Analyses of pig genomes provide insight into porcine demography and evolution

Research output: Contribution to journal/Conference contribution in journal/Contribution to newspaperJournal articleResearchpeer-review

  • Martien A M Groenen, Animal Breeding and Genomics Centre, Wageningen University, Netherlands
  • Alan L Archibald, The Roslin Institute and R(D)SVS, University of Edinburgh, United Kingdom
  • Hirohide Uenishi, National Institute of Agrobiological Sciences, Japan
  • Christopher K Tuggle, Department of Animal Science and Center for Integrated Animal Genomics, Iowa State University, United States
  • Yasuhiro Takeuchi, MRC/UCL Centre for Medical Molecular Virology and Wohl Virion Centre, Division of Infection & Immunity, University College London, United Kingdom
  • Max F Rothschild, Department of Animal Science and Center for Integrated Animal Genomics, Iowa State University, United States
  • Claire Rogel-Gaillard, INRA, Laboratory of Animal Genetics and Integrative Biology/AgroParisTech, Laboratory of Animal Genetics and Integrative Biology/CEA, DSV, IRCM, Laboratoire de Radiobiologie et Etude du Ge´nome, France
  • Chankyu Park, Department of Animal Biotechnology, Konkuk University, 1 Hwayang-dong, Kwangjin-gu, Seoul, Korea, Republic of
  • Denis Milan, Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, United Kingdom
  • Hendrik-Jan Megens, Animal Breeding and Genomics Centre, Wageningen University, Netherlands
  • Shengting Li, Denmark
  • Denis M Larkin, Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, United Kingdom
  • Heebal Kim, Department of Agricultural Biotechnology and C&K Genomics, Seoul National University, Korea, Republic of
  • Laurent A F Frantz, Animal Breeding and Genomics Centre, Wageningen University, Netherlands
  • Mario Caccamo, The Genome Analysis Centre, Norwich Research Park, United Kingdom
  • Hyeonju Ahn, Department of Agricultural Biotechnology and C&KGenomics, Seoul NationalUniversity, Korea, Republic of
  • Bronwen L Aken, Wellcome Trust Sanger Institute, WellcomeTrust Genome Campus, United Kingdom
  • Anna Anselmo, Parco Tecnologico Padano, Italy
  • Christian Anthon, Center for non-coding RNA in Technology and Health, IBHV University of Copenhagen, Denmark
  • Loretta Auvil, Illinois Informatics Institute, University of Illinois, United States
  • Bouabid Badaoui, Parco Tecnologico Padano, Italy
  • Craig W Beattie, Department of Surgery, University of Illinois, United States
  • Christian Bendixen
  • Daniel Berman, USDA ARS BARC Animal Parasitic Diseases Laboratory, United States
  • Frank Blecha, Department of Anatomy and Physiology, College of Veterinary Medicine, Kansas State University, United States
  • Jonas Blomberg, 22Clinical Virology, Department of Medical Sciences, Uppsala University, Sweden
  • Lars Bolund
  • Mirte Bosse, Animal Breeding and Genomics Centre, Wageningen University, Netherlands
  • Sara Botti, Parco Tecnologico Padano, Italy
  • Bujie Zhan
  • ,
  • Megan Bystrom, Department of Animal Science and Center for Integrated Animal Genomics, Iowa State University, United States
  • Boris Capitanu, Illinois Informatics Institute, University of Illinois, United States
  • Denise Carvalho-Silva, European Bioinformatics Institute, Wellcome Trust Genome Campus, United Kingdom
  • Patrick Chardon, INRA, Laboratory of Animal Genetics and Integrative Biology/AgroParisTech, Laboratory of Animal Genetics and Integrative Biology, France
  • Celine Chen, Diet, Genomics, Immunology Laboratory, Beltsville Human Nutrition Research Center, United States Department of Agriculture, United States
