We have adapted the Location Database (LDB) map-integration strategy of Morton et al. [Ann Hum Genet 56:223–232] (1992) as above to create an integrated map for each of several species for which fully annotated genome sequences are not yet available (sheep, cattle, pig, wallaby), using all types of partial maps for that species, including cytogenetic, linkage, somatic-cell hybrid, and radiation hybrid maps. An integrated map provides not only predictions of the kilobase location of every locus, but also predicts locations (in cM) and cytogenetic band locations for every locus. In this way a comprehensive linkage map and a comprehensive cytogenetic map are created, including all loci, irrespective of whether they have ever been linkage mapped or physically mapped, respectively. High-resolution physical maps from annotated sequenced species have also been placed alongside the integrated maps. This has created a powerful tool for comparative genomics. The LDB map-integration strategy has been extended to make use of zoo-FISH comparative information. It has also been extended to enable the creation of a “virtual” map for each species not yet sequenced by using mapping data from fully sequenced species. All of the partial maps, together with the integrated map, for each species have been placed in a database called Comparative Location Database (CompLDB), which is available for querying, browsing, or download in tabular form at http://medvet.angis.org.au/ldb/.
Radiation Hybrid Band File Anchor Locus Cytogenetic Band Comparative Mapping Data
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.
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This work was supported in part by the Cooperative Research Centre for Innovative Dairy Products and by SheepGenomics. The authors thank the many researchers who have generated the data incorporated into the integrated maps. In particular, they thank Dr. Jill Maddox for much of the data on which the example of OAR18 was based. The authors also thank the referees for many helpful suggestions.
Furey TS, Haussler D (2003) Integration of the cytogenetic map with the draft human genome sequence. Hum Mol Genet 12:1037–1044PubMedCrossRefGoogle Scholar
Iannuzzi L, Di Meo GO, Perucatti A, Incarnato D (1999) Comparison of the human with the sheep genomes by use of human chromosome-specific painting probes. Mamm Genome 10:719–723PubMedCrossRefGoogle Scholar
ISCNDB (2000) International system for chromosome nomenclature of domestic bovids. In: Di Berardino D, Di Miro DP, Gallagher DS, Hayes H, Iannuzzi L (coordinator) (eds) Cytogenetics and cell genetics, vol 92. pp 283–299Google Scholar
Ke X, Tapper W, Collins A (2001) LDB2000: Sequence based integrated maps of the human genome. Bioinformatics 17:1581–1586Google Scholar
Maddox JF, Davies KP, Crawford AM, Hulme DJ, Vaiman D, et al. (2001) An enhanced linkage map of the sheep genome comprising more than 1000 loci. Genome Res 11:1275–1289PubMedCrossRefGoogle Scholar
Maniatis N, Collins A, Ku X-F, McCarthy LC, Hewett DR, et al. (2002) The first linkage disequilibrium (LD) maps: delineation of hot and cold blocks by diplotype analysis. Proc Natl Acad Sci U S A 99:2228–2233PubMedCrossRefGoogle Scholar
McCoard SA, Fahrenkrug SC, Alexander LJ, Freking BA, Rohrer GA, et al. (2002) An integrated comparative map of the porcine X chromosome. Anim Genet 33:178–185PubMedCrossRefGoogle Scholar
Morton NE, Collins A, Lawrence S, Shields DC (1992) Algorithms for a location database. Ann Hum Genet 56:223–232PubMedGoogle Scholar
Murphy WJ, Larkin DM, Everts-van der Wind A, Bourque G, Tesler G, et al. (2005) Dynamics of mammalian chromosome evolution inferred from multispecies comparative maps. Science 309:613–617PubMedCrossRefGoogle Scholar
Nievergelt CM, Smith DW, Kohlenberg JB, Schork NJ (2004) Large-scale integration of human genetic and physical maps. Genome Res 14:1199–1205PubMedCrossRefGoogle Scholar
Perrocheau M, Boutreux V, Chadi S, Mata X, Decaunes P, et al. (2006) Construction of a medium-density horse gene map. Anim Genet 37:145–155PubMedCrossRefGoogle Scholar
Snelling WM, Gautier M, Keele JW, Smith TP, Stone RT, et al. (2004) Integrating linkage and radiation hybrid mapping data for bovine chromosome 15. BMC Genomics 5:77PubMedCrossRefGoogle Scholar
Tapper W, Maniatis N, Morton NE, Collins A (2003) A metric linkage disequilibrium map of a human chromosome. Ann Hum Genet 67:487–494PubMedCrossRefGoogle Scholar
Tapper W, Collins A, Gibson J, Maniatis N, Ennis S, et al. (2005) A map of the human genome in linkage disequilibrium units. Proc Natl Acad Sci U S A 102:11835–11839PubMedCrossRefGoogle Scholar
Yap IV, Schneider D, Kleinberg J, Matthews D, Cartinhour S, et al. (2003) A graph-theoretic approach to comparing and integrating genetic, physical and sequence-based maps. Genetics 165:2235–2247PubMedGoogle Scholar