Evaluation of genomic selection for replacement strategies using selection index theory

Our objective was to investigate the economic effect of prioritizing heifers for replacement at the herd level based on genomic estimated breeding values, and to compute break-even genotyping costs across a wide range of scenarios. Specifically, we aimed to determine the optimal proportion of preselection based on parent average information for all scenarios considered. Considered replacement strategies include a range of different selection intensities by considering different numbers of heifers available for replacement (15-45 in a herd with 100 dairy cows) as well as different replacement rates (15-40%). Use of conventional versus sexed semen was considered, where the latter resulted in having twice as many heifers available for replacement. The baseline scenario relies on prioritization of replacement heifers based on parent average. The first alternative scenario involved genomic selection of heifers, considering that all heifers were genotyped. The benefits of genomic selection in this scenario were computed using a simple formula that only requires the number of lactating animals, the difference in accuracy between parent average and genomic selection (GS), and the selection intensity as input. When all heifers were genotyped, using GS for replacement of heifers was beneficial in most scenarios for current genotyping prices, provided some room exists for selection, in the sense that at least 2 more heifers are available than needed for replacement. In those scenarios, minimum break-even genotyping costs were equal to half the economic value of a standard deviation of the breeding goal. The second alternative scenario involved a preselection based on parent average, followed by GS among all the preselected heifers. It was in almost all cases beneficial to genotype all heifers when conventional semen was used (i.e., to do no preselection). The optimal proportion of preselection based on parent average was at least 0.63 when sexed semen was used. Use of sexed semen increased the potential benefit of using GS, because it increased the room for selection. Critical assumptions that should not be ignored when calculating the benefit of GS are (1) a decrease in replacement rate can only be achieved by increasing productive life in the herd, and (2) accuracies of selection should be used rather than accuracies of estimated breeding values based on the prediction error variance and base-generation genetic variance, because the latter lead to underestimation of the potential of G