  • Ryan Cheng, Department of Animal Science and Center for Integrated Animal Genomics, Iowa State University, United States
  • Sang-Haeng Choi, Korean Research Institute of Bioscience and Biotechnology, Korea, Republic of
  • William Chow, Wellcome Trust Sanger Institute,WellcomeTrust Genome Campus, United Kingdom
  • Richard C Clark, Wellcome Trust Sanger Institute,WellcomeTrust Genome Campus, United Kingdom
  • Christopher Clee, Wellcome Trust Sanger Institute,WellcomeTrust Genome Campus, United Kingdom
  • Richard P M A Crooijmans, Animal Breeding and Genomics Centre, Wageningen University, Netherlands
  • Harry D Dawson, Diet, Genomics, Immunology Laboratory, Beltsville Human Nutrition Research Center, United States Department of Agriculture, BARC-East, United States
  • Patrice Dehais, INRA, Laboratoire de Ge´ne´tique Cellulaire, Chemin de Borde-Rouge, France
  • Fioravante De Sapio, The Roslin Institute and R(D)SVS, University of Edinburgh, United Kingdom
  • Bert Dibbits, Animal Breeding and Genomics Centre, Wageningen University, Netherlands
  • Nizar Drou, The Genome Analysis Centre, Norwich Research Park, United Kingdom
  • Zhi-Qiang Du, Department of Animal Science and Center for Integrated Animal Genomics, Iowa State University, United States
  • Kellye Eversole, Eversole Associates and the Alliance for Animal Genome Research, United States
  • João Fadista
  • ,
  • Susan Fairley, Wellcome Trust Sanger Institute,WellcomeTrust Genome Campus, United Kingdom
  • Thomas Faraut, INRA, Laboratoire de Ge´ne´tique Cellulaire, Chemin de Borde-Rouge, France
  • Geoffrey J Faulkner, The Roslin Institute and R(D)SVS, University of Edinburgh, United Kingdom
  • Katie E Fowler, The Roslin Institute and R(D)SVS, University of Edinburgh, United Kingdom
  • Merete Fredholm, Center for non-coding RNA in Technology and Health, IBHV University of Copenhagen, Denmark
  • Eric Fritz, Department of Animal Science and Center for Integrated Animal Genomics, Iowa State University, United States
  • James G R Gilbert, Wellcome Trust Sanger Institute,WellcomeTrust Genome Campus, United Kingdom
  • Elisabetta Giuffra, INRA, Laboratory of Animal Genetics and Integrative Biology/AgroParisTech, Laboratory of Animal Genetics and Integrative Biology/CEA, DSV, IRCM, Laboratoire de Radiobiologie et Etude du Ge´nome, France
  • Jan Gorodkin, Center for non-coding RNA in Technology and Health, IBHV University of Copenhagen, Denmark
  • Darren K Griffin, School of Biosciences, The University of Kent, United Kingdom
  • Jennifer L Harrow, Wellcome Trust Sanger Institute,WellcomeTrust Genome Campus, United Kingdom
  • Alexander Hayward, Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Sweden
  • Kerstin Howe, Wellcome Trust Sanger Institute,WellcomeTrust Genome Campus, United Kingdom
  • Zhi-Liang Hu, Department of Animal Science and Center for Integrated Animal Genomics, Iowa State University, United States
  • Sean J Humphray, Wellcome Trust Sanger Institute,WellcomeTrust Genome Campus, United Kingdom
  • Toby Hunt, Wellcome Trust Sanger Institute,WellcomeTrust Genome Campus, United Kingdom
  • Henrik Hornshøj, Denmark
  • Jin-Tae Jeon, Department of Animal Sciences, College of Agriculture and Life Sciences, Gyeongsang National University, Korea, Republic of
  • Patric Jern, Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Sweden
  • Matthew Jones, Wellcome Trust Sanger Institute,WellcomeTrust Genome Campus, United Kingdom
  • Jerzy Jurka, Genetic Information Research Institute, United States
  • Hiroyuki Kanamori, National Institute of Agrobiological Sciences, Japan
  • Ronan Kapetanovic, The Roslin Institute and R(D)SVS, University of Edinburgh, United Kingdom
