*4.4. Candidate Gene qRT-PCR Analysis*

Our qRT-PCR outcomes indicate that the expression patterns of three genes (*Capana05g000595*, *Capana05g000596*, and *Capana05g000597*) are up-regulated in both the resistant "PI201234" and susceptible "Early calwonder" lines after pathogen inoculation. *Capana05g000598* was down-regulated in "PI201234" with pathogen inoculation and upregulated in "Early calwonder." We infer that *Capana05g000598* may have the part of the negative regulator of resistance to *P. capsici* in PI201234. *Capana05g000604* was up-regulated in "Early calwonder" at post-infection, while its expression level was significantly lower throughout in "PI201234". Interestingly, the expression of five genes in "PI201234" peaked 2–3 days after pathogen infection, in contrast, expression in "Early calwonder peaked at 5 day after pathogen infection." Therefore, we deduced that *Capana05g000595*, *Capana05g000596*, and *Capana05g000597* might be related to resistance to *P. capsici*. These three genes are highly associated with *CQPc5.1*, but functional validation has not been reported. Therefore, it is essential to conduct functional analysis of these genes to verify their molecular functions in *P. capsici* resistance in pepper. The result of this study would provide information for the next stage of research such as gene functional analysis, pyramiding breeding, and marker-assisted selection (MAS) as well.

**Author Contributions:** Conceptualization, Y.-F.L.; methodology, Y.-F.L., S.-C.Z., and C.-P.W.; investigation, Y.-F.L., S.-C.Z., and X.-M.Y.; writing—original draft preparation, Y.-F.L.; writing—review and editing, S.-C.Z., Q.-Z.H., and R.-Z.H.; funding acquisition, R.-Z.H. All authors have read and agreed to the published version of the manuscript.

**Funding:** This research was financially supported by the National Key R&D Program of China (2017YFD0101903).

**Institutional Review Board Statement:** Not applicable for studies not involving humans or animals.

**Informed Consent Statement:** Not applicable.

**Data Availability Statement:** The sequencing data accession number (PRJNA669602).

**Acknowledgments:** We acknowledge Yu Pan for her efforts in revising the manuscript.

**Conflicts of Interest:** The authors declare no conflict of interest.
