A high utility integrated map of the pig genome

Sean J. Humphray, Carol E. Scott, Richard Clark, Brandy Marron, Clare Bender, Nick Camm, Jayne Davis, Andrew Jenks, Angela Noon, Manish Patel, Harminder Sehra, Fengtang Yang, Margarita B. Rogatcheva, Denis Milan, Patrick Chardon, Gary Rohrer, Dan Nonneman, Pieter de Jong, Stacey N. Meyers, Alan ArchibaldJonathan E. Beever, Lawrence B. Schook, Jane Rogers

Research output: Contribution to journalArticle

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 artificial 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.

Original languageEnglish (US)
Article numberR139
JournalGenome biology
Volume8
Issue number7
DOIs
StatePublished - Jul 11 2007

ASJC Scopus subject areas

  • Ecology, Evolution, Behavior and Systematics
  • Genetics
  • Cell Biology

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    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., ... Rogers, J. (2007). A high utility integrated map of the pig genome. Genome biology, 8(7), [R139]. https://doi.org/10.1186/gb-2007-8-7-r139