**1. Introduction**

Pepper plants (*Capsicum* spp.) derived from the regions of American tropics belong to the Capsicum genus and Solanaceae family, including peppers, paprika, tomatoes, eggplants, and potatoes. It is regarded as one of the most important vegetable crops worldwide owing to diverse positive aspects in field of cuisine, medicine and healthcare, and economy [1–3]. Pepper fruits are largely consumed as fresh and dried ingredients as well as processed foods and render a wide variety of essential bioactive elements, such as vitamins, minerals, phenolics, carotenoids, and capsaicinoids [4–8]. The consumption of pepper has been gradually increased for several decades, together with the cultivation area and production in agriculture (http://www.fao.org/faostat (accessed on 9 August 2021) [9]. On the basis of Food and Agriculture Organization (FAO) [9], the cultivation area has occupied around 4.5 million hectare, and pepper production has reached around 67 million

**Citation:** Chae, S.-Y.; Lee, K.; Do, J.-W.; Hong, S.-C.; Lee, K.-H.; Cho, M.-C.; Yang, E.-Y.; Yoon, J.-B. QTL Mapping of Resistance to Bacterial Wilt in Pepper Plants (*Capsicum annuum*) Using Genotyping-by-Sequencing (GBS). *Horticulturae* **2022**, *8*, 115. https://doi.org/10.3390/ horticulturae8020115

Academic Editors: Fei Chen and Jia-Yu Xue

Received: 23 November 2021 Accepted: 25 January 2022 Published: 27 January 2022

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tons, including fresh and dried peppers, in the world [10]. Moreover, in terms of the world trade value of crops, the amount of chili peppers has ranked with the second position after tomato plants among the Solanaceae family [11]. However, pepper production is naturally threatened by biotic factors, including bacteria, fungi, and viruses in the agronomic field [12]. In particular, bacterial wilt (BW) is one of most destructive diseases throughout the world and has been widely spread in pepper crops across all over the Asia [13–15]. In 2017, BW led to a significant reduction of pepper yields and productions ranging from over 20 to less than 50% at most in the world cultivation area [16].

BW disease is caused by a soil-borne bacterial pathogen, *R. solanacearum,* and it is one of the global plant diseases [17]. The BW is seriously harmful for a large amount of the solanaceous family, including the vegetable crops of chili and sweet peppers, paprika, tomatoes, potatoes, and eggplants, which cause a plant-wilting disease. It is recognized as a wide range of hosts by invading over 450 different plant species through the broad climate spectrums containing tropical, subtropical, and temperate regions [18–20]. The pathogen of *R. solanacearum* enters plants via the natural opening and the wounded layers at the emergence sites of secondary roots or at root tips, which immigrate and colonize the host root cortex [21,22]. Subsequently, the *R. solanacearum* infects the parenchyma of the plant vascular system. The success of the invasion into xylem causes plant pathogenicity, including high population of the increased bacterial cells, diverse enzymes, and viscous di-and poly-saccharides by *R. solanacearum*. As such, the xylem vessels in plant roots are filled and blocked by the pathogenicity [23,24]. Interestingly, several reports have studied that the resistant cultivars possess an ability to restore the xylem transport system directly after the bacterial attacks, whereas the susceptible cultivars are observed with the xylem blocked by the occlusion derived from bacteria [25,26], leading to the damage of the water flow system inside the plant's xylem. The malfunction results from plant yellowing, wilting, and dying depending on the severity of the disease symptoms [25].

To date, multiple management methods to govern the BW disease have been developed and applied in agriculture. Indeed, the effects of combatting the devastating BW have been shown with agronomical, physical, chemical, and cultural methods, including the crop rotation of different types, utilization of bactericides, and plant breeding programs [26]. However, the management strategies have been reported with limited and insufficient effects on the BW disease regulation owing to the wide variety of host range, diverse genetic variations of the pathogen, and long-term survival in plants [26–28].

In general, it is considered that the most effective control method is to breed elite, resistant cultivars in the pepper crops against the BW [29]. Remarkably, a wide variety of BW resistant-pepper accessions have been determined. For example, the BW resistantpepper accessions (*Capsicum* spp.) with LS2341, PI358812, Kerting, PI322726, PI322727, PI369998, PI377688, PI322728, Jatilaba, MC4, MC5, PBC 066, PBC 437, PBC 631, and PBC 1347 display high BW resistance against a wide array of BW pathogens [30–33]. In addition to this, some researches have studied that BW resistance is involved in a quantitative inheritance and is polygenically governed by multiple genes (≥2 genes) in the pepper cultivar Mie-Midori [29]. A pepper cultivar, PM687, has been determined to have additive effects, which are influenced by the involvement of 2 to 5 candidate genes to regulate the BW resistance [34]. Additionally, A pepper accession called LS2341 has been identified with polygenes and linkage to a major quantitative trait loci (QTL), *Bw1,* located on chromosome 08, which possesses putative 44 candidate-resistance genes against *R. solanacearum* [35]. A recent report has uncovered a marker ID10-194305124 on the major QTL *qRRs-10.1* on chromosome 10, which consists of five candidate R genes containing putative leucinerich repeat (LRR) receptor or NB-ARC proteins and three defense-associated genes in the resistance pepper cultivar BVRC1 [36].

QTL mapping is a basic and powerful tool for genetic investigation of quantitative traits and high-density linked markers. Although the conventional QTL mapping is a time-consuming, labor-intensive, and costly procedure [37], advances in next-generation sequencing (NGS) technologies reduce sequencing cost and contribute to the rapid identification of QTL and the assessment of genome-wide single nucleotide polymorphism (SNP) in pepper crop [38]. The utilization of NGS for SNP discovery is beneficial, as it generates a large amount of sequence data that can be used for genotype-phenotype association [37,39,40]. Genotyping-by-sequencing (GBS) technology is a simple and robust method that is practical as a high-throughput genotyping tool for a large number and huge amount of DNA as well as for complex genomes of crop species [41,42]. Furthermore, GBS is a cost-effective technique with the advantages of reduced sampling time, decreased sequencing cost, and no limited reference genome sequences [37,43]. Recent studies have reported that the GBS tool is successfully applied to the various crops, including chickpea, maize, wheat, onion, soybean, pepper, and rice, for QTL mapping, high-density genetic mapping, SNP discovery, GWAS, genomic selection (GS), and genotyping [44–52]. Since the GBS tool possesses a wide applicability of QTL identification in pepper (*C. annuum*), genetic analysis of quantitative traits and high-resolution-linked markers for BW would contribute to more accurate marker-assisted selection (MAS) in plant genetics and breeding via GBS.

In this study, we produced 94 F2 recombinant lines derived from a cross between a resistant source of *C. annuum,* KC352, and a susceptible source of *C. annuum,* 14F6002-14, for QTL mapping of BW resistance to *R. solanacearum* isolates. Next, we constructed a genetic map with 94 F2 recombinant offspring. High-resolution SNP markers associated with BW resistance revealed novel QTL regions on chromosome 01 via GBS. The result will be utilized for developing SNP markers involved in BW resistance and for selecting and breeding elite BW-resistant pepper plants.
