Study imputation efficiency and low density panels of SNPs in Quarter Horse Breed

Abstract

The cost of genotyping panels is still high and it is influenced by level of genomic information. Genotype imputation has been explored as strategy to reduce the cost of implementation of molecular tools in animal breeding. The objective of this study will be to study imputation efficiency obtained from analysis of low density panels of SNPs (1k, 3k, 6k and 9k) and high density commercial panels in order to verify the use of low density panels in improvement of the Quarter Horse breed. A total of 356 horses of racing lines, including both sex and genotyped with high density panel, will be used. Low density panels of SNPs will be generated through selection of SNPs considering distance along the chromosome and high frequency of the minor allele. Genotype imputation will be performed with the use of FImpute v.2.2. Imputation efficiency will be evaluated according to the following criteria: 1) non-imputed genotypes percentage (PGNI); 2) correctly attributed genotypes percentage (PGIC); 3) correlation between observed genotype and imputed genotype (CORR). (AU)