  • Jaebum Kim, Department of Animal Biotechnology, Konkuk University, Korea, Republic of
  • Jae-Hwan Kim, Animal Genetic Resources Station, National Institute of Animal Science, Korea, Republic of
  • Kyu-Won Kim, C&K Genomics, Korea, Republic of
  • Tae-Hun Kim, 35Animal Genomics and Bioinformatics Division, National Institute of Animal Science, Korea, Republic of
  • Greger Larson, Durham Evolution and Ancient DNA, Department of Archaeology, Durham University, United Kingdom
  • Kyooyeol Lee, Department of Animal Biotechnology, Konkuk University, Korea, Republic of
  • Kyung-Tai Lee, C&K Genomics, Korea, Republic of
  • Richard Leggett, The Genome Analysis Centre, Norwich Research Park, United Kingdom
  • Harris A Lewin, Department of Evolution and Ecology, The UC Davis Genome Center, United States
  • Yingrui Li, BGI-Shenzhen, China
  • Wansheng Liu, Department of Dairy and Animal Sciences, Center for Reproductive Biology and Health (CRBH), College of Agricultural Sciences, The Pennsylvania State University, United States
  • Jane E Loveland, Wellcome Trust Sanger Institute,WellcomeTrust Genome Campus, United Kingdom
  • Yao Lu, BGI-Shenzhen, China
  • Joan K Lunney, 0USDA ARS BARC Animal Parasitic Diseases Laboratory, United States
  • Jian Ma, Department of Bioengineering and Institute for Genomic Biology, University of Illinois, United States
  • Ole Madsen, Animal Breeding and Genomics Centre, Wageningen University, De Elst 1, 6708 WD, Wageningen, Netherlands
  • Katherine Mann, 0USDA ARS BARC Animal Parasitic Diseases Laboratory, United States
  • Lucy Matthews, Wellcome Trust Sanger Institute,WellcomeTrust Genome Campus, United Kingdom
  • Stuart McLaren, Wellcome Trust Sanger Institute,WellcomeTrust Genome Campus, United Kingdom
  • Takeya Morozumi, Institute of Japan Association for Techno-innovation in Agriculture, Forestry and Fisheries, Japan
  • Michael P Murtaugh, Department of Veterinary and Biomedical Sciences, University of Minnesota, United States
  • Jitendra Narayan, Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, United Kingdom
  • Dinh Truong Nguyen, Department of Animal Biotechnology, Konkuk University, Korea, Republic of
  • Peixiang Ni, BGI-Shenzhen, China
  • Song-Jung Oh, Jeju National University, Korea, Republic of
  • Suneel Onteru, Department of Animal Science and Center for Integrated Animal Genomics, Iowa State University, United States
  • Frank Panitz
  • Eung-Woo Park, Animal Genomics and Bioinformatics Division, National Institute of Animal Science, Korea, Republic of
  • Hong-Seog Park, Korean Research Institute of Bioscience and Biotechnology, Korea, Republic of
  • Geraldine Pascal, INRA UMR85/CNRS UMR7247 Physiologie de la Reproduction et des Comportements/IFCE, France
  • Yogesh Paudel, Animal Breeding and Genomics Centre, Wageningen University, Netherlands
  • Miguel Perez-Enciso, ICREA, Centre for Research in Agricultural Genomics (CRAG) and Facultat de Veterinaria UAB, Campus Universitat Autonoma Barcelona, Spain
  • Ricardo Ramirez-Gonzalez, The Genome Analysis Centre, Norwich Research Park, United Kingdom
  • James M Reecy, Department of Animal Science and Center for Integrated Animal Genomics, Iowa State University, United States
  • Sandra Rodriguez-Zas, Department of Animal Sciences, University of Illinois, United States
  • Gary A Rohrer, USDA, ARS, USMeat Animal Research Center, Clay Center, United States
  • Lauretta Rund, Department of Animal Sciences, University of Illinois, United States
  • Yongming Sang, Department of Anatomy and Physiology, College of Veterinary Medicine, Kansas State University, United States
