10.5061/DRYAD.J9KD51CB0
Seddon, Jenny
0000-0003-3789-6878
University of Queensland
Sommerlad, Susan
University of Queensland
Fortes, Marina
0000-0002-7254-1960
University of Queensland
Deafness in Australian Cattle Dogs associated to QTL on chromosome 20 in
GWAS analyses
Dryad
dataset
2020
FOS: Veterinary science
Australian National Kennel Council *
Australian National Kennel Council
https://ror.org/00xny7d86
Australian National Kennel Council
2021-05-07T00:00:00Z
2021-05-07T00:00:00Z
en
849691833 bytes
3
CC0 1.0 Universal (CC0 1.0) Public Domain Dedication
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.
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.
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.