A compendium of genetic regulatory effects across pig tissues.

Journal

Nature genetics
ISSN: 1546-1718
Titre abrégé: Nat Genet
Pays: United States
ID NLM: 9216904

Informations de publication

Date de publication:
04 Jan 2024
Historique:
received: 23 11 2022
accepted: 13 10 2023
medline: 5 1 2024
pubmed: 5 1 2024
entrez: 4 1 2024
Statut: aheadofprint

Résumé

The Farm Animal Genotype-Tissue Expression (FarmGTEx) project has been established to develop a public resource of genetic regulatory variants in livestock, which is essential for linking genetic polymorphisms to variation in phenotypes, helping fundamental biological discovery and exploitation in animal breeding and human biomedicine. Here we show results from the pilot phase of PigGTEx by processing 5,457 RNA-sequencing and 1,602 whole-genome sequencing samples passing quality control from pigs. We build a pig genotype imputation panel and associate millions of genetic variants with five types of transcriptomic phenotypes in 34 tissues. We evaluate tissue specificity of regulatory effects and elucidate molecular mechanisms of their action using multi-omics data. Leveraging this resource, we decipher regulatory mechanisms underlying 207 pig complex phenotypes and demonstrate the similarity of pigs to humans in gene expression and the genetic regulation behind complex phenotypes, supporting the importance of pigs as a human biomedical model.

Identifiants

DOI: 10.1038/s41588-023-01585-7 PMID: 38177344
pubmed: 38177344
doi: 10.1038/s41588-023-01585-7
pii: 10.1038/s41588-023-01585-7
doi:

Types de publication

Journal Article

Langues

eng

Sous-ensembles de citation

IM

Subventions

Organisme : RCUK | Medical Research Council (MRC)
ID : MR/R025851/1
Organisme : RCUK | Medical Research Council (MRC)
ID : MR/P015514/1
Organisme : RCUK | Biotechnology and Biological Sciences Research Council (BBSRC)
ID : BBS/E/D/10002070
Organisme : RCUK | Biotechnology and Biological Sciences Research Council (BBSRC)
ID : BBS/E/D/30002275
Organisme : United States Department of Agriculture | Agricultural Research Service (USDA Agricultural Research Service)
ID : 2019-67015-29321
Organisme : United States Department of Agriculture | Agricultural Research Service (USDA Agricultural Research Service)
ID : 2021-67015-33409
Organisme : National Natural Science Foundation of China (National Science Foundation of China)
ID : 32022078

Informations de copyright

© 2024. The Author(s).

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Auteurs

Jinyan Teng (J)

State Key Laboratory of Swine and Poultry Breeding Industry, National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University (SCAU), Guangzhou, China.
ORCID: 0000-0002-3046-1452

Yahui Gao (Y)

State Key Laboratory of Swine and Poultry Breeding Industry, National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University (SCAU), Guangzhou, China.
Animal Genomics and Improvement Laboratory, Henry A. Wallace Beltsville Agricultural Research Center, Agricultural Research Service (ARS), U.S. Department of Agriculture (USDA), Beltsville, MD, USA.
Department of Animal and Avian Sciences, University of Maryland, College Park, MD, USA.

Hongwei Yin (H)

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.
ORCID: 0000-0002-9373-5166

Zhonghao Bai (Z)

Center for Quantitative Genetics and Genomics, Aarhus University, Aarhus, Denmark.
MRC Human Genetics Unit at the Institute of Genetics and Cancer, The University of Edinburgh, Edinburgh, UK.

Shuli Liu (S)

Animal Genomics and Improvement Laboratory, Henry A. Wallace Beltsville Agricultural Research Center, Agricultural Research Service (ARS), U.S. Department of Agriculture (USDA), Beltsville, MD, USA.
School of Life Sciences, Westlake University, Hangzhou, China.

Haonan Zeng (H)

State Key Laboratory of Swine and Poultry Breeding Industry, National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University (SCAU), Guangzhou, China.

Lijing Bai (L)

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.

Zexi Cai (Z)

Center for Quantitative Genetics and Genomics, Aarhus University, Aarhus, Denmark.
ORCID: 0000-0002-9579-3415

Bingru Zhao (B)

College of Animal Science and Technology, China Agricultural University, Beijing, China.

Xiujin Li (X)

Guangdong Provincial Key Laboratory of Waterfowl Healthy Breeding, College of Animal Science and Technology, Zhongkai University of Agriculture and Engineering, Guangzhou, China.

Zhiting Xu (Z)

State Key Laboratory of Swine and Poultry Breeding Industry, National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University (SCAU), Guangzhou, China.

Qing Lin (Q)

State Key Laboratory of Swine and Poultry Breeding Industry, National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University (SCAU), Guangzhou, China.

