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A physical map of the bovine genome

Warren M Snelling1 email, Readman Chiu2 email, Jacqueline E Schein2 email, Matthew Hobbs3 email, Colette A Abbey4 email, David L Adelson4 email, Jan Aerts5 email, Gary L Bennett1 email, Ian E Bosdet2 email, Mekki Boussaha6 email, Rudiger Brauning7 email, Alexandre R Caetano8 email, Marcos M Costa8 email, Allan M Crawford7 email, Brian P Dalrymple9 email, André Eggen6 email, Annelie Everts-van der Wind10 email, Sandrine Floriot6 email, Mathieu Gautier6 email, Clare A Gill4 email, Ronnie D Green11 email, Robert Holt2 email, Oliver Jann5 email, Steven JM Jones2 email, Steven M Kappes11 email, John W Keele1 email, Pieter J de Jong12 email, Denis M Larkin10 email, Harris A Lewin10,13 email, John C McEwan7 email, Stephanie McKay14 email, Marco A Marra2 email, Carrie A Mathewson2 email, Lakshmi K Matukumalli15 email, Stephen S Moore14 email, Brenda Murdoch14 email, Frank W Nicholas3 email, Kazutoyo Osoegawa12 email, Alice Roy16 email, Hanni Salih4 email, Laurent Schibler6 email, Robert D Schnabel17 email, Licia Silveri18 email, Loren C Skow4 email, Timothy PL Smith1 email, Tad S Sonstegard15 email, Jeremy F Taylor17 email, Ross Tellam9 email, Curtis P Van Tassell15 email, John L Williams5,19 email, James E Womack4 email, Natasja H Wye2 email, George Yang2 email and Shaying Zhao20,21 email for the International Bovine BAC Mapping Consortium

1  USDA, ARS, US Meat Animal Research Center, Clay Center, NE 68933, USA

2  Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, Canada

3  Cooperative Research Centre for Innovative Dairy Products, Reprogen, Faculty of Veterinary Science, University of Sydney, NSW 2006, Australia

4  Texas A&M University, College Station, TX 77843, USA

5  Roslin Institute, Roslin, Midlothian EH25 9PS, UK

6  INRA, UR339 Laboratoire de Génétique Biochimique et de Cytogénétique, 78350 Jouy-en-Josas, France

7  AgResearch, Invermay, Mosgiel, New Zealand

8  Embrapa Recursos Geneticos e Biotecnologia, Parque Estacao Biologica, Final Av. W/5 Norte, Brasilia-DF, CP 02372 70770-900, Brasil

9  CSIRO Livestock Industries, Carmody Road, St Lucia, Queensland 4067, Australia

10  Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA

11  USDA-ARS - National Program Staff, Beltsville, MD 20705-5134, USA

12  Children's Hospital Oakland Research Institute, Oakland, California 94609, USA

13  Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA

14  Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta T6G 2P5, Canada

15  USDA, ARS, BARC Bovine Functional Genomics Laboratory, Maryland, USA

16  Genoscope, rue Gaston Cremieux, 91057 Evry, France

17  Animal Science Research Center, Division of Animal Sciences, University of Missouri, Columbia, MO 65211, USA

18  Istituto di Zootecnica Università Cattolica del S Cuore, via E Parmense, 84 29100 Piacenza, Italy

19  Current address: Parco Tecnologico Padano, Via Einstein, Polo Universitario, Lodi 26900, Italy

20  The Institute for Genomic Research, Rockville, Maryland 20850, USA

21  Current address: Department of Biochemistry and Molecular Biology, University of Georgia, Green Street, Athens, GA 30602-7229, USA

author email corresponding author email

Genome Biology 2007, 8:R165doi:10.1186/gb-2007-8-8-r165

Published: 14 August 2007

Subject areas: Biochemistry and structural biology, Genome studies, Genetics

Abstract

Background

Cattle are important agriculturally and relevant as a model organism. Previously described genetic and radiation hybrid (RH) maps of the bovine genome have been used to identify genomic regions and genes affecting specific traits. Application of these maps to identify influential genetic polymorphisms will be enhanced by integration with each other and with bacterial artificial chromosome (BAC) libraries. The BAC libraries and clone maps are essential for the hybrid clone-by-clone/whole-genome shotgun sequencing approach taken by the bovine genome sequencing project.

Results

A bovine BAC map was constructed with HindIII restriction digest fragments of 290,797 BAC clones from animals of three different breeds. Comparative mapping of 422,522 BAC end sequences assisted with BAC map ordering and assembly. Genotypes and pedigree from two genetic maps and marker scores from three whole-genome RH panels were consolidated on a 17,254-marker composite map. Sequence similarity allowed integrating the BAC and composite maps with the bovine draft assembly (Btau3.1), establishing a comprehensive resource describing the bovine genome. Agreement between the marker and BAC maps and the draft assembly is high, although discrepancies exist. The composite and BAC maps are more similar than either is to the draft assembly.

Conclusion

Further refinement of the maps and greater integration into the genome assembly process may contribute to a high quality assembly. The maps provide resources to associate phenotypic variation with underlying genomic variation, and are crucial resources for understanding the biology underpinning this important ruminant species so closely associated with humans.

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