Abstract
BackgroundExtending the reference set for genomic predictions in dairy cattle by adding large numbers of cows with genotypes and phenotypes has been proposed as a means to increase reliability of selection decisions for candidates.MethodsIn this study, we explored the potential of increasing the reliability of breeding values of young selection candidates by genotyping a fixed number of first-crop daughters of each sire from one or two generations in a balanced and regular system of genotyping. Using stochastic simulation, we developed a basic population scenario that mimics the situation in dual-purpose Fleckvieh cattle with respect to important key parameters. Starting with a reference set consisting of only genotyped bulls, we extended this reference set by including increasing numbers of daughter genotypes and phenotypes. We studied the effects on model-derived reliabilities, validation reliabilities and unbiasedness of predicted values for selection candidates. We also illustrate and discuss the effects of a selected sample and an unbalanced sampling of daughters. Furthermore, we quantified the role of selection with respect to the influence on validation reliabilities and contrasted these to model-derived reliabilities.ResultsIn the most extended design, with 200 daughters per sire genotyped from two generations, single nucleotide polymorphism (SNP) effects were estimated from a reference set of 420,000 cows and 4200 bulls. For this design, the validation reliabilities for candidates reached 80 % or more, thereby exceeding the reliabilities that were achieved in traditional progeny-testing designs for a trait with moderate to high heritability. We demonstrate that even a moderate number of 25 genotyped daughters per sire will lead to considerable improvement in the reliability of predicted breeding values for selection candidates. Our results illustrate that the strategy applied to sample females for genotyping has a large impact on the benefits that can be achieved.Electronic supplementary materialThe online version of this article (doi:10.1186/s12711-016-0250-9) contains supplementary material, which is available to authorized users.
Highlights
Extending the reference set for genomic predictions in dairy cattle by adding large numbers of cows with genotypes and phenotypes has been proposed as a means to increase reliability of selection decisions for candidates
Schaeffer [11] predicted a situation where considerable bias was introduced on genomic evaluations by strong preselection [12,13,14] of young bulls based on their genomic breeding values
Simulation For ease of interpretation, we separated the presentation of results for generation 9 from those for generation 10, in order to highlight the fact that generation 9 represents a group of individuals that are already pre-selected on an estimated breeding value (EBV) including Mendelian sampling information in the course of the simulation process
Summary
Extending the reference set for genomic predictions in dairy cattle by adding large numbers of cows with genotypes and phenotypes has been proposed as a means to increase reliability of selection decisions for candidates. Most opportunities to increase the genotype pool by exchanging genotypes have been exploited and, in most cases, the growth of reference sets within breeds is restricted to the yearly increase in number of genomically preselected young bulls receiving daughter proofs. As a demonstration of that effect, Cooper et al [10], for example, excluded subsets of old bulls and found that older bulls in the reference set had only a minimal impact on the reliability of the genomic breeding values of predicted animals. Schaeffer [11] predicted a situation where considerable bias was introduced on genomic evaluations by strong preselection [12,13,14] of young bulls based on their genomic breeding values
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