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Animal Science Publications Animal Science 8-2015 Third Report on Chicken Genes and Chromosomes 2015 M. Schmid University of Würzburg J. Smith The Roslin Institute and R(D)SVS D. W. Burt The Roslin Institute and R(D)SVS B. L. Aken European Bioinformatics Institute, EMBL P. B. Antin University of Arizona SeFoe nelloxtw pa thige fors aaddndition addal aitutionhorsal works at: http://lib.dr.iastate.edu/ans_pubs Part of the Agriculture Commons, Genetics and Genomics Commons, and the Poultry or Avian Science Commons The ompc lete bibliographic information for this item can be found at http://lib.dr.iastate.edu/ ans_pubs/175. For information on how to cite this item, please visit http://lib.dr.iastate.edu/ howtocite.html. This Article is brought to you for free and open access by the Animal Science at Iowa State University Digital Repository. It has been accepted for inclusion in Animal Science Publications by an authorized administrator of Iowa State University Digital Repository. For more information, please contact [email protected]. Third Report on Chicken Genes and Chromosomes 2015 Abstract Following on from the First Report on Chicken Genes and Chromosomes [Schmid et al., 2000] and the Second Report in 2005 [Schmid et al., 2005], we are pleased to publish this long-awaited Third Report on the latest developments in chicken genomics. The irF st Report highlighted the availability of genetic and physical maps, while the Second Report was published as the chicken genome sequence was released. This report comes at a time of huge technological advances (particularly in sequencing methodologies) which have allowed us to examine the chicken genome in detail not possible until now. This has also heralded an explosion in avian genomics, with the current availability of more than 48 bird genomes [Zhang G et al., 2014b; Eöry et al., 2015], with many more planned. Disciplines Agriculture | Animal Sciences | Genetics and Genomics | Poultry or Avian Science Comments This article is from Cytogenic and Genome Research 145 (2015): 78, doi:10.1159/000430927. Rights Works produced by employees of the U.S. Government as part of their official duties are not copyrighted within the U.S. The onc tent of this document is not copyrighted. Authors M. Schmid, J. Smith, D. W. Burt, B. L. Aken, P. B. Antin, A. L. Archibald, C. Ashwell, P. J. Blackshear, C. Boschiero, C. T. Brown, S. C. Burgess, H. H. Cheng, W. Chow, D. J. Coble, A. Cooksey, R. P. M. A.. Crooijmans, J. Damas, R. V. N. Davis, D.-J. de Koning, M. E. Delany, T. Derrien, T. T. Desta, I. C Dunn, M. Dunn, H. Ellegren, L. Eöry, I. Erb, M. Farré, M. Fasold, D. Fleming, P. Flicek, K. E. Fowler, L. Frésard, D. P. Froman, V. Garceau, P. P. Gardner, A. A. Gheyas, D. K. Griffin, M. A. M. Groenen, T. Haaf, O. Hanotte, A. Hart, J. Häsler, S. B. Hedges, J. Hertel, K. Howe, A. Hubbard, D. A. Hume, P. Kaiser, D. Kedra, S. J. Kemp, C. Klopp, K. E. Kniel, R. Kuo, S. Lagarrigue, Susan J. Lamont, D. M. Larkin, R. A. Lawal, S. M. Markland, F. McCarthy, H. A. McCormack, M. C. McPherson, A. Motegi, S. A. Muljo, A. Münsterberg, R. Nag, I. Nanda, M. Neuberger, A. Nitsche, C. Notredame, H. Noyes, R. O'Connor, E. A. O'Hare, A. J. Oler, S. C. Ommeh, H. Pais, M. Persia, F. Pitel, L. Preeyanon, P. Prieto Barja, E. M. Pritchett, D. D. Rhoads, C. M. Robinson, M. N. Romanov, M. Rothschild, P.