Abstract
Genetic mutation and drift, coupled with natural and human-mediated selection and migration, have produced a wide variety of genotypes and phenotypes in farmed animals. We here introduce the Farm Animal Genotype–Tissue Expression (FarmGTEx) Project, which aims to elucidate the genetic determinants of gene expression across 16 terrestrial and aquatic domestic species under diverse biological and environmental contexts. For each species, we aim to collect multiomics data, particularly genomics and transcriptomics, from 50 tissues of 1,000 healthy adults and 200 additional animals representing a specific context. This Perspective provides an overview of the priorities of FarmGTEx and advocates for coordinated strategies of data analysis and resource-sharing initiatives. FarmGTEx aims to serve as a platform for investigating context-specific regulatory effects, which will deepen our understanding of molecular mechanisms underlying complex phenotypes. The knowledge and insights provided by FarmGTEx will contribute to improving sustainable agriculture-based food systems, comparative biology and eventual human biomedicine.
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Fig. 1: Overview of the FarmGTEx Project.
Fig. 2: The overall data analysis pipeline of FarmGTEx.
Fig. 3: Potential applications of FarmGTEx resources.
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Acknowledgements
L. Fang is supported by Agriculture and Food Research Initiative Competitive grant 2022-67015-36215 from the USDA National Institute of Food and Agriculture, and seed funding from CellFood Hub (Aarhus University Foundation). Y. Luo is supported by the Innovative Health Initiative Joint Undertaking under grant agreement 101165643. Z. Zhang is supported by funding from the China Agriculture Research System (CARS-35). We thank all the researchers who have contributed to the generation and analyses of both publicly available and newly generated data used in the pilot phase of FarmGTEx. We thank I. Kaplow at the Department of Biological Sciences and the Ray and Stephanie Lane Computational Biology Department, Carnegie Mellon University for valuable comments on the manuscript.
Author information
Authors and Affiliations
Center for Quantitative Genetics and Genomics, Aarhus University, Aarhus, Denmark
Lingzhao Fang, Qing Lin, Zhonghao Bai, Mian Gong, Peter Sørensen, Goutam Sahana, Mogens Sandø Lund, Jing Li & Xinfeng Liu
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, Guangzhou, China
Jinyan Teng, Qing Lin, Yahui Gao, Xiangchun Pan, Wentao Gong, Xiaolong Yuan, Jiaqi Li & Zhe Zhang
Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, China
Shuli Liu & Jian Yang
School of Life Sciences, Westlake University, Hangzhou, China
Shuli Liu & Jian Yang
Department of Animal Science, University of California, Davis, Davis, CA, USA
Dailu Guan, Hao Cheng & Huaijun Zhou
Department of Animal and Veterinary Sciences, Scotland’s Rural College, Midlothian, UK
Bingjie Li
Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
Yali Hou, Mian Gong, Zhangyuan Pan, Fuping Zhao, Lin Jiang, Guiping Zhao, Zhengkui Zhou & Rong Zhou
National Engineering Laboratory for Animal Breeding, State Key Laboratory of Animal Biotech Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction of the Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural University, Beijing, China
