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Journal Articles Nature Genetics Year : 2024

A compendium of genetic regulatory effects across pig tissues

Jinyan Teng (1) , Yahui Gao (2, 3, 4) , Hongwei Yin (5, 6) , Zhonghao Bai (7) , Shuli Liu (8, 9) , Haonan Zeng (1) , Lijing Bai (5) , Zexi Cai (7, 10) , Bingru Zhao (2) , Xiujin Li (11) , Zhiting Xu (12) , Qing Lin (13) , Zhangyuan Pan (14, 5) , Wenjing Yang (15, 2, 14) , Xiaoshan Yu (6) , Dailu Guan (16) , Yali Hou (17, 18) , Brittney Keel (8) , Gary Rohrer (8) , Amanda Lindholm-Perry (8) , William Oliver (8) , Maria Ballester (19) , Daniel Crespo-Piazuelo (19) , Raquel Quintanilla (19) , Oriol Canela-Xandri (6, 20) , Konrad Rawlik (21) , Charley Xia (21) , Yuelin Yao , Qianyi Zhao , Wenye Yao , Liu Yang , Houcheng Li , Huicong Zhang , Wang Liao , Tianshuo Chen , Peter Karlskov-Mortensen , Merete Fredholm , Marcel Amills , Alex Clop , Elisabetta Giuffra (22) , Jun Wu , Xiaodian Cai , Shuqi Diao , Xiangchun Pan , Chen Wei , Jinghui Li , Hao Cheng , Sheng Wang , Guosheng Su , Goutam Sahana , Mogens Sandø Lund , Jack Dekkers , Luke Kramer , Christopher Tuggle , Ryan Corbett , Martien Groenen , Ole Madsen , Marta Gòdia , Dominique Rocha (22) , Mathieu Charles (22) , Cong-Jun Li , Hubert Pausch , Xiaoxiang Hu , Laurent Frantz , Yonglun Luo , Lin Lin , Zhongyin Zhou , Zhe Zhang , Zitao Chen , Leilei Cui , Ruidong Xiang , Xia Shen , Pinghua Li , Ruihua Huang , Guoqing Tang , Mingzhou Li , Yunxiang Zhao , Guoqiang Yi , Zhonglin Tang , Jicai Jiang , Fuping Zhao , Xiaolong Yuan , Xiaohong Liu , Yaosheng Chen , Xuewen Xu , Shuhong Zhao , Pengju Zhao , Chris Haley , Huaijun Zhou , Qishan Wang , Yuchun Pan , Xiangdong Ding , Li Ma , Jiaqi Li , Pau Navarro , Qin Zhang , Bingjie Li , Albert Tenesa (21) , Kui Li , George Liu , Zhe Zhang , Lingzhao Fang
Jinyan Teng
Zhiting Xu
  • Function : Author
Dailu Guan
Gary Rohrer
Konrad Rawlik
Yuelin Yao
Qianyi Zhao
  • Function : Author
Wenye Yao
  • Function : Author
Liu Yang
  • Function : Author
Houcheng Li
  • Function : Author
Huicong Zhang
  • Function : Author
Wang Liao
  • Function : Author
Tianshuo Chen
  • Function : Author
Peter Karlskov-Mortensen
Merete Fredholm
  • Function : Author
Marcel Amills
Alex Clop
Jun Wu
  • Function : Author
Xiaodian Cai
  • Function : Author
Shuqi Diao
  • Function : Author
Xiangchun Pan
  • Function : Author
Chen Wei
  • Function : Author
Jinghui Li
  • Function : Author
Hao Cheng
  • Function : Author
Sheng Wang
  • Function : Author
Guosheng Su
  • Function : Author
Goutam Sahana
Mogens Sandø Lund
  • Function : Author
Jack Dekkers
  • Function : Author
Luke Kramer
  • Function : Author
Christopher Tuggle
Ryan Corbett
  • Function : Author
Martien Groenen
Ole Madsen
  • Function : Author
Marta Gòdia
  • Function : Author
Cong-Jun Li
Hubert Pausch
Xiaoxiang Hu
Laurent Frantz
  • Function : Author
Yonglun Luo
Lin Lin
Zhongyin Zhou
  • Function : Author
Zhe Zhang
  • Function : Author
Zitao Chen
  • Function : Author
Leilei Cui
  • Function : Author
Ruidong Xiang
  • Function : Author
Xia Shen
Pinghua Li
  • Function : Author
Ruihua Huang
  • Function : Author
Guoqing Tang
  • Function : Author
Mingzhou Li
Yunxiang Zhao
  • Function : Author
Guoqiang Yi
Zhonglin Tang
Jicai Jiang
  • Function : Author
Fuping Zhao
  • Function : Author
Xiaolong Yuan
  • Function : Author
Xiaohong Liu
  • Function : Author
Yaosheng Chen
  • Function : Author
Xuewen Xu
  • Function : Author
Shuhong Zhao
Pengju Zhao
  • Function : Author
Chris Haley
  • Function : Author
Huaijun Zhou
Qishan Wang
Yuchun Pan
  • Function : Author
Xiangdong Ding
  • Function : Author
Li Ma
Jiaqi Li
  • Function : Author
Pau Navarro
Qin Zhang
  • Function : Author
Bingjie Li
Albert Tenesa
Connectez-vous pour contacter l'auteur
Kui Li
George Liu
Zhe Zhang
  • Function : Author
Lingzhao Fang

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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hal-04599954 , version 1 (06-06-2024)

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Jinyan Teng, Yahui Gao, Hongwei Yin, Zhonghao Bai, Shuli Liu, et al.. A compendium of genetic regulatory effects across pig tissues. Nature Genetics, 2024, 56 (1), pp.112-123. ⟨10.1038/s41588-023-01585-7⟩. ⟨hal-04599954⟩
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