Imputation of genotypes in Danish two-way crossbred pigs using low density panels

Abstract Text: Genotype imputation is commonly used as an initial step of genomic selection. Studies on humans, plants and ruminants suggested many factors would affect the performance of imputation. However, studies rarely investigated on crossbred pigs. In this study, firstly, different scenarios of imputing 7K SNPs from 5K panel on Danish Landrace, Yorkshire, and crossbred Landrace-Yorkshire were compared by using Beagle. In conclusion, genotype imputation on crossbreds performs equally well as in purebreds, when parental breeds are used as the reference panel. When the size of reference is considerably large, it is redundant to use a combined reference to impute the purebred because a within breed reference can already ensure an outstanding imputation accuracy, but in crossbreds, using a combined reference increased the imputation accuracy greatly. Secondly, 60K crossbred genotypes were accurately imputed from 7K panel. This dataset will be analyzed for genomic selection in the future.  

Keywords: imputation crossbred purebred