Accuracy of genotype imputation with different low density panels in Braford and Hereford cattle

Abstract Text: The objective of this research was to test alternative low-density panels to impute Illumina 50K SNP genotypes. Genotypes from 3,768 Hereford, Braford and Nellore animals were used for testing imputation from low-density panels to the 50K SNP panel under four different scenarios: including or not Nellore genotypes in the reference population in combination with the use or not pedigree information. There were no significant differences in imputation accuracy among these four scenarios within each panel. However, significant differences between the panels were found. The concordance rates were 0.872, 0.952, 0.957, 0.977 and 0.958 for 3K, 6K, 8K, 15K and 20K SNP panels, respectively. In this study, all the alternative panels denser than 3K could be used for imputing to the 50K SNP panel with overall high imputation accuracy. The use of Nellore genotypes and pedigree information did not increase accuracy of imputation in this population

Keywords: imputation, low-density panel, SNP