Ying Yu, Siqian Chen, Zhuocheng Hou, Qin Wang, Yi Zhang, Xiangdong Ding, Dongxiao Sun, Hao Zhang & Ning Yang
The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, UK
Emily L. Clark & Jacqueline Smith
Baillie Gifford Pandemic Science Hub, Centre for Inflammation Research, Institute for Regeneration and Repair, the University of Edinburgh, Edinburgh, UK
Konrad Rawlik
Agriculture Victoria Research, AgriBio, Centre for AgriBioscience, Bundoora, Victoria, Australia
Ruidong Xiang, Amanda J. Chamberlain & Michael E. Goddard
Cambridge Baker Systems Genomics Initiative, Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia
Ruidong Xiang
School of Agriculture, Food and Ecosystem Sciences, the University of Melbourne, Parkville, Victoria, Australia
Ruidong Xiang & Michael E. Goddard
School of Applied Systems Biology, La Trobe University, Bundoora, Victoria, Australia
Amanda J. Chamberlain
Research and Development, Livestock Improvement Corporation, Hamilton, New Zealand
Mathew Littlejohn
AL Rae Centre for Genetics and Breeding, Massey University, Palmerston North, New Zealand
Mathew Littlejohn
The Palaeogenomics and Bio-Archaeology Research Network, School of Archaeology, University of Oxford, Oxford, UK
Greger Larson
UCD School of Agriculture and Food Science, University College Dublin, Belfield, Dublin, Ireland
David E. MacHugh & John F. O’Grady
UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Belfield, Dublin, Ireland
David E. MacHugh
UCD One Health Centre, University College Dublin, Belfield, Dublin, Ireland
David E. MacHugh
Department of Animal Sciences and Center for Reproductive Biology, Washington State University, Pullman, WA, USA
Zhihua Jiang
College of Animal Science and Technology, Hunan Agricultural University, Changsha, China
Haihan Zhang, Xi He, Yuebo Zhang, Ning Gao & Jun He
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
Guoqiang Yi, Yuwen Liu, Zhonglin Tang & Kui Li
Hainan Institute, Zhejiang University, Yongyou Industry Park, Yazhou Bay Sci–Tech City, Sanya, China
Pengju Zhao
Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of the Ministry of Education, Huazhong Agricultural University, Wuhan, China
Yang Zhou, Liangliang Fu & Shuhong Zhao
Yazhouwan National Laboratory, Sanya, China
Yang Zhou, Lei Liu & Shuhong Zhao
Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, China
Xiao Wang
Poultry Institute, Shandong Academy of Agricultural Sciences, Jinan, China
Dan Hao
Usher Institute, University of Edinburgh, Edinburgh, UK
Robert S. Young & Xia Shen
Zhejiang University–University of Edinburgh Institute, Zhejiang University, Haining, P. R. China
Robert S. Young
State Key Laboratory of Genetic Engineering, Center for Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai, China
Xia Shen
Center for Intelligent Medicine Research, Greater Bay Area Institute of Precision Medicine (Guangzhou), Fudan University, Guangzhou, China
Xia Shen
Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
Xia Shen
Lothian Birth Cohort studies, University of Edinburgh, Edinburgh, UK
Charley Xia
Department of Psychology, University of Edinburgh, Edinburgh, UK
Charley Xia
Department of Animal and Avian Sciences, University of Maryland, College Park, MD, USA
Li Ma & Jiuzhou Song
Council on Dairy Cattle Breeding, Bowie, MD, USA
John B. Cole
Department of Animal Sciences, Donald Henry Barron Reproductive and Perinatal Biology Research Program and the Genetics Institute, University of Florida, Gainesville, FL, USA
John B. Cole
