A physical map of the bovine genome |
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| Authors: | Snelling Warren M Chiu Readman Schein Jacqueline E Hobbs Matthew Abbey Colette A Adelson David L Aerts Jan Bennett Gary L Bosdet Ian E Boussaha Mekki Brauning Rudiger Caetano Alexandre R Costa Marcos M Crawford Allan M Dalrymple Brian P Eggen André Everts-van der Wind Annelie Floriot Sandrine Gautier Mathieu Gill Clare A Green Ronnie D Holt Robert Jann Oliver Jones Steven Jm Kappes Steven M Keele John W de Jong Pieter J Larkin Denis M Lewin Harris A McEwan John C McKay Stephanie Marra Marco A Mathewson Carrie A Matukumalli Lakshmi K Moore Stephen S Murdoch Brenda Nicholas Frank W |
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| Affiliation: | USDA, ARS, US Meat Animal Research Center, Clay Center, NE 68933, USA. warren.snelling@ars.usda.gov |
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| Abstract: | BackgroundCattle 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.ResultsA 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.ConclusionFurther 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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