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United States Department of Agriculture

Agricultural Research Service

Research Project: ENHANCING GENETIC MERIT OF DAIRY CATTLE THROUGH GENOME SELECTION AND ANALYSIS Title: A high-resolution radiation hybrid map of the bovine genome

Authors
item Grant, Jason - UNIVERSITY OF ALBERTA
item Stothard, Paul - UNIVERSITY OF ALBERTA
item Wang, Zhiquant - UNIVERSITY OF ALBERTA
item Cai, Zhipeng - UNIVERSITY OF ALBERTA
item Xu, Jiaofen - UNIVERSITY OF ALBERTA
item Lin, Guohui - UNIVERSITY OF ALBERTA
item Prasad, Aparna - UNIVERSITY OF ALBERTA
item Moon, Debra - UNIVERSITY OF ALBERTA
item Sonstegard, Tad
item Van Tassell, Curtis

Submitted to: Plant and Animal Genome Conference Proceedings
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: January 5, 2008
Publication Date: January 12, 2008
Citation: Grant, J.R., Stothard, P., Wang, Z., Cai, Z., Xu, J., Lin, G., Prasad, A., Moon, D., Sonstegard, T.S., Van Tassell, C.P. 2008. A high-resolution radiation hybrid map of the bovine genome. Plant and Animal Genome Conference Proceedings.

Technical Abstract: We are building high-resolution radiation hybrid maps of all 29 bovine autosomes and chromosome X, using a 58,000-marker genotyping assay, and a 12,000-rad whole-genome radiation hybrid (RH) panel. To accommodate the large number of markers, and to automate the map building procedure, a software pipeline was constructed to process the data in the following manner. First, a custom program is used to parse the output from the Illumina genotyping system, to determine which markers are present in each RH cell line. In parallel to this procedure, each marker is located on the current bovine and human genome assemblies using BLAST. The marker positions on the bovine assembly and the marker calls are then analyzed using CarthaGene’s comparative mapping algorithm, which uses both sets of information to determine marker order. Lastly, maps are visualized and compared to the bovine and human genome assemblies using AutoGRAPH. The entire process runs in a distributed fashion on a 30-node computing cluster, allowing maps to be rebuilt relatively quickly using alternative parameters or reference assemblies. This pipeline should be applicable to other species for which similar RH panel and genotyping resources are available. The maps generated using this approach should aid in the assembly of problematic genome regions, and in turn facilitate haplotype construction and candidate gene searches.

Last Modified: 9/20/2014
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