Optimal strategies for the use of genomic selection in dairy cattle breeding programs

The objective of the present study was to conduct a stochastic simulation study on the possible benefits of an application of genomic selection in dairy cattle breeding programs according to a variety of selection schemes. In addition, the heritability of the trait in question, the accuracy of genomic breeding values, and the number of animals to be genotyped were varied. Specifically, the question of genotyping males, females, or both, was addressed. Selection schemes were compared with a young bull breeding program. The main criterion for comparison was the average of true breeding values of selected young males to be used as replacements for artificial insemination bulls. Stochastic simulations were run with 50 repetitions each to generate individuals with phenotypes, breeding values estimated by BLUP, and true breeding values. Genomic breeding values were generated from true breeding values with defined accuracy. Examined scenarios included a group of selection schemes that featured genotyping of parents of future bulls only. Such schemes can be viewed as improvements of young bull programs, and they were found to be competitive with or superior to a classical young bull program. However, a genomic breeding program usually involves at least genotyping young male candidates. A second group of selection schemes reflected this requirement. Scenarios in this group were found to be superior over the young bull program by 1.0 to 1.2 standard deviations of the average true breeding value of young male candidates. Within this group of scenarios, one scheme referred to an ideal situation under which genotypes for male calves were available without limitation. Using the average of true breeding values as the criterion for comparison, this idealistic scenario was competitive with other scenarios only if the reliability of genomic breeding values was larger than 0.50. Conventionally, not all males available will have genotypes, and the 2 most promising scenarios included a preselection step for dams of future bulls. This preselection step can be based on conventional BLUP estimated breeding values for bull dams, because differences with a scheme under which both parents and the resulting male offspring are genotyped were marginal. Genotyping of young male candidates should be the focus of activities of today's breeding organizations.