A compendium of genetic regulatory effects across pig tissues
Teng, Jinyan (South China Agricultural University. National Engineering Research Center for Breeding Swine Industry)
Gao, Yahui (University of Maryland. Department of Animal and Avian Sciences)
Yin, Hongwei (Chinese Academy of Agricultural Sciences. Agricultural Genomics Institute at Shenzhen)
Bai, Zhonghao (The University of Edinburgh)
Liu, Shuli (Westlake University)
Zeng, Haonan (South China Agricultural University. National Engineering Research Center for Breeding Swine Industry)
Bai, Lijing (Chinese Academy of Agricultural Sciences. Agricultural Genomics Institute at Shenzhen)
Cai, Zexi (Aarhus University. Center for Quantitative Genetics and Genomics)
Zhao, Bingru (China Agricultural University)
Li, Xiujin (Zhongkai University of Agriculture and Engineering)
Xu, Zhiting (South China Agricultural University. National Engineering Research Center for Breeding Swine Industry)
Lin, Qing (South China Agricultural University. National Engineering Research Center for Breeding Swine Industry)
Pan, Zhangyuan (Chinese Academy of Agricultural Sciences. Institute of Animal Science)
Yang, Wenjing (University of California, Davis. Department of Animal Science)
Yu, Xiaoshan (The University of Edinburgh. MRC Human Genetics Unit at the Institute of Genetics and Cancer)
Guan, Dailu (University of California. Department of Animal Science)
Hou, Yali (Chinese Academy of Sciences and China National Center for Bioinformation)
Keel, Brittney N. (U.S. Meat Animal Research Center)
Rohrer, Gary A. (U.S. Meat Animal Research Center)
Lindholm-Perry, Amanda K. (U.S. Meat Animal Research Center)
Oliver, William T. (U.S. Meat Animal Research Center)
Ballester Devis, Maria (Unitat mixta d'investigació IRTA-UAB en Sanitat Animal. Centre de Recerca en Sanitat Animal)
Crespo-Piazuelo, Daniel (Unitat mixta d'investigació IRTA-UAB en Sanitat Animal. Centre de Recerca en Sanitat Animal)
Quintanilla, Raquel (Unitat mixta d'investigació IRTA-UAB en Sanitat Animal. Centre de Recerca en Sanitat Animal)
Canela-Xandri, Oriol (University of Edinburgh)
Rawlik, Konrad (University of Edinburgh. Baillie Gifford Pandemic Science Hub)
Xia, Charley (University of Edinburgh. Department of Psychology)
Yao, Yuelin (University of Edinburgh)
Zhao, Qianyi (Chinese Academy of Agricultural Sciences. Agricultural Genomics Institute at Shenzhen)
Yao, Wenye (Wageningen University and Research)
Yang, Liu (Chinese Academy of Agricultural Sciences. Agricultural Genomics Institute at Shenzhen)
Li, Houcheng (Aarhus University. Center for Quantitative Genetics and Genomics)
Zhang, Huicong (Aarhus University. Center for Quantitative Genetics and Genomics)
Liao, Wang (The University of Edinburgh. Human Genetics Unit at the Institute of Genetics and Cancer)
Chen, Tianshuo (The University of Edinburgh. Human Genetics Unit at the Institute of Genetics and Cancer)
Karlskov-Mortensen, Peter (University of Copenhagen. Department of Veterinary and Animal Sciences)
Fredholm, Merete (University of Copenhagen. Department of Veterinary and Animal Sciences)
Amills i Eras, Marcel (Universitat Autònoma de Barcelona. Departament de Ciència Animal i dels Aliments)
Clop, Alex (Consejo Superior de Investigaciones Científicas)
Giuffra, Elisabetta (Paris-Saclay University)
Wu, Jun (South China Agricultural University. National Engineering Research Center for Breeding Swine Industry)
Cai, Xiaodian (South China Agricultural University. National Engineering Research Center for Breeding Swine Industry)
Diao, Shuqi (South China Agricultural University. National Engineering Research Center for Breeding Swine Industry)
Pan, Xiangchun (South China Agricultural University. National Engineering Research Center for Breeding Swine Industry)
Wei, Chen (South China Agricultural University. National Engineering Research Center for Breeding Swine Industry)
Li, Jinghui (University of California, Davis. Department of Animal Science)
Cheng, Hao (University of California, Davis. Department of Animal Science)
Wang, Sheng (Chinese Academy of Sciences. Kunming Institute of Zoology)
Su, Guosheng (Aarhus University. Center for Quantitative Genetics and Genomics)
Sahana, Goutam (Aarhus University. Center for Quantitative Genetics and Genomics)
Lund, Mogens Sandø (Aarhus University. Center for Quantitative Genetics and Genomics)
Dekkers, Jack C. M. (Iowa State University. Department of Animal Science)
Kramer, Luke (Iowa State University. Department of Animal Science)
Tuggle, Christopher K. (Iowa State University. Department of Animal Science)
Corbett, Ryan (Iowa State University. Department of Animal Science)
Groenen, Martien A. M. (Wageningen University and Research. Animal Breeding and Genomics)
Madsen, Ole (Wageningen University and Research. Animal Breeding and Genomics)
