Key message: For genomic selection in clonal breeding programs to be 14 effective, crossing parents should be selected based on genomic predicted cross 15 performance unless dominance is negligible. Genomic prediction of cross performance 16 enables a balanced exploitation of the additive and dominance value simultaneously. A 17 two-part breeding program with parent selection based on genomic predicted cross 18 performance to rapidly drive population improvement has great potential to improve 19 breeding clonally propagated crops. 20 Abstract 21For genomic selection in clonal breeding programs to be effective, crossing 22 parents should be selected based on genomic predicted cross performance unless 23 dominance is negligible. Genomic prediction of cross performance enables a balanced 24 exploitation of the additive and dominance value simultaneously. Here, we compared 25 different strategies for the implementation of genomic selection in clonal plant breeding 26 programs. We used stochastic simulations to evaluate six combinations of three 27 breeding programs and two parent selection methods. The three breeding programs 28 included i) a breeding program that introduced genomic selection in the first clonal 29 testing stage, and ii) two variations of a two-part breeding program with one and three 30 crossing cycles per year, respectively. The two parent selection methods were i) 31 selection of parents based on genomic estimated breeding values, and ii) selection of 32 parents based on genomic predicted cross performance. Selection of parents based on 33 genomic predicted cross performance produced faster genetic gain than selection of 34 parents based on genomic estimated breeding values because it substantially reduced 35 inbreeding when the dominance degree increased. The two-part breeding programs 36 with one and three crossing cycles per year using genomic prediction of cross 37 performance always produced the most genetic gain unless dominance was negligible. 38We conclude that i) in clonal breeding programs with genomic selection, parents should 39 be selected based on genomic predicted cross performance, and ii) a two-part breeding 40 program with parent selection based on genomic predicted cross performance to rapidly 41 drive population improvement has great potential to improve breeding clonally 42 propagated crops. 43 additive genetic effects in a given breeding population. As a result, heterozygosity is 55 reduced. Although selection for the genomic estimated breeding value will increase the 56 additive value over time, it may lead to a reduction of the dominance value, unless 57 dominance is negligible. In the long term, using the genomic estimated breeding value 58 to select new parents in breeding programs which deliver outbred varieties, such as in 59 clonal plant breeding programs, might not be the optimal method to use in order to 60 maximize the total genetic value of the breeding population in a sustainable fashion. 61Many major food crops, including nearly all types of fruit and all importa...