A high utility integrated map of the pig genome

Sean J Humphray¹ , Carol E Scott¹ , Richard Clark¹ , Brandy Marron² , Clare Bender¹ , Nick Camm¹ , Jayne Davis¹ , Andrew Jenks¹ , Angela Noon¹ , Manish Patel¹ , Harminder Sehra¹ , Fengtang Yang¹ , Margarita B Rogatcheva² , Denis Milan³ , Patrick Chardon⁴ , Gary Rohrer⁵ , Dan Nonneman⁵ , Pieter de Jong⁶ , Stacey N Meyers² , Alan Archibald⁷ , Jonathan E Beever² , Lawrence B Schook² and Jane Rogers¹

¹The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA UK

²College of Agriculture, Consumer and Environmental Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801 USA

³Laboratoire de Génétique Cellulaire, INRA, 31326 Castanet-Tolosan, France

⁴INRA-CEA, Domaine de Vilvert, 78352, Jouy en Josas cedex, France

⁵US Department of Agriculture, Agricultural Research Service, US Meat Animal Research Center, Clay Center, NE 68933-0166, USA

⁶Children's Hospital Oakland-BACPAC Resources, Oakland, California 94609, USA

⁷Roslin Institute, Roslin, Midlothian EH25 9PS, UK

author email corresponding author email

Genome Biology 2007, 8:R139doi:10.1186/gb-2007-8-7-r139


Published:	11 July 2007

Subject areas: Bioinformatics, Genome studies, Genetics

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.