Abstract
BackgroundThe 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.MethodsDirect 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.ResultsAs 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.ConclusionsGenetic 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.
Highlights
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
This genomic model assumes that, all the loci that affect the trait are in linkage disequilibrium (LD) with at least one single nucleotide polymorphism (SNP) marker and marker genotypes can be used as predictors for breeding values
The tremendous advances in conventional genetic evaluations during the last decades have formed a solid basis for genomic evaluation and selection in dairy cattle
Summary
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. In order to model genetic variation for quantitative traits, Meuwissen et al [10] have proposed a genetic evaluation model that includes a large number of SNP markers simultaneously. Genomic models [10,15,16,17,19] usually assume that a given SNP marker chip, such as the Illumina Bovine54K (Illumina Inc., San Diego, CA), explains all the genetic variation of a trait, and as a consequence no residual polygenic effect (RPG) is typically fitted in genomic prediction [10,15,16,17,19]. The objectives of this study were to investigate (1) the impact of the size of a genomic reference population using German reference bulls on the estimation of SNP effects and on direct genomic values (DGV) and (2) the impact of including an RPG effect on the accuracy of genomic prediction using EuroGenomics reference bulls
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