Zhangyuan Pan (Z)

Department of Animal Science, University of California, Davis, Davis, CA, USA.
Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China.

Wenjing Yang (W)

College of Animal Science and Technology, China Agricultural University, Beijing, China.
Department of Animal Science, University of California, Davis, Davis, CA, USA.

Xiaoshan Yu (X)

MRC Human Genetics Unit at the Institute of Genetics and Cancer, The University of Edinburgh, Edinburgh, UK.

Dailu Guan (D)

Department of Animal Science, University of California, Davis, Davis, CA, USA.
ORCID: 0000-0001-8800-3158

Yali Hou (Y)

Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, China.
ORCID: 0000-0002-7421-2431

Brittney N Keel (BN)

ARS, USDA, U.S. Meat Animal Research Center, Clay Center, NE, USA.

Gary A Rohrer (GA)

ARS, USDA, U.S. Meat Animal Research Center, Clay Center, NE, USA.
ORCID: 0000-0002-8252-9308

Amanda K Lindholm-Perry (AK)

ARS, USDA, U.S. Meat Animal Research Center, Clay Center, NE, USA.

William T Oliver (WT)

ARS, USDA, U.S. Meat Animal Research Center, Clay Center, NE, USA.

Maria Ballester (M)

Animal Breeding and Genetics Programme, Institut de Recerca i Tecnologia Agroalimentàries (IRTA), Torre Marimon, Caldes de Montbui, Spain.
ORCID: 0000-0002-5413-4640

Daniel Crespo-Piazuelo (D)

Animal Breeding and Genetics Programme, Institut de Recerca i Tecnologia Agroalimentàries (IRTA), Torre Marimon, Caldes de Montbui, Spain.
ORCID: 0000-0001-7896-2507

Raquel Quintanilla (R)

Animal Breeding and Genetics Programme, Institut de Recerca i Tecnologia Agroalimentàries (IRTA), Torre Marimon, Caldes de Montbui, Spain.

Oriol Canela-Xandri (O)

MRC Human Genetics Unit at the Institute of Genetics and Cancer, The University of Edinburgh, Edinburgh, UK.

Konrad Rawlik (K)

Baillie Gifford Pandemic Science Hub, University of Edinburgh, Edinburgh, UK.
ORCID: 0000-0002-0010-370X

Charley Xia (C)

Lothian Birth Cohort studies, University of Edinburgh, Edinburgh, UK.
Department of Psychology, University of Edinburgh, Edinburgh, UK.

Yuelin Yao (Y)

MRC Human Genetics Unit at the Institute of Genetics and Cancer, The University of Edinburgh, Edinburgh, UK.
School of Informatics, The University of Edinburgh, Edinburgh, UK.
ORCID: 0000-0001-9868-2801

Qianyi Zhao (Q)

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.

Wenye Yao (W)

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.
Animal Breeding and Genomics, Wageningen University and Research, Wageningen, The Netherlands.

Liu Yang (L)

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.

Houcheng Li (H)

Center for Quantitative Genetics and Genomics, Aarhus University, Aarhus, Denmark.

Huicong Zhang (H)

Center for Quantitative Genetics and Genomics, Aarhus University, Aarhus, Denmark.

Wang Liao (W)

MRC Human Genetics Unit at the Institute of Genetics and Cancer, The University of Edinburgh, Edinburgh, UK.

Tianshuo Chen (T)

MRC Human Genetics Unit at the Institute of Genetics and Cancer, The University of Edinburgh, Edinburgh, UK.

Peter Karlskov-Mortensen (P)

Animal Genetics, Bioinformatics and Breeding, Department of Veterinary and Animal Sciences, University of Copenhagen, Copenhagen, Denmark.
ORCID: 0000-0002-2491-2763

Merete Fredholm (M)

Animal Genetics, Bioinformatics and Breeding, Department of Veterinary and Animal Sciences, University of Copenhagen, Copenhagen, Denmark.

Marcel Amills (M)

Department of Animal Genetics, Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus de la Universitat Autònoma de Barcelona, Bellaterra, Spain.
Departament de Ciència Animal i dels Aliments, Universitat Autònoma de Barcelona, Bellaterra, Spain.
ORCID: 0000-0002-8999-0770

Alex Clop (A)

Department of Animal Genetics, Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus de la Universitat Autònoma de Barcelona, Bellaterra, Spain.
Consejo Superior de Investigaciones Científicas, Barcelona, Spain.
ORCID: 0000-0001-9238-2728

Elisabetta Giuffra (E)

Paris-Saclay University, INRAE, AgroParisTech, GABI, Jouy-en-Josas, France.
ORCID: 0000-0001-9568-2056

Jun Wu (J)

State Key Laboratory of Swine and Poultry Breeding Industry, National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University (SCAU), Guangzhou, China.

