Guangdong, China
| | - Zhanwei Zhuang
- State Key Laboratory of Swine and Poultry Breeding Industry, National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong, China
- Guangdong Provincial Key Laboratory of Agro-animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou, Guangdong, China
| | - Shenping Zhou
- State Key Laboratory of Swine and Poultry Breeding Industry, National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong, China
- Guangdong Provincial Key Laboratory of Agro-animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou, Guangdong, China
| | - Suxu Tan
- Department of Animal Science, Michigan State University, East Lansing, MI, USA
| | - Donglin Ruan
- State Key Laboratory of Swine and Poultry Breeding Industry, National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong, China
- Guangdong Provincial Key Laboratory of Agro-animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou, Guangdong, China
| | - Jiajin Wu
- State Key Laboratory of Swine and Poultry Breeding Industry, National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong, China
- State Regional Livestock and Poultry Genebank, Guangdong Genebank of Livestock and Poultry, South China Agricultural University, Guangzhou, Guangdong, China
- Guangdong Provincial Key Laboratory of Agro-animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou, Guangdong, China
| | - Enqin Zheng
- State Key Laboratory of Swine and Poultry Breeding Industry, National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong, China
- State Regional Livestock and Poultry Genebank, Guangdong Genebank of Livestock and Poultry, South China Agricultural University, Guangzhou, Guangdong, China
- Guangdong Provincial Key Laboratory of Agro-animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou, Guangdong, China
| | - Zebin Zhang
- State Key Laboratory of Swine and Poultry Breeding Industry, National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong, China
- State Regional Livestock and Poultry Genebank, Guangdong Genebank of Livestock and Poultry, South China Agricultural University, Guangzhou, Guangdong, China
- Guangdong Provincial Key Laboratory of Agro-animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou, Guangdong, China
| | - Langqing Liu
- State Key Laboratory of Swine and Poultry Breeding Industry, National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong, China
- State Regional Livestock and Poultry Genebank, Guangdong Genebank of Livestock and Poultry, South China Agricultural University, Guangzhou, Guangdong, China
- Guangdong Provincial Key Laboratory of Agro-animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou, Guangdong, China
| | - Fanming Meng
- State Key Laboratory of Swine and Poultry Breeding Industry, National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong, China
- Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangdong Key Laboratory of Animal Breeding and Nutrition, Guangzhou, Guangdong, China
| | - Jie Wu
- State Key Laboratory of Swine and Poultry Breeding Industry, National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong, China
- Guangdong Provincial Key Laboratory of Agro-animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou, Guangdong, China
| | - Cineng Xu
- State Key Laboratory of Swine and Poultry Breeding Industry, National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong, China
- Guangdong Provincial Key Laboratory of Agro-animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou, Guangdong, China
| | - Yibin Qiu
- State Key Laboratory of Swine and Poultry Breeding Industry, National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong, China
- Guangdong Provincial Key Laboratory of Agro-animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou, Guangdong, China
| | - Shiyuan Wang
- State Key Laboratory of Swine and Poultry Breeding Industry, National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong, China
- Guangdong Provincial Key Laboratory of Agro-animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou, Guangdong, China
| | - Meng Lin
- State Key Laboratory of Swine and Poultry Breeding Industry, National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong, China
- State Regional Livestock and Poultry Genebank, Guangdong Genebank of Livestock and Poultry, South China Agricultural University, Guangzhou, Guangdong, China
| | - Shaoyun Li
- State Key Laboratory of Swine and Poultry Breeding Industry, National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong, China
- Guangdong Provincial Key Laboratory of Agro-animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou, Guangdong, China
| | - Yong Ye
- State Key Laboratory of Swine and Poultry Breeding Industry, National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong, China
- Guangdong Provincial Key Laboratory of Agro-animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou, Guangdong, China
| | - Fuchen Zhou
- State Key Laboratory of Swine and Poultry Breeding Industry, National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong, China
- Guangdong Provincial Key Laboratory of Agro-animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou, Guangdong, China
| | - Danyang Lin
- State Key Laboratory of Swine and Poultry Breeding Industry, National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong, China
- Guangdong Provincial Key Laboratory of Agro-animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou, Guangdong, China
| | - Xuehua Li
- State Key Laboratory of Swine and Poultry Breeding Industry, National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong, China
