Direct-to-consumer (DTC) genetic testing – the service offered by companies like 23andMe and Ancestry DNA – is revolutionizing the study of human genetics by creating databases of gene sequence examples far larger than those collected by academic institutions.
And although we simply don’t yet know enough about our genomes to be able to diagnose or predict complex diseases based on DTC results, scientists have been able to use these databases to gain key insights into the origins of numerous traits and conditions.
This also holds true for the emerging field of dog genome analysis.
Writing in the open-access journal PLOS Genetics, a team from the canine DNA testing company Embark Veterinary describe how they used samples from over 3,000 dogs to determine the genetics responsible for the vivid blue eyes of huskies.
As the researchers explain, variants of two genes also involved in coat coloration had been previously identified as the cause of solid or partially blue irises in one or both eyes of many dogs, but these sequences were not found in Siberian Huskies or in the rare non-merle Australian Shepherds that have distinctively bright, solid blue eyes.
To determine the genetics underlying this unique feature, the team first performed what is known as a genome-wide association study (GWAS). Using a panel of 3,180 diverse purebreds and mutts whose DNA had been tested with a platform that probes for sequence markers at over 214,000 spots throughout the dog genome, they looked for correlations between the presence of certain variants and blue eyes. Each dog’s actual eye color was listed in the owner report or confirmed by an uploaded photo.
This process identified one of the known blue eye genes as well as a never-before-seen combination of variations – called a haplotype – on chromosome 18: a duplication of a mutation-bearing sequence of 98,600 base pairs located near the beginning of the ALX4 gene. Quite tellingly, this haplotype was carried by 100 percent of the panel’s blue-eyed purebred Siberian Huskies and 78 percent of the blue-eyed shepherds.
To confirm the findings of the GWAS, the corporate researchers repeated the analysis on a panel of 2,890 additional dogs. All but one of the dogs in this sample who carried one or two copies of the same chromosome 18 duplication had either blue or heterochromatic blue eyes instead of brown. The one husky who broke this pattern had the haplotype on one chromosome but still had solid brown eyes, though a query sent out to the owner confirmed that the pup’s parents had blue eyes.
“In this study, we discovered a haplotype containing a 98.6-kb duplication that is strongly predictive of blue eyes and heterochromia in dogs. While we cannot definitively rule out a different typed or untyped variant on this haplotype causing the trait, we feel that the duplication is a plausible causal candidate worthy of further functional investigation," the authors concluded.