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. 2004 Sep 13:5:65.
doi: 10.1186/1471-2164-5-65.

An integrated 4249 marker FISH/RH map of the canine genome

Affiliations

An integrated 4249 marker FISH/RH map of the canine genome

Matthew Breen et al. BMC Genomics. .

Abstract

Background: The 156 breeds of dog recognized by the American Kennel Club offer a unique opportunity to map genes important in genetic variation. Each breed features a defining constellation of morphological and behavioral traits, often generated by deliberate crossing of closely related individuals, leading to a high rate of genetic disease in many breeds. Understanding the genetic basis of both phenotypic variation and disease susceptibility in the dog provides new ways in which to dissect the genetics of human health and biology.

Results: To facilitate both genetic mapping and cloning efforts, we have constructed an integrated canine genome map that is both dense and accurate. The resulting resource encompasses 4249 markers, and was constructed using the RHDF5000-2 whole genome radiation hybrid panel. The radiation hybrid (RH) map features a density of one marker every 900 Kb and contains 1760 bacterial artificial chromosome clones (BACs) localized to 1423 unique positions, 851 of which have also been mapped by fluorescence in situ hybridization (FISH). The two data sets show excellent concordance. Excluding the Y chromosome, the map features an RH/FISH mapped BAC every 3.5 Mb and an RH mapped BAC-end, on average, every 2 Mb. For 2233 markers, the orthologous human genes have been established, allowing the identification of 79 conserved segments (CS) between the dog and human genomes, dramatically extending the length of most previously described CS.

Conclusions: These results provide a necessary resource for the canine genome mapping community to undertake positional cloning experiments and provide new insights into the comparative canine-human genome maps.

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Figures

Figure 1
Figure 1
Integrated FISH/RH map and dog/human comparative data for CFA1. BAC-ends also localized by FISH mapping are reported in the left panel, symbolized by a vertical bar along with BAC addresses. Asterisks (**) represent BAC clones that did not have a unique cytogenetic location (multiples hits are listed on SOM). RH mapped markers and their cumulative positions in centiRay 5000 units are reported to the right of the FISH map. Connecting lines between FISH and RH maps indicate integration points between maps. The right panel shows the human evolutionarily conserved segments, represented by colored boxes as determined by RH data. Human coordinates (in Mb) identified from dog/human sequence alignments (see Methods) are reported on the right most vertical bar. RH markers and their corresponding human sites are connected by lines and illustrate the rearrangement within synteny blocks.
Figure 2
Figure 2
Assignment of 60 canine BAC clones to CFA 1. BAC addresses alongside the ideogram of CFA 1 refer to clones from the RPCI-81 canine BAC library. A pair of colored spots spanning an interval of approximately 4 Mb represents the cytogenetic assignment of each clone. The color of the spots identifies the fluorochrome used to label the clone as follows: red = Spectrum Red; orange = Spectrum Orange; green = Spectrum Green; blue = DEAC; purple = Cy5. Multi-color FISH of neighboring clones, using both metaphase and interphase analyses, was used to establish the precise order of the clones along the length of the chromosome. Clones whose assignment is represented by a circular rainbow have been tentatively placed, but not yet co-localized with neighboring clones to establish one equivocal, linear order. BAC addresses followed by ** identify those clones that resulted in fluorescent signal at more than one location. Human orthologous regions (HSA) are reported on the left of the figure by vertical bars.

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