ArticleNature genetics2025
Genetic regulation of gene expression across multiple tissues in chickens.
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Article in Nature genetics, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 44 papers, 1 of them a synthesis that pooled it.
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44citing papers in PubMed, 1 pooled it
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Who cites it
44 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Pooled it
- Advances in Poultry RNA-Omics Research: Technologies, RNA Information Layers, and Applications in Complex Traits.Animals : an open access journal from MDPI · 2026Review
- Bridging precision agriculture and human medicine through comparative genetics.Nature reviews. Genetics · 2026Review
- Low-Coverage Whole-Genome Resequencing in Livestock and Poultry: Statistical Foundations, Applications and Future Directions.Biology · 2026Review
- Identification of candidate genes and regulatory mechanisms for thick shank phenotype of Dong Tao chickens.Poultry science · 2026Article
- Integrated Analysis of SNPs and Structural Variations via High-depth Whole-genome Sequencing Reveals the Genetic Architecture and Optimizes Genomic Prediction in Chickens.Poultry science · 2026Article
- Whole-transcriptome analysis reveals key transcriptional and noncoding RNA regulators of skeletal muscle satellite cell differentiation in quail.Poultry science · 2026Article
- Microbiomics and metabolomics reveal microbial-metabolic signatures associated with body weight variation in chickens.Poultry science · 2026Article
- Integrative Multi-Omics Analysis Reveals the Genetic Architecture Landscape of the Blood Metabolome in Jersey Cattle.Animals : an open access journal from MDPI · 2026Article
- Integrating bulk and single-cell RNA sequencing with GWAS reveals regulatory networks underpinning complex traits in beef cattle.Journal of animal science and biotechnology · 2026Article
- Insights from adaptive immune regulation for disease resistance breeding in livestock and poultry.Science China. Life sciences · 2026Review
- Divergent jejunal cis- and trans-eQTLs and their microbiome associations following a diet lacking mineral phosphorus supplements in laying hens.BMC genomics · 2026Article
- Integrative genomic analysis and gene expression patterns reveal a cardio-neuroendocrine signaling network for heat adaptation in geographically diverse chickens.Poultry science · 2026Article
- Identification and Characterization of sQTLs and eQTLs Associated with Growth Traits in Yellow-Feathered Broilers.Poultry science · 2026Article
- Whole genome analysis of selection associated with resistance to heat stress in chickens.Scientific reports · 2026Article
- Multi-Tissue Omics Analysis Uncovers Translational Regulation Underlying Complex Traits in Pigs.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Pan-3D Genome Analysis Reveals the Roles of Structural Variation in Chicken Chromatin Architectures, Domestication and Production Traits.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Pan-Transcriptome Analyses of Multiple Tissues and Growth Stages Create Expression Atlases for the SilkwormAnimals : an open access journal from MDPI · 2026Article
- Meta-GWAS of Pig Semen Quality Traits Reveals Conserved Genes Regulating Mammalian Fertility.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Multi-Tissue Genetic Regulation of RNA Editing in Pigs.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
Corrections and comments
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Authors and funding
63 authors.
Dailu Guan *Department of Animal Science, University of California-Davis, Davis, CA, USA.ORCID http://orcid.org/0000-0001-8800-3158
Zhonghao Bai *Center for Quantitative Genetics and Genomics (QGG), Aarhus University, Aarhus, Denmark.
Xiaoning Zhu *State Key Laboratory of Animal Biotech Breeding, College of Biological Sciences, China Agricultural University, Beijing, China.ORCID http://orcid.org/0000-0001-5743-879X
Conghao Zhong *State Key Laboratory of Animal Biotech Breeding and Frontier Science Center of Molecular Design Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China.ORCID http://orcid.org/0000-0003-0063-4970
Yali Hou *Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China.ORCID http://orcid.org/0000-0002-7421-2431
Di Zhu *Center for Quantitative Genetics and Genomics (QGG), Aarhus University, Aarhus, Denmark.
ChickenGTEx Consortium
Houcheng LiCenter for Quantitative Genetics and Genomics (QGG), Aarhus University, Aarhus, Denmark.
Fangren LanState Key Laboratory of Animal Biotech Breeding and Frontier Science Center of Molecular Design Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China.
Shuqi DiaoState Key Laboratory of Swine and Poultry Breeding Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, China.
Yuelin YaoMRC Human Genetics Unit at the Institute of Genetics and Cancer, The University of Edinburgh, Edinburgh, UK.ORCID http://orcid.org/0000-0001-9868-2801
Bingru ZhaoJiangsu Livestock Embryo Engineering Laboratory, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China.
Xiaochang LiState Key Laboratory of Animal Biotech Breeding and Frontier Science Center of Molecular Design Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China.
Zhangyuan PanInstitute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China.
Yahui GaoState Key Laboratory of Swine and Poultry Breeding Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, China.
Yuzhe WangState Key Laboratory of Animal Biotech Breeding, College of Biological Sciences, China Agricultural University, Beijing, China.ORCID http://orcid.org/0000-0003-3474-7957
Dong ZouBeijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, China.
Ruizhen WangBeijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, China.
Tianyi XuBeijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, China.ORCID http://orcid.org/0000-0003-4197-8163
Congjiao SunState Key Laboratory of Animal Biotech Breeding and Frontier Science Center of Molecular Design Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China.
Hongwei YinShenzhen 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.ORCID http://orcid.org/0000-0002-9373-5166
Jinyan TengState Key Laboratory of Swine and Poultry Breeding Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, China.ORCID http://orcid.org/0000-0002-3046-1452
Zhiting XuState Key Laboratory of Swine and Poultry Breeding Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, China.ORCID http://orcid.org/0000-0001-8830-3580
Qing LinState Key Laboratory of Swine and Poultry Breeding Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, China.
Shourong ShiPoultry Institute, Chinese Academy of Agricultural Sciences, Yangzhou, China.
Dan ShaoPoultry Institute, Chinese Academy of Agricultural Sciences, Yangzhou, China.
Fabien DegalezPEGASE, INRAE, Institut Agro, Saint Gilles, France.ORCID http://orcid.org/0000-0001-8252-6425
Sandrine LagarriguePEGASE, INRAE, Institut Agro, Saint Gilles, France.
Ying WangDepartment of Animal Science, University of California-Davis, Davis, CA, USA.
Mingshan WangState Key Laboratory of Genetic Evolution & Animal Models and Yunnan Key Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.ORCID http://orcid.org/0000-0003-4663-2735
Minsheng PengState Key Laboratory of Genetic Evolution & Animal Models and Yunnan Key Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.ORCID http://orcid.org/0000-0002-6301-9599
Dominique RochaINRAE, GABI, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France.
Mathieu CharlesINRAE, GABI, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France.ORCID http://orcid.org/0000-0001-6491-1928
Jacqueline SmithThe Roslin Institute, Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Midlothian, UK.ORCID http://orcid.org/0000-0002-2813-7872
Kellie WatsonThe Roslin Institute, Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Midlothian, UK.
Albert Johannes BuitenhuisCenter for Quantitative Genetics and Genomics (QGG), Aarhus University, Aarhus, Denmark.ORCID http://orcid.org/0000-0002-4953-3081
Goutam SahanaCenter for Quantitative Genetics and Genomics (QGG), Aarhus University, Aarhus, Denmark.ORCID http://orcid.org/0000-0001-7608-7577
Mogens Sandø LundCenter for Quantitative Genetics and Genomics (QGG), Aarhus University, Aarhus, Denmark.
Wesley WarrenDepartment of Animal Sciences, Data Science and Informatics Institute, University of Missouri, Columbia, MO, USA.ORCID http://orcid.org/0000-0003-2255-2730
Laurent FrantzPalaeogenomics Group, Department of Veterinary Sciences, Ludwig Maximilian University, Munich, Germany.
Greger LarsonThe Palaeogenomics & Bio-Archaeology Research Network, School of Archaeology, University of Oxford, Oxford, UK.ORCID http://orcid.org/0000-0002-4092-0392
Susan J LamontDepartment of Animal Science, Iowa State University, Ames, IA, USA.
Wei SiInstitute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China.
Xin ZhaoDepartment of Animal Science, McGill University, Montreal, Quebec, Canada.ORCID http://orcid.org/0000-0002-1078-7332
Bingjie LiScotland's Rural College (SRUC), Roslin Institute Building, Midlothian, UK.ORCID http://orcid.org/0000-0002-8528-1889
Haihan ZhangCollege of Animal Science and Technology, Hunan Agricultural University, Changsha, China.
