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United States Department of Agriculture

Agricultural Research Service

Title: A high utility integrated map of the pig genome

Authors
item Humphray, Sean -
item Scott, Carol - WTSI, CAMBRIDGE, UK
item Clark, Richard - WTSI, CAMBRIDGE, UL
item Marron, Brandy - UNIV. IL, URBANA, IL
item Bender, Clare - WTSI, CAMBRIDGE, UK
item Camm, Nick - WTSI, CAMBRIDGE, UK
item Davis, Jayne - WTSI, CAMBRIDGE, UK
item Jenks, Andrew - WTSI, CAMBRIDGE, UK
item Noon, Angela - WTSI, CAMBRIDGE, UK
item Patel, Manish - WTSI, CAMBRIDGE, UK
item Sehra, Harminder - WTSI, CAMBRIDGE, UK
item Yang, Fengtang - WTSI, CAMBRIDGE, UK
item Rogatcheva, Margarita - UNIV. IL, URBANA, IL
item Milan, Denis - LGC, INRA, FRANCE
item Chardon, Patrick - INRA-CEA, FRANCE
item Rohrer, Gary
item Nonneman, Danny
item DE Jong, Pieter - CHO-BACPACR, OAKLAND, CA
item Meyers, Stacey - UNIV. IL, URBANA, IL
item Archibald, Alan - ROSLIN INSTITUTE, UK
item Beever, Johathan - UNIV. IL, URBANA, IL
item Schook, Lawrence - UNIV. IL, URBANA, IL
item Rogers, Jane - WTSI, CAMBRIDGE, UK

Submitted to: Genome Biology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: July 11, 2007
Publication Date: July 11, 2007
Citation: Humphray, S.J., Scott, C.E., Clark, R., Marron, B., Bender, C., Camm, N., Davis, J., Jenks, A., Noon, A., Patel, M., Sehra, H., Yang, F., Rogatcheva, M.B., Milan, D., Chardon, P., Rohrer, G., Nonneman, D., de Jong, P., Meyers, S.N., Archibald, A., Beever, J.E., Schook, L.B., Rogers, J. 2007. A high utility integrated map of the pig genome. Genome Biology. 8(7):R139.

Interpretive Summary: We have constructed a comprehensive physical map of the pig genome. The physical map integrates previous landmark maps with a fingerprint map developed from large segments of DNA from the pig genome known as bacterial artificial chromosomes (BACs). In addition, we used sequence information from over 260,000 BACs compared to the human genome to improve the continuity and local ordering of the BAC segments. We estimate that approximately 98% of the pig genome is represented in 172 contigs or groups of BACs.Some chromosomes are well mapped and the entire chromosome is represented by only a few contigs, while other chromosomes have many contigs. The extreme cases are the X chromosome represented by 27 contigs and chromosome 13 assembled in a single contig. The Y chromosome is currently represented by sparse coverage in specific regions. The map is accessible on the internet (http://pre.ensembl.org/Sus_scrofa/index.html). This physical map will provide a framework for the generation and assembly of the pig genome sequence. Furthermore, the map is immediately useful to the pig research community to identify genes and fine mapping of quantitative trait loci.

Technical Abstract: Background: The domestic pig is being increasingly exploited as a system for modeling human disease. It also has substantial economic importance for meat-based protein production. Physical clone maps have underpinned large-scale genomic sequencing and enabled focused cloning efforts for many genomes. Comparative genetic maps indicate that there is more structural similarity between pig and human than, for example, mouse and human, and we have used this close relationship between human and pig as a way of facilitating map construction. Results: Here we report the construction of the most highly continuous bacterial artifical chromosome (BAC) map of any mammalian genome, for the pig (Sus scrofa domestica) genome. The map provides a template for the generation and assembly of high-quality anchored sequence across the genome. The physical map integrates previous landmark maps with restriction fingerprints and BAC end sequences from over 260,000 BACs derived from 4 BAC libraries and takes advantage of alignments to the human genome to improve the continuity and local ordering of the clone contigs. We estimate that over 98% of the euchromatin of the 18 pig autosomes and the X chromosome along with localized coverage on Y is represented in 172 contigs, with chromosome 13 (218 Mb) represented by a single contig. The map is accessible through pre-Ensembl, where links to marker and sequence data can be found. Conclusion: The map will enable immediate electronic positional cloning of genes, benefiting the pig research community and further facilitating use of the pig as an alternative animal model for human disease. The clone map and BAC end sequence data can also help to support the assembly of maps and genome sequences of other artiodactyls.

Last Modified: 11/27/2014