Prioritizing animals for dense genotyping in order to impute missing genotypes of sparsely genotyped animals.

ABSTRACT:

Background

Genotyping accounts for a substantial part of the cost of genomic selection (GS). Using both dense and sparse SNP chips, together with imputation of missing genotypes, can reduce these costs. The aim of this study was to identify the set of candidates that are most important for dense genotyping, when they are used to impute the genotypes of sparsely genotyped animals. In a real pig pedigree, the 2500 most recently born pigs of the last generation, i.e. the target animals, were used for sparse genotyping. Their missing genotypes were imputed using either Beagle or LDMIP from T densely genotyped candidates chosen from the whole pedigree. A new optimization method was derived to identify the best animals for dense genotyping, which minimized the conditional genetic varianc

SUBMITTER: Yu X 

PROVIDER: S-EPMC4283150 | biostudies-literature | 2014 Aug

REPOSITORIES: biostudies-literature