ArticleNature communications2024
Multi-omic characterization of allele-specific regulatory variation in hybrid pigs.
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Who cites it
20 citing papers in PubMed.
- Bridging precision agriculture and human medicine through comparative genetics.Nature reviews. Genetics · 2026Review
- Article
- Mapping the landscape of allele-specific expression in porcine genomes.Genome biology · 2026Article
- ATAC-seq and RNA-seq reveal key genes and pathways regulating lactation in the mammary gland of Yili horses.BMC genomics · 2026Article
- A comprehensive genome-wide scan for parent-of-origin expressed genes in the pig clarifies the conservation landscape of genomic imprinting.Genetics, selection, evolution : GSE · 2026Article
- Farm animal evolution demonstrates hidden molecular basis of human traits.bioRxiv : the preprint server for biology · 2026Article
- Tissue-Specific Chromatin Accessibility Regions and Transcription Factor Binding Sites in Pig Brain and Endocrine Tissues.Molecular neurobiology · 2025Article
- A New Family-Based Approach for Detecting Allele-Specific Expression and for Mapping Possible eQTLs.Animals : an open access journal from MDPI · 2025Article
- Conservation of Domestic Animal Genetic Resources in China: Overview of the Status, Activities, Policies, and Challenges.Life (Basel, Switzerland) · 2025Review
- Multitissue single-nucleus RNA-seq reveals cell type-specific regulatory patterns of alternative polyadenylation in pigs.Genome research · 2025Article
- Mechanism of parent-of-origin effects revealed by multi-omic data in euro-chinese hybrid pigs.Nature communications · 2025Article
- A pilot multi-omics study reveals genetic mechanisms regulating milk component traits in dairy cattle.Communications biology · 2025Article
- Integration ATAC-Seq and RNA-Seq Analysis of Mammary Placodes in Erhualian and Bamaxiang Pigs Identified Candidate Genes Influencing Pig Teat Number Variation.Evolutionary applications · 2025Article
- Cell-cell communication-mediated cell-type-specific parent-of-origin effects in mammals.Nature communications · 2025Article
- A multi-tissue atlas of allelic-specific expression reveals the characteristics, mechanisms, and relationship with dominant effects in cattle.BMC biology · 2025Article
- Parental Phasing Study Identified Lineage-Specific Variants Associated with Gene Expression and Epigenetic Modifications in European-Chinese Hybrid Pigs.Animals : an open access journal from MDPI · 2025Article
- Regulatory signatures involved in the cell cycle pathway contribute to egg production heterosis in chicken.Journal of animal science and biotechnology · 2025Article
- Uncovering Molecular Mechanisms of Feed Efficiency in Pigs Through Multi-Omics Analysis of the Jejunum.Animals : an open access journal from MDPI · 2025Article
- Comparative epigenetics of domestic animals: focusing on DNA accessibility and its impact on gene regulation and traits.Journal of veterinary science · 2025Review
- Integration of ATAC-Seq and RNA-Seq Reveals VDR-SELENBP1 Axis Promotes Adipogenesis of Porcine Intramuscular Preadipocytes.International journal of molecular sciences · 2024Article
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Authors and funding
46 authors.
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.ORCID 0000-0002-7064-080X
Ming Yang *College of Animal Science and Technology, Zhongkai University of Agriculture and Engineering, Guangzhou, 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.
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.
Rongrong DingState 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.
Zhanwei ZhuangState 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.
Shenping ZhouState 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.
Suxu TanDepartment of Animal Science, Michigan State University, East Lansing, MI, USA.
Donglin RuanState 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.
Jiajin WuState 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.
Enqin ZhengState 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.
Zebin ZhangState 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.
Langqing LiuState 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.ORCID 0000-0003-4868-087X
Fanming MengState 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.
Jie WuState 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.
Cineng XuState 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.
Yibin QiuState 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.
Shiyuan WangState 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.
Meng LinState 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.
Shaoyun LiState 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.
Yong YeState 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.
Fuchen ZhouState 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.
Danyang LinState 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.
Xuehua LiState 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.
Shaoxiong DengState 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.
Yuling ZhangState 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.
Zekai YaoState 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.
Xin GaoCollege of Animal Science and Technology, Zhongkai University of Agriculture and Engineering, Guangzhou, Guangdong, China.
Yingshan YangState 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.
Yiyi LiuState 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.
Yuexin ZhanState 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.
Zhihong LiuCollege of Animal Science and Technology, Zhongkai University of Agriculture and Engineering, Guangzhou, Guangdong, China.
Jiaming ZhangState 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.
Fucai MaState 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.
Jifei YangState 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.
Qiaoer ChenState 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 YangState 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 YeGuangdong Zhongxin Breeding Technology Co., Ltd, Guangzhou, Guangdong, China.
Linsong DongGuangdong Zhongxin Breeding Technology Co., Ltd, Guangzhou, Guangdong, China.
Ting GuState 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.
Sixiu HuangState 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.
Zheng XuState 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.
Zicong LiState 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.
Jie YangState 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. jieyang2012@hotmail.com.ORCID 0000-0002-7031-2160
Wen HuangDepartment of Animal Science, Michigan State University, East Lansing, MI, USA. huangw53@msu.edu.ORCID 0000-0001-6788-8364
Zhenfang WuState 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. wzfemail@163.com.
Funding
No grant is acknowledged in the PubMed record.
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.
Indexed as
AllelesDNA MethylationAnimalsBrainChromatinFemaleLiverMaleMultiomicsOrgan SpecificityPlacentaPregnancySus scrofaSwineWhole Genome SequencingChromatin
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