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dc.contributor.authorFriedrich Jen
dc.contributor.authorAntolin Ren
dc.contributor.authorEdwards SMen
dc.contributor.authorSanchez-Molano Een
dc.contributor.authorHaskell MJen
dc.contributor.authorHickey JMen
dc.contributor.authorWiener Pen
dc.date.accessioned2018-07-09T10:49:32Z
dc.date.available2018-07-09T10:49:32Z
dc.date.issued2018
dc.identifier.citation49:4
dc.identifier.urihttps://doi.org/10.1111/age.12677
dc.identifier.urihttp://hdl.handle.net/11262/11474
dc.description.abstractThe 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 masking level of 87.5% ranged from 0.92 to 0.97, depending on the scenario used. A correlation of 0.92 was found for a likely scenario (10% of dogs genotyped using HighD, 87.5% of HighD SNPs masked in the LowD array), which indicates that genotype imputation in Labrador Retrievers can be a valuable tool to reduce experimental costs while increasing sample size. Furthermore, we show that genotype imputation can be performed successfully even without pedigree information and with low relatedness between dogs in the reference and validation sets. Based on these results, the impact of genotype imputation was evaluated in a genome‐wide association analysis and genomic prediction in Labrador Retrievers.en
dc.description.sponsorshipScottish Government RESAS Strategic Research Programme (RD2.2.9)en
dc.language.isoenen
dc.relation.isformatof14890en
dc.relation.ispartofAnimal Geneticsen
dc.rights© 2018 The Authors. Animal Genetics published by John Wiley & Sons Ltd on behalf of Stichting International Foundation for Animal Genetics. This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.
dc.subjectGenome-wide association studiesen
dc.subjectGenomic predictionen
dc.subjectImputation accuracyen
dc.subjectLow-density array designen
dc.subjectPedigree informationen
dc.subjectReference seten
dc.titleAccuracy of genotype imputation in Labrador Retrieversen
dc.typeArticleen
dc.description.versionVersion of Record
dc.extent.pageNumbers303-311
rioxxterms.publicationdate2018-07-05
rioxxterms.typeJournal Article/Reviewen
dcterms.dateAccepted2018-04-05
refterms.accessExceptionNAen
refterms.dateDeposit2018-07-09
refterms.depositExceptionpublishedGoldOAen
refterms.depositExceptionExplanationGoldOAen
refterms.panelUnspecifieden
refterms.technicalExceptionNAen
refterms.versionVoRen


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