Department of Animal Science, North Carolina State University, Raleigh, NC, USA
John B. Cole
Animal Genomics and Improvement Laboratory, Henry A. Wallace Beltsville Agricultural Research Center, Agricultural Research Service, USDA, Beltsville, MD, USA
Ransom L. Baldwin VI, Cong-jun Li, Curtis P. Van Tassell, Benjamin D. Rosen, Nayan Bhowmik, George E. Liu & Curtis P. Van Tassell
Animal Parasitic Diseases Laboratory, BARC, NEA, ARS, USDA, Beltsville, MD, USA
Joan Lunney
Department of Animal Science, Center for Reproductive Biology and Health, College of Agricultural Sciences, the Pennsylvania State University, University Park, PA, USA
Wansheng Liu
Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta, Canada
Leluo Guan
Faculty of Land and Food Systems, University of British Columbia, Vancouver, British Columbia, Canada
Leluo Guan
Department of Animal Science, McGill University, Sainte-Anne-de-Bellevue, Quebec, Canada
Xin Zhao
Sherbrooke Research and Development Centre, Agriculture and Agri-Food Canada, Sherbrooke, Quebec, Canada
Eveline M. Ibeagha-Awemu
Department of Biomedicine, Aarhus University, Aarhus, Denmark
Yonglun Luo & Lin Lin
Steno Diabetes Center Aarhus, Aarhus University Hospital, Aarhus, Denmark
Yonglun Luo & Lin Lin
MRC Human Genetics Unit at the Institute of Genetics and Cancer, the University of Edinburgh, Edinburgh, UK
Oriol Canela-Xandri
Animal Breeding and Genomics, Wageningen University & Research, Wageningen, the Netherlands
Martijn F. L. Derks, Richard P. M. A. Crooijmans, Marta Gòdia, Ole Madsen & Martien A. M. Groenen
Department of Animal Science, Iowa State University, Ames, IA, USA
James E. Koltes & Christopher K. Tuggle
University of Arizona, Tucson, AZ, USA
Fiona M. McCarthy
GABI, AgroParisTech, INRAE, Paris-Saclay University, Jouy-en-Josas, France
Dominique Rocha & Elisabetta Giuffra
Department of Animal Genetics, Centre for Research in Agricultural Genomics, CSIC-IRTA-UAB-UB, Campus de la Universitat Autònoma de Barcelona, Bellaterra, Spain
Marcel Amills & Alex Clop
Departament de Ciència Animal i dels Aliments, Universitat Autònoma de Barcelona, Bellaterra, Spain
Marcel Amills
Consejo Superior de Investigaciones Científicas, Barcelona, Spain
Alex Clop
Animal Breeding and Genetics Programme, Institut de Recerca i Tecnologia Agroalimentàries (IRTA), Torre Marimon, Caldes de Montbui, Spain
Maria Ballester
GenPhySE, INRAE, ENVT, Université de Toulouse, Castanet-Tolosan, France
Gwenola Tosser-Klopp
School of Agriculture and Life Sciences, Kunming University, Kunming, China
Jing Li
LC-Bio Technologies, Co., Ltd, Hangzhou, China
Chao Fang
Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture and Rural Affairs, Jimei University, Xiamen, China
Ming Fang
College of Animal Sciences, Zhejiang University, Hangzhou, China
Qishan Wang
College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
Hehe Liu, Juan Deng, Long Jin & Mingzhou Li
State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
Delin Mo, Xiaohong Liu & Yaosheng Chen
Key Laboratory of Dairy Cow Genetic Improvement and Milk Quality Research of Zhejiang Province, College of Animal Sciences, Zhejiang University, Hangzhou, China
Hui-Zeng Sun
College of Animal Science and Technology, Northwest A&F University, Yangling, China
Cong Li, Yu Wang & Yu Jiang
Key Laboratory of Genetic Evolution and Animal Models, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
Dongdong Wu
