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Analyses of pig genomes provide insight into porcine demography and evolution

Author

Listed:
  • Martien A. M. Groenen

    (Animal Breeding and Genomics Centre, Wageningen University, De Elst 1, 6708 WD, Wageningen, The Netherlands.)

  • Alan L. Archibald

    (The Roslin Institute and R(D)SVS, University of Edinburgh, Easter Bush, Midlothian EH25 9RG, UK.)

  • Hirohide Uenishi

    (National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602, Japan.)

  • Christopher K. Tuggle

    (Iowa State University, 2255 Kildee Hall, Ames 50011, USA.)

  • Yasuhiro Takeuchi

    (MRC/UCL Centre for Medical Molecular Virology and Wohl Virion Centre, University College London, Cruciform Building, Gower Street, London WC1E 6BT, UK.)

  • Max F. Rothschild

    (Iowa State University, 2255 Kildee Hall, Ames 50011, USA.)

  • 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 Génome, Domaine de Vilvert, F-78350 Jouy-en-Josas, France.)

  • Chankyu Park

    (Konkuk University, 1 Hwayang-dong, Kwangjin-gu, Seoul 143-701, South Korea.)

  • Denis Milan

    (INRA, Laboratoire de Génétique Cellulaire, Chemin de Borde-Rouge, Auzeville, 31320 Castanet Tolosan, France.)

  • Hendrik-Jan Megens

    (Animal Breeding and Genomics Centre, Wageningen University, De Elst 1, 6708 WD, Wageningen, The Netherlands.)

  • Shengting Li

    (BGI-Shenzhen
    Aarhus University)

  • Denis M. Larkin

    (Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Penglais Campus, Aberystwyth, Ceredigion SY23 3DA, UK.)

  • Heebal Kim

    (Seoul National University, Gwanakgu, Seoul 151-742, South Korea.)

  • Laurent A. F. Frantz

    (Animal Breeding and Genomics Centre, Wageningen University, De Elst 1, 6708 WD, Wageningen, The Netherlands.)

  • Mario Caccamo

    (The Genome Analysis Centre, Norwich Research Park)

  • Hyeonju Ahn

    (Seoul National University, Gwanakgu, Seoul 151-742, South Korea.)

  • Bronwen L. Aken

    (Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK.)

  • Anna Anselmo

    (Parco Tecnologico Padano, Via Einstein, Loc. C. Codazza, 26900 Lodi, Italy.)

  • Christian Anthon

    (Center for non-coding RNA in Technology and Health, IBHV University of Copenhagen, Frederiksberg)

  • Loretta Auvil

    (Illinois Informatics Institute, University of Illinois)

  • Bouabid Badaoui

    (Parco Tecnologico Padano, Via Einstein, Loc. C. Codazza, 26900 Lodi, Italy.)

  • Craig W. Beattie

    (University of Illinois)

  • Christian Bendixen

    (Aarhus University)

  • Daniel Berman

    (USDA ARS BARC Animal Parasitic Diseases Laboratory)

  • Frank Blecha

    (College of Veterinary Medicine, Kansas State University)

  • Jonas Blomberg

    (Clinical Virology, Uppsala University, Building D1, Academic Hospital, 751 85 Uppsala, Sweden.)

  • Lars Bolund

    (BGI-Shenzhen
    Aarhus University)

  • Mirte Bosse

    (Animal Breeding and Genomics Centre, Wageningen University, De Elst 1, 6708 WD, Wageningen, The Netherlands.)

  • Sara Botti

    (Parco Tecnologico Padano, Via Einstein, Loc. C. Codazza, 26900 Lodi, Italy.)

  • Zhan Bujie

    (Aarhus University)

  • Megan Bystrom

    (Iowa State University, 2255 Kildee Hall, Ames 50011, USA.)

  • Boris Capitanu

    (Illinois Informatics Institute, University of Illinois)

  • Denise Carvalho-Silva

    (European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton)

  • Patrick Chardon

    (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 Génome, Domaine de Vilvert, F-78350 Jouy-en-Josas, France.)

  • Celine Chen

    (Diet, Genomics, Immunology Laboratory, Beltsville Human Nutrition Research Center, BARC-East 10300 Baltimore Ave Beltsville, Maryland 20705, USA.)

  • Ryan Cheng

    (Iowa State University, 2255 Kildee Hall, Ames 50011, USA.)

  • Sang-Haeng Choi

    (Korean Research Institute of Bioscience and Biotechnology, 125 Gwahak ro, Yuseong gu, Daejeon 305-806, South Korea.)

  • William Chow

    (Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK.)

  • Richard C. Clark

    (Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK.)

  • Christopher Clee

    (Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK.)

