A comparative approach to physical and linkage mapping of genes on canine chromosomes using gene-associated simple sequence repeat polymorphisms illustrated by studies of dog chromosome 9

We describe and illustrate a comparative approach to creating physical and linkage maps of genes on dog chromosomes, The approach is particularly usef ul in species, like the dog, which have a rudimentary gene map not integrat ed with microsatellite loci. Human or mouse cDNAs for genes to be mapped ar e used to isolate cosmid or phage clones from dog genomic libraries. Clones verified to contain the homologous canine gene coding sequences are screen ed for "gene-associated" simple sequence repeat polymorphisms (SSRPs), The unique sequences flanking the repeats are used to design PCR primers to amp lify the repeat and gene-associated SSR length differences that are informa tive for linkage analysis used in canine pedigrees to study linkage between loci or with diseases. The same canine clones are employed as probes in fl uorescence in situ hybridization (FISH) studies to physically map the loci to specific sites on dog chromosomes. This approach creates a combined gene and gene-associated microsatellite anchor locus framework map, In this art icle we review our recent use of this approach to map a series of genes fou nd on human chromosome 17 (HSA17) to two dog chromosomes. Canine chromosome 9 (CFA9) contains 11 loci found on HSA17q, while two genes from HSA17p map to CFA5, demonstrating disruption of HSA17 synteny at the centromere, The order of 11 HSA17q genes on CFA9 was conserved in the dog, but the entire g roup is inverted with respect to the centromere when compared to human and mouse. Maps created by this approach can be used to advantage for integrati ng anonymous microsatellites with gene maps, including microsatellites foun d in genome scans to be linked to canine diseases, This makes it possible t o identify the homologous chromosomal region in the human or mouse genome a nd to make use of this information in formulating hypotheses regarding cand idate genes, as has recently been illustrated by other investigators.