The dog is an attractive model for genetic studies of complex disease. With drafts of the canine genome complete, a large number of single-nucleotide polymorphisms (SNPs) that are potentially useful for gene-mapping studies and empirical estimations of canine diversity and linkage disequilibrium (LD) are now available. Unfortunately, most canine SNPs remain uncharacterized, and the amount and quality of DNA available from population-based samples are limited. We assessed how these real-world challenges influence automated SNP genotyping methods such as Illumina's GoldenGate assay. We examined 384 SNPs on canine chromosome 9 and successfully genotyped a minimum of 217 and a maximum of 275 SNPs using buccal swab samples for 181 dogs (86 beagles, 76 border collies, and 15 Australian shepherds). Call rates per SNP and sample averaged 97%, with reproducibility within and between analyses averaging 98%. The majority of these SNPs were polymorphic across all 3 breeds. We observed extensive LD, albeit less than reported for surveys using fewer dogs, consistent between breeds. Analyses of population substructure indicated that beagles are distinct from border collies and Australian shepherds. These results demonstrate the suitability of amplified canine buccal samples for high-throughput multiplex genotyping and confirm extensive LD in the dog.

Over the past decade, a number of researchers have advocated the use of the dog as a model system for understanding the genetic basis of disease, morphology, and behavior (Barsoum et al. 2000; Ostrander and Kruglyak 2000; Ponder et al. 2002; Galibert et al. 2004; Sutter and Ostrander 2004). Due to its history of domestication (Savolainen et al. 2002), the dog offers a number of advantages for gene-mapping studies. Most extant breeds were developed through selection for specific types of tasks or work (Clutton-Brock 1999; Koskinen and Bredbacka 2000) and are less than 150 years old, resulting in reduced heterogeneity within breeds and increased heterogeneity between breeds (Parker et al. 2004). As breeds represent canalization of genetic variation, different breeds may vary with respect to genes responsible for biological processes, including growth, cognitive development, and liability for the development of behavioral or disease pathologies.

Gene-mapping studies require adequate numbers of informative markers (Ostrander and Kruglyak 2000; Brooks and Sargan 2001). Large numbers of short tandem repeat markers (STRs) have been described for the dog (Guyon et al. 2003), with a subset defined for linkage studies (Clark et al. 2004). With draft sequences of the canine genome complete (Kirkness et al. 2003; Lindblad-Toh et al. 2005), a large number of single-nucleotide polymorphisms (SNPs) are now available for the domestic dog. A small subset of these have already been used to develop empirical estimations of diversity and linkage disequilibrium (LD) in the canine genome (Sutter et al. 2004; Lindblad-Toh et al. 2005), and panels of SNPs for linkage analysis and whole-genome association studies are being developed to facilitate the identification of traits of interest. However, almost all known canine SNPs remain uncharacterized, and what would constitute an adequate set of SNPs for LD-mapping efforts remains unknown. Although recently developed platforms for genotyping large numbers of SNPs (i.e., Illumina, Inc., San Diego, CA; Affymetrix, Inc., Santa Clara, CA) can facilitate efficient data collection, the feasibility of large-scale genetic analyses in dogs is complicated by a number of challenges; the potential for low net yield of canine DNA from population-based samples (characteristically extracted from buccal swabs) is particularly daunting. The amount of target DNA that can be retrieved from canine buccal swab samples is low, and the total DNA extracted from buccal swabs is invariably contaminated by large amounts of microbial DNA.

For the present study, we assessed how real-world challenges inherent to genetic investigations in the dog influence automated SNP genotyping methods. We chose 384 SNPs on canine chromosome 9 from the Broad Institute's set of approximately 2.55 million uncharacterized canine SNPs (Lindblad-Toh et al. 2005), and evaluated their performance on the Illumina BeadArray genotyping platform using whole-genome–amplified DNA samples extracted from buccal swabs. In the process, we were able to use the data produced for an assessment of LD and population structure in a sample of 86 purebred beagles, 76 purebred border collies, and 15 purebred Australian shepherds. Our results indicate that amplified buccal samples yield enough canine DNA for use in standard high-throughput multiplex genotyping assays and confirm that LD is extensive in the dog. To our knowledge, no other group has successfully genotyped from canine buccal swab DNA samples using the Illumina platform.