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A genome-wide association study of deafness in three canine breeds

Citation

Hayward, Jessica et al. (2020), A genome-wide association study of deafness in three canine breeds, Dryad, Dataset, https://doi.org/10.5061/dryad.sf7m0cg2n

Abstract

Congenital deafness in the domestic dog is usually related to the presence of white pigmentation, which is controlled primarily by the piebald locus on chromosome 20 and also by merle on chromosome 10. Pigment-associated deafness is also seen in other species, including cats, mice, sheep, alpacas, horses, cows, pigs, and humans, but the genetic factors determining why some piebald or merle dogs develop deafness while others do not have yet to be determined.

Here we perform a genome-wide association study (GWAS) to identify regions of the canine genome significantly associated with deafness in three dog breeds carrying piebald: Dalmatian, Australian cattle dog, and English setter. We include bilaterally deaf, unilaterally deaf, and matched control dogs from the same litter, phenotyped using the brainstem auditory evoked response (BAER) hearing test.

Principal component analysis showed that we have different distributions of cases and controls in genetically distinct Dalmatian populations, therefore GWAS was performed separately for North American and UK samples. We identified one genome-wide significant association and 14  suggestive (chromosome-wide) associations using the GWAS design of bilaterally deaf vs. control Australian cattle dogs,. However, these associations were not located on the same chromosome as the piebald locus, indicating the complexity of the genetics underlying this disease in the domestic dog. Because of this apparent complex genetic architecture, larger sample sizes may be needed to detect the genetic loci modulating risk in piebald dogs.

Methods

Genotype data of 503 dogs from three breeds (dalmatian, australian cattle dog, english setter) run on the semi-custom 220k CanineHD array (Illumina), with positions in CanFam3.1 reference. After quality control filters performed in PLINK, there are 201,020 SNPs. 

Funding

American Kennel Club Canine Health Foundation, Award: CHF2172

American Kennel Club Canine Health Foundation, Award: CHF2387