BMC Genomics 2004, 5:65 http://www.biomedcentral.com/1471-2164/5/65 Background Three major advances in the development of resources for mapping canine disease genes have been: 1) the develop- ment of a radiation hybrid (RH) map composed of large numbers of microsatellite markers and genes that link the canine and human genomes [1], 2) the development of canine specific whole chromosome paints that have allowed preliminary assignment of conserved segments between human and dog [3-5]; and 3) the publication of a 1.5x genome sequence of the dog [2]. The most recently published RH map of the dog comprises 3270 markers including 1596 microsatellite-based markers, 900 canine- specific cloned gene sequences and expressed sequence tags (ESTs), and an initial set of 668 canine-specific BAC- ends [1]. The map was constructed using the RHDF5000- 2 whole genome radiation hybrid panel [6] and features markers mapped to 3009 unique positions, defining an average inter-marker distance of one megabase (Mb). The map also defines a minimal screening set of 325 highly informative well-spaced markers, to be used in the initia- tion of genome-wide scans [1]. A well-defined synteny between the dog and human genomes was established as a function of this work [1] and from extensive reciprocal chromosome painting studies [3,5,7]. The above mapping efforts are complemented by the recent release of a 1.5x sequence of a Standard Poodle genome [2]. The sequence includes 6.2 million sequence reads that span approximately 78% of the genome. More than 650 million base pairs (>25%) align uniquely to the human genome, and the resulting alignment includes fragments of putative orthologs for 18,473 of 24,567 annotated human genes. The current alignment supports most of the proposed comparative segments, but suggests that the final comparative dog-human map will be com- posed of at least 160 comparative blocks [2]. Using the above resources, canine researchers have under- taken genome-wide screens for linkage to a variety of dis- ease loci as well as morphological traits defining differences between breeds. Many of these studies have met with success. Disease loci have been genetically mapped or otherwise localized in the dog for several dis- orders including: vision-associated disease such as pro- gressive rod cone degeneration, early retinal degeneration, cone degeneration, and collie eye anomaly [8-11], kidney cancer [12,13], narcolepsy [14], rheumatoid arthritis [15], Severe Combined Immunodeficiency (SCID) [16], hip dysplasia [17], cystinuria [18], bleeding disorders [19,20], ceroid lipofuscinosis [21], and copper toxicosis [22,23]. In addition, quantitative trait loci (QTL) have been iden- tified for principal components defining skeletal variation and hip dysplasia [17,24]. In general, investigators have been able to use the existing resources to localize traits of interest to an interval of 10–20 Mb, but in most cases the causative gene remains to be identified. To facilitate positional cloning efforts in the canine com- munity, we have localized a large set of randomly selected canine-specific BACs onto the canine 5000-rad RH map, a subset of which we have also localized cytogenetically. The resulting map of 4249 markers includes 1760 mapped BAC-ends, 851 of which have been FISH mapped, to generate a dense, accurate and highly inte- grated map of the canine genome. Results General RH map characteristics This novel RH map of the dog genome contains 4249 markers of three different types: 900 genes, 1589 micros- atellites and 1760 BACs. The map was generated by geno- typing 1092 new BAC-end markers on the RHDF5000-2 panel, and recomputing the new vectors with those from the previous map [1] using MULTIMAP [25] and TSP/ CONCORDE [26]. Table 1 summarizes the key features of the new map. The typing of 4249 markers resulted in an RH map containing 4106 markers that were eventually grouped and assigned to each of the canine chromo- somes, leaving only 143 unlinked markers. Human orthologs were identified for 2233 mapped markers. The resolution limit of the RHDF5000 panel has been deter- mined to be 4 cR5000 (600 Kb) [6]. Thus, markers falling within any 4 cR5000 or 600 Kb stretch cannot be ordered relative to one another with high confidence and, conse- quently, are reported as co-localized on the map. Analysis of the entire dataset of 4249 RH vectors by MUL- TIMAP [25] at a Lod score of 8.0, and for a subset of regions a Lod of 9.0, resulted in 60 individual linkage groups that could be assigned to the 38 canine autosomes and two sex chromosomes. For chromosomes that were covered by multiple linkage groups, the data were merged and ordered as described in the Methods. FISH data com- bined with significant Lod scores between selected mark- ers led to the unambiguous assignment and orientation of specific linkage groups to chromosomes and, ultimately, complete coverage of each chromosome. The resulting 4106 linked markers defined 3090 unique positions regularly spaced across all autosomes. The larg- est chromosome, canine chromosome 1 (CFA 1), con- tains 220 markers, while CFA 38, the smallest chromosome at 38 Mb, has only 32 markers (Figure 1). Excluding the sex chromosomes, the least dense chromo- some, CFA 38, has a marker located every 1.2 Mb, while the most dense, CFA 12 and CFA 20, have markers posi- tioned at an average of every 0.47 Mb. The increase in den- sity is due solely to the addition of 1092 new BAC-ends, bringing the total to 1760 from the 668 reported in the Page 2 of 11 (page number not for citation purposes)