  • Kyle Schachtschneider, Department of Animal Sciences, University of Illinois, United States
  • Joshua G Schraiber, Department of Integrative Biology, University of California, United States
  • John Schwartz, Department of Veterinary and Biomedical Sciences, University of Minnesota, United States
  • Linda Scobie, Department of Life Sciences, Glasgow Caledonian University, United Kingdom
  • Carol Scott, Wellcome Trust Sanger Institute,WellcomeTrust Genome Campus, United Kingdom
  • Stephen Searle, Wellcome Trust Sanger Institute,WellcomeTrust Genome Campus, United Kingdom
  • Bertrand Servin, INRA, Laboratoire de Ge´ne´tique Cellulaire, Chemin de Borde-Rouge, France
  • Bruce R Southey, Department of Animal Sciences, University of Illinois, United States
  • Goran Sperber, Department of Neuroscience, Biomedical Centre, Uppsala University, Sweden
  • Peter Stadler, Bioinformatics Group, Department of Computer Science, Interdisciplinary Center for Bioinformatics, Universität Leipzig, Germany
  • Jonathan V Sweedler, Department of Chemistry, University of Illinois, United States
  • Hakim Tafer, Bioinformatics Group, Department of Computer Science, Interdisciplinary Center for Bioinformatics, Universität Leipzig, Germany
  • Bo Thomsen
  • Rashmi Wali, Department of Life Sciences, Glasgow Caledonian University, United Kingdom
  • Jian Wang, BGI-Shenzhen, China
  • Jun Wang, BGI-Shenzhen, China
  • Simon White, Wellcome Trust Sanger Institute,WellcomeTrust Genome Campus, United Kingdom
  • Xun Xu, BGI-Shenzhen, China
  • Martine Yerle, INRA, Laboratoire de Ge´ne´tique Cellulaire, Chemin de Borde-Rouge, France
  • Guojie Zhang, BGI-Europe, Denmark
  • Jianguo Zhang, BGI-Shenzhen, China
  • Jie Zhang, Key Lab of Animal Genetics, Breeding, and Reproduction of Ministry Education, Huazhong Agricultural University, China
  • Shuhong Zhao, 53Key Lab of Animal Genetics, Breeding, and Reproduction of Ministry Education, Huazhong Agricultural University, China
  • Jane Rogers, The Genome Analysis Centre, Norwich Research Park, United Kingdom
  • Carol Churcher, Wellcome Trust Sanger Institute,WellcomeTrust Genome Campus, United Kingdom
  • Lawrence B Schook, Department of Animal Sciences and Institute for Genomic Biology, University of Illinois, United States
For 10,000 years pigs and humans have shared a close and complex relationship. From domestication to modern breeding practices, humans have shaped the genomes of domestic pigs. Here we present the assembly and analysis of the genome sequence of a female domestic Duroc pig (Sus scrofa) and a comparison with the genomes of wild and domestic pigs from Europe and Asia. Wild pigs emerged in South East Asia and subsequently spread across Eurasia. Our results reveal a deep phylogenetic split between European and Asian wild boars ∼1 million years ago, and a selective sweep analysis indicates selection on genes involved in RNA processing and regulation. Genes associated with immune response and olfaction exhibit fast evolution. Pigs have the largest repertoire of functional olfactory receptor genes, reflecting the importance of smell in this scavenging animal. The pig genome sequence provides an important resource for further improvements of this important livestock species, and our identification of many putative disease-causing variants extends the potential of the pig as a biomedical model.
Original languageEnglish
JournalNature
Volume491
Issue7424
Pages (from-to)393-398
Number of pages6
ISSN0028-0836
DOIs
Publication statusPublished - 15 Nov 2012

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