biostudies-literatureFriedrich JDogs Trust (UK)Rural and Environment Science and Analytical Services DivisionBiotechnology and Biological Sciences Research Council303-311https://www.ebi.ac.uk/biostudies/studies/S-EPMC6055857biostudies-literatureUnknown49(4)The dog is a valuable model species for the genetic analysis of complex traits, and the use of genotype imputation in dogs will be an important tool for future studies. It is of particular interest to analyse the effect of factors like single nucleotide polymorphism (SNP) density of genotyping arrays and relatedness between dogs on imputation accuracy due to the acknowledged genetic and pedigree structure of dog breeds. In this study, we simulated different genotyping strategies based on data from 1179 Labrador Retriever dogs. The study involved 5826 SNPs on chromosome 1 representing the high density (HighD) array; the low-density (LowD) array was simulated by masking different proportions of SNPs on the HighD array. The correlations between true and imputed genotypes for a realistic maskiAnimal geneticsAccuracy of genotype imputation in Labrador Retrievers.PMC6055857BBS/E/D/30002275BBS/E/D/05191132BB/H019073/1Friedrich JWiener PHickey JMSanchez-Molano EAntolin RHaskell MJEdwards SMfalseAccuracy of genotype imputation in Labrador Retrievers.The dog is a valuable model species for the genetic analysis of complex traits, and the use of genotype imputation in dogs will be an important tool for future studies. It is of particular interest to analyse the effect of factors like single nucleotide polymorphism (SNP) density of genotyping arrays and relatedness between dogs on imputation accuracy due to the acknowledged genetic and pedigree structure of dog breeds. In this study, we simulated different genotyping strategies based on data from 1179 Labrador Retriever dogs. The study involved 5826 SNPs on chromosome 1 representing the high density (HighD) array; the low-density (LowD) array was simulated by masking different proportions of SNPs on the HighD array. The correlations between true and imputed genotypes for a realistic maski2018-01-01T00:00:00Z2018 Aug2025-04-04T23:42:40.009Z2019-03-26T23:48:17ZS-EPMC60558572997496610.1111/age.12677