  • Richard P. M. A. Crooijmans

    (Animal Breeding and Genomics Centre, Wageningen University, De Elst 1, 6708 WD, Wageningen, The Netherlands.)

  • Harry D. Dawson

    (Diet, Genomics, Immunology Laboratory, Beltsville Human Nutrition Research Center, BARC-East 10300 Baltimore Ave Beltsville, Maryland 20705, USA.)

  • Patrice Dehais

    (INRA, Laboratoire de Génétique Cellulaire, Chemin de Borde-Rouge, Auzeville, 31320 Castanet Tolosan, France.)

  • Fioravante De Sapio

    (The Roslin Institute and R(D)SVS, University of Edinburgh, Easter Bush, Midlothian EH25 9RG, UK.)

  • Bert Dibbits

    (Animal Breeding and Genomics Centre, Wageningen University, De Elst 1, 6708 WD, Wageningen, The Netherlands.)

  • Nizar Drou

    (The Genome Analysis Centre, Norwich Research Park)

  • Zhi-Qiang Du

    (Iowa State University, 2255 Kildee Hall, Ames 50011, USA.)

  • Kellye Eversole

    (Eversole Associates and the Alliance for Animal Genome Research, 5207 Wyoming Road, Bethesda, Maryland 20816, USA.)

  • João Fadista

    (Aarhus University
    Present addresses: Lund University Diabetes Centre, CRC, Malmö University Hospital, SE-205 02 Malmö, Sweden (J.F.); Mater Medical Research Institute, and School of Biomedical Sciences, University of Queensland, Brisbane, 4072 Queensland, Australia (G.J.F.); Illumina Inc. Chesterford Research Park, Little Chesterford, Nr Saffron Walden, Essex CB10 1XL, UK (S.J.H.); Department of Molecular Microbiology, Washington University School of Medicine, Saint Louis, Missouri 63110, USA (K.M.).)

  • Susan Fairley

    (Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK.)

  • Thomas Faraut

    (INRA, Laboratoire de Génétique Cellulaire, Chemin de Borde-Rouge, Auzeville, 31320 Castanet Tolosan, France.)

  • Geoffrey J. Faulkner

    (The Roslin Institute and R(D)SVS, University of Edinburgh, Easter Bush, Midlothian EH25 9RG, UK.
    Present addresses: Lund University Diabetes Centre, CRC, Malmö University Hospital, SE-205 02 Malmö, Sweden (J.F.); Mater Medical Research Institute, and School of Biomedical Sciences, University of Queensland, Brisbane, 4072 Queensland, Australia (G.J.F.); Illumina Inc. Chesterford Research Park, Little Chesterford, Nr Saffron Walden, Essex CB10 1XL, UK (S.J.H.); Department of Molecular Microbiology, Washington University School of Medicine, Saint Louis, Missouri 63110, USA (K.M.).)

  • Katie E. Fowler

    (School of Biosciences, The University of Kent, Giles Lane, Canterbury)

  • Merete Fredholm

    (Center for non-coding RNA in Technology and Health, IBHV University of Copenhagen, Frederiksberg)

  • Eric Fritz

    (Iowa State University, 2255 Kildee Hall, Ames 50011, USA.)

  • James G. R. Gilbert

    (Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK.)

  • 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 Génome, Domaine de Vilvert, F-78350 Jouy-en-Josas, France.
    Parco Tecnologico Padano, Via Einstein, Loc. C. Codazza, 26900 Lodi, Italy.)

  • Jan Gorodkin

    (Center for non-coding RNA in Technology and Health, IBHV University of Copenhagen, Frederiksberg)

  • Darren K. Griffin

    (School of Biosciences, The University of Kent, Giles Lane, Canterbury)

  • Jennifer L. Harrow

    (Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK.)

  • Alexander Hayward

    (Science for Life Laboratory, Uppsala University, BMC, Box 582, SE75123 Uppsala, Sweden.)

  • Kerstin Howe

    (Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK.)

  • Zhi-Liang Hu

    (Iowa State University, 2255 Kildee Hall, Ames 50011, USA.)

  • Sean J. Humphray

    (Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK.
    Present addresses: Lund University Diabetes Centre, CRC, Malmö University Hospital, SE-205 02 Malmö, Sweden (J.F.); Mater Medical Research Institute, and School of Biomedical Sciences, University of Queensland, Brisbane, 4072 Queensland, Australia (G.J.F.); Illumina Inc. Chesterford Research Park, Little Chesterford, Nr Saffron Walden, Essex CB10 1XL, UK (S.J.H.); Department of Molecular Microbiology, Washington University School of Medicine, Saint Louis, Missouri 63110, USA (K.M.).)

  • Toby Hunt

    (Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK.)

