A compendium of genetic regulatory effects across pig tissues
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Published:2024-01
Issue:1
Volume:56
Page:112-123
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ISSN:1061-4036
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Container-title:Nature Genetics
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language:en
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Short-container-title:Nat Genet
Author:
Teng JinyanORCID, Gao Yahui, Yin HongweiORCID, Bai Zhonghao, Liu Shuli, Zeng Haonan, Bai Lijing, Cai ZexiORCID, Zhao Bingru, Li Xiujin, Xu Zhiting, Lin Qing, Pan Zhangyuan, Yang Wenjing, Yu Xiaoshan, Guan DailuORCID, Hou YaliORCID, Keel Brittney N., Rohrer Gary A.ORCID, Lindholm-Perry Amanda K., Oliver William T., Ballester MariaORCID, Crespo-Piazuelo DanielORCID, Quintanilla Raquel, Canela-Xandri Oriol, Rawlik KonradORCID, Xia Charley, Yao YuelinORCID, Zhao Qianyi, Yao Wenye, Yang Liu, Li Houcheng, Zhang Huicong, Liao Wang, Chen Tianshuo, Karlskov-Mortensen PeterORCID, Fredholm Merete, Amills MarcelORCID, Clop AlexORCID, Giuffra ElisabettaORCID, Wu Jun, Cai Xiaodian, Diao Shuqi, Pan Xiangchun, Wei Chen, Li Jinghui, Cheng Hao, Wang Sheng, Su Guosheng, Sahana GoutamORCID, Lund Mogens Sandø, Dekkers Jack C. M., Kramer Luke, Tuggle Christopher K.ORCID, Corbett Ryan, Groenen Martien A. M.ORCID, Madsen Ole, Gòdia Marta, Rocha Dominique, Charles MathieuORCID, Li Cong-junORCID, Pausch HubertORCID, Hu XiaoxiangORCID, Frantz Laurent, Luo YonglunORCID, Lin LinORCID, Zhou Zhongyin, Zhang Zhe, Chen Zitao, Cui Leilei, Xiang Ruidong, Shen XiaORCID, Li Pinghua, Huang Ruihua, Tang Guoqing, Li MingzhouORCID, Zhao Yunxiang, Yi GuoqiangORCID, Tang ZhonglinORCID, Jiang Jicai, Zhao Fuping, Yuan Xiaolong, Liu Xiaohong, Chen Yaosheng, Xu Xuewen, Zhao ShuhongORCID, Zhao Pengju, Haley Chris, Zhou HuaijunORCID, Wang QishanORCID, Pan Yuchun, Ding Xiangdong, Ma LiORCID, Li Jiaqi, Navarro PauORCID, Zhang Qin, Li BingjieORCID, Tenesa AlbertORCID, Li KuiORCID, Liu George E.ORCID, Zhang Zhe, Fang LingzhaoORCID,
Abstract
AbstractThe 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.
Funder
RCUK | Medical Research Council RCUK | Biotechnology and Biological Sciences Research Council United States Department of Agriculture | Agricultural Research Service National Natural Science Foundation of China
Publisher
Springer Science and Business Media LLC
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