Accuracy of genotype imputation in Nelore cattle

• DOI: 10.1186/s12711-014-0069-1
• Publication Date: 2014-10-09T16:58:41Z
• Authors: Roberto Carvalheiro; Solomon A Boison; Haroldo H R Neves; Mehdi Sargolzaei; Flavio S Schenkel; Yuri T Utsunomiya; Ana Maria Pérez O...; Johann Sölkner; John C McEwan; Curtis P Van Tassell; Tad S Sonstegard; José Fernando Garcia
• Keywords: Imputation (statistics); Linkage Disequilibrium; Genomic Selection; SNP; SNP genotyping; Minor allele frequency; Genetic Association

Genotype imputation from low-density (LD) to high-density single nucleotide polymorphism (SNP) chips is an important step before applying genomic selection, since denser tend provide more reliable predictions. Imputation methods rely partially on linkage disequilibrium between markers infer unobserved genotypes. Bos indicus cattle (e.g. Nelore breed) are characterized, in general, by lower levels of genetic at short distances, compared taurine breeds. Thus, it evaluate the accuracy better define which method and chip most appropriate for applications indicine Accuracy genotype was evaluated using different LD chips, software sets animals. Twelve commercial customized with densities ranging 7 K 75 were tested. Customized virtually designed taking into account minor allele frequency, distance markers. Software programs FImpute BEAGLE applied impute From 995 bulls 1247 cows that genotyped Illumina® BovineHD (HD), 793 sires composed reference set, remaining 202 younger all two separate validation genotypes masked except SNPs be increased SNP density chip. However, gain than 15 relatively small because already high this density. Commercial equivalent presented similar results. outperformed sets. Regardless used, tended increase as relatedness imputed animals increased, especially If considered target breed, cost-effectiveness can improved genotyping part a containing around useful imputing their missing FImpute.