title: Impacts of both reference population size and inclusion of a residual polygenic effect on the accuracy of genomic prediction.
abstract: BACKGROUND
  The purpose of this work was to study the impact of both the size of genomic reference populations and the inclusion of a residual polygenic effect on dairy cattle genetic evaluations enhanced with genomic information.
  
  
  METHODS
  Direct genomic values were estimated for German Holstein cattle with a genomic BLUP model including a residual polygenic effect. A total of 17,429 genotyped Holstein bulls were evaluated using the phenotypes of 44 traits. The Interbull genomic validation test was implemented to investigate how the inclusion of a residual polygenic effect impacted genomic estimated breeding values.
  
  
  RESULTS
  As the number of reference bulls increased, both the variance of the estimates of single nucleotide polymorphism effects and the reliability of the direct genomic values of selection candidates increased. Fitting a residual polygenic effect in the model resulted in less biased genome-enhanced breeding values and decreased the correlation between direct genomic values and estimated breeding values of sires in the reference population.
  
  
  CONCLUSIONS
  Genetic evaluation of dairy cattle enhanced with genomic information is highly effective in increasing reliability, as well as using large genomic reference populations. We found that fitting a residual polygenic effect reduced the bias in genome-enhanced breeding values, decreased the correlation between direct genomic values and sire's estimated breeding values and made genome-enhanced breeding values more consistent in mean and variance as is the case for pedigree-based estimated breeding values.
authors.affiliation: Christian-Albert-University, Institute of Animal Breeding and Husbandry, 24908 Kiel, Germany. zengting.liu@vit.de
authors.forename: Zengting
authors.initials: Z
authors.lastname: Liu
authors.forename: Franz R
authors.initials: FR
authors.lastname: Seefried
authors.forename: Friedrich
authors.initials: F
authors.lastname: Reinhardt
authors.forename: Stephan
authors.initials: S
authors.lastname: Rensing
authors.forename: Georg
authors.initials: G
authors.lastname: Thaller
authors.forename: Reinhard
authors.initials: R
authors.lastname: Reents
mesh_terms: D000818:Animals; D001947:Breeding / Q000706:statistics & numerical data*; D002417:Cattle; D003612:Dairying; D005260:Female; D056726:Genetic Association Studies; D016678:Genome; D008297:Male; D008957:Models, Genetic; D020412:Multifactorial Inheritance / Q000235:genetics*; D020641:Polymorphism, Single Nucleotide / Q000235:genetics; D011156:Population Density; D012641:Selection, Genetic