The Farm Animal Genotype-Tissue Expression (FarmGTEx) Project

Lingzhao Fang¹, Jinyan Teng², Qing Lin^{3

2}, Zhonghao Bai³, Shuli Liu^{4

5}, Dailu Guan⁶, Bingjie Li⁷, Yahui Gao², Yali Hou⁸, Mian Gong^{3

8}, Zhangyuan Pan⁸, Ying Yu⁹, Emily L Clark¹⁰, Jacqueline Smith¹⁰, Konrad Rawlik¹¹, Ruidong Xiang^{12

13

14}, Amanda J Chamberlain^{12

15}, Michael E Goddard^{12

14}, Mathew Littlejohn^{16

17}, Greger Larson¹⁸, David E MacHugh^{19

20

21}, John F O'Grady¹⁹, Peter Sørensen³, Goutam Sahana³, Mogens Sandø Lund³, Zhihua Jiang²², Xiangchun Pan², Wentao Gong², Haihan Zhang²³, Xi He²³, Yuebo Zhang²³, Ning Gao²³, Jun He²³, Guoqiang Yi²⁴, Yuwen Liu²⁴, Zhonglin Tang²⁴, Pengju Zhao²⁵, Yang Zhou^{26

27}, Liangliang Fu²⁶, Xiao Wang²⁸, Dan Hao²⁹, Lei Liu²⁷, Siqian Chen⁹, Robert S Young^{30

31}, Xia Shen^{30

32

33

34}, Charley Xia^{35

36}, Hao Cheng⁶, Li Ma³⁷, John B Cole^{38

39

40}, Ransom L Baldwin 6th⁴¹, Cong-Jun Li⁴¹, Curtis P Van Tassell⁴¹, Benjamin D Rosen⁴¹, Nayan Bhowmik⁴¹, Joan Lunney⁴², Wansheng Liu⁴³, Leluo Guan^{44

45}, Xin Zhao⁴⁶, Eveline M Ibeagha-Awemu⁴⁷, Yonglun Luo^{48

49}, Lin Lin^{48

49}, Oriol Canela-Xandri⁵⁰, Martijn F L Derks⁵¹, Richard P M A Crooijmans⁵¹, Marta Gòdia⁵¹, Ole Madsen⁵¹, Martien A M Groenen⁵¹, James E Koltes⁵², Christopher K Tuggle⁵², Fiona M McCarthy⁵³, Dominique Rocha⁵⁴, Elisabetta Giuffra⁵⁴, Marcel Amills^{55

56}, Alex Clop^{55

57}, Maria Ballester⁵⁸, Gwenola Tosser-Klopp⁵⁹, Jing Li^{3

60}, Chao Fang⁶¹, Ming Fang⁶², Qishan Wang⁶³, Zhuocheng Hou⁹, Qin Wang⁹, Fuping Zhao⁸, Lin Jiang⁸, Guiping Zhao⁸, Zhengkui Zhou⁸, Rong Zhou⁸, Hehe Liu⁶⁴, Juan Deng⁶⁴, Long Jin⁶⁴, Mingzhou Li⁶⁴, Delin Mo⁶⁵, Xiaohong Liu⁶⁵, Yaosheng Chen⁶⁵, Xiaolong Yuan², Jiaqi Li², Shuhong Zhao^{26

27}, Yi Zhang⁹, Xiangdong Ding⁹, Dongxiao Sun⁹, Hui-Zeng Sun⁶⁶, Cong Li⁶⁷, Yu Wang⁶⁷, Yu Jiang⁶⁷, Dongdong Wu⁶⁸, Wenwen Wang⁶⁹, Xinzhong Fan⁶⁹, Qin Zhang⁶⁹, Kui Li²⁴, Hao Zhang⁹, Ning Yang⁹, Xiaoxiang Hu⁷⁰, Wen Huang⁷¹, Jiuzhou Song³⁷, Yang Wu⁷², Jian Yang^{4

5}, Weiwei Wu⁷³, Claudia Kasper⁷⁴, Xinfeng Liu^{3

75}, Xiaofei Yu⁷⁶, Leilei Cui^{77

78}, Xiang Zhou⁷⁹, Seyoung Kim⁸⁰, Wei Li⁸¹, Hae Kyung Im⁸², Edward S Buckler^{83

84

85}, Bing Ren⁸⁶, Michael C Schatz⁸⁷, Jingyi Jessica Li⁸⁸, Abraham A Palmer^{89

90}, Laurent Frantz^{91

92}, Huaijun Zhou⁹³, Zhe Zhang⁹⁴, George E Liu⁹⁵; FarmGTEx Consortium

Collaborators, Affiliations

Collaborators

FarmGTEx Consortium:
Curtis P Van Tassell

Affiliations

¹ Center for Quantitative Genetics and Genomics, Aarhus University, Aarhus, Denmark. lingzhao.fang@qgg.au.dk.
² 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.
³ Center for Quantitative Genetics and Genomics, Aarhus University, Aarhus, Denmark.
⁴ Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, China.
⁵ School of Life Sciences, Westlake University, Hangzhou, China.
⁶ Department of Animal Science, University of California, Davis, Davis, CA, USA.
⁷ Department of Animal and Veterinary Sciences, Scotland's Rural College, Midlothian, UK.
⁸ Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China.
⁹ 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.
¹⁰ The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, UK.
¹¹ Baillie Gifford Pandemic Science Hub, Centre for Inflammation Research, Institute for Regeneration and Repair, the University of Edinburgh, Edinburgh, UK.
¹² Agriculture Victoria Research, AgriBio, Centre for AgriBioscience, Bundoora, Victoria, Australia.
¹³ Cambridge Baker Systems Genomics Initiative, Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia.
¹⁴ School of Agriculture, Food and Ecosystem Sciences, the University of Melbourne, Parkville, Victoria, Australia.
¹⁵ School of Applied Systems Biology, La Trobe University, Bundoora, Victoria, Australia.
¹⁶ Research and Development, Livestock Improvement Corporation, Hamilton, New Zealand.
¹⁷ AL Rae Centre for Genetics and Breeding, Massey University, Palmerston North, New Zealand.
¹⁸ The Palaeogenomics and Bio-Archaeology Research Network, School of Archaeology, University of Oxford, Oxford, UK.
¹⁹ UCD School of Agriculture and Food Science, University College Dublin, Belfield, Dublin, Ireland.
²⁰ UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Belfield, Dublin, Ireland.
²¹ UCD One Health Centre, University College Dublin, Belfield, Dublin, Ireland.
²² Department of Animal Sciences and Center for Reproductive Biology, Washington State University, Pullman, WA, USA.
²³ College of Animal Science and Technology, Hunan Agricultural University, Changsha, China.
²⁴ 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.
²⁵ Hainan Institute, Zhejiang University, Yongyou Industry Park, Yazhou Bay Sci-Tech City, Sanya, China.
²⁶ Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of the Ministry of Education, Huazhong Agricultural University, Wuhan, China.
²⁷ Yazhouwan National Laboratory, Sanya, China.
²⁸ Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, China.
²⁹ Poultry Institute, Shandong Academy of Agricultural Sciences, Jinan, China.
³⁰ Usher Institute, University of Edinburgh, Edinburgh, UK.
³¹ Zhejiang University-University of Edinburgh Institute, Zhejiang University, Haining, P. R. China.
³² State Key Laboratory of Genetic Engineering, Center for Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai, China.
³³ Center for Intelligent Medicine Research, Greater Bay Area Institute of Precision Medicine (Guangzhou), Fudan University, Guangzhou, China.
³⁴ Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden.
³⁵ Lothian Birth Cohort studies, University of Edinburgh, Edinburgh, UK.
³⁶ Department of Psychology, University of Edinburgh, Edinburgh, UK.
³⁷ Department of Animal and Avian Sciences, University of Maryland, College Park, MD, USA.
³⁸ Council on Dairy Cattle Breeding, Bowie, MD, USA.
³⁹ Department of Animal Sciences, Donald Henry Barron Reproductive and Perinatal Biology Research Program and the Genetics Institute, University of Florida, Gainesville, FL, USA.
⁴⁰ Department of Animal Science, North Carolina State University, Raleigh, NC, USA.
⁴¹ Animal Genomics and Improvement Laboratory, Henry A. Wallace Beltsville Agricultural Research Center, Agricultural Research Service, USDA, Beltsville, MD, USA.
⁴² Animal Parasitic Diseases Laboratory, BARC, NEA, ARS, USDA, Beltsville, MD, USA.
⁴³ Department of Animal Science, Center for Reproductive Biology and Health, College of Agricultural Sciences, the Pennsylvania State University, University Park, PA, USA.
⁴⁴ Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta, Canada.
⁴⁵ Faculty of Land and Food Systems, University of British Columbia, Vancouver, British Columbia, Canada.
⁴⁶ Department of Animal Science, McGill University, Sainte-Anne-de-Bellevue, Quebec, Canada.
⁴⁷ Sherbrooke Research and Development Centre, Agriculture and Agri-Food Canada, Sherbrooke, Quebec, Canada.
⁴⁸ Department of Biomedicine, Aarhus University, Aarhus, Denmark.
⁴⁹ Steno Diabetes Center Aarhus, Aarhus University Hospital, Aarhus, Denmark.
⁵⁰ MRC Human Genetics Unit at the Institute of Genetics and Cancer, the University of Edinburgh, Edinburgh, UK.
⁵¹ Animal Breeding and Genomics, Wageningen University & Research, Wageningen, the Netherlands.
⁵² Department of Animal Science, Iowa State University, Ames, IA, USA.
⁵³ University of Arizona, Tucson, AZ, USA.
⁵⁴ GABI, AgroParisTech, INRAE, Paris-Saclay University, Jouy-en-Josas, France.
⁵⁵ Department of Animal Genetics, Centre for Research in Agricultural Genomics, CSIC-IRTA-UAB-UB, Campus de la Universitat Autònoma de Barcelona, Bellaterra, Spain.
⁵⁶ Departament de Ciència Animal i dels Aliments, Universitat Autònoma de Barcelona, Bellaterra, Spain.
⁵⁷ Consejo Superior de Investigaciones Científicas, Barcelona, Spain.
⁵⁸ Animal Breeding and Genetics Programme, Institut de Recerca i Tecnologia Agroalimentàries (IRTA), Torre Marimon, Caldes de Montbui, Spain.
⁵⁹ GenPhySE, INRAE, ENVT, Université de Toulouse, Castanet-Tolosan, France.
⁶⁰ School of Agriculture and Life Sciences, Kunming University, Kunming, China.
⁶¹ LC-Bio Technologies, Co., Ltd, Hangzhou, China.
⁶² Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture and Rural Affairs, Jimei University, Xiamen, China.
⁶³ College of Animal Sciences, Zhejiang University, Hangzhou, China.
⁶⁴ College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China.
⁶⁵ State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China.
⁶⁶ Key Laboratory of Dairy Cow Genetic Improvement and Milk Quality Research of Zhejiang Province, College of Animal Sciences, Zhejiang University, Hangzhou, China.
⁶⁷ College of Animal Science and Technology, Northwest A&F University, Yangling, China.
⁶⁸ Key Laboratory of Genetic Evolution and Animal Models, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.
⁶⁹ Shandong Provincial Key Laboratory for Livestock Germplasm Innovation and Utilization, College of Animal Science, Shandong Agricultural University, Tai'an, China.
⁷⁰ State Key Laboratory of Animal Biotech Breeding, College of Biological Sciences, China Agricultural University, Beijing, China.
⁷¹ Department of Animal Science, Michigan State University, East Lansing, MI, USA.
⁷² Institute of Rare Diseases, West China Hospital of Sichuan University, Chengdu, China.
⁷³ Institute of Animal Science, Xinjiang Academy of Animal Science, Ürümqi City, China.
⁷⁴ Animal GenoPhenomics, Animal Production Systems and Animal Health, Agroscope Posieux, Fribourg, Switzerland.
⁷⁵ State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystem, College of Ecology, Lanzhou University, Lanzhou, China.
⁷⁶ College of Marine Life Sciences, Ocean University of China, Qingdao, China.
⁷⁷ School of Life Sciences, Nanchang University, Nanchang, China.
⁷⁸ Jiangxi Province Key Laboratory of Aging and Disease, Human Aging Research Institute and School of Life Science, Nanchang University, Jiangxi, China.
⁷⁹ Department of Biostatistics, University of Michigan, Ann Arbor, MI, USA.
⁸⁰ Department of Epidemiology, School of Public Health, University of Pittsburgh, Pittsburgh, PA, USA.
⁸¹ Division of Computational Biomedicine, Department of Biological Chemistry, School of Medicine, University of California, Irvine, Irvine, CA, USA.
⁸² Department of Medicine and Human Genetics, the University of Chicago, Chicago, IL, USA.
⁸³ Section of Plant Breeding and Genetics, Cornell University, Ithaca, NY, USA.
⁸⁴ Institute for Genomic Diversity, Cornell University, Ithaca, NY, USA.
⁸⁵ Agricultural Research Service, United States Department of Agriculture, Ithaca, NY, USA.
⁸⁶ 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.
⁸⁷ Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA.
⁸⁸ Department of Statistics and Data Science, University of California, Los Angeles, Los Angeles, CA, USA. lijy03@g.ucla.edu.
⁸⁹ Department of Psychiatry, University of California San Diego, La Jolla, CA, USA. aap@ucsd.edu.
⁹⁰ Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA. aap@ucsd.edu.
⁹¹ Palaeogenomics Group, Institute of Palaeoanatomy, Domestication Research and the History of Veterinary Medicine, Ludwig-Maximilians-Universität, Munich, Germany. laurent.frantz@lmu.de.
⁹² School of Biological and Behavioural Sciences, Queen Mary University of London, London, UK. laurent.frantz@lmu.de.
⁹³ Department of Animal Science, University of California, Davis, Davis, CA, USA. hzhou@ucdavis.edu.
⁹⁴ 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. zhezhang@scau.edu.cn.
⁹⁵ Animal Genomics and Improvement Laboratory, Henry A. Wallace Beltsville Agricultural Research Center, Agricultural Research Service, USDA, Beltsville, MD, USA. george.liu@usda.gov.

PMID: 40097783
DOI: 10.1038/s41588-025-02121-5

Review

The Farm Animal Genotype-Tissue Expression (FarmGTEx) Project

Lingzhao Fang et al. Nat Genet. 2025 Apr.

. 2025 Apr;57(4):786-796.

doi: 10.1038/s41588-025-02121-5. Epub 2025 Mar 17.

Authors

Collaborators

FarmGTEx Consortium:
Curtis P Van Tassell

Affiliations

¹ Center for Quantitative Genetics and Genomics, Aarhus University, Aarhus, Denmark. lingzhao.fang@qgg.au.dk.
² 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.
³ Center for Quantitative Genetics and Genomics, Aarhus University, Aarhus, Denmark.
⁴ Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, China.
⁵ School of Life Sciences, Westlake University, Hangzhou, China.
⁶ Department of Animal Science, University of California, Davis, Davis, CA, USA.
⁷ Department of Animal and Veterinary Sciences, Scotland's Rural College, Midlothian, UK.
⁸ Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China.
⁹ 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.
¹⁰ The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, UK.
¹¹ Baillie Gifford Pandemic Science Hub, Centre for Inflammation Research, Institute for Regeneration and Repair, the University of Edinburgh, Edinburgh, UK.
¹² Agriculture Victoria Research, AgriBio, Centre for AgriBioscience, Bundoora, Victoria, Australia.
¹³ Cambridge Baker Systems Genomics Initiative, Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia.
¹⁴ School of Agriculture, Food and Ecosystem Sciences, the University of Melbourne, Parkville, Victoria, Australia.
¹⁵ School of Applied Systems Biology, La Trobe University, Bundoora, Victoria, Australia.
¹⁶ Research and Development, Livestock Improvement Corporation, Hamilton, New Zealand.
¹⁷ AL Rae Centre for Genetics and Breeding, Massey University, Palmerston North, New Zealand.
¹⁸ The Palaeogenomics and Bio-Archaeology Research Network, School of Archaeology, University of Oxford, Oxford, UK.
¹⁹ UCD School of Agriculture and Food Science, University College Dublin, Belfield, Dublin, Ireland.
²⁰ UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Belfield, Dublin, Ireland.
²¹ UCD One Health Centre, University College Dublin, Belfield, Dublin, Ireland.
²² Department of Animal Sciences and Center for Reproductive Biology, Washington State University, Pullman, WA, USA.
²³ College of Animal Science and Technology, Hunan Agricultural University, Changsha, China.
²⁴ 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.
²⁵ Hainan Institute, Zhejiang University, Yongyou Industry Park, Yazhou Bay Sci-Tech City, Sanya, China.
²⁶ Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of the Ministry of Education, Huazhong Agricultural University, Wuhan, China.
²⁷ Yazhouwan National Laboratory, Sanya, China.
²⁸ Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, China.
²⁹ Poultry Institute, Shandong Academy of Agricultural Sciences, Jinan, China.
³⁰ Usher Institute, University of Edinburgh, Edinburgh, UK.
³¹ Zhejiang University-University of Edinburgh Institute, Zhejiang University, Haining, P. R. China.
³² State Key Laboratory of Genetic Engineering, Center for Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai, China.
³³ Center for Intelligent Medicine Research, Greater Bay Area Institute of Precision Medicine (Guangzhou), Fudan University, Guangzhou, China.
³⁴ Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden.
³⁵ Lothian Birth Cohort studies, University of Edinburgh, Edinburgh, UK.
³⁶ Department of Psychology, University of Edinburgh, Edinburgh, UK.
³⁷ Department of Animal and Avian Sciences, University of Maryland, College Park, MD, USA.
³⁸ Council on Dairy Cattle Breeding, Bowie, MD, USA.
³⁹ Department of Animal Sciences, Donald Henry Barron Reproductive and Perinatal Biology Research Program and the Genetics Institute, University of Florida, Gainesville, FL, USA.
⁴⁰ Department of Animal Science, North Carolina State University, Raleigh, NC, USA.
⁴¹ Animal Genomics and Improvement Laboratory, Henry A. Wallace Beltsville Agricultural Research Center, Agricultural Research Service, USDA, Beltsville, MD, USA.
⁴² Animal Parasitic Diseases Laboratory, BARC, NEA, ARS, USDA, Beltsville, MD, USA.
⁴³ Department of Animal Science, Center for Reproductive Biology and Health, College of Agricultural Sciences, the Pennsylvania State University, University Park, PA, USA.
⁴⁴ Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta, Canada.
⁴⁵ Faculty of Land and Food Systems, University of British Columbia, Vancouver, British Columbia, Canada.
⁴⁶ Department of Animal Science, McGill University, Sainte-Anne-de-Bellevue, Quebec, Canada.
⁴⁷ Sherbrooke Research and Development Centre, Agriculture and Agri-Food Canada, Sherbrooke, Quebec, Canada.
⁴⁸ Department of Biomedicine, Aarhus University, Aarhus, Denmark.
⁴⁹ Steno Diabetes Center Aarhus, Aarhus University Hospital, Aarhus, Denmark.
⁵⁰ MRC Human Genetics Unit at the Institute of Genetics and Cancer, the University of Edinburgh, Edinburgh, UK.
⁵¹ Animal Breeding and Genomics, Wageningen University & Research, Wageningen, the Netherlands.
⁵² Department of Animal Science, Iowa State University, Ames, IA, USA.
⁵³ University of Arizona, Tucson, AZ, USA.
⁵⁴ GABI, AgroParisTech, INRAE, Paris-Saclay University, Jouy-en-Josas, France.
⁵⁵ Department of Animal Genetics, Centre for Research in Agricultural Genomics, CSIC-IRTA-UAB-UB, Campus de la Universitat Autònoma de Barcelona, Bellaterra, Spain.
⁵⁶ Departament de Ciència Animal i dels Aliments, Universitat Autònoma de Barcelona, Bellaterra, Spain.
⁵⁷ Consejo Superior de Investigaciones Científicas, Barcelona, Spain.
⁵⁸ Animal Breeding and Genetics Programme, Institut de Recerca i Tecnologia Agroalimentàries (IRTA), Torre Marimon, Caldes de Montbui, Spain.
⁵⁹ GenPhySE, INRAE, ENVT, Université de Toulouse, Castanet-Tolosan, France.
⁶⁰ School of Agriculture and Life Sciences, Kunming University, Kunming, China.
⁶¹ LC-Bio Technologies, Co., Ltd, Hangzhou, China.
⁶² Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture and Rural Affairs, Jimei University, Xiamen, China.
⁶³ College of Animal Sciences, Zhejiang University, Hangzhou, China.
⁶⁴ College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China.
⁶⁵ State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China.
⁶⁶ Key Laboratory of Dairy Cow Genetic Improvement and Milk Quality Research of Zhejiang Province, College of Animal Sciences, Zhejiang University, Hangzhou, China.
⁶⁷ College of Animal Science and Technology, Northwest A&F University, Yangling, China.
⁶⁸ Key Laboratory of Genetic Evolution and Animal Models, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.
⁶⁹ Shandong Provincial Key Laboratory for Livestock Germplasm Innovation and Utilization, College of Animal Science, Shandong Agricultural University, Tai'an, China.
⁷⁰ State Key Laboratory of Animal Biotech Breeding, College of Biological Sciences, China Agricultural University, Beijing, China.
⁷¹ Department of Animal Science, Michigan State University, East Lansing, MI, USA.
⁷² Institute of Rare Diseases, West China Hospital of Sichuan University, Chengdu, China.
⁷³ Institute of Animal Science, Xinjiang Academy of Animal Science, Ürümqi City, China.
⁷⁴ Animal GenoPhenomics, Animal Production Systems and Animal Health, Agroscope Posieux, Fribourg, Switzerland.
⁷⁵ State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystem, College of Ecology, Lanzhou University, Lanzhou, China.
⁷⁶ College of Marine Life Sciences, Ocean University of China, Qingdao, China.
⁷⁷ School of Life Sciences, Nanchang University, Nanchang, China.
⁷⁸ Jiangxi Province Key Laboratory of Aging and Disease, Human Aging Research Institute and School of Life Science, Nanchang University, Jiangxi, China.
⁷⁹ Department of Biostatistics, University of Michigan, Ann Arbor, MI, USA.
⁸⁰ Department of Epidemiology, School of Public Health, University of Pittsburgh, Pittsburgh, PA, USA.
⁸¹ Division of Computational Biomedicine, Department of Biological Chemistry, School of Medicine, University of California, Irvine, Irvine, CA, USA.
⁸² Department of Medicine and Human Genetics, the University of Chicago, Chicago, IL, USA.
⁸³ Section of Plant Breeding and Genetics, Cornell University, Ithaca, NY, USA.
⁸⁴ Institute for Genomic Diversity, Cornell University, Ithaca, NY, USA.
⁸⁵ Agricultural Research Service, United States Department of Agriculture, Ithaca, NY, USA.
⁸⁶ 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.
⁸⁷ Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA.
⁸⁸ Department of Statistics and Data Science, University of California, Los Angeles, Los Angeles, CA, USA. lijy03@g.ucla.edu.
⁸⁹ Department of Psychiatry, University of California San Diego, La Jolla, CA, USA. aap@ucsd.edu.
⁹⁰ Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA. aap@ucsd.edu.
⁹¹ Palaeogenomics Group, Institute of Palaeoanatomy, Domestication Research and the History of Veterinary Medicine, Ludwig-Maximilians-Universität, Munich, Germany. laurent.frantz@lmu.de.
⁹² School of Biological and Behavioural Sciences, Queen Mary University of London, London, UK. laurent.frantz@lmu.de.
⁹³ Department of Animal Science, University of California, Davis, Davis, CA, USA. hzhou@ucdavis.edu.
⁹⁴ 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. zhezhang@scau.edu.cn.
⁹⁵ Animal Genomics and Improvement Laboratory, Henry A. Wallace Beltsville Agricultural Research Center, Agricultural Research Service, USDA, Beltsville, MD, USA. george.liu@usda.gov.

PMID: 40097783
DOI: 10.1038/s41588-025-02121-5

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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Conflict of interest statement

Competing interests: The authors declare no competing interests.

References

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The Farm Animal Genotype-Tissue Expression (FarmGTEx) Project

Collaborators

Affiliations

The Farm Animal Genotype-Tissue Expression (FarmGTEx) Project

Authors

Collaborators

Affiliations

Abstract

Conflict of interest statement

References

Publication types

MeSH terms

Grants and funding

LinkOut - more resources

Full Text Sources

Medical