Supplemental Material for Schlather et al., 2019 (in review)

File S1: Additional method section on setting a target coverage.<br><br>File S2: Additional method section on the graphical representation of haplotype blocks.<br><br>File S3: Additional method section - toy example for calculation of bEHH.<br><br>File S4: Script to simulate a diallel design in MoBPS<br><br>Table S1: Proportion of variance explained between the full SNP-dataset (X), a SNP-subset (Xs) and the block dataset (Z). For comparability the number of parameters in Xs and Z were chosen equally using traditionally heritability estimation as in de los Campos (2017).<br><br>Table S2: Influence of the window size on the haplotype library for chromosome 1 in the KE DH-lines with a target coverage of 95%.<br><br>Table S3: Influence of the weighting of block length (wl) and number of haplotypes (wn) on the haplotype library for chromosome 1 in the KE DH-lines with a target coverage of 95%.<br><br>Table S4: Influence of using the extended-block-identification on the haplotype library in dependency of the parameter t of the extended-block-identification-step for chromosome 1 in the KE DH-lines with a target coverage of 95%.<br><br>Figure S1: Dataset for the toy example used in File S3.<br><br>Figure S2: Comparison of the block structure and a bifurcation plot (Sabeti et al., 2002, Gautier and Vitalis, 2012) according SNP 10,000 on chromosome 1 in the KE DH-lines.<br><br>Figure S3: Comparison of the block structure for MCMB=1000 (A), MCMB=5000 (B), MCMB=20,000 (C) for the first 20,000 SNPs of chromosome 1 in the KE DH-lines.<br><br><br>

补充文件S1：关于目标覆盖度设置的补充方法章节。
补充文件S2：关于单体型块（haplotype blocks）图形化展示的补充方法章节。
补充文件S3：补充方法章节——bEHH计算的演示示例。
补充文件S4：在MoBPS中模拟双列杂交设计的脚本。
补充表S1：完整单核苷酸多态性（Single Nucleotide Polymorphism, SNP）数据集（X）、SNP子集（Xs）与单体型块数据集（Z）之间的方差解释比例。为保证可比性，参照de los Campos（2017）提出的传统遗传力估计方法，使Xs与Z中的参数数量保持一致。
补充表S2：针对KE双单倍体（double haploid, DH）系的1号染色体，当目标覆盖度为95%时，窗口大小对单倍型库的影响。
补充表S3：针对KE DH系的1号染色体，当目标覆盖度为95%时，单体型长度权重（wl）与单倍型数量权重（wn）对单倍型库的影响。
补充表S4：针对KE DH系的1号染色体，当目标覆盖度为95%时，延伸块识别步骤的参数t对单倍型库的影响（延伸块识别的使用效果随参数t变化）。
补充图S1：用于补充文件S3中演示示例的数据集。
补充图S2：针对KE DH系的1号染色体上第10000号SNP，单体型块结构与分叉图（Sabeti等，2002；Gautier & Vitalis，2012）的对比。
补充图S3：针对KE DH系的1号染色体前20000个SNP，分别展示MCMB=1000（A组）、MCMB=5000（B组）与MCMB=20000（C组）对应的单体型块结构对比。