Xiaodian Cai (X)

State Key Laboratory of Swine and Poultry Breeding Industry, National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University (SCAU), Guangzhou, China.

Shuqi Diao (S)

State Key Laboratory of Swine and Poultry Breeding Industry, National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University (SCAU), Guangzhou, China.

Xiangchun Pan (X)

State Key Laboratory of Swine and Poultry Breeding Industry, National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University (SCAU), Guangzhou, China.

Chen Wei (C)

State Key Laboratory of Swine and Poultry Breeding Industry, National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University (SCAU), Guangzhou, China.

Jinghui Li (J)

Department of Animal Science, University of California, Davis, Davis, CA, USA.

Hao Cheng (H)

Department of Animal Science, University of California, Davis, Davis, CA, USA.

Sheng Wang (S)

State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.

Guosheng Su (G)

Center for Quantitative Genetics and Genomics, Aarhus University, Aarhus, Denmark.

Goutam Sahana (G)

Center for Quantitative Genetics and Genomics, Aarhus University, Aarhus, Denmark.
ORCID: 0000-0001-7608-7577

Mogens Sandø Lund (MS)

Center for Quantitative Genetics and Genomics, Aarhus University, Aarhus, Denmark.

Jack C M Dekkers (JCM)

Department of Animal Science, Iowa State University, Ames, IA, USA.

Luke Kramer (L)

Department of Animal Science, Iowa State University, Ames, IA, USA.

Christopher K Tuggle (CK)

Department of Animal Science, Iowa State University, Ames, IA, USA.
ORCID: 0000-0002-4229-5316

Ryan Corbett (R)

Department of Animal Science, Iowa State University, Ames, IA, USA.

Martien A M Groenen (MAM)

Animal Breeding and Genomics, Wageningen University and Research, Wageningen, The Netherlands.
ORCID: 0000-0003-0484-4545

Ole Madsen (O)

Animal Breeding and Genomics, Wageningen University and Research, Wageningen, The Netherlands.

Marta Gòdia (M)

Animal Breeding and Genomics, Wageningen University and Research, Wageningen, The Netherlands.
Department of Animal Genetics, Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus de la Universitat Autònoma de Barcelona, Bellaterra, Spain.

Dominique Rocha (D)

Paris-Saclay University, INRAE, AgroParisTech, GABI, Jouy-en-Josas, France.

Mathieu Charles (M)

Paris-Saclay University, INRAE, AgroParisTech, GABI, SIGENAE, Jouy-en-Josas, France.
ORCID: 0000-0001-6491-1928

Cong-Jun Li (CJ)

Animal Genomics and Improvement Laboratory, Henry A. Wallace Beltsville Agricultural Research Center, Agricultural Research Service (ARS), U.S. Department of Agriculture (USDA), Beltsville, MD, USA.
ORCID: 0000-0003-1389-9820

Hubert Pausch (H)

Animal Genomics, ETH Zurich, Universitaetstrasse 2, Zurich, Switzerland.
ORCID: 0000-0002-0501-6760

Xiaoxiang Hu (X)

State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China.
ORCID: 0000-0001-7045-0283

Laurent Frantz (L)

Palaeogenomics Group, Department of Veterinary Sciences, Ludwig Maximilian University, Munich, Germany.
School of Biological and Behavioural Sciences, Queen Mary University of London, London, UK.

Yonglun Luo (Y)

Department of Biomedicine, Aarhus University, Aarhus, Denmark.
Steno Diabetes Center Aarhus, Aarhus University Hospital, Aarhus, Denmark.
Lars Bolund Institute of Regenerative Medicine, Qingdao-Europe Advanced Institute for Life Sciences, BGI-Research, Qingdao, China.
ORCID: 0000-0002-0007-7759

Lin Lin (L)

Department of Biomedicine, Aarhus University, Aarhus, Denmark.
Steno Diabetes Center Aarhus, Aarhus University Hospital, Aarhus, Denmark.
ORCID: 0000-0002-7546-4948

Zhongyin Zhou (Z)

State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.

Zhe Zhang (Z)

Department of Animal Science, College of Animal Sciences, Zhejiang University, Hangzhou, China.

Zitao Chen (Z)

Department of Animal Science, College of Animal Sciences, Zhejiang University, Hangzhou, China.

Leilei Cui (L)

School of Life Sciences, Nanchang University, Nanchang, China.
Human Aging Research Institute and School of Life Science, Nanchang University, and Jiangxi Key Laboratory of Human Aging, Jiangxi, China.
UCL Genetics Institute, University College London, London, UK.