  • Henrik Hornshøj

    (Aarhus University)

  • Jin-Tae Jeon

    (College of Agriculture and Life Sciences, Gyeongsang National University, Jinju 660-701, South Korea.)

  • Patric Jern

    (Science for Life Laboratory, Uppsala University, BMC, Box 582, SE75123 Uppsala, Sweden.)

  • Matthew Jones

    (Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK.)

  • Jerzy Jurka

    (Genetic Information Research Institute, 1925 Landings Drive)

  • Hiroyuki Kanamori

    (National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602, Japan.
    Institute of Japan Association for Techno-innovation in Agriculture, Forestry and Fisheries, 446-1 Ippaizuka, Kamiyokoba, Tsukuba, Ibaraki 305-0854, Japan.)

  • Ronan Kapetanovic

    (The Roslin Institute and R(D)SVS, University of Edinburgh, Easter Bush, Midlothian EH25 9RG, UK.)

  • Jaebum Kim

    (Konkuk University, 1 Hwayang-dong, Kwangjin-gu, Seoul 143-701, South Korea.
    Institute for Genomic Biology, University of Illinois)

  • Jae-Hwan Kim

    (Animal Genetic Resources Station, National Institute of Animal Science, RDA, San 4, Yongsanri, Unbong eup, Namwon 590-832, South Korea.)

  • Kyu-Won Kim

    (C&K Genomics, Gwanakgu)

  • Tae-Hun Kim

    (National Institute of Animal Science, RDA, 77 Chuksan gil, Kwonsun gu, Suwon 441-706, South Korea.)

  • Greger Larson

    (Durham Evolution and Ancient DNA, Durham University)

  • Kyooyeol Lee

    (Konkuk University, 1 Hwayang-dong, Kwangjin-gu, Seoul 143-701, South Korea.)

  • Kyung-Tai Lee

    (National Institute of Animal Science, RDA, 77 Chuksan gil, Kwonsun gu, Suwon 441-706, South Korea.)

  • Richard Leggett

    (The Genome Analysis Centre, Norwich Research Park)

  • Harris A. Lewin

    (The UC Davis Genome Center, University of California)

  • Yingrui Li

    (BGI-Shenzhen)

  • Wansheng Liu

    (Center for Reproductive Biology and Health (CRBH), College of Agricultural Sciences, The Pennsylvania State University, 305 Henning Building, University Park, Pennsylvania 16802, USA.)

  • Jane E. Loveland

    (Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK.)

  • Yao Lu

    (BGI-Shenzhen)

  • Joan K. Lunney

    (USDA ARS BARC Animal Parasitic Diseases Laboratory)

  • Jian Ma

    (University of Illinois)

  • Ole Madsen

    (Animal Breeding and Genomics Centre, Wageningen University, De Elst 1, 6708 WD, Wageningen, The Netherlands.)

  • Katherine Mann

    (USDA ARS BARC Animal Parasitic Diseases Laboratory
    Present addresses: Lund University Diabetes Centre, CRC, Malmö University Hospital, SE-205 02 Malmö, Sweden (J.F.); Mater Medical Research Institute, and School of Biomedical Sciences, University of Queensland, Brisbane, 4072 Queensland, Australia (G.J.F.); Illumina Inc. Chesterford Research Park, Little Chesterford, Nr Saffron Walden, Essex CB10 1XL, UK (S.J.H.); Department of Molecular Microbiology, Washington University School of Medicine, Saint Louis, Missouri 63110, USA (K.M.).)

  • Lucy Matthews

    (Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK.)

  • Stuart McLaren

    (Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK.)

  • Takeya Morozumi

    (Institute of Japan Association for Techno-innovation in Agriculture, Forestry and Fisheries, 446-1 Ippaizuka, Kamiyokoba, Tsukuba, Ibaraki 305-0854, Japan.)

  • Michael P. Murtaugh

    (University of Minnesota, 1971 Commonwealth Avenue, St Paul, Minnesota 55108, USA.)

  • Jitendra Narayan

    (Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Penglais Campus, Aberystwyth, Ceredigion SY23 3DA, UK.)

  • Dinh Truong Nguyen

    (Konkuk University, 1 Hwayang-dong, Kwangjin-gu, Seoul 143-701, South Korea.)

  • Peixiang Ni

    (BGI-Shenzhen)

  • Song-Jung Oh

    (Jeju National University, 102 Jejudaehakno, Jeju 690-756, South Korea.)

  • Suneel Onteru

    (Iowa State University, 2255 Kildee Hall, Ames 50011, USA.)

  • Frank Panitz

    (Aarhus University)

  • Eung-Woo Park

    (National Institute of Animal Science, RDA, 77 Chuksan gil, Kwonsun gu, Suwon 441-706, South Korea.)

