What Is a SNP? Single-Nucleotide Polymorphisms in Dogs

A SNP, pronounced "snip", is a single-nucleotide polymorphism: a position in the genome where dogs differ by a single DNA letter, such as an A in some dogs and a G in others. SNPs are the most common markers used to compare dogs' DNA, both to estimate breed ancestry and to find the genes behind traits like body size and coat colour.

The short version

• One letter: a SNP is a single position where the DNA letter varies between dogs.
• Two copies: each dog carries two letters at a SNP, one from each parent, such as AA, AG or GG.
• Mostly markers: most SNPs don't change a trait, but they flag nearby DNA that's inherited along with them.
• Some matter directly: a SNP inside or near a gene can change how it works.
• DNA tests read SNPs with genotyping arrays, also called SNP chips, or by sequencing.

What a SNP looks like

DNA is written in four chemical letters: A, C, G and T. At most positions, nearly every dog has the same letter. At a SNP, some dogs have one letter and some have another. Because a dog has two copies of each chromosome, it carries two letters at each SNP, which can be the same or different, just like the alleles of a gene. A dog with two matching letters is homozygous at that SNP, and a dog with two different letters is heterozygous.

How SNPs helped find dog genes

The dog genome, published in 2005, came with a dense map of SNPs across breeds, which its authors said made genome-wide association studies possible: comparing dogs with and without a trait to find the DNA linked to it. A 2007 study then described a genotyping array with about 27,000 SNPs and showed that single-gene traits in dog breeds could be mapped with only about 20 dogs. That study traced the major white-spotting locus to the MITF gene, one of the genes in our coat colour hub.

SNPs also helped explain body size. A 2007 study of size found a single IGF1 SNP haplotype, a set of SNP letters inherited together, that was common to all small breeds and nearly absent from giant breeds. Our guide to whether DNA can predict adult size explains what that means for your dog.

How DNA tests read SNPs

There are two main approaches. A genotyping array, or SNP chip, reads a fixed set of SNPs chosen in advance. Sequencing reads DNA letters directly, and low-pass sequencing reads positions across the whole genome thinly, filling in the rest by genotype imputation. As a 2022 study noted, SNP chips are ultimately limited to the SNPs chosen when the chip was designed.

The PuppyGenes report combines sequencing evidence with reference-based predictions. Our science page explains what that means for each section of the report.