Replacement of microsatellite markers by imputed medium-density SNP arrays for parentage control in German warmblood horses

In horses, parentage control is currently performed based on an internationally standardized panel of 17 microsatellite (MS) markers comprising 12 mandatory and five optional markers. Unlike MS, single nucleotide polymorphism (SNP) profiles support a wider portfolio of genomic applications, including parentage control. A transition to SNP-based parentage control is favorable, but requires additional efforts for ensuring generation-overlapping availability of marker genotypes of the same type. To avoid double genotyping of either parents or offspring for changing to SNP technology and enable efficient transition, we tested whether MS genotypes used for parentage control could be reliably imputed from a medium-density SNP panel in German warmblood horses. Imputation accuracy was tested in a tenfold cross-validation with two approaches: within breed (option A) and across breeds (option B). Average imputation accuracies of 97.98% (A) and 96.17% (B) were achieved, respectively. Due to interbreed differences in genotyping rates, five MS markers of low genotyping rate (GTR; < 90%) could be imputed with higher accuracy within breed (98.18%) than across breeds (90.73%). MS markers with high GTR performed homogeneously well in option B (98.44%) and showed slightly lower accuracy in option A (97.90%). Among these markers, AHT5 proved to be problematic for imputation regardless of the approach, revealing accuracies of 86.40% (A) and 88.70% (B). Better results for MS markers with high GTR and savings in computational processing justified the choice of option B for routine implementation. To date, more than 9500 horses have undergone the new parentage control based on imputed MS genotypes. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s13353-022-00725-9.