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Deafness in Australian Cattle Dogs associated to QTL on chromosome 20 in GWAS analyses

Citation

Seddon, Jenny; Sommerlad, Susan; Fortes, Marina (2021), Deafness in Australian Cattle Dogs associated to QTL on chromosome 20 in GWAS analyses, Dryad, Dataset, https://doi.org/10.5061/dryad.j9kd51cb0

Abstract

Pigment-associated deafness is a common hereditary condition in a range of dog breeds. The aim of this study was to perform a genome-wide association analysis to investigate the genetic architecture of deafness in Australian Cattle Dogs. Genotypes for 104,757 polymorphisms in 96 Australian dogs were available for analyses after quality control and included here. Further samples from US and UK are available here (https://doi.org/10.5061/dryad.sf7m0cg2n). A genomic relationship matrix was used in the mixed model analyses to account for polygenic effects, as we tested each polymorphism for its association with deafness, in a case/control experimental design. Three approaches were used to code the genotypes and test for additive, recessive and dominant SNP effects. Analysing all samples together, GWAS analyses identified a clear association peak on CFA20, with the most significant SNPs on this chromosome (-log10 p value = 3.89) in the vicinity of MITF. Mutations in MITF have been associated with white pigmentation in dogs and with deafness in humans and other species, supporting the premise that canine deafness is associated with mutations in or near this gene.  A recessive inheritance for the peak in CFA20 is possible given the significant results in the recessive model; however, the estimated heritability was low (4.54 x10-5). Further validation, identification of mutations and testing in other dog breeds are needed.

Methods

Hearing status was confirmed in Australian Cattle Dogs by means of the brainstem auditory evoked response (BAER). In Australia, blood samples were collected into EDTA at the time of BAER testing. Samples were genotyped using the Illumina CanineHD BeadChip array. This array is a chip that contains more than 170,000 single nucleotide polymorphisms (SNPs) and was mapped to the CanFam3.1 reference genome. SNPs with a call rate lower than 0.8 or a minor allele frequency (MAF) lower than 0.05 were removed from the analyses.

Usage Notes

Phenotypes are indicated in the sample ID:

D=bilaterally deaf, L=unilaterally deaf in left ear; R=unilaterally deaf in right ear; N=not deaf i.e. hearing.

Funding

Australian National Kennel Council

Canine Research Foundation

Australian National Kennel Council