Gòdia, Marta (Universitat Autònoma de Barcelona. Departament de Ciència Animal i dels Aliments)
Rocha, Dominique (Paris-Saclay University)
Charles, Mathieu (Paris-Saclay University)
Li, Cong-jun (Henry A. Wallace Beltsville Agricultural Research Center)
Pausch, Hubert (Animal Genomics)
Hu, Xiaoxiang (China Agricultural University. State Key Laboratory of Agrobiotechnology)
Frantz, Laurent (Queen Mary University of London. School of Biological and Behavioural Sciences)
Luo, Yonglun (Qingdao-Europe Advanced Institute for Life Sciences. Lars Bolund Institute of Regenerative Medicine)
Lin, Lin (Aarhus University Hospital. Steno Diabetes Center Aarhus)
Zhou, Zhongyin (Chinese Academy of Sciences. Kunming Institute of Zoology)
Zhang, Zhe (Zhejiang University. Department of Animal Science)
Chen, Zitao (Zhejiang University. Department of Animal Science)
Cui, Leilei (University College London. UCL Genetics Institute)
Xiang, Ruidong (Centre for AgriBiosciences)
Shen, Xia (University of Edinburgh. Centre for Global Health Research)
Li, Pinghua (Nanjing Agricultural University. Institute of Swine Science)
Huang, Ruihua (Nanjing Agricultural University. Institute of Swine Science)
Tang, Guoqing (Sichuan Agricultural University. Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province)
Li, Mingzhou (Sichuan Agricultural University. Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province)
Zhao, Yunxiang (Guangxi University. College of Animal Science and Technology)
Yi, Guoqiang (Chinese Academy of Agricultural Sciences. Agricultural Genomics Institute at Shenzhen)
Tang, Zhonglin (Chinese Academy of Agricultural Sciences. Agricultural Genomics Institute at Shenzhen)
Jiang, Jicai (North Carolina State University. Department of Animal Science)
Zhao, Fuping (Chinese Academy of Agricultural Sciences. Institute of Animal Science)
Yuan, Xiaolong (South China Agricultural University. National Engineering Research Center for Breeding Swine Industry)
Liu, Xiaohong (Sun Yat-sen University. State Key Laboratory of Biocontrol)
Chen, Yaosheng (Sun Yat-sen University. State Key Laboratory of Biocontrol)
Xu, Xuewen (Huazhong Agricultural University. Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction)
Zhao, Shuhong (Huazhong Agricultural University. Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction)
Zhao, Pengju (Hainan Institute, Zhejiang University)
Haley, Chris (The University of Edinburgh. Royal (Dick) School of Veterinary Studies)
Zhou, Huaijun (University of California. Department of Animal Science)
Wang, Qishan (Zhejiang University. Department of Animal Science)
Pan, Yuchun (Zhejiang University. Department of Animal Science)
Ding, Xiangdong (China Agricultural University. College of Animal Science and Technology)
Ma, Li (University of Maryland. Department of Animal and Avian Sciences)
Li, Jiaqi (South China Agricultural University. National Engineering Research Center for Breeding Swine Industry)
Navarro, Pau (The University of Edinburgh. Royal (Dick) School of Veterinary Studies)
Zhang, Qin (Shandong Agricultural University. College of Animal Science and Technology)
Li, Bingjie (Scotland's Rural College. Roslin Institute Building)
Tenesa, Albert (The University of Edinburgh. Royal (Dick) School of Veterinary Studies)
Li, Kui (Chinese Academy of Agricultural Sciences. Agricultural Genomics Institute at Shenzhen)
Liu, George E. (U.S. Department of Agriculture)
Zhang, Zhe (South China Agricultural University. National Engineering Research Center for Breeding Swine Industry)
Fang, Lingzhao (The University of Edinburgh. MRC Human Genetics Unit at the Institute of Genetics and Cancer)

Data:	2024
Resum:	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. The pilot phase of PigGTEx, re-analyzing 5,457 published RNA-seq samples, presents a pan-tissue catalog of molecular quantitative trait loci. Cross-species comparisons identify traits with shared genetic regulation in humans.
Nota:	Altres ajuts: Medical Research Council (MRC) MR/R025851/1 i MR/P015514/1. Biotechnology and Biological Sciences Research Council BBS/E/D/10002070 i BBS/E/D/30002275. United States Department of Agriculture 2019-67015-29321 i 2021-67015-33409. National Natural Science Foundation of China (National Science Foundation of China) 32022078.
Drets:	Aquest document està subjecte a una llicència d'ús Creative Commons. Es permet la reproducció total o parcial, la distribució, la comunicació pública de l'obra i la creació d'obres derivades, fins i tot amb finalitats comercials, sempre i quan es reconegui l'autoria de l'obra original.
Llengua:	Anglès
Document:	Article ; recerca ; Versió publicada
Matèria:	Gene regulation ; Data mining ; Transcriptomics
Publicat a:	Nature genetics, Vol. 56 (january 2024) , p. 112-123, ISSN 1546-1718

DOI: 10.1038/s41588-023-01585-7
PMID: 38177344

34 p, 19.3 MB

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