Analysis of different genotyping and selection strategies in laying hen breeding programs

Genomic selection has become an integral component of modern animal breeding programs, having the potential to improve the efficiency of layer breeding programs both by obtaining higher prediction accuracies and reducing the generation interval, particularly for males, who cannot be phenotyped for sex-limited traits such as laying performance. In the current study, we investigate different strategies to reduce the generation interval either for both sexes or only for the male side of the breeding scheme based on stochastic simulation using the software MoBPS. Additionally, prediction accuracies based on varying proportions of genotyping and phenotype- and pedigree-based selection as well as genomic breeding values are compared. Selection of hens based on estimated breeding values, either pedigree-based or genomic, increased genetic gain compared to selection based on phenotypes only. The use of two time-shifted subpopulations with exchange of males between subpopulations to reduce the generation interval on the male side led to significantly higher genetic gains. Reducing the generation interval for both males and females was only efficient when population sizes were maintained, which result in doubling of the number of females to genotype and phenotype within the same time frame compared to the scenarios with the longer generation intervals. Although substantially higher gains were obtained by in particular pedigree-based selection of females and a reduction of generation intervals this led to substantially greater rates of inbreeding per year. The use of a genomic relationship matrix in breeding value estimation instead of a pedigree-based relationship matrix not only increased genetic gains but also reduced inbreeding rates. The use of optimum contribution selection led to basically the same genetic gains as without it but reduced inbreeding rates. However, overall differences obtained with optimal contribution selection were small compared to differences caused by the other effects that were considered. The reduction of the generation interval on the male side by the use of genomic estimated breeding values was highly beneficial. Reduction of the generation interval on the female side was only beneficial when a high proportion of hens was genotyped and housing capacities were increased. On the female side of a layer breeding program, selection based on pedigree-based estimated breeding values was inferior to phenotypic selection, as it resulted in a substantial increase in inbreeding rates.