Genomic breeding value prediction: methods and procedures

Animal breeding faces one of the most significant changes of the past decades - the implementation of genomic selection. Genomic selection uses dense marker maps to predict the breeding value of animals with reported accuracies that are up to 0.31 higher than those of pedigree indexes, without the need to phenotype the animals themselves, or close relatives thereof. The basic principle is that because of the high marker density, each quantitative trait loci (QTL) is in linkage disequilibrium (LD) with at least one nearby marker. The process involves putting a reference population together of animals with known phenotypes and genotypes to estimate the marker effects. Marker effects have been estimated with several different methods that generally aim at reducing the dimensions of the marker data. Nearly all reported models only included additive effects. Once the marker effects are estimated, breeding values of young selection candidates can be predicted with reported accuracies up to 0.85. Although results from simulation studies suggest that different models may yield more accurate genomic estimated breeding values (GEBVs) for different traits, depending on the underlying QTL distribution of the trait, there is so far only little evidence from studies based on real data to support this. The accuracy of genomic predictions strongly depends on characteristics of the reference populations, such as number of animals, number of markers, and the heritability of the recorded phenotype. Another important factor is the relationship between animals in the reference population and the evaluated animals. The breakup of LD between markers and QTL across generations advocates frequent re-estimation of marker effects to maintain the accuracy of GEBVs at an acceptable level. Therefore, at low frequencies of re-estimating marker effects, it becomes more important that the model that estimates the marker effects capitalizes on LD information that is persistent across generations.