CanineHD 230 K BeadChip data from Miniature Dachshunds

Abstract Several hundred disease-causing mutations are currently known in
domestic dogs. Breeding management is therefore required to minimize their
spread. Recently, genetic methods such as direct-to-consumer testing have
gained popularity; however, their effects on dog populations are
unclear.  A variant in the RPGRIP1 gene is a causative element
associated with cone-rod dysplasia 1 (cord1) and progressive retinal
atrophy (PRA) in dogs, notably purebred Miniature Dachshunds (DHMs). Here,
we aimed to evaluate the influence of genetic testing on the frequency of
mutations responsible for canine PRA and assess the changes in the genetic
structure of a DHMs population from Japan. To evaluate the influence of
genetic testing on the frequency of mutations causing canine degenerative
myelopathy and changes to genetic structure in the Pembroke Welsh corgi
population from Japan, 117 dogs were genotyped. Weir and Cockerham
population differentiation (FST) based on genome-wide single-nucleotide
polymorphism (SNP) detected the SNP with the highest FST located in the
intron of SOD1 adjacent to the c.118G>A mutation, supporting a
selection signature on SOD1. Further genome-wide SNP analyses revealed no
obvious changes in inbreeding levels between the 2019 and 2022
populations. Our study highlights that genetic testing can help inform
improved mating choices in breeding programs to reduce the frequency of
risk variants and avoid inbreeding.