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.

图S1为快速轮回育种方案的示意图，蓝色框代表各批次育种株系，框内数字标注了对应批次包含的株系数量。该可视化结果基于Pook等人（2020）提出的MoBPS交互式环境生成。
图S2展示F2群体株系的补充表型数据，图S3展示双单倍体（Double Haploid, DH）株系的补充表型数据，图S4则展示新引入的外源遗传材料。
图S5提供了基线情景下，三个目标性状分别在不同育种周期中，F2群体株系的育种值估计精度相关信息。
图S6概述了不同情景下，各性状在不同育种周期中的预测精度。
图S7对比了不同基线情景下的剩余遗传多样性，该对比以每个育种周期引入的育种项目外源遗传材料占比为依据。
图S8对比了不同基线情景下的剩余遗传多样性，该对比以每个育种周期中AlphaMate（Gorjanc与Hickey，2018）所采用的参数角度为依据。
表S1提供了所有情景及所有育种周期下的杂合变异位点占比相关信息。
表S2提供了所有情景及所有育种周期下的固定标记占比相关信息。