Shandong Provincial Key Laboratory for Livestock Germplasm Innovation and Utilization, College of Animal Science, Shandong Agricultural University, Tai’an, China
Wenwen Wang, Xinzhong Fan & Qin Zhang
State Key Laboratory of Animal Biotech Breeding, College of Biological Sciences, China Agricultural University, Beijing, China
Xiaoxiang Hu
Department of Animal Science, Michigan State University, East Lansing, MI, USA
Wen Huang
Institute of Rare Diseases, West China Hospital of Sichuan University, Chengdu, China
Yang Wu
Institute of Animal Science, Xinjiang Academy of Animal Science, Ürümqi City, China
Weiwei Wu
Animal GenoPhenomics, Animal Production Systems and Animal Health, Agroscope Posieux, Fribourg, Switzerland
Claudia Kasper
State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystem, College of Ecology, Lanzhou University, Lanzhou, China
Xinfeng Liu
College of Marine Life Sciences, Ocean University of China, Qingdao, China
Xiaofei Yu
School of Life Sciences, Nanchang University, Nanchang, China
Leilei Cui
Jiangxi Province Key Laboratory of Aging and Disease, Human Aging Research Institute and School of Life Science, Nanchang University, Jiangxi, China
Leilei Cui
Department of Biostatistics, University of Michigan, Ann Arbor, MI, USA
Xiang Zhou
Department of Epidemiology, School of Public Health, University of Pittsburgh, Pittsburgh, PA, USA
Seyoung Kim
Division of Computational Biomedicine, Department of Biological Chemistry, School of Medicine, University of California, Irvine, Irvine, CA, USA
Wei Li
Department of Medicine and Human Genetics, the University of Chicago, Chicago, IL, USA
Hae Kyung Im
Section of Plant Breeding and Genetics, Cornell University, Ithaca, NY, USA
Edward S. Buckler
Institute for Genomic Diversity, Cornell University, Ithaca, NY, USA
Edward S. Buckler
Agricultural Research Service, United States Department of Agriculture, Ithaca, NY, USA
Edward S. Buckler
Department of Cellular and Molecular Medicine, Center for Epigenomics, Moores Cancer Center and Institute of Genomic Medicine, University of California San Diego, School of Medicine, La Jolla, CA, USA
Bing Ren
Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA
Michael C. Schatz
Department of Statistics and Data Science, University of California, Los Angeles, Los Angeles, CA, USA
Jingyi Jessica Li
Department of Psychiatry, University of California San Diego, La Jolla, CA, USA
Abraham A. Palmer
Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
Abraham A. Palmer
Palaeogenomics Group, Institute of Palaeoanatomy, Domestication Research and the History of Veterinary Medicine, Ludwig-Maximilians-Universität, Munich, Germany
Laurent Frantz
School of Biological and Behavioural Sciences, Queen Mary University of London, London, UK
Laurent Frantz
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Lingzhao Fang
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Consortia
The FarmGTEx Consortium
Lingzhao Fang
, Jinyan Teng
, Qing Lin
, Zhonghao Bai
, Shuli Liu
, Dailu Guan
, Bingjie Li
, Yahui Gao
, Yali Hou
, Mian Gong
, Zhangyuan Pan
, Ying Yu
, Emily L. Clark
, Jacqueline Smith
, Konrad Rawlik
, Ruidong Xiang
, Amanda J. Chamberlain
, Michael E. Goddard
, Mathew Littlejohn
, Greger Larson
, David E. MacHugh
, John F. O’Grady
, Peter Sørensen
, Goutam Sahana
, Mogens Sandø Lund
, Zhihua Jiang
, Xiangchun Pan
, Wentao Gong
, Haihan Zhang
, Xi He
, Yuebo Zhang
, Ning Gao
, Jun He
, Guoqiang Yi
, Yuwen Liu
, Zhonglin Tang
, Pengju Zhao
