*3.3. Quality and Accuracy of the Genetic Map*

The quality and accuracy of the genetic map were assessed based on collinearity between the genetic and physical maps. The average integrity of each marker was 99.91% (Figure 3). Furthermore, among the 12 linkage groups, Chr03 showed the highest collinearity, with a correlation coefficient of 0.9979, and the average Spearman's rank correlation coefficient was 0.9758 (Table 3). On average, the coverage of these markers was 108.74-fold in PI201234 (male parent), 126.25-fold in 1287 (female parent), and 22.73-fold in every F2 individual (Table 4), thereby indicating genotyping accuracy. Furthermore, collinearity with the physical map was utilized to examine the quality of the genetic map. Figure 4 shows that most of the genetically mapped loci were collinear with their physical positions on the reference genome sequence of *C. annuum* cv. Zunla-1 v2.0 [45]. Every correlation coefficient of 12 linkage groups was also assessed. The correlation coefficients of the 12 linkage groups

were all close to 1, which indicated relatively high collinearity between linkage groups and the pepper reference genome (Figure 3).

**Table 3.** Basic information of the 12 linkage groups. The closer the Spearman's rank correlation coefficient is to 1, the better the collinearity.


**Figure 3.** Collinearity between genetic and physical maps. The correlation between the pepper chromosomes (Chr) and the linkage group (LG) of the genetic map is illustrated.


**Figure 4.** Quantitative trait locus (QTL) analysis of the *P. capsici* resistance trait of pepper. The *x*-axis indicates linkage group in pepper, and the *y*-axis presents LOD values. The blue line indicates the additive effect, and the red line represents the dominant effect.