Ruidong Xiang (R)

Faculty of Veterinary and Agricultural Science, The University of Melbourne, Parkville, Victoria, Australia.
Agriculture Victoria, AgriBio, Centre for AgriBiosciences, Bundoora, Victoria, Australia.

Xia Shen (X)

State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China.
Center for Intelligent Medicine Research, Greater Bay Area Institute of Precision Medicine, Fudan University, Guangzhou, China.
Centre for Global Health Research, Usher Institute, University of Edinburgh, Edinburgh, UK.
ORCID: 0000-0003-4390-1979

Pinghua Li (P)

Institute of Swine Science, Nanjing Agricultural University, Nanjing, China.

Ruihua Huang (R)

Institute of Swine Science, Nanjing Agricultural University, Nanjing, China.

Guoqing Tang (G)

Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China.

Mingzhou Li (M)

Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China.
ORCID: 0000-0001-8681-7684

Yunxiang Zhao (Y)

College of Animal Science and Technology, Guangxi University, Nanning, China.

Guoqiang Yi (G)

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.
ORCID: 0000-0001-8248-9126

Zhonglin Tang (Z)

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.
ORCID: 0000-0002-4538-4349

Jicai Jiang (J)

Department of Animal Science, North Carolina State University, Raleigh, NC, USA.

Fuping Zhao (F)

Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China.

Xiaolong Yuan (X)

State Key Laboratory of Swine and Poultry Breeding Industry, National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University (SCAU), Guangzhou, China.

Xiaohong Liu (X)

State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China.

Yaosheng Chen (Y)

State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China.

Xuewen Xu (X)

Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education and College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China.

Shuhong Zhao (S)

Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education and College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China.
ORCID: 0000-0002-3997-2320

Pengju Zhao (P)

Hainan Institute, Zhejiang University, Yongyou Industry Park, Yazhou Bay Sci-Tech City, Sanya, China.

Chris Haley (C)

MRC Human Genetics Unit at the Institute of Genetics and Cancer, The University of Edinburgh, Edinburgh, UK.
The Roslin Institute, Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Midlothian, UK.

Huaijun Zhou (H)

Department of Animal Science, University of California, Davis, Davis, CA, USA.
ORCID: 0000-0001-6023-9521

Qishan Wang (Q)

Department of Animal Science, College of Animal Sciences, Zhejiang University, Hangzhou, China.
ORCID: 0000-0002-6475-0009

Yuchun Pan (Y)

Department of Animal Science, College of Animal Sciences, Zhejiang University, Hangzhou, China.

Xiangdong Ding (X)

College of Animal Science and Technology, China Agricultural University, Beijing, China.

Li Ma (L)

Department of Animal and Avian Sciences, University of Maryland, College Park, MD, USA.
ORCID: 0000-0003-1038-1081

Jiaqi Li (J)

State Key Laboratory of Swine and Poultry Breeding Industry, National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University (SCAU), Guangzhou, China.

Pau Navarro (P)

MRC Human Genetics Unit at the Institute of Genetics and Cancer, The University of Edinburgh, Edinburgh, UK.
The Roslin Institute, Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Midlothian, UK.
ORCID: 0000-0001-5576-8584

Qin Zhang (Q)

College of Animal Science and Technology, Shandong Agricultural University, Tai'an, China.

Bingjie Li (B)

Scotland's Rural College (SRUC), Roslin Institute Building, Midlothian, UK.
ORCID: 0000-0002-8528-1889

Albert Tenesa (A)

MRC Human Genetics Unit at the Institute of Genetics and Cancer, The University of Edinburgh, Edinburgh, UK. albert.tenesa@ed.ac.uk.
The Roslin Institute, Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Midlothian, UK. albert.tenesa@ed.ac.uk.
ORCID: 0000-0003-4884-4475

Kui Li (K)

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. likui@caas.cn.
ORCID: 0000-0002-5686-3898

George E Liu (GE)

Animal Genomics and Improvement Laboratory, Henry A. Wallace Beltsville Agricultural Research Center, Agricultural Research Service (ARS), U.S. Department of Agriculture (USDA), Beltsville, MD, USA. george.liu@usda.gov.
ORCID: 0000-0003-0192-6705

Zhe Zhang (Z)

State Key Laboratory of Swine and Poultry Breeding Industry, National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University (SCAU), Guangzhou, China. zhezhang@scau.edu.cn.

Lingzhao Fang (L)

Center for Quantitative Genetics and Genomics, Aarhus University, Aarhus, Denmark. lingzhao.fang@qgg.au.dk.
MRC Human Genetics Unit at the Institute of Genetics and Cancer, The University of Edinburgh, Edinburgh, UK. lingzhao.fang@qgg.au.dk.
ORCID: 0000-0003-1103-3679

Classifications MeSH