Impacts of both reference population size and inclusion of a residual polygenic effect on the accuracy of genomic prediction

Genet Sel Evol. 2011 May 17;43(1):19. doi: 10.1186/1297-9686-43-19.


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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Breeding / statistics & numerical data*
  • Cattle
  • Dairying*
  • Female
  • Genetic Association Studies
  • Genome
  • Male
  • Models, Genetic
  • Multifactorial Inheritance / genetics*
  • Polymorphism, Single Nucleotide / genetics
  • Population Density
  • Selection, Genetic