Service Communautaire d'Information sur la Recherche et le Développement - CORDIS

Genomic tools for bovine sequencing and mapping

We have produced radiation hybrid (RH) maps for BTA9 and BTA11. The RH maps produced by this project are the most concise produced for BTA9 AND BTA11 to date. In addition to RH maps we also thought it important to create contig maps of BTA9 and BTA11.

These maps underpin detailed construction of the bovine chromosome at a fine scale. To date the sequence has a 6X coverage (although unpublished to date) although the true coverage along with the reliability of the build means that although the genome has been sequenced there are a number of problems with the sequence. (i) As with the human chromosome the bovine genome contains a large number of gaps between areas of sequence. These gaps are of particular importance when it comes to the positioning of markers as a gap is usually unknown and may be given a fixed size i.e. 10,000bp when in fact in reality the gap could be a hundred fold greater or a hundred fold less than this.(ii) Not only are the gaps a problem but also the orientation of the scaffolds is often incorrect due to the lack of information concerning the sequence and the large gaps in the genome sequence mentioned previously.

The contig maps for BTA9 and BTA11 were developed by comparing the contig information to the bovine genome sequence and producing an output that would allow identification of areas within the chromosomes that may be prone to sequence assembly error. This review process combined with the RH maps for yet finer scale mapping yields a more precise and more reliable assembly of the sequence. This is essential for fine scale mapping of QTL.

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Genomics and Bioinformatics
United Kingdom