- Guangdong Provincial Key Laboratory of Agro-animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou, Guangdong, China
| | - Shaoxiong Deng
- State Key Laboratory of Swine and Poultry Breeding Industry, National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong, China
- Guangdong Provincial Key Laboratory of Agro-animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou, Guangdong, China
| | - Yuling Zhang
- State Key Laboratory of Swine and Poultry Breeding Industry, National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong, China
- Guangdong Provincial Key Laboratory of Agro-animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou, Guangdong, China
| | - Zekai Yao
- State Key Laboratory of Swine and Poultry Breeding Industry, National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong, China
- Guangdong Provincial Key Laboratory of Agro-animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou, Guangdong, China
| | - Xin Gao
- College of Animal Science and Technology, Zhongkai University of Agriculture and Engineering, Guangzhou, Guangdong, China
| | - Yingshan Yang
- State Key Laboratory of Swine and Poultry Breeding Industry, National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong, China
- Guangdong Provincial Key Laboratory of Agro-animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou, Guangdong, China
| | - Yiyi Liu
- State Key Laboratory of Swine and Poultry Breeding Industry, National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong, China
- Guangdong Provincial Key Laboratory of Agro-animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou, Guangdong, China
| | - Yuexin Zhan
- State Key Laboratory of Swine and Poultry Breeding Industry, National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong, China
- Guangdong Provincial Key Laboratory of Agro-animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou, Guangdong, China
| | - Zhihong Liu
- College of Animal Science and Technology, Zhongkai University of Agriculture and Engineering, Guangzhou, Guangdong, China
| | - Jiaming Zhang
- State Key Laboratory of Swine and Poultry Breeding Industry, National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong, China
- Guangdong Provincial Key Laboratory of Agro-animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou, Guangdong, China
| | - Fucai Ma
- State Key Laboratory of Swine and Poultry Breeding Industry, National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong, China
- Guangdong Provincial Key Laboratory of Agro-animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou, Guangdong, China
| | - Jifei Yang
- State Key Laboratory of Swine and Poultry Breeding Industry, National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong, China
- Guangdong Provincial Key Laboratory of Agro-animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou, Guangdong, China
| | - Qiaoer Chen
- State Key Laboratory of Swine and Poultry Breeding Industry, National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong, China
| | - Jisheng Yang
- State Key Laboratory of Swine and Poultry Breeding Industry, National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong, China
| | - Jian Ye
- Guangdong Zhongxin Breeding Technology Co., Ltd, Guangzhou, Guangdong, China
- Yunfu Subcenter of Guangdong Laboratory for Lingnan Modern Agriculture, Yunfu, Guangdong, China
| | - Linsong Dong
- Guangdong Zhongxin Breeding Technology Co., Ltd, Guangzhou, Guangdong, China
- Yunfu Subcenter of Guangdong Laboratory for Lingnan Modern Agriculture, Yunfu, Guangdong, China
| | - Ting Gu
- State Key Laboratory of Swine and Poultry Breeding Industry, National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong, China
- Guangdong Provincial Key Laboratory of Agro-animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou, Guangdong, China
| | - Sixiu Huang
- State Key Laboratory of Swine and Poultry Breeding Industry, National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong, China
- State Regional Livestock and Poultry Genebank, Guangdong Genebank of Livestock and Poultry, South China Agricultural University, Guangzhou, Guangdong, China
| | - Zheng Xu
- State Key Laboratory of Swine and Poultry Breeding Industry, National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong, China
- Guangdong Provincial Key Laboratory of Agro-animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou, Guangdong, China
| | - Zicong Li
- State Key Laboratory of Swine and Poultry Breeding Industry, National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong, China
- Guangdong Provincial Key Laboratory of Agro-animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou, Guangdong, China
| | - Jie Yang
- State Key Laboratory of Swine and Poultry Breeding Industry, National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong, China.
- State Regional Livestock and Poultry Genebank, Guangdong Genebank of Livestock and Poultry, South China Agricultural University, Guangzhou, Guangdong, China.
- Guangdong Provincial Key Laboratory of Agro-animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou, Guangdong, China.
| | - Wen Huang
- Department of Animal Science, Michigan State University, East Lansing, MI, USA.
| | - Zhenfang Wu
- State Key Laboratory of Swine and Poultry Breeding Industry, National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong, China.
- Guangdong Zhongxin Breeding Technology Co., Ltd, Guangzhou, Guangdong, China.
- Yunfu Subcenter of Guangdong Laboratory for Lingnan Modern Agriculture, Yunfu, Guangdong, China.
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