BMC Genomics 2004, 5:65 http://www.biomedcentral.com/1471-2164/5/65 other markers of different types, i.e. BACs and microsatel- lites, or microsatellite and genes, etc. Thus, all of the data will likely prove useful for mapping and cloning genes of interest, as the information provided at each location is non redundant. In addition, even when markers of the same type are co-localized, they are likely to be of value; any given microsatellite is not informative in every pedi- gree, and closely localized BACs may represent the begin- ning of an overlapping contig. A direct consequence of markers mapping to the same positions is that the mean distance between two adjacent positions is now 0.9 Mb, which is very similar to the 1 Mb calculated for the most recent published version of the canine map [1]. Again, this reflects the resolving power of the 5000 rad panel [6], as well as the method of map com- putation. TSP/CONCORDE considers markers co-local- ized if they map to a region of 0.9 Mb or less, regardless of RH panel mapping power [26]. The number and identity of conserved segments (CS) between the human and the dog genomes is 79. CS were identified by both FISH localization and RH mapping with four chromosomes showing four human/dog CS, and the remainder showing one to three. The number of markers and the resolving power of the 5000 rad panel allowed us to detect several instances in which CS appear to be split in sub-segments. In several such cases, the order of markers in the two adjacent sub-fragments is conserved, although the two sub-fragments are oriented in opposing directions. Following the previously agreed definitions, these sub-fragments are termed CSO for "con- served segment order" [28]. Such a situation is observed in CFA 1 (Figure 1). In other instances, one of the two adja- cent sub-fragments appears to correspond to a CSO, while the other corresponds to a CS. Obviously a better distinc- tion between CS and CSO segments would require geno- typing of additional markers, ideally on a panel constructed with a higher dose of radiation, and with con- comitantly higher resolution. Such experiments are cur- rently underway using 10,000 genes derived from the available dog genome sequence [2] and a newly con- structed 9000 rad panel (data not shown). As shown in Table 1, and as indicated in the Results, 851 BACs were localized both by FISH and RH mapping, with a high level of concordance between the two methods. Thus, the map presented here provides a verified anchor point every 3.48 Mb. Unlike a FISH map that is not altered or modified by the addition of a new dataset, an RH map does change after adding information because different algorithms provide different solutions for local marker order. Each is statistically valid when ordering the same set of markers. However, discrepancies may arise as more markers are added to the map. Moreover, even one algorithm can generate maps with slightly different marker orders within localized regions, even when only minor adjustments are made to the dataset like removing seemingly redundant markers [29]. In the present study, the high degree of anchorage by a set of markers localized in different laboratories with differing technologies yields a high level of confidence for the integrated FISH/RH map. Of interest to many researchers will be the multiple appli- cations that a cytogenetically defined and RH verified set of canine BAC clones can provide. For example, the ordered set of 981 FISH mapped canine BAC clones with a unique cytogenetic location will be welcomed by cancer geneticists as a means to characterize chromosome aberra- tions in canine tumors. The dense cytogenetic coverage available for most chromosomes allows the use of serial differential labeling of some or all clones in chromosome- specific panels designed to 'tile' structurally aberrant chro- mosomes. This approach will allow a much more accurate assessment of chromosome rearrangements than is possi- ble with single color whole chromosome paint probes. In addition, the ordered clones will allow expansion of the current canine BAC microarrays, which in turn may be used for a variety of applications including array-based Comparative Genome Hybridization (CGH) analysis of canine tumors [30], array-painting of aberrant canine chromosomes, and investigation of cytogenetically cryptic copy number changes and gene dosage alterations in con- genital abnormality syndromes. In addition, ordered arrays of BAC clones will be an important resource for refining the comparative cytogenetic data within the diverse karyotypes that comprise the Canidae. Finally, with the imminent release of the 7x canine genome assembly, the resources described in this paper will pro- vide a long-awaited means to translate canine cytogenetics data into canine DNA sequence data, thus advancing our knowledge of canine and comparative genomics. Conclusions The presentation of a map containing 900 canine specific genes, 1589 microsatellites and 1760 BACs provides the canine genetics community with nearly all the resources it needs to undertake experiments aimed at both mapping and cloning traits of interest. A dense set of microsatellite markers (MSS-2) for undertaking genome wide scans was provided in the previous iteration of the map [1]. These same markers are integrated into the current map. Thus, within 0.7/0.8 Mb of any linked marker on the current map is now an array of anchored BACs for contig build- ing, comparative mapping, and searching for new genes and splice variants. The current map defines some 79 con- served segments between human and dog. While we expect this number to approximately double when the 7x canine genome sequence is completed, we speculate that Page 7 of 11 (page number not for citation purposes)