A compendium of genetic regulatory effects across pig tissues.

Autor:	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., 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., 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., 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., 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., 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., 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., Cai Z; Center for Quantitative Genetics and Genomics, Aarhus University, Aarhus, Denmark., Zhao B; College of Animal Science and Technology, China Agricultural University, Beijing, China., Li X; Guangdong Provincial Key Laboratory of Waterfowl Healthy Breeding, College of Animal Science and Technology, Zhongkai University of Agriculture and Engineering, Guangzhou, China., 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., 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., Pan Z; Department of Animal Science, University of California, Davis, Davis, CA, USA.; Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China., Yang W; College of Animal Science and Technology, China Agricultural University, Beijing, China.; Department of Animal Science, University of California, Davis, Davis, CA, USA., Yu X; MRC Human Genetics Unit at the Institute of Genetics and Cancer, The University of Edinburgh, Edinburgh, UK., Guan D; Department of Animal Science, University of California, Davis, Davis, CA, USA., Hou Y; Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, China., Keel BN; ARS, USDA, U.S. Meat Animal Research Center, Clay Center, NE, USA., Rohrer GA; ARS, USDA, U.S. Meat Animal Research Center, Clay Center, NE, USA., Lindholm-Perry AK; ARS, USDA, U.S. Meat Animal Research Center, Clay Center, NE, USA., Oliver WT; ARS, USDA, U.S. Meat Animal Research Center, Clay Center, NE, USA., Ballester M; Animal Breeding and Genetics Programme, Institut de Recerca i Tecnologia Agroalimentàries (IRTA), Torre Marimon, Caldes de Montbui, Spain., Crespo-Piazuelo D; Animal Breeding and Genetics Programme, Institut de Recerca i Tecnologia Agroalimentàries (IRTA), Torre Marimon, Caldes de Montbui, Spain., Quintanilla R; Animal Breeding and Genetics Programme, Institut de Recerca i Tecnologia Agroalimentàries (IRTA), Torre Marimon, Caldes de Montbui, Spain., Canela-Xandri O; MRC Human Genetics Unit at the Institute of Genetics and Cancer, The University of Edinburgh, Edinburgh, UK., Rawlik K; Baillie Gifford Pandemic Science Hub, University of Edinburgh, Edinburgh, UK., Xia C; Lothian Birth Cohort studies, University of Edinburgh, Edinburgh, UK.; Department of Psychology, University of Edinburgh, Edinburgh, UK., 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., 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., 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., 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., Li H; Center for Quantitative Genetics and Genomics, Aarhus University, Aarhus, Denmark., Zhang H; Center for Quantitative Genetics and Genomics, Aarhus University, Aarhus, Denmark., Liao W; MRC Human Genetics Unit at the Institute of Genetics and Cancer, The University of Edinburgh, Edinburgh, UK., Chen T; MRC Human Genetics Unit at the Institute of Genetics and Cancer, The University of Edinburgh, Edinburgh, UK., Karlskov-Mortensen P; Animal Genetics, Bioinformatics and Breeding, Department of Veterinary and Animal Sciences, University of Copenhagen, Copenhagen, Denmark., Fredholm M; Animal Genetics, Bioinformatics and Breeding, Department of Veterinary and Animal Sciences, University of Copenhagen, Copenhagen, Denmark., 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., 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., Giuffra E; Paris-Saclay University, INRAE, AgroParisTech, GABI, Jouy-en-Josas, France., 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., 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., 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., 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., 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., Li J; Department of Animal Science, University of California, Davis, Davis, CA, USA., Cheng H; Department of Animal Science, University of California, Davis, Davis, CA, USA., Wang S; State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China., Su G; Center for Quantitative Genetics and Genomics, Aarhus University, Aarhus, Denmark., Sahana G; Center for Quantitative Genetics and Genomics, Aarhus University, Aarhus, Denmark., Lund MS; Center for Quantitative Genetics and Genomics, Aarhus University, Aarhus, Denmark., Dekkers JCM; Department of Animal Science, Iowa State University, Ames, IA, USA., Kramer L; Department of Animal Science, Iowa State University, Ames, IA, USA., Tuggle CK; Department of Animal Science, Iowa State University, Ames, IA, USA., Corbett R; Department of Animal Science, Iowa State University, Ames, IA, USA., Groenen MAM; Animal Breeding and Genomics, Wageningen University and Research, Wageningen, The Netherlands., Madsen O; Animal Breeding and Genomics, Wageningen University and Research, Wageningen, The Netherlands., 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., Rocha D; Paris-Saclay University, INRAE, AgroParisTech, GABI, Jouy-en-Josas, France., Charles M; Paris-Saclay University, INRAE, AgroParisTech, GABI, SIGENAE, Jouy-en-Josas, France., 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., Pausch H; Animal Genomics, ETH Zurich, Universitaetstrasse 2, Zurich, Switzerland., Hu X; State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China., 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., 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., Lin L; Department of Biomedicine, Aarhus University, Aarhus, Denmark.; Steno Diabetes Center Aarhus, Aarhus University Hospital, Aarhus, Denmark., Zhou Z; State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China., Zhang Z; Department of Animal Science, College of Animal Sciences, Zhejiang University, Hangzhou, China., Chen Z; Department of Animal Science, College of Animal Sciences, Zhejiang University, Hangzhou, China., 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., Xiang R; Faculty of Veterinary and Agricultural Science, The University of Melbourne, Parkville, Victoria, Australia.; Agriculture Victoria, AgriBio, Centre for AgriBiosciences, Bundoora, Victoria, Australia., 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., Li P; Institute of Swine Science, Nanjing Agricultural University, Nanjing, China., Huang R; Institute of Swine Science, Nanjing Agricultural University, Nanjing, China., Tang G; Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China., Li M; Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China., Zhao Y; College of Animal Science and Technology, Guangxi University, Nanning, China., 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., 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., Jiang J; Department of Animal Science, North Carolina State University, Raleigh, NC, USA., Zhao F; Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China., 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., Liu X; State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China., Chen Y; State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China., 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., 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., Zhao P; Hainan Institute, Zhejiang University, Yongyou Industry Park, Yazhou Bay Sci-Tech City, Sanya, China., 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., Zhou H; Department of Animal Science, University of California, Davis, Davis, CA, USA., Wang Q; Department of Animal Science, College of Animal Sciences, Zhejiang University, Hangzhou, China., Pan Y; Department of Animal Science, College of Animal Sciences, Zhejiang University, Hangzhou, China., Ding X; College of Animal Science and Technology, China Agricultural University, Beijing, China., Ma L; Department of Animal and Avian Sciences, University of Maryland, College Park, MD, USA., 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., 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., Zhang Q; College of Animal Science and Technology, Shandong Agricultural University, Tai'an, China., Li B; Scotland's Rural College (SRUC), Roslin Institute Building, Midlothian, UK., 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., 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., 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., 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., 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.
Jazyk:	angličtina
Zdroj:	Nature genetics [Nat Genet] 2024 Jan; Vol. 56 (1), pp. 112-123. Date of Electronic Publication: 2024 Jan 04.
DOI:	10.1038/s41588-023-01585-7
Abstrakt:	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. (© 2024. The Author(s).)
Databáze:	MEDLINE
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