BMC Genomics 2004, 5:65 http://www.biomedcentral.com/1471-2164/5/65 FAisgsuigrnem2ent of 60 canine BAC clones to CFA 1 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 neigh- boring 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. previous version of the map. The mean interval size is now 1.59 Mb. The chromosome with the most BACs mapped to it is CFA 1, featuring 104 localized to 83 unique positions (Figure 1). See all chromosomes in the Supporting Online Material (SOM) at http://www-recom gen.univ-rennes1.fr/doggy.html. Again, the chromosome with the fewest is CFA 38, with 16 BACs localized to 14 unique positions. This resource provides a dense scaffold on which to build regional physical maps and search for new genes. Of particular interest to disease gene mappers will be the 26 BACs that are RH mapped to the X chromo- some, 13 of which are also localized by FISH. Only two BACs were localized to the Y chromosome, one of which is also FISH mapped. See Table 1 for details. FISH mapped BACs A total of 1,000 BACs were assigned to a chromosome band, and then ordered along the length of the corre- sponding chromosome using a combination of met- aphase and interphase multi-color FISH. CFA 1 is shown, for example, in Figure 2. The panel of FISH mapped clones included clones representing both ends of each chromosome, with the exception of the centromeric end of CFA 6 (6q11-q12) and the centromeric 20% of CFA 9 (9q11-q12). Nine hundred and eighty-one out of 1,000 BACs had a unique cytogenetic location, and 851 were also ordered on the RH map. This yielded an average of one BAC-end that was both FISH and RH mapped every 3.48 Mb. See SOM material for data on all chromosomes and http://www.cvm.ncsu.edu/mbs/breen_matthew.htm. Integration of FISH and RH data Analysis of co-linearity between the two maps was per- formed by connecting the BAC markers in common between the RH map and FISH data. This approach allowed the identification of markers that serve as anchors to each chromosome for both RH and FISH maps, thus validating their localization and marker order. Early in the assembly process, a small number of discrepancies between the two maps were easily identified through graphical drawings of all chromosomes, leading to a sys- tematic re-examination of experimental data and, in most cases, consensus resolution. However, 19 BACs did not have one unique cytogenetic location. These are indicated with a double asterisk in Figure 1 and 2, as well as the SOM and figures provided on all web sites. For each of these 19, one of their FISH localizations was in agreement with the corresponding RH map position. In addition, seven (7/19) had an identified human ortholog that was in agreement with the RH map localization. For an addi- tional set of 24 BACs, conflict remained after rechecking both the FISH and RH data. These are indicated by "#" in all Figures. Interestingly, the DNA used to obtain FISH data for these clones PCR amplified successfully with the same primers used to obtain RH data, indicating that the Page 5 of 11 (page number not for citation purposes)