*3.6. Candidate Gene Prediction and qRT-PCR Analysis*

According to the annotations of the *C. annuum* cv. Zunla-1 v2.0 genome, 23 predicted candidate genes were determined in the physical interval of *CQPc5.1* on Chr05 (Table 7). Among these, nine candidate genes were identified in the COG database, including 11 genes with KEGG annotations and 12 genes with Swiss-Prot annotations. Furthermore, 5 of the 23 genes were related to disease resistance or defense, and thus might be involved in *P. capsici* resistance in pepper; the *Capana05g000595* gene was annotated as disease resistance protein, RPP8-like; two genes (*Capana05g000596* and *Capana05g000597*) were annotated as disease resistance protein, RPP13-like; *Capana05g000598* was annotated as likely LRR receptor-like serine/threonine-protein kinase; and *Capana05g000604* was annotated as an F-box/LRR-repeat protein. These five genes were then analyzed by qRT-PCR. The primer sequences are listed in Table 8. The results showed that three genes (i.e., *Capana05g000595*, *Capana05g000596*, and *Capana05g000597*) were up-regulated in "PI201234," and expression levels peaked 2–3 days after pathogen inoculation (Figure 5). Five genes were up-regulated in "Early calwonder" after pathogen inoculation, and expression levels peaked at 5 days. In "Early calwonder," the expression of *Capana05g000604* gradually increased over time; however, it was expressed at a markedly lower level in "PI201234."



*Horticulturae* **2021** , *7*, 92

**Table 7.** *Cont.*

**Figure 5.** qPCR analysis of five genes in PI201234 and Early calwonder that are related to disease resistance or defense. PI: PI201234 inoculated using *P. capsici* zoospore suspension; EA: Early calwonder inoculated using *P. capsici* zoospore suspension. The *x*-axis shows the time points of sample collection, d: days post-inoculation. The *y*-axis shows the relative expression quantity of genes. Gene expression was normalized to that of actin, and the data were expressed as the mean ± standard deviation of two biological replicates and three technical replicates. A Student's *t*-test was used to analyze statistical significance of differences. \* 0.05 level of significance; \*\* 0.01 level of significance.

