Supplemental Material for Pook, Tost, and Simianer, 2025

Figure S1 provides a schematic overview of the rapid cycle breeding scheme with blue boxes indicating cohorts of lines with numbers indicating the number of lines included in a particular cohort. This visualization was generated via the MoBPS interactive environment from Pook et al. (2020), Figure S2 with additional phenotyping of F2 lines, Figure S3 with additional phenotyping of DH lines and Figure S4 with newly introduced additional genetic material. Figure S5 provides information on the accuracy of the breeding value estimation for the F2 lines in the different breeding cycles for each of the three traits in the baseline scenario. Figure S6 provides an overview of prediction accuracies per trait and breeding cycle for the different scenarios. Figure S7 provides a comparison of the remaining genetic diversity for the different base scenarios depending on the amount of genetic material from outside of the breeding program introduced in each cycle. Figure S8 provides a comparison of the remaining genetic diversity for the base scenarios depending on the angle used in AlphaMate (Gorjanc and Hickey, 2018) in each cycle. Table S1 provides information on the share of heterozygous variants for all scenarios and cycles. Table S2 provides information on the share of fixed markers for all scenarios and breeding cycles.