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Imputation of high density genotypes from medium density genotypes in various French equine breeds.
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Edité par CCSD ; Massey University -
International audience. The objective of the study was to estimate the efficiency of genotypes imputation of the Affymetrix Axiom Equine genotyping array (670 806 SNPs), from genotypes of the Illumina Equine SNP50 BeadChip (54 602 SNPs) and the Illumina Equine SNP-74k-chip (65 157 SNPs). Genotypes from 5 populations: Arabs (AR, 1 207 horses), Trotteurs Français (TF, 979 horses), Selle Français (SF, 1 979 horses), Anglo-Arabs (AA, 229 horses), and various foreign sport horses (FH, 209 horses) were available. In AR, 15% of horses were genotyped with the high density chip, in SF 57%, in TF 30%, in AA 10% and FH 15%. A validation set equal to the third of the sample was drawn in horses genotyped with high density chip and their genotypes suppressed. Two strategies were compared, one with a reference population with only the horses of the same breed as the validation set and another one with horses from multi-breeds. The software FImpute was used. For the first strategy, the mean error rates were 0.97% in TF, 1.29% in SF and 2.16% in AR populations. For the second strategy, the mean error rates ranged from 1.11% (TF) to 2.63% (AR). SF, FH and AA populations had intermediate error rates: 1.35%, 1.55% and 1.87% respectively. For each population and each strategy, the mean error rates were inferior to 3% which indicates that imputation of high density genotypes from medium density genotypes is feasible and accurate. The imputation accuracy depended on the size of the reference population, the genetic diversity of the breed, the importance of relationship between validation and reference populations and the linkage disequilibrium (LD). The comparison between the two imputation strategies showed that the addition of horses from different populations in the reference population did not improve the imputation accuracy.
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