Chenglong LuoState Key Laboratory of Swine and Poultry Breeding Industry, Guangdong Key Laboratory of Animal Breeding and Nutrition, Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou, China.
Dingming ShuState Key Laboratory of Swine and Poultry Breeding Industry, Guangdong Key Laboratory of Animal Breeding and Nutrition, Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou, China.
Hao QuState Key Laboratory of Swine and Poultry Breeding Industry, Guangdong Key Laboratory of Animal Breeding and Nutrition, Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou, China.
Wei LuoState Key Laboratory of Swine and Poultry Breeding Industry, Guangdong Key Laboratory of Animal Breeding and Nutrition, Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou, China.
Zhenhui LiState Key Laboratory of Swine and Poultry Breeding Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, China.
Qinghua NieState Key Laboratory of Swine and Poultry Breeding Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, China.
Xiquan ZhangState Key Laboratory of Swine and Poultry Breeding Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, China.
Ruidong XiangAgriculture Victoria, Agribio, Centre for AgriBiosciences, Bundoora, Victoria, Australia.ORCID http://orcid.org/0000-0002-1584-7605
Shuli LiuSchool of Life Sciences, Westlake University, Hangzhou, China.
Zhe ZhangState Key Laboratory of Swine and Poultry Breeding Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, China.ORCID http://orcid.org/0000-0001-7338-7718
Zhang ZhangBeijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, China.ORCID http://orcid.org/0000-0001-6603-5060
George E LiuAnimal Genomics and Improvement Laboratory, Henry A. Wallace Beltsville Agricultural Research Center, Agricultural Research Service, USDA, Beltsville, MD, USA.ORCID http://orcid.org/0000-0003-0192-6705
Hans ChengAvian Disease and Oncology Laboratory, USDA, ARS, USNPRC, East Lansing, MI, USA.
Ning YangState Key Laboratory of Animal Biotech Breeding and Frontier Science Center of Molecular Design Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China. nyang@cau.edu.cn.ORCID http://orcid.org/0000-0001-5772-3320
Xiaoxiang HuState Key Laboratory of Animal Biotech Breeding, College of Biological Sciences, China Agricultural University, Beijing, China. huxx@cau.edu.cn.ORCID http://orcid.org/0000-0001-7045-0283
Huaijun ZhouDepartment of Animal Science, University of California-Davis, Davis, CA, USA. hzhou@ucdavis.edu.ORCID http://orcid.org/0000-0001-6023-9521
Lingzhao FangCenter for Quantitative Genetics and Genomics (QGG), Aarhus University, Aarhus, Denmark. lingzhao.fang@qgg.au.dk.ORCID http://orcid.org/0000-0003-1103-3679
Funding
National Natural Science Foundation of China (National Science Foundation of China) 31961133003United States Department of Agriculture | Agricultural Research Service (USDA Agricultural Research Service) 2022-67015-36215
Abstract
The chicken is a valuable model for understanding fundamental biology and vertebrate evolution and is a major global source of nutrient-dense and lean protein. Despite being the first non-mammalian amniote to have its genome sequenced, a systematic characterization of functional variation on the chicken genome remains lacking. Here, we integrated bulk RNA sequencing (RNA-seq) data from 7,015 samples, single-cell RNA-seq data from 127,598 cells and 2,869 whole-genome sequences to present a pilot atlas of regulatory variants across 28 chicken tissues. This atlas reveals millions of regulatory effects on primary expression (protein-coding genes, long non-coding RNA and exons) and post-transcriptional modifications (alternative splicing and 3'-untranslated region alternative polyadenylation). We highlighted distinct molecular mechanisms underlying these regulatory variants, their context-dependent behavior and their utility in interpreting genome-wide associations for 39 chicken complex traits. Finally, our comparative analyses of gene regulation between chickens and mammals demonstrate how this resource can facilitate cross-species gene mapping of complex traits.
Indexed as
ChickensGene Expression RegulationAlternative SplicingAnimalsExonsGenomeGenome-Wide Association StudyOrgan SpecificityRNA, Long NoncodingSequence Analysis, RNARNA, Long Noncoding
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