-F. Roux, C. J. Schmidt, A.-S. Schneider, M. G. Schwartz, S. M. Searle, M. A. Skinner, C. A. Smith, P. F. Stadler, T. E. Steeves, C. Steinlein, L. Sun, M. Takata, I. Ulitsky, Q. Wang, Y. Wang, W. C. Warren, J. M. D. Wood, D. Wragg, and H. Zhou This article is available at Iowa State University Digital Repository: http://lib.dr.iastate.edu/ans_pubs/175 Report Cytogenet Genome Res 2015;145:78–179 Published online: July 14, 2015 DOI: 10.1159/000430927 Third Report on Chicken Genes and Chromosomes 2015 Prepared by 1 3 3 5 26 3 Michael Schmid Jacqueline Smith David W. Burt Bronwen L. Aken Parker B. Antin Alan L. Archibald 29 30 48 31, 32 27 Chris Ashwell Perry J. Blackshear Clarissa Boschiero C. Titus Brown Shane C. Burgess 33 6 40 28 17 Hans H. Cheng William Chow Derrick J. Coble Amanda Cooksey Richard P.M.A. Crooijmans 8 34 18 36 20 10 Joana Damas Richard V.N. Davis Dirk-Jan de Koning Mary E. Delany Thomas Derrien Takele T. Desta 3 6 19 3 24 8 2 Ian C. Dunn Matthew Dunn Hans Ellegren Lél Eöry Ionas Erb Marta Farré Mario Fasold 40 5 11 22 38 3 Damarius Fleming Paul Flicek Katie E. Fowler Laure Frésard David P. Froman Valerie Garceau 51, 52 3 12 17 1 Paul P. Gardner Almas A. Gheyas Darren K. Griffin Martien A.M. Groenen Thomas Haaf 10 3, 13 7 39 2 6 35 Olivier Hanotte Alan Hart Julien Häsler S. Blair Hedges Jana Hertel Kerstin Howe Allen Hubbard 3 4 24 14 23 35 David A. Hume Pete Kaiser Darek Kedra Stephen J. Kemp Christophe Klopp Kalmia E. Kniel 3 21 40 8 10 Richard Kuo Sandrine Lagarrigue Susan J. Lamont Denis M. Larkin Raman A. Lawal 35 28 3 36 53 Sarah M. Markland Fiona McCarthy Heather A. McCormack Marla C. McPherson Akira Motegi 41 15 5 1 7 2 Stefan A. Muljo Andrea Münsterberg Rishi Nag Indrajit Nanda Michael Neuberger Anne Nitsche 24 14 12 43 42 Cedric Notredame Harry Noyes Rebecca O’Connor Elizabeth A. O’Hare Andrew J. Oler Sheila C. Ommeh49 Helio Pais16 Michael Persia44 Frédérique Pitel22 Likit Preeyanon31 Pablo Prieto Barja24 Elizabeth M. Pritchett35 Douglas D. Rhoads45 Charmaine M. Robinson37 Michael N. Romanov12 Max Rothschild40 Pierre-François Roux21 Carl J. Schmidt35 Alisa-Sophia Schneider1 Matthew G. Schwartz46 Steve M. Searle6 Michael A. Skinner9 Craig A. Smith50 Peter F. Stadler2 Tammy E. Steeves51 Claus Steinlein1 Liang Sun35 Minoru Takata54 Igor Ulitsky25 Qing Wang35 Ying Wang36 Wesley C. Warren27 Jonathan M.D. Wood6 David Wragg22 Huaijun Zhou36 1 2 Department of Human Genetics, University of Würzburg, Würzburg , and Bioinformatics Group, Department of Computer Science and 3 Interdisciplinary Centre for Bioinformatics, University of Leipzig, Leipzig , Germany; Division of Genetics and Genomics, The Roslin 4 5 Institute and R(D)SVS, and Division of Infection and Immunity, The Roslin Institute, University of Edinburgh, Edinburgh , European 6 7 Bioinformatics Institute, EMBL, and Wellcome Trust Sanger Institute, Hinxton, Medical Research Council Laboratory of Molecular Biology, 8 9 Cambridge , Department of Comparative Biomedical Sciences, Royal Veterinary College, University of London, and Section of Virology, 10 Department of Medicine, Imperial College London, London , School of Life Sciences, University of Nottingham, Nottingham , Supported by Biotechnology and Biological Sciences