A compendium of genetic regulatory effects across pig tissues,Nature Genetics

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A compendium of genetic regulatory effects across pig tissues
Nature Genetics ( IF 31.7 ) Pub Date : 2024-01-04 , DOI: 10.1038/s41588-023-01585-7
Jinyan Teng ₁ , Yahui Gao _{1,

2,

3} , Hongwei Yin ₄ , Zhonghao Bai _{5,

6} , Shuli Liu _{2,

7} , Haonan Zeng ₁ , , Lijing Bai ₄ , Zexi Cai ₅ , Bingru Zhao ₈ , Xiujin Li ₉ , Zhiting Xu ₁ , Qing Lin ₁ , Zhangyuan Pan _{10,

11} , Wenjing Yang _{8,

10} , Xiaoshan Yu ₆ , Dailu Guan ₁₀ , Yali Hou ₁₂ , Brittney N Keel ₁₃ , Gary A Rohrer ₁₃ , Amanda K Lindholm-Perry ₁₃ , William T Oliver ₁₃ , Maria Ballester ₁₄ , Daniel Crespo-Piazuelo ₁₄ , Raquel Quintanilla ₁₄ , Oriol Canela-Xandri ₆ , Konrad Rawlik ₁₅ , Charley Xia _{16,

17} , Yuelin Yao _{6,

18} , Qianyi Zhao ₄ , Wenye Yao _{4,

19} , Liu Yang ₄ , Houcheng Li ₅ , Huicong Zhang ₅ , Wang Liao ₆ , Tianshuo Chen ₆ , Peter Karlskov-Mortensen ₂₀ , Merete Fredholm ₂₀ , Marcel Amills _{21,

22} , Alex Clop _{21,

23} , Elisabetta Giuffra ₂₄ , Jun Wu ₁ , Xiaodian Cai ₁ , Shuqi Diao ₁ , Xiangchun Pan ₁ , Chen Wei ₁ , Jinghui Li ₁₀ , Hao Cheng ₁₀ , Sheng Wang ₂₅ , Guosheng Su ₅ , Goutam Sahana ₅ , Mogens Sandø Lund ₅ , Jack C M Dekkers ₂₆ , Luke Kramer ₂₆ , Christopher K Tuggle ₂₆ , Ryan Corbett ₂₆ , Martien A M Groenen ₁₉ , Ole Madsen ₁₉ , Marta Gòdia _{19,

21} , Dominique Rocha ₂₄ , Mathieu Charles ₂₇ , Cong-Jun Li ₂ , Hubert Pausch ₂₈ , Xiaoxiang Hu ₂₉ , Laurent Frantz _{30,

31} , Yonglun Luo _{32,

33,

34} , Lin Lin _{32,

33} , Zhongyin Zhou ₂₅ , Zhe Zhang ₃₅ , Zitao Chen ₃₅ , Leilei Cui _{36,

37,

38} , Ruidong Xiang _{39,

40} , Xia Shen _{41,

42,

43} , Pinghua Li ₄₄ , Ruihua Huang ₄₄ , Guoqing Tang ₄₅ , Mingzhou Li ₄₅ , Yunxiang Zhao ₄₆ , Guoqiang Yi ₄ , Zhonglin Tang ₄ , Jicai Jiang ₄₇ , Fuping Zhao ₁₁ , Xiaolong Yuan ₁ , Xiaohong Liu ₄₈ , Yaosheng Chen ₄₈ , Xuewen Xu ₄₉ , Shuhong Zhao ₄₉ , Pengju Zhao ₅₀ , Chris Haley _{6,

51} , Huaijun Zhou ₁₀ , Qishan Wang ₃₅ , Yuchun Pan ₃₅ , Xiangdong Ding ₈ , Li Ma ₃ , Jiaqi Li ₁ , Pau Navarro _{6,

