*Article* **Generation of a High-Density Genetic Map of Pepper (***Capsicum annuum* **L.) by SLAF-seq and QTL Analysis of** *Phytophthora capsici* **Resistance**

**Yi-Fei Li 1,†, Shi-Cai Zhang 1,†, Xiao-Miao Yang 1, Chun-Ping Wang 2,\*, Qi-Zhong Huang 1,\* and Ren-Zhong Huang 1,\***

<sup>1</sup> The Institute of Vegetable and Flower Research, Chongqing Academy of Agricultural Sciences,

Chongqing 401329, China; liyifei201@163.com (Y.-F.L.); shicaiz@126.com (S.-C.Z.); xiaomiaoyangy@sina.com (X.-M.Y.) <sup>2</sup> Chongqing Key Laboratory of Adversity Agriculture, Biotechnology Research Institute, Chongqing Academy of Agricultural Sciences, Chongqing 401329, China


**Abstract:** Pepper (*Capsicum annuum* L.) is an economically significant global crop and condiment. Its yield can be severely reduced by the oomycete plant pathogen, *Phytophthora capsici* (*P. capsici*). Here, a high-density genetic map was created with a mapping panel of F2 populations obtained from 150 individuals of parental lines PI201234 and 1287 and specific-locus amplified fragment sequencing (SLAF) that was then utilized to identify loci that are related to resistance to *P. capsici*. The sequencing depth of the genetic map was 108.74-fold for the male parent, 126.25-fold for the female parent, and 22.73-fold for the offspring. A high-resolution genetic map consisting of 5565 markers and 12 linkage groups was generated for pepper, covering 1535.69 cM and an average marker distance of 0.28 cM. One major quantitative trait locus (QTL) for the *P. capsici* resistance (*CQPc5.1*) was identified on Chr05 that explained the observed 11.758% phenotypic variance. A total of 23 candidate genes located within the QTL *CQPc5.1* interval were identified, which included the candidate gene *Capana05g000595* that encodes the RPP8-like protein as well as two candidate genes *Capana05g000596* and *Capana05g000597* that encodes a RPP13-like protein. Quantitative reverse-transcription PCR (qRT-PCR) revealed higher expression levels of *Capana05g000595, Capana05g000596*, and *Capana05g000597* in *P. capsici* resistance accessions, suggesting their association with *P. capsici* resistance in pepper.

**Keywords:** pepper; *Capsicum annuum*; *Phytophthora capsici*; high-density genetic map; QTL
