SNP Genotyping in Dogs: How Does a SNP Array Work?

Key Takeaways

• SNP is a position where DNA differs by just one spot — a genetic "signpost."
• A SNP array tests hundreds of thousands to millions of SNPs at once on a single chip.
• It can reveal a dog's breed, disease risk, and specific traits.
• It's a stable, accurate, and cost-effective technology for wide-scale testing.

When talking about dog DNA testing with Microarray, the term you hear often is "SNP genotyping." But what is it, and how does it work? This article explains the principle behind it in simple terms, from a bioinformatics perspective.

What Is a SNP?

SNP (Single Nucleotide Polymorphism) is a position on DNA that differs by just "one base" between organisms — for example, at one position some are A and some are G. These tiny differences are scattered across the genome and act like "signposts" indicating genetic differences between individual dogs and breeds.

How Does a SNP Array Work?

A SNP array, or genotyping chip, works by having hundreds of thousands to millions of probes on a small chip. Each probe is designed to bind to one specific SNP position — for instance, the CanineHD array carries over 170,000 SNPs spaced on average every 13 kb across the genome (Vaysse et al., PLoS Genetics, 2011). When a dog's DNA is placed on the chip, each position gives a signal telling which base that dog has there. This lets us read hundreds of thousands of genetic positions at once, quickly and to a high standard.

What Can SNPs Tell Us About a Dog?

By gathering SNP patterns across the genome, we can read several things — breed (comparing SNP patterns against a reference breed database, where research shows SNP positions correlate clearly with between-breed differences), genetic disease risk (looking at SNPs in disease-associated positions via within-breed GWAS) (Friedenberg et al., PLoS Genetics, 2019), and specific traits like coat color or body size — with research identifying variants that explain over 90% of dog body-size variation (Plassais et al., Nature Communications, 2019). The SNP pattern is like a genetic fingerprint of each individual dog. This connects with dog breed DNA testing.

Why SNP Arrays Fit Real Testing

The strength of SNP arrays is cost-effectiveness and stability, because they test only positions with scientific support already, giving accurate, reproducible, and straightforward-to-interpret results — and research confirms an array of this density is sufficient for detecting genetic associations within a breed. This differs from reading the whole genome, which produces enormous data mostly unused in routine testing. For breed and disease screening in dogs, this is the most fitting tool. This connects with genetic diseases by dog breed.

Author's Final Note

SNP genotyping is a beautiful example of using "tiny differences" on DNA to tell big stories about our dogs. This technology makes DNA testing accessible, accurate, and reliable. If you're interested in DNA testing for your pet, feel free to consult the Geneus Pet team.

References

1. Vaysse A, et al. Identification of Genomic Regions Associated with Phenotypic Variation between Dog Breeds using Selection Mapping. PLoS Genetics. 2011;7(10):e1002316. NCBI PMC
2. Imputation of canine genotype array data using 365 whole-genome sequences improves power of genome-wide association studies. PLoS Genetics. 2019. NCBI PMC
3. Plassais J, et al. Whole genome sequencing of canids reveals genomic regions under selection and variants influencing morphology. Nature Communications. 2019;10:1489. Nature
4. A Genome-Wide Detection of Copy Number Variations Using SNP Genotyping Arrays in Dogs. Genes. 2019. NCBI PMC