This NCBI Map Viewer presents a whole-genome radiation hybrid (RH) map of the domestic cat (Felis catus) genome. The RH map for the X chromosome and 18 autosomes has 2662 markers of which 1602 are on maximum likelihood (MLE-)consensus (also known as framework) maps, 779 are placed at centiRay positions in relation to the MLE-consensus maps, and 281 are assigned to bins spanned by two or more consecutive MLE-consensus markers. There are 733 intragenic markers called by gene names, 783 microsatellite markers, and 1146 other sequenced-tagged site (STS) markers on the map. The process of checking the map included fluorescence in situ hybridization (FISH) mapping of 129 BAC clones that confirmed the long-range marker order. This cat map supersedes earlier cat autosomal and X chromosome RH maps, the most recent of which was described in (Murphy WJ, et al., 2007).

The marker development and RH map construction are described in (Davis BW, et al., 2008). The map computation was done at NCBI using the software packages rh_tsp_map and CONCORDE linked to Qsopt. The package rh_tsp_map is described in (Agarwala R, et al., 2000, and Schaffer AA, et al., 2007). CONCORDE is described in "The Traveling Salesman Problem: A Computational Study" (Applegate D, et al., Princeton University Press, 2006). rh_tsp_map includes a lengthy, detailed tutorial on how to construct RH maps, and the instructions in the tutorial were used for constructing this map.

The Y chromosome RH map is based on (Murphy WJ, et al., 2006).

Some marker names consist of only digits; to search for such markers by name, the user must add "[name]" to the query. For example: 39025064[name].

The genetic linkage map entitled "Genetic2009" is generated from a large, multi-generation pedigree of domestic cats, Felis catus, and is based on (Menotti-Raymond et al., 2009) for the autosomes and (Schmidt-Küntzel et al., 2009) for the X chromosome. This map has 529 markers and, unlike previous maps, has one linkage group per autosome. On the X chromosome, the pseudoautosomal region is treated as one linkage group and the remainder of the chromosome as a second linkage group. By convention, the positions are in gender-averaged centiMorgans for the autosomes and the pseudoautosomal region, and in female-specific centiMorgans for the remainder of the X chromosome. The genetic linkage map entitled "Genetic" is generated from a hybrid pedigree between the domestic cat and the Asian leopard cat and is based on (Menotti-Raymond et al., 2003a) and (Menotti-Raymond et al., 2003b).

Please note that other genomes can also be viewed in the NCBI Map Viewer resource. The Map Viewer Home Page provides a current list. Consider also reviewing the resources listed on the Genomic Biology site.

Available Documentation:

• NCBI Handbook: Map Viewer chapter - resource description
• NCBI Handbook: Map Viewer Exercises - tutorials and examples
• Map Viewer Help - details about navigation and customizing your display
• Genome Assembly - description of genome assembly and annotation process
• Gnomon - description of NCBI's Hidden Markov Model (HMM) ab initio prediction program

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