, Yang Zhou
, Liangliang Fu
, Xiao Wang
, Dan Hao
, Lei Liu
, Siqian Chen
, Robert S. Young
, Xia Shen
, Charley Xia
, Hao Cheng
, Li Ma
, John B. Cole
, Ransom L. Baldwin VI
, Cong-jun Li
, Curtis P. Van Tassell
, Benjamin D. Rosen
, Nayan Bhowmik
, Joan Lunney
, Wansheng Liu
, Leluo Guan
, Xin Zhao
, Eveline M. Ibeagha-Awemu
, Yonglun Luo
, Lin Lin
, Oriol Canela-Xandri
, Martijn F. L. Derks
, Richard P. M. A. Crooijmans
, Marta Gòdia
, Ole Madsen
, Martien A. M. Groenen
, James E. Koltes
, Christopher K. Tuggle
, Fiona M. McCarthy
, Dominique Rocha
, Elisabetta Giuffra
, Marcel Amills
, Alex Clop
, Maria Ballester
, Gwenola Tosser-Klopp
, Jing Li
, Chao Fang
, Ming Fang
, Qishan Wang
, Zhuocheng Hou
, Qin Wang
, Fuping Zhao
, Lin Jiang
, Guiping Zhao
, Zhengkui Zhou
, Rong Zhou
, Hehe Liu
, Juan Deng
, Long Jin
, Mingzhou Li
, Delin Mo
, Xiaohong Liu
, Yaosheng Chen
, Xiaolong Yuan
, Jiaqi Li
, Shuhong Zhao
, Yi Zhang
, Xiangdong Ding
, Dongxiao Sun
, Hui-Zeng Sun
, Cong Li
, Yu Wang
, Yu Jiang
, Dongdong Wu
, Wenwen Wang
, Xinzhong Fan
, Qin Zhang
, Kui Li
, Hao Zhang
, Ning Yang
, Xiaoxiang Hu
, Wen Huang
, Jiuzhou Song
, Yang Wu
, Jian Yang
, Weiwei Wu
, Claudia Kasper
, Xinfeng Liu
, Xiaofei Yu
, Leilei Cui
, Xiang Zhou
, Seyoung Kim
, Wei Li
, Hae Kyung Im
, Edward S. Buckler
, Bing Ren
, Michael C. Schatz
, Jingyi Jessica Li
, Abraham A. Palmer
, Laurent Frantz
, Huaijun Zhou
, Zhe Zhang
& George E. Liu
Contributions
L. Fang took the lead in writing the manuscript with input from all authors. J.J.L., A.A.P., L. Frantz, H. Zhou, Z. Zhang and G.E.L. made critical revisions to the manuscript and made major contributions to the pilot phase of FarmGTEx. L. Fang, J.T., Q.L., Z.B., Y.H., X.P. and W.G. contributed to figure generation. S.L., D.G., B.L., Y.G., Y.H., M. Gong, Z.P., Y.Y., E.L.C., J. Smith., K.R., R.X., A.J.C., M.E.G., M. Littlejohn, G.L., D.E.M., J.F.O’G., P.S., G.S., M.S.L., Z.J., X.P., W.G., Haihan Zhang, X. He, Yuebo Zhang, N.G., J.H., G.Y., Y. Liu, Z.T., P.Z., Y. Zhou, L. Fu, X.W., D.H., L. Liu, S.C., R.S.Y., X.S., C.X., H.C., L.M., J.B.C., R.L.B., C.j.L., C.P.V.T., B.D.R., N.B., J. Lunney., W. Liu., L.G., X. Zhao., E.M.I.-A., Y. Luo, L. Lin, O.C.-X., M.F.L.D., R.P.M.A.C., M. Gòdia, O.M., M.A.M.G., J.E.K., C.K.T., F.M.M., D.R., E.G., M.A., A.C., M.B., G.T.-K., Jing Li, C.F., M.F., Qishan Wang, Z.H., Qin Wang, F.Z., L. Jiang, G.Z., Z. Zhou, R.Z., H.L., J.D., L. Jin, M. Li, D.M., Xiaohong Liu, Y.C., X. Yuan, Jiaqi Li, S.Z., Yi Zhang, X.D., D.S., H.-Z.S., C.L., Y. Wang, Y.J., D.W., W. Wang, X.F., Q.Z., K.L., Hao Zhang, N.Y., X. Hu, W.H., J. Song., Y. Wu, J.Y., W. Wu, C.K., Xinfeng Liu, X. Yu., L.C., X. Zhou, S.K., W. Li, H.K.I., E.S.B., B.R. and M.C.S. have provided valuable comments and edits to the manuscript. All authors provided critical feedback and helped shape the manuscript.
Corresponding authors
Correspondence to Lingzhao Fang, Jingyi Jessica Li, Abraham A. Palmer, Laurent Frantz, Huaijun Zhou, Zhe Zhang or George E. Liu.
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Fang, L., Teng, J., Lin, Q. et al. The Farm Animal Genotype–Tissue Expression (FarmGTEx) Project. Nat Genet (2025). https://doi.org/10.1038/s41588-025-02121-5
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Received:21 May 2024
Accepted:06 February 2025
Published:17 March 2025
DOI:https://doi.org/10.1038/s41588-025-02121-5
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