  • Hong-Seog Park

    (Korean Research Institute of Bioscience and Biotechnology, 125 Gwahak ro, Yuseong gu, Daejeon 305-806, South Korea.)

  • Geraldine Pascal

    (INRA UMR85/CNRS UMR7247 Physiologie de la Reproduction et des Comportements/IFCE, F-37380 Nouzilly, France and Université François Rabelais de Tours)

  • Yogesh Paudel

    (Animal Breeding and Genomics Centre, Wageningen University, De Elst 1, 6708 WD, Wageningen, The Netherlands.)

  • Miguel Perez-Enciso

    (ICREA, Centre for Research in Agricultural Genomics (CRAG) and Facultat de Veterinaria UAB, Campus Universitat Autonoma Barcelona)

  • Ricardo Ramirez-Gonzalez

    (The Genome Analysis Centre, Norwich Research Park)

  • James M. Reecy

    (Iowa State University, 2255 Kildee Hall, Ames 50011, USA.)

  • Sandra Rodriguez-Zas

    (University of Illinois)

  • Gary A. Rohrer

    (USDA, ARS, US Meat Animal Research Center, Clay Center)

  • Lauretta Rund

    (University of Illinois)

  • Yongming Sang

    (College of Veterinary Medicine, Kansas State University)

  • Kyle Schachtschneider

    (University of Illinois)

  • Joshua G. Schraiber

    (University of California)

  • John Schwartz

    (University of Minnesota, 1971 Commonwealth Avenue, St Paul, Minnesota 55108, USA.)

  • Linda Scobie

    (Glasgow Caledonian University)

  • Carol Scott

    (Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK.)

  • Stephen Searle

    (Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK.)

  • Bertrand Servin

    (INRA, Laboratoire de Génétique Cellulaire, Chemin de Borde-Rouge, Auzeville, 31320 Castanet Tolosan, France.)

  • Bruce R. Southey

    (University of Illinois)

  • Goran Sperber

    (Biomedical Centre, Uppsala University, PO Box 593, 751 24 Uppsala, Sweden.)

  • Peter Stadler

    (Bioinformatics Group, Interdisciplinary Center for Bioinformatics, Universität Leipzig)

  • Jonathan V. Sweedler

    (University of Illinois)

  • Hakim Tafer

    (Bioinformatics Group, Interdisciplinary Center for Bioinformatics, Universität Leipzig)

  • Bo Thomsen

    (Aarhus University)

  • Rashmi Wali

    (Glasgow Caledonian University)

  • Jian Wang

    (BGI-Shenzhen)

  • Jun Wang

    (BGI-Shenzhen
    University of Copenhagen)

  • Simon White

    (Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK.)

  • Xun Xu

    (BGI-Shenzhen)

  • Martine Yerle

    (INRA, Laboratoire de Génétique Cellulaire, Chemin de Borde-Rouge, Auzeville, 31320 Castanet Tolosan, France.)

  • Guojie Zhang

    (BGI-Shenzhen
    BGI-Europe, DK-2200 Copenhagen N, Denmark.)

  • Jianguo Zhang

    (BGI-Shenzhen)

  • Jie Zhang

    (Key Lab of Animal Genetics, Breeding, and Reproduction of Ministry Education, Huazhong Agricultural University, Wuhan 430070 PR China, Huazhong Agricultural University, Wuhan 430070, China.)

  • Shuhong Zhao

    (Key Lab of Animal Genetics, Breeding, and Reproduction of Ministry Education, Huazhong Agricultural University, Wuhan 430070 PR China, Huazhong Agricultural University, Wuhan 430070, China.)

  • Jane Rogers

    (The Genome Analysis Centre, Norwich Research Park)

  • Carol Churcher

    (Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK.)

  • Lawrence B. Schook

    (University of Illinois, Urbana, Illinois 61801, USA.)

Abstract

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.

Suggested Citation

  • Martien A. M. Groenen & Alan L. Archibald & Hirohide Uenishi & Christopher K. Tuggle & Yasuhiro Takeuchi & Max F. Rothschild & Claire Rogel-Gaillard & Chankyu Park & Denis Milan & Hendrik-Jan Megens &, 2012. "Analyses of pig genomes provide insight into porcine demography and evolution," Nature, Nature, vol. 491(7424), pages 393-398, November.
    • Handle: RePEc:nat:nature:v:491:y:2012:i:7424:d:10.1038_nature11622
    DOI: 10.1038/nature11622
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    Cited by:

    1. W. Wang & W. Xue & X. Xu & B. Jin & X. Zhang, 2016. "Correlations of genes expression in PPAR signalling pathway with porcine meat quality traits," Czech Journal of Animal Science, Czech Academy of Agricultural Sciences, vol. 61(7), pages 333-339.

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