![]() However, the gain in accuracy with LD chips with more than 15 K SNPs was relatively small because accuracy was already high at this density. Imputation accuracy increased with the SNP density of the LD chip. From 995 bulls and 1247 cows that were genotyped with the Illumina® BovineHD chip (HD), 793 sires composed the reference set, and the remaining 202 younger sires and all the cows composed two separate validation sets for which genotypes were masked except for the SNPs of the LD chip that were to be tested. Software programs FImpute and BEAGLE were applied to impute genotypes. Customized LD chips were virtually designed taking into account minor allele frequency, linkage disequilibrium and distance between markers. Twelve commercial and customized LD chips with densities ranging from 7 K to 75 K were tested. MethodsĪccuracy of genotype imputation in Nelore cattle was evaluated using different LD chips, imputation software and sets of animals. Thus, it is important to evaluate the accuracy of imputation to better define which imputation method and chip are most appropriate for genomic applications in indicine breeds. ![]() Nelore breed) are characterized, in general, by lower levels of linkage disequilibrium between genetic markers at short distances, compared to taurine breeds. Imputation methods rely partially on linkage disequilibrium between markers to infer unobserved genotypes. Genotype imputation from low-density (LD) to high-density single nucleotide polymorphism (SNP) chips is an important step before applying genomic selection, since denser chips tend to provide more reliable genomic predictions. ![]()
0 Comments
Leave a Reply. |
AuthorWrite something about yourself. No need to be fancy, just an overview. ArchivesCategories |