*3.2. Linkage Map*

A linkage analysis was done in the F1 mapping population consisting of 62 individuals from a cross 'GX71' (high regeneration rate) between 'GX50' (low regeneration rate). Two individuals were excluded from the analyses because they have too many missing genotypes. We keep the missing rate below 30% so that the linkage analysis is properly performed. As a result, a total of 4462 SNPs were selected by first classifying genotypes into lm × ll, nn × np, and hk × hk types (see the Section 2.5 for details). Finally, based on the genotypes of the parents, monomorphic markers were removed. Consequently, the total number of SNPs for genetic mapping was chosen as follows: 1295, 1325, and 1852 segregating SNPs with the classes of lm × ll, hk × hk, and nn × np, respectively (Figure 2). Markers deviating significantly ( *P* < 0.05) from the Mendelian segregation ratio for dominant and codominant markers, respectively, were excluded from the analysis. To increase the mapping e fficiency, locus pairs or locus groups with identical genotypes were identified and a single marker was selected to represent the group. After removing the redundant SNP markers, the final set of 178 SNPs remained for linkage map construction. The linkage maps were constructed using Joinmap 4.1 software (logarithm

of odds (LOD) ≥5). The linkage maps contained nine linkage groups, which were consistent with the basal chromosome number of the radish. Because of the lack of bi-parental marker types that can connect parental genetic maps in this study, we first identified a set of SNP markers to assign the nine radish chromosomes to nine LGs. For the maternal linkage map, 87 markers were mapped from all three pseudo-testcross segregation types (Table 1, Figure 3). The length of the maternal linkage map was 439.2 cM, with the longest linkage group, LG5 (56.0 cM), and the shortest linkage group, LG2 (36.7 cM). The average interval marker distance was 5.9 cM and the maximum gap size ranged from 7.7 cM (LG9) to 13.4 cM (LG5). For the paternal linkage map, 91 markers were mapped from all three pseudo-testcross segregation types (Table 2, Figure 4). The length of the paternal linkage map was 420.8 cM, with the longest linkage group, LG5 (53.3 cM), and the shortest linkage group, LG8 (40.6 cM). The average interval marker distance was 5.2 cM and the maximum gap size ranged from 3.1 cM (LG1) to 11.3 cM (LG3). Owing to this unambiguous assignment of linkage groups to chromosomes, the linkage groups were designated with the chromosome numbers (e.g., chromosome 1 = LG 1 etc.).

**Figure 2.** Segregation types of polymorphic SNP markers. The *x-axis* indicates the three segregation types; the *y-axis* indicates the number of markers included in each marker type. lm × ll = 'GX50' heterozygous 'GX71' homozygous. hk × hk = 'GX50' heterozygous 'GX71' heterozygous. nn × np = 'GX50' homozygous 'GX71' heterozygous.


**Table 1.** Length, number of markers, average spacing, and largest intervals of GX50 genetic maps (LG; linkage group, SNP; single nucleotide polymorphism, cM; centi-Morgan).

**Table 2.** Length, number of markers, average spacing, and largest intervals of GX71 genetic maps.