51} , Qin Zhang ₅₂ , Bingjie Li ₅₃ , Albert Tenesa _{6,

51} , Kui Li ₄ , George E Liu ₂ , Zhe Zhang ₁ , Lingzhao Fang _{5,

6}

Affiliation

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.
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.
Department of Animal and Avian Sciences, University of Maryland, College Park, MD, USA.
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.
Center for Quantitative Genetics and Genomics, Aarhus University, Aarhus, Denmark.
MRC Human Genetics Unit at the Institute of Genetics and Cancer, The University of Edinburgh, Edinburgh, UK.
School of Life Sciences, Westlake University, Hangzhou, China.
College of Animal Science and Technology, China Agricultural University, Beijing, China.
Guangdong Provincial Key Laboratory of Waterfowl Healthy Breeding, College of Animal Science and Technology, Zhongkai University of Agriculture and Engineering, Guangzhou, China.
Department of Animal Science, University of California, Davis, Davis, CA, USA.
Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China.
Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, China.
ARS, USDA, U.S. Meat Animal Research Center, Clay Center, NE, USA.
Animal Breeding and Genetics Programme, Institut de Recerca i Tecnologia Agroalimentàries (IRTA), Torre Marimon, Caldes de Montbui, Spain.
Baillie Gifford Pandemic Science Hub, University of Edinburgh, Edinburgh, UK.
Lothian Birth Cohort studies, University of Edinburgh, Edinburgh, UK.
Department of Psychology, University of Edinburgh, Edinburgh, UK.
School of Informatics, The University of Edinburgh, Edinburgh, UK.
Animal Breeding and Genomics, Wageningen University and Research, Wageningen, The Netherlands.
Animal Genetics, Bioinformatics and Breeding, Department of Veterinary and Animal Sciences, University of Copenhagen, Copenhagen, Denmark.
Department of Animal Genetics, Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus de la Universitat Autònoma de Barcelona, Bellaterra, Spain.
Departament de Ciència Animal i dels Aliments, Universitat Autònoma de Barcelona, Bellaterra, Spain.
Consejo Superior de Investigaciones Científicas, Barcelona, Spain.
Paris-Saclay University, INRAE, AgroParisTech, GABI, Jouy-en-Josas, France.
State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.
Department of Animal Science, Iowa State University, Ames, IA, USA.
Paris-Saclay University, INRAE, AgroParisTech, GABI, SIGENAE, Jouy-en-Josas, France.
Animal Genomics, ETH Zurich, Universitaetstrasse 2, Zurich, Switzerland.
State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China.
Palaeogenomics Group, Department of Veterinary Sciences, Ludwig Maximilian University, Munich, Germany.
School of Biological and Behavioural Sciences, Queen Mary University of London, London, UK.
Department of Biomedicine, Aarhus University, Aarhus, Denmark.
Steno Diabetes Center Aarhus, Aarhus University Hospital, Aarhus, Denmark.
Lars Bolund Institute of Regenerative Medicine, Qingdao-Europe Advanced Institute for Life Sciences, BGI-Research, Qingdao, China.
Department of Animal Science, College of Animal Sciences, Zhejiang University, Hangzhou, China.
School of Life Sciences, Nanchang University, Nanchang, China.
Human Aging Research Institute and School of Life Science, Nanchang University, and Jiangxi Key Laboratory of Human Aging, Jiangxi, China.
UCL Genetics Institute, University College London, London, UK.
Faculty of Veterinary and Agricultural Science, The University of Melbourne, Parkville, Victoria, Australia.
Agriculture Victoria, AgriBio, Centre for AgriBiosciences, Bundoora, Victoria, Australia.
State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China.
Center for Intelligent Medicine Research, Greater Bay Area Institute of Precision Medicine, Fudan University, Guangzhou, China.
Centre for Global Health Research, Usher Institute, University of Edinburgh, Edinburgh, UK.
Institute of Swine Science, Nanjing Agricultural University, Nanjing, China.
Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China.
College of Animal Science and Technology, Guangxi University, Nanning, China.
Department of Animal Science, North Carolina State University, Raleigh, NC, USA.
State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China.
Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education and College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China.
Hainan Institute, Zhejiang University, Yongyou Industry Park, Yazhou Bay Sci-Tech City, Sanya, China.
The Roslin Institute, Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Midlothian, UK.
College of Animal Science and Technology, Shandong Agricultural University, Tai'an, China.
Scotland's Rural College (SRUC), Roslin Institute Building, Midlothian, UK.

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.

中文翻译：

猪组织中遗传调控作用的纲要

农场动物基因型-组织表达（FarmGTEx）项目已经建立，旨在开发牲畜遗传调控变异的公共资源，这对于将遗传多态性与表型变异联系起来至关重要，有助于动物育种和人类生物医学的基础生物学发现和开发。在这里，我们展示了 PigGTEx 试点阶段的结果，通过处理 5,457 个 RNA 测序和 1,602 个通过猪质量控制的全基因组测序样本。我们建立了一个猪基因型插补面板，并将数百万个遗传变异与 34 个组织中的五种转录组表型相关联。我们使用多组学数据评估调节作用的组织特异性并阐明其作用的分子机制。利用这一资源，我们破译了 207 种猪复合体表型背后的调控机制，并证明了猪与人类在基因表达方面的相似性以及复杂表型背后的遗传调控，支持了猪作为人类生物医学模型的重要性。

更新日期：2024-01-04

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