Research Council (BBSRC); USDA Correspondence to: Agriculture and Food Research Initiative Competitive Grant; NIH Intramural Research Michael Schmid Program of the National Institute of Allergy and Infectious Diseases; European Union Department of Human Genetics, University of Würzburg FP-7 project QUANTOMICS; Deutsche Forschungsgemeinschaft (DFG); Swiss National Biozentrum, Am Hubland Science Foundation; Lady Tata Memorial Trust; French ‘Agence Nationale de la Recher- DE–97074 Würzburg (Germany) che’ EpiBird; Intramural Research Program of the NIEHS, NIH; Department for Interna- E-Mail m.schmid @ biozentrum.uni-wuerzburg.de tional Development (DFID). Jacqueline Smith Division of Genetics and Genomics The Roslin Institute, University of Edinburgh Edinburgh EH25 9RG (UK) E-Mail jacqueline.smith @ roslin.ed.ac.uk © 2015 S. Karger AG, Basel David W. Burt 1424–8581/15/1452–0078$39.50/0 Division of Genetics and Genomics The Roslin Institute, University of Edinburgh E-Mail [email protected] Edinburgh EH25 9RG (UK) www.karger.com/cgr E-Mail dave.burt @ roslin.ed.ac.uk Downloaded by: Iowa State University 198.143.32.1 - 11/11/2015 11:02:55 PM 11 12 School of Human and Life Sciences, Canterbury Christ Church University, and School of Biosciences, University of Kent, Canterbury , 13 14 Biological Services, Royal Hallamshire Hospital, University of Sheffield, Sheffield , Institute of Integrative Biology, University of 15 16 Liverpool, Liverpool , School of Biological Sciences, University of East Anglia, Norwich , and Weatherall Institute of Molecular Medicine, 17 University of Oxford, John Radcliffe Hospital, Oxford , UK; Animal Breeding and Genomics Centre, Wageningen University, Wageningen , 18 19 The Netherlands; Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, and Department of 20 Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Uppsala , Sweden; Institut de Génétique et Développement de 21 22 23 Rennes, Université de Rennes1, and Equipe Génétique et Génomique, PEGASE, INRA, Rennes , GenPhySE, INRA, and Plateforme 24 Bioinformatique Toulouse Midi-Pyrénées, INRA, Biométrie et Intelligence Artificielle, Castanet-Tolosan , France; Comparative 25 Bioinformatics Group, Bioinformatics and Genomics Programme, Centre for Genomic Regulation, Barcelona , Spain; Department of 26 27 Biological Regulation, Weizmann Institute of Science, Rehovot , Israel; Department of Cellular and Molecular Medicine, College of 28 29 Agriculture and Life Sciences, and Department of Veterinary Science and Microbiology, University of Arizona, Tucson, Ariz. , Department 30 31 of Poultry Science, Raleigh, N.C. , Department of Biochemistry, Duke University School of Medicine, NIEHS, Durham, N.C. , Microbiology 32 33 and Molecular Genetics, Michigan State University, Computer Science and Engineering, Michigan State University, and Avian Disease 34 35 and Oncology Laboratory, USDA, ARS, East Lansing, Mich. , Department of Biology, University of Delaware, and Department of Animal 36 37 and Food Sciences, University of Delaware, Newark, Del. , Department of Animal Science, University of California, Davis, Calif. , Division 38 of Science and Environmental Policy, California State University Monterey Bay, Seaside, Calif. , Department of Animal and Rangeland 39 40 Sciences, Oregon State University, Corvallis, Oreg.