**1. Introduction**

Pepper (*Capsicum annuum* L.) is a common condiment and an economically significant vegetable crop. It is not only used in many cuisines but also found to have many medicinal properties. In 2019, approximately 212.04 million tons of chilies and peppers were grown on about 49.31 Mha around the world (http://www.fao.org/faostat/zh/#data/QC). However, pepper is susceptible to a variety of pathogens such as CMV, TMV, *Colletotrichum* spp., and *Phytophthora capsici* (*P. capsici*) [1–4]. *Phytophthora* blight can significantly decrease pepper yield and quality [5]. The disease is caused by the oomycete plant pathogen *P. capsici* that initially infects the roots and crown roots, then subsequently spread to every plant part, including the roots, stems, fruits, and leaves [6]. *Phytophthora* blight is a severe disease that commonly occurs under warm (25–28 ◦C) and highly humid conditions [7–9]. No effective and safe measures to control *Phytophthora* blight have been established to date, except for chemical control [10–13]. Therefore, the utilization of resistant varieties has become a simple, effective, and safe way of resolving *Phytophthora* blight occurrence in pepper. Plant breeders have also focused on selecting varieties with high levels of resistance.

The three physiological races of *P. capsici*, named "races 1–3," have been determined by their virulence on four pepper varieties: early calwonder (sensitive), PI201234 (resistant),

**Citation:** Li, Y.-F.; Zhang, S.-C.; Yang, X.-M.; Wang, C.-P.; Huang, Q.-Z.; Huang, R.-Z. Generation of a High-Density Genetic Map of Pepper (*Capsicum annuum* L.) by SLAF-seq and QTL Analysis of *Phytophthora capsici* Resistance. *Horticulturae* **2021**, *7*, 92. https://doi.org/10.3390/ horticulturae7050092

Academic Editor: Yuyang Zhang

Received: 5 March 2021 Accepted: 16 April 2021 Published: 1 May 2021

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PBC137 (partially resistant), and PBC602 (partial resistance) [14]. Previous studies have reported several pepper accessions that are resistant to *P. capsici*, including PI123469, PI201232, PI201234, AC2258, and CM334 (Criollo de Morelos 334) [4,14–18]. Resistance to *P. capsici* is mainly regulated by a single dominant gene in PI201234 or by one dominant gene in the presence of modifiers [9,19–21], and AC2258, which has been derived from PI201234, is resistant to *P. capsici* [17,18]. Studies have shown that resistance to *P. capsici* in CM334 is controlled by a minimum of two genes [22,23]. In addition, these reports revealed that the regulatory mechanism underlying *P. capsici* resistance in pepper is highly complex. Numerous reports have investigated the effect of a pepper QTLs on chromosomes that are associated with resistance against *P. capsici* [18,23–31]. *Pc5.1* is a homologous QTL on chromosome 5 of CM334, PI201234, and Perennial that has been associated with resistance to *P. capsici* [23,29,31]. Mallard et al. (2013) have identified resistance QTLs among three meta-QTLs (*MetaPc5.1*, *MetaPc5.2*, and *MetaPc5.3*) by meta-analysis [31]. Siddique et al. (2019) identified three QTLs on chromosome P5, including *QTL5.1*, *QTL5.2,* and *QTL5.3*, which were associated with resistance to three *P. capsici* isolates (race 1, race 2, and race 3) by traditional QTL mapping combined with GWAS strategy [30]. In addition, a few minor-effect QTLs has been identified on different chromosomes [23,27,28,32].

Large-scale SNP markers have recently been discovered by next-generation sequencing (NGS) that have expedited the construction of the pepper genetic map. SLAF-seq is a novel high-throughput sequencing technique that is less expensive and complex than high-quality reference genome libraries [33]. In addition, the SLAF-seq strategy has been generally utilized in constructing high-density genetic maps of different species and in QTL mapping [34–42]. This strategy had also been successfully used in the creating high-density pepper genetic maps [40,43,44]. For instance, Guo et al. (2017) determined two candidate CMV resistance genes on pepper chromosomes 2 and 11 using SLAF-seq along with BSA technologies [43]. In addition, Zhang et al. (2019) utilized SLAF-seq in detecting two major QTLs that were strongly associated with FFN [40].

In this work, we developed a high-density pepper linkage map with SLAF-seq as well as identified QTLs that are related to *P. capsici* resistance using F2 populations that were obtained from a cross between parental lines 1287 (*P. capsici* susceptible, female) and PI201234 (*P. capsici* resistant, male). Finally, we investigated the main effect of QTLs as well as select candidate genes. Our results could potentially facilitate the elucidation of the genetic mechanism underlying *P. capsici* resistance in pepper and lay the foundation for breeding highly resistance pepper cultivars.
