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A compendium of genetic regulatory effects across pig tissues.
Teng, Jinyan; Gao, Yahui; Yin, Hongwei; Bai, Zhonghao; Liu, Shuli; Zeng, Haonan; Bai, Lijing; Cai, Zexi; Zhao, Bingru; Li, Xiujin; Xu, Zhiting; Lin, Qing; Pan, Zhangyuan; Yang, Wenjing; Yu, Xiaoshan; Guan, Dailu; Hou, Yali; Keel, Brittney N; Rohrer, Gary A; Lindholm-Perry, Amanda K; Oliver, William T; Ballester, Maria; Crespo-Piazuelo, Daniel; Quintanilla, Raquel; Canela-Xandri, Oriol; Rawlik, Konrad; Xia, Charley; Yao, Yuelin; Zhao, Qianyi; Yao, Wenye; Yang, Liu; Li, Houcheng; Zhang, Huicong; Liao, Wang; Chen, Tianshuo; Karlskov-Mortensen, Peter; Fredholm, Merete; Amills, Marcel; Clop, Alex; Giuffra, Elisabetta; Wu, Jun; Cai, Xiaodian; Diao, Shuqi; Pan, Xiangchun; Wei, Chen; Li, Jinghui; Cheng, Hao; Wang, Sheng; Su, Guosheng; Sahana, Goutam.
Affiliation
  • 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.
  • Yin H; 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.
  • Bai Z; Department of Animal and Avian Sciences, University of Maryland, College Park, MD, USA.
  • Liu S; 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.
  • Zeng H; Center for Quantitative Genetics and Genomics, Aarhus University, Aarhus, Denmark.
  • Bai L; 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.
  • Cai Z; School of Life Sciences, Westlake University, Hangzhou, China.
  • Zhao B; 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.
  • Xu 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.
  • Lin Q; Center for Quantitative Genetics and Genomics, Aarhus University, Aarhus, Denmark.
  • Pan Z; College of Animal Science and Technology, China Agricultural University, Beijing, China.
  • Yang W; Guangdong Provincial Key Laboratory of Waterfowl Healthy Breeding, College of Animal Science and Technology, Zhongkai University of Agriculture and Engineering, Guangzhou, China.
  • Yu 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.
  • Guan D; 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.
  • Hou Y; Department of Animal Science, University of California, Davis, Davis, CA, USA.
  • Keel BN; Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China.
  • Rohrer GA; College of Animal Science and Technology, China Agricultural University, Beijing, China.
  • Lindholm-Perry AK; Department of Animal Science, University of California, Davis, Davis, CA, USA.
  • Oliver WT; MRC Human Genetics Unit at the Institute of Genetics and Cancer, The University of Edinburgh, Edinburgh, UK.
  • Ballester M; Department of Animal Science, University of California, Davis, Davis, CA, USA.
  • Crespo-Piazuelo D; Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, China.
  • Quintanilla R; ARS, USDA, U.S. Meat Animal Research Center, Clay Center, NE, USA.
  • Canela-Xandri O; ARS, USDA, U.S. Meat Animal Research Center, Clay Center, NE, USA.
  • Rawlik K; ARS, USDA, U.S. Meat Animal Research Center, Clay Center, NE, USA.
  • Xia C; ARS, USDA, U.S. Meat Animal Research Center, Clay Center, NE, USA.
  • Yao Y; Animal Breeding and Genetics Programme, Institut de Recerca i Tecnologia Agroalimentàries (IRTA), Torre Marimon, Caldes de Montbui, Spain.
  • Zhao Q; Animal Breeding and Genetics Programme, Institut de Recerca i Tecnologia Agroalimentàries (IRTA), Torre Marimon, Caldes de Montbui, Spain.
  • Yao W; Animal Breeding and Genetics Programme, Institut de Recerca i Tecnologia Agroalimentàries (IRTA), Torre Marimon, Caldes de Montbui, Spain.
  • Yang L; MRC Human Genetics Unit at the Institute of Genetics and Cancer, The University of Edinburgh, Edinburgh, UK.
  • Li H; Baillie Gifford Pandemic Science Hub, University of Edinburgh, Edinburgh, UK.
  • Zhang H; Lothian Birth Cohort studies, University of Edinburgh, Edinburgh, UK.
  • Liao W; Department of Psychology, 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; School of Informatics, The University of Edinburgh, Edinburgh, UK.
  • Fredholm M; 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.
  • Amills M; 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.
  • Clop A; Animal Breeding and Genomics, Wageningen University and Research, Wageningen, The Netherlands.
  • Giuffra E; 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.
  • Wu J; Center for Quantitative Genetics and Genomics, Aarhus University, Aarhus, Denmark.
  • Cai X; Center for Quantitative Genetics and Genomics, Aarhus University, Aarhus, Denmark.
  • Diao S; MRC Human Genetics Unit at the Institute of Genetics and Cancer, The University of Edinburgh, Edinburgh, UK.
  • Pan X; MRC Human Genetics Unit at the Institute of Genetics and Cancer, The University of Edinburgh, Edinburgh, UK.
  • Wei C; Animal Genetics, Bioinformatics and Breeding, Department of Veterinary and Animal Sciences, University of Copenhagen, Copenhagen, Denmark.
  • Li J; Animal Genetics, Bioinformatics and Breeding, Department of Veterinary and Animal Sciences, University of Copenhagen, Copenhagen, Denmark.
  • Cheng H; Department of Animal Genetics, Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus de la Universitat Autònoma de Barcelona, Bellaterra, Spain.
  • Wang S; Departament de Ciència Animal i dels Aliments, Universitat Autònoma de Barcelona, Bellaterra, Spain.
  • Su G; Department of Animal Genetics, Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus de la Universitat Autònoma de Barcelona, Bellaterra, Spain.
  • Sahana G; Consejo Superior de Investigaciones Científicas, Barcelona, Spain.
Nat Genet ; 56(1): 112-123, 2024 Jan.
Article in En | MEDLINE | ID: mdl-38177344
ABSTRACT
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.
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Full text: 1 Collection: 01-internacional Database: MEDLINE Main subject: Gene Expression Regulation / Gene Expression Profiling Limits: Animals / Humans Language: En Journal: Nat Genet Journal subject: GENETICA MEDICA Year: 2024 Document type: Article Affiliation country:
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Full text: 1 Collection: 01-internacional Database: MEDLINE Main subject: Gene Expression Regulation / Gene Expression Profiling Limits: Animals / Humans Language: En Journal: Nat Genet Journal subject: GENETICA MEDICA Year: 2024 Document type: Article Affiliation country: