Evidence map›Paper›PMID 38177344›Full record

ArticleNature genetics2024

A compendium of genetic regulatory effects across pig tissues.

Jinyan Teng, Yahui Gao, Hongwei Yin, Zhonghao Bai, Shuli Liu, Haonan Zeng, PigGTEx Consortium, Lijing Bai, Zexi Cai, Bingru Zhao and 93 more

Open access · hybridAbstract read
In one paragraph

Article in Nature genetics, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 164 papers, 4 of them syntheses that pooled it.

0numbers the graph read from it
0cells of the map it votes in
164citing papers in PubMed, 4 pooled it
147.5field-weighted citation impact, top 1% of its field
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

164 citing papers in PubMed, 4 syntheses or guidelines pooled it, 236 citations in OpenAlex.

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104 more citing papers are in PubMed but not listed here.

4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

103 authors at 20 institutions in 10 countries.

Jinyan Teng *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.ORCID http://orcid.org/0000-0002-3046-1452
Yahui Gao *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.
Hongwei Yin *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.ORCID http://orcid.org/0000-0002-9373-5166
Zhonghao Bai *Center for Quantitative Genetics and Genomics, Aarhus University, Aarhus, Denmark.
Shuli Liu *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.
Haonan Zeng *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.
PigGTEx Consortium
Lijing BaiShenzhen 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.
Zexi CaiCenter for Quantitative Genetics and Genomics, Aarhus University, Aarhus, Denmark.ORCID http://orcid.org/0000-0002-9579-3415
Bingru ZhaoCollege of Animal Science and Technology, China Agricultural University, Beijing, China.
Xiujin LiGuangdong Provincial Key Laboratory of Waterfowl Healthy Breeding, College of Animal Science and Technology, Zhongkai University of Agriculture and Engineering, Guangzhou, China.
Zhiting XuState 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.
Qing LinState 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.
Zhangyuan PanDepartment of Animal Science, University of California, Davis, Davis, CA, USA.
Wenjing YangCollege of Animal Science and Technology, China Agricultural University, Beijing, China.
Xiaoshan YuMRC Human Genetics Unit at the Institute of Genetics and Cancer, The University of Edinburgh, Edinburgh, UK.
Dailu GuanDepartment of Animal Science, University of California, Davis, Davis, CA, USA.ORCID http://orcid.org/0000-0001-8800-3158
Yali HouBeijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, China.ORCID http://orcid.org/0000-0002-7421-2431
Brittney N KeelARS, USDA, U.S. Meat Animal Research Center, Clay Center, NE, USA.
Gary A RohrerARS, USDA, U.S. Meat Animal Research Center, Clay Center, NE, USA.ORCID http://orcid.org/0000-0002-8252-9308
Amanda K Lindholm-PerryARS, USDA, U.S. Meat Animal Research Center, Clay Center, NE, USA.
William T OliverARS, USDA, U.S. Meat Animal Research Center, Clay Center, NE, USA.
Maria BallesterAnimal Breeding and Genetics Programme, Institut de Recerca i Tecnologia Agroalimentàries (IRTA), Torre Marimon, Caldes de Montbui, Spain.ORCID http://orcid.org/0000-0002-5413-4640
Daniel Crespo-PiazueloAnimal Breeding and Genetics Programme, Institut de Recerca i Tecnologia Agroalimentàries (IRTA), Torre Marimon, Caldes de Montbui, Spain.ORCID http://orcid.org/0000-0001-7896-2507
Raquel QuintanillaAnimal Breeding and Genetics Programme, Institut de Recerca i Tecnologia Agroalimentàries (IRTA), Torre Marimon, Caldes de Montbui, Spain.
Oriol Canela-XandriMRC Human Genetics Unit at the Institute of Genetics and Cancer, The University of Edinburgh, Edinburgh, UK.
Konrad RawlikBaillie Gifford Pandemic Science Hub, University of Edinburgh, Edinburgh, UK.ORCID http://orcid.org/0000-0002-0010-370X
Charley XiaLothian Birth Cohort studies, University of Edinburgh, Edinburgh, UK.
Yuelin YaoMRC Human Genetics Unit at the Institute of Genetics and Cancer, The University of Edinburgh, Edinburgh, UK.ORCID http://orcid.org/0000-0001-9868-2801
Qianyi ZhaoShenzhen 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.
Wenye YaoShenzhen 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.
Liu YangShenzhen 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.
Houcheng LiCenter for Quantitative Genetics and Genomics, Aarhus University, Aarhus, Denmark.
Huicong ZhangCenter for Quantitative Genetics and Genomics, Aarhus University, Aarhus, Denmark.
Wang LiaoMRC Human Genetics Unit at the Institute of Genetics and Cancer, The University of Edinburgh, Edinburgh, UK.
Tianshuo ChenMRC Human Genetics Unit at the Institute of Genetics and Cancer, The University of Edinburgh, Edinburgh, UK.
Peter Karlskov-MortensenAnimal Genetics, Bioinformatics and Breeding, Department of Veterinary and Animal Sciences, University of Copenhagen, Copenhagen, Denmark.ORCID http://orcid.org/0000-0002-2491-2763
Merete FredholmAnimal Genetics, Bioinformatics and Breeding, Department of Veterinary and Animal Sciences, University of Copenhagen, Copenhagen, Denmark.
Marcel AmillsDepartment of Animal Genetics, Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus de la Universitat Autònoma de Barcelona, Bellaterra, Spain.ORCID http://orcid.org/0000-0002-8999-0770
Alex ClopDepartment of Animal Genetics, Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus de la Universitat Autònoma de Barcelona, Bellaterra, Spain.ORCID http://orcid.org/0000-0001-9238-2728
Elisabetta GiuffraParis-Saclay University, INRAE, AgroParisTech, GABI, Jouy-en-Josas, France.ORCID http://orcid.org/0000-0001-9568-2056
Jun WuState 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.
Xiaodian CaiState 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.
Shuqi DiaoState 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.
Xiangchun PanState 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.
Chen WeiState 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.
Jinghui LiDepartment of Animal Science, University of California, Davis, Davis, CA, USA.
Hao ChengDepartment of Animal Science, University of California, Davis, Davis, CA, USA.
Sheng WangState Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.
Guosheng SuCenter for Quantitative Genetics and Genomics, Aarhus University, Aarhus, Denmark.
Goutam SahanaCenter for Quantitative Genetics and Genomics, Aarhus University, Aarhus, Denmark.ORCID http://orcid.org/0000-0001-7608-7577
Mogens Sandø LundCenter for Quantitative Genetics and Genomics, Aarhus University, Aarhus, Denmark.
Jack C M DekkersDepartment of Animal Science, Iowa State University, Ames, IA, USA.
Luke KramerDepartment of Animal Science, Iowa State University, Ames, IA, USA.
Christopher K TuggleDepartment of Animal Science, Iowa State University, Ames, IA, USA.ORCID http://orcid.org/0000-0002-4229-5316
Ryan CorbettDepartment of Animal Science, Iowa State University, Ames, IA, USA.
Martien A M GroenenAnimal Breeding and Genomics, Wageningen University and Research, Wageningen, The Netherlands.ORCID http://orcid.org/0000-0003-0484-4545
Ole MadsenAnimal Breeding and Genomics, Wageningen University and Research, Wageningen, The Netherlands.
Marta GòdiaAnimal Breeding and Genomics, Wageningen University and Research, Wageningen, The Netherlands.
Dominique RochaParis-Saclay University, INRAE, AgroParisTech, GABI, Jouy-en-Josas, France.
Mathieu CharlesParis-Saclay University, INRAE, AgroParisTech, GABI, SIGENAE, Jouy-en-Josas, France.ORCID http://orcid.org/0000-0001-6491-1928
Cong-Jun LiAnimal Genomics and Improvement Laboratory, Henry A. Wallace Beltsville Agricultural Research Center, Agricultural Research Service (ARS), U.S. Department of Agriculture (USDA), Beltsville, MD, USA.ORCID http://orcid.org/0000-0003-1389-9820
Hubert PauschAnimal Genomics, ETH Zurich, Universitaetstrasse 2, Zurich, Switzerland.ORCID http://orcid.org/0000-0002-0501-6760
Xiaoxiang HuState Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China.ORCID http://orcid.org/0000-0001-7045-0283
Laurent FrantzPalaeogenomics Group, Department of Veterinary Sciences, Ludwig Maximilian University, Munich, Germany.
Yonglun LuoDepartment of Biomedicine, Aarhus University, Aarhus, Denmark.ORCID http://orcid.org/0000-0002-0007-7759
Lin LinDepartment of Biomedicine, Aarhus University, Aarhus, Denmark.ORCID http://orcid.org/0000-0002-7546-4948
Zhongyin ZhouState Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.
Zhe ZhangDepartment of Animal Science, College of Animal Sciences, Zhejiang University, Hangzhou, China.
Zitao ChenDepartment of Animal Science, College of Animal Sciences, Zhejiang University, Hangzhou, China.
Leilei CuiSchool of Life Sciences, Nanchang University, Nanchang, China.
Ruidong XiangFaculty of Veterinary and Agricultural Science, The University of Melbourne, Parkville, Victoria, Australia.
Xia ShenState Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China.ORCID http://orcid.org/0000-0003-4390-1979
Pinghua LiInstitute of Swine Science, Nanjing Agricultural University, Nanjing, China.
Ruihua HuangInstitute of Swine Science, Nanjing Agricultural University, Nanjing, China.
Guoqing TangFarm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China.
Mingzhou LiFarm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China.ORCID http://orcid.org/0000-0001-8681-7684
Yunxiang ZhaoCollege of Animal Science and Technology, Guangxi University, Nanning, China.
Guoqiang YiShenzhen 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.ORCID http://orcid.org/0000-0001-8248-9126
Zhonglin TangShenzhen 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.ORCID http://orcid.org/0000-0002-4538-4349
Jicai JiangDepartment of Animal Science, North Carolina State University, Raleigh, NC, USA.
Fuping ZhaoInstitute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China.
Xiaolong YuanState 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.
Xiaohong LiuState Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China.
Yaosheng ChenState Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China.
Xuewen XuKey Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education and College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China.
Shuhong ZhaoKey Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education and College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China.ORCID http://orcid.org/0000-0002-3997-2320
Pengju ZhaoHainan Institute, Zhejiang University, Yongyou Industry Park, Yazhou Bay Sci-Tech City, Sanya, China.
Chris HaleyMRC Human Genetics Unit at the Institute of Genetics and Cancer, The University of Edinburgh, Edinburgh, UK.
Huaijun ZhouDepartment of Animal Science, University of California, Davis, Davis, CA, USA.ORCID http://orcid.org/0000-0001-6023-9521
Qishan WangDepartment of Animal Science, College of Animal Sciences, Zhejiang University, Hangzhou, China.ORCID http://orcid.org/0000-0002-6475-0009
Yuchun PanDepartment of Animal Science, College of Animal Sciences, Zhejiang University, Hangzhou, China.
Xiangdong DingCollege of Animal Science and Technology, China Agricultural University, Beijing, China.
Li MaDepartment of Animal and Avian Sciences, University of Maryland, College Park, MD, USA.ORCID http://orcid.org/0000-0003-1038-1081
Jiaqi LiState 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.
Pau NavarroMRC Human Genetics Unit at the Institute of Genetics and Cancer, The University of Edinburgh, Edinburgh, UK.ORCID http://orcid.org/0000-0001-5576-8584
Qin ZhangCollege of Animal Science and Technology, Shandong Agricultural University, Tai'an, China.
Bingjie LiScotland's Rural College (SRUC), Roslin Institute Building, Midlothian, UK.ORCID http://orcid.org/0000-0002-8528-1889
Albert TenesaMRC Human Genetics Unit at the Institute of Genetics and Cancer, The University of Edinburgh, Edinburgh, UK. albert.tenesa@ed.ac.uk.ORCID http://orcid.org/0000-0003-4884-4475
Kui LiShenzhen 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. likui@caas.cn.ORCID http://orcid.org/0000-0002-5686-3898
George E LiuAnimal Genomics and Improvement Laboratory, Henry A. Wallace Beltsville Agricultural Research Center, Agricultural Research Service (ARS), U.S. Department of Agriculture (USDA), Beltsville, MD, USA. george.liu@usda.gov.ORCID http://orcid.org/0000-0003-0192-6705
Zhe ZhangState 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. zhezhang@scau.edu.cn.
Lingzhao FangCenter for Quantitative Genetics and Genomics, Aarhus University, Aarhus, Denmark. lingzhao.fang@qgg.au.dk.ORCID http://orcid.org/0000-0003-1103-3679
South China Agricultural University · CNAarhus University · DKAgricultural Genomics Institute at Shenzhen · CNInstitute of Genetics and Cancer · GBRoman L. Hruska U.S. Meat Animal Research Center · USChina Agricultural University · CNIowa State University · USRoslin Institute · GBAgricultural Research Service · USAgroParisTech · FRInstitute of Agrifood Research and Technology · ESUniversitat Autònoma de Barcelona · ESUniversity of California, Davis · USZhejiang University · CNChinese Academy of Agricultural Sciences · CNHuazhong Agricultural University · CNKunming Institute of Zoology · CNNanjing Agricultural University · CNSichuan Agricultural University · CNSteno Diabetes Centers · DK

Funding

National Natural Science Foundation of China (National Science Foundation of China) 32022078RCUK | Biotechnology and Biological Sciences Research Council (BBSRC) BBS/E/D/10002070RCUK | Biotechnology and Biological Sciences Research Council (BBSRC) BBS/E/D/30002275RCUK | Medical Research Council (MRC) MR/P015514/1RCUK | Medical Research Council (MRC) MR/R025851/1United States Department of Agriculture | Agricultural Research Service (USDA Agricultural Research Service) 2019-67015-29321United States Department of Agriculture | Agricultural Research Service (USDA Agricultural Research Service) 2021-67015-33409
6 · The paper itself

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.

Indexed as

Gene Expression ProfilingGene Expression RegulationAnimalsGenotypeHumansPhenotypeSequence Analysis, RNASwine

Identifiers

PMID38177344
PMCPMC10786720
OpenAlexW4390582245

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.