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Open Access Research article

A high resolution radiation hybrid map of bovine chromosome 14 identifies scaffold rearrangement in the latest bovine assembly

Elisa Marques1, Simon de Givry2, Paul Stothard1, Brenda Murdoch1, Zhiquan Wang1, James Womack3 and Stephen S Moore1*

Author Affiliations

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

2 Unité de Biométrie et d'Intelligence Artificielle INRA, BP 52627, 31326 Castanet-Tolosan, France

3 Department of Veterinary Pathobiology, Texas A & M University, College Station, TX 77843, USA

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BMC Genomics 2007, 8:254  doi:10.1186/1471-2164-8-254

Published: 26 July 2007

Abstract

Background

Radiation hybrid (RH) maps are considered to be a tool of choice for fine mapping closely linked loci, considering that the resolution of linkage maps is determined by the number of informative meiosis and recombination events which may require very large mapping populations. Accurately defining the marker order on chromosomes is crucial for correct identification of quantitative trait loci (QTL), haplotype map construction and refinement of candidate gene searches.

Results

A 12 k Radiation hybrid map of bovine chromosome 14 was constructed using 843 single nucleotide polymorphism markers. The resulting map was aligned with the latest version of the bovine assembly (Btau_3.1) as well as other previously published RH maps. The resulting map identified distinct regions on Bovine chromosome 14 where discrepancies between this RH map and the bovine assembly occur. A major region of discrepancy was found near the centromere involving the arrangement and order of the scaffolds from the assembly. The map further confirms previously published conserved synteny blocks with human chromosome 8. As well, it identifies an extra breakpoint and conserved synteny block previously undetected due to lower marker density. This conserved synteny block is in a region where markers between the RH map presented here and the latest sequence assembly are in very good agreement.

Conclusion

The increase of publicly available markers shifts the rate limiting step from marker discovery to the correct identification of their order for further use by the research community. This high resolution map of bovine chromosome 14 will facilitate identification of regions in the sequence assembly where additional information is required to resolve marker ordering.