A compendium of genetic regulatory effects across pig tissues
Jinyan Teng(South China Agricultural University), Yahui Gao(South China Agricultural University), Hongwei Yin(Agricultural Genomics Institute at Shenzhen), Zhonghao Bai(Aarhus University), Shuli Liu(Agricultural Research Service), Haonan Zeng(South China Agricultural University), Lijing Bai(Agricultural Genomics Institute at Shenzhen), Zexi Cai(Aarhus University), Bingru Zhao(China Agricultural University), Xiujin Li(Zhongkai University of Agriculture and Engineering), Zhiting Xu(South China Agricultural University), Qing Lin(South China Agricultural University), Zhangyuan Pan(Chinese Academy of Agricultural Sciences), Wenjing Yang(China Agricultural University), Xiaoshan Yu(Institute of Genetics and Cancer), Dailu Guan(University of California, Davis), Yali Hou(Chinese Academy of Sciences), Brittney N. Keel(Roman L. Hruska U.S. Meat Animal Research Center), G. A. Rohrer(Roman L. Hruska U.S. Meat Animal Research Center), Amanda K. Lindholm‐Perry(Roman L. Hruska U.S. Meat Animal Research Center), William T. Oliver(Roman L. Hruska U.S. Meat Animal Research Center), María Ballester(Institute of Agrifood Research and Technology), Daniel Crespo‐Piazuelo(Institute of Agrifood Research and Technology), Raquel Quintanilla(Institute of Agrifood Research and Technology), Oriol Canela‐Xandri(Institute of Genetics and Cancer), Konrad Rawlik(University of Edinburgh), Charley Xia(NHS Lothian), Yuelin Yao(Institute of Genetics and Cancer), Qianyi Zhao(Agricultural Genomics Institute at Shenzhen), Wenye Yao(Agricultural Genomics Institute at Shenzhen), Liu Yang(Agricultural Genomics Institute at Shenzhen), Houcheng Li(Aarhus University), Huicong Zhang(Aarhus University), Wang Liao(Institute of Genetics and Cancer), Tianshuo Chen(Institute of Genetics and Cancer), Peter Karlskov‐Mortensen(University of Copenhagen), Merete Fredholm(University of Copenhagen), Marcel Amills(Universitat Autònoma de Barcelona), Alex Clop(Universitat Autònoma de Barcelona), Elisabetta Giuffra(AgroParisTech), Jun Wu(South China Agricultural University), Xiaodian Cai(South China Agricultural University), Shuqi Diao(South China Agricultural University), Xiangchun Pan(South China Agricultural University), Wei Chen(South China Agricultural University), Jinghui Li(South China Agricultural University), Hao Cheng(University of California, Davis), Sheng Wang(Kunming Institute of Zoology), Guosheng Su(Aarhus University), Goutam Sahana(Aarhus University), Mogens Sandø Lund(Aarhus University), Jack C. M. Dekkers(Iowa State University), Luke Kramer(Iowa State University), Christopher K. Tuggle(Iowa State University), Ryan J. Corbett(Iowa State University), Martien A. M. Groenen(Wageningen University & Research), Ole Madsen(Wageningen University & Research), Marta Gòdia(Universitat Autònoma de Barcelona), Dominique Rocha(AgroParisTech), Mathieu Charles(AgroParisTech), Congjun Li(Agricultural Research Service), Hubert Pausch(ETH Zurich), Xiaoxiang Hu(China Agricultural University), Laurent Frantz(Queen Mary University of London), Yonglun Luo(Steno Diabetes Centers), Lin Lin(Steno Diabetes Centers), Zhongyin Zhou(Kunming Institute of Zoology), Zhe Zhang(South China Agricultural University), Zitao Chen(Zhejiang University), Leilei Cui(Nanchang University), Ruidong Xiang(The University of Melbourne), Xia Shen(Fudan University), Pinghua Li(Nanjing Agricultural University), Ruihua Huang(Nanjing Agricultural University), Guoqing Tang(Sichuan Agricultural University), Mingzhou Li(Sichuan Agricultural University), Yunxiang Zhao(Guangxi University), Guoqiang Yi(Agricultural Genomics Institute at Shenzhen), Zhonglin Tang(Agricultural Genomics Institute at Shenzhen), Jicai Jiang(North Carolina State University), Fuping Zhao(Chinese Academy of Agricultural Sciences), Xiaolong Yuan(South China Agricultural University), Xiaohong Liu(Sun Yat-sen University), Yaosheng Chen(Sun Yat-sen University), Xuewen Xu(Huazhong Agricultural University), Shuhong Zhao(Huazhong Agricultural University), Pengju Zhao, Chris Haley(Roslin Institute), Huaijun Zhou(University of California, Davis), Qishan Wang(Zhejiang University), Yuchun Pan(Zhejiang University), Xiangdong Ding(China Agricultural University), Li Ma(Roman L. Hruska U.S. Meat Animal Research Center), Jiaqi Li(South China Agricultural University), Pau Navarro(Roslin Institute), Qin Zhang(Shandong Agricultural University), Bingjie Li(Roslin Institute), Albert Tenesa(Roslin Institute), Kui Li(Agricultural Genomics Institute at Shenzhen), George E. Liu(Agricultural Research Service), Zhe Zhang(South China Agricultural University), Lingzhao Fang(Aarhus University)
Cited by 247Open Access
Abstract
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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