Open Access Highly Accessed Research

A physical map of the bovine genome

Warren M Snelling1*, Readman Chiu2, Jacqueline E Schein2, Matthew Hobbs3, Colette A Abbey4, David L Adelson4, Jan Aerts5, Gary L Bennett1, Ian E Bosdet2, Mekki Boussaha6, Rudiger Brauning7, Alexandre R Caetano8, Marcos M Costa8, Allan M Crawford7, Brian P Dalrymple9, André Eggen6, Annelie Everts-van der Wind10, Sandrine Floriot6, Mathieu Gautier6, Clare A Gill4, Ronnie D Green11, Robert Holt2, Oliver Jann5, Steven JM Jones2, Steven M Kappes11, John W Keele1, Pieter J de Jong12, Denis M Larkin10, Harris A Lewin1013, John C McEwan7, Stephanie McKay14, Marco A Marra2, Carrie A Mathewson2, Lakshmi K Matukumalli15, Stephen S Moore14, Brenda Murdoch14, Frank W Nicholas3, Kazutoyo Osoegawa12, Alice Roy16, Hanni Salih4, Laurent Schibler6, Robert D Schnabel17, Licia Silveri18, Loren C Skow4, Timothy PL Smith1, Tad S Sonstegard15, Jeremy F Taylor17, Ross Tellam9, Curtis P Van Tassell15, John L Williams195, James E Womack4, Natasja H Wye2, George Yang2, Shaying Zhao2021 and the International Bovine BAC Mapping Consortium

Author Affiliations

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

For all author emails, please log on.

Genome Biology 2007, 8:R165  doi:10.1186/gb-2007-8-8-r165

Published: 14 August 2007

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.