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Accuracy of genotype imputation in Labrador Retrievers
Author(s) -
Friedrich J.,
Antolín R.,
Edwards S. M.,
SánchezMolano E.,
Haskell M. J.,
Hickey J. M.,
Wiener P.
Publication year - 2018
Publication title -
animal genetics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.756
H-Index - 81
eISSN - 1365-2052
pISSN - 0268-9146
DOI - 10.1111/age.12677
Subject(s) - imputation (statistics) , genotyping , biology , snp , genotype , single nucleotide polymorphism , labrador retriever , snp genotyping , genetics , genome wide association study , statistics , missing data , gene , mathematics , medicine , pathology
Summary 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 SNP s on chromosome 1 representing the high density (HighD) array; the low‐density (LowD) array was simulated by masking different proportions of SNP s 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 SNP s 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.