*4.4. pBWR-1 Candidate Genes for Resistance to R. solanacearum*

We annotated the 31 candidate genes on the basis of sequence alignment using CM334 reference genome, KEGG, Swiss-Prot, GO, and NR databases (Table 4). Among them, four candidate genes were annotated as defense-associated genes: one gene, CA01g18650 (putative disease-resistance protein RPM1), in ch01\_156505108 marker and three genes, such as nearly tandem-arrayed genes CA01g20110 (GO: 0006952, Thaumatin-like protein), CA01g20130 (putative disease-resistance protein RPM1, KO: 13457), and CA01g20140 (NB-ARC domain-containing protein), in ch01\_161127926 marker. In comparison with previous publications, the identified candidate genes might not be similar to Mathew's (2020) results on chromosome 08, whereas the genes encoding LRR proteins and NB-ARC domain-containing protein on chromosome 10 in Du et al. (2019) are shared with our results, implying that these genes are possibly indispensable for BW resistance.

Previous studies have reported that pathogen defense-associated R genes are tandemly located in chromosomes [74–76]. For example, eight genes encoding an amino terminal coiled-coil domain (CC), a central nucleotide binding (NB) site, leucine-rich repeat (LRR) domain are tandemly arrayed in the *Pvr4* locus of CM334 genome in *C. annuum*. Fourteen genes encoding NB-LRR tandemly lie on the *Tsw* locus of PI159236 genome in *C. chinense*. Moreover, among of three tandem-arrayed R genes within the *qRRS-10.1* QTL, two genes, including CA10g13010 and CA10g13020, were annotated as *Bs2,* which is classified into the NB-LRR family, suggesting that NB-LRR proteins play a crucial role in disease resistance against pathogens [75]. It has been studied that elongation factor tu receptor (EFR) from *Arabidopsis* and *Bs2* from pepper are expressed in tomato plant for controlling BW and bacterial spot (BS), respectively [77]. Intriguingly, the EFR was determined as a critical component in plant defense of PAMP-triggered immunity (PTI) via the interaction between conserved PAMPs and bacterial pathogens [78]. Furthermore, Du et al. (2019) reported that CA10g12520 within the *qRRS-10.1* QTL encodes PR-1 gene, indicating the participation in the interaction of plant and pathogen via PTI. In similar line with previous results, we identified CA01g18650 and CA01g20130 encoding putative disease-resistance protein RPM1. The bacterial resistance to *Pseudomonas syringae pv. maculicola 1* (RPM1) encodes a CC-NB-LRR family protein, which is a peripheral plasma membrane protein [79,80]. The RPM1 recognizes the effector proteins of *avrB* or *avrRpm1* of *Pseudomonas syringae* in *Arabidopsis*, resulting in the rapid generation of a hypersensitive response (HR) [79–81]. Moreover, identified CA01g20140 harbors NB-ARC domain-containing protein. It has been shown that effector-triggered immunity (ETI) is associated with nucleotide-binding leucine-rich repeat (NLR) proteins [82]. A variety of plant NLRs possess an NB-ARC domain (nucleotide-binding adaptor shared by Apaf-1, R proteins, and CED4), which is able to interact with NLR domain-containing proteins, indicating that an NB-ARC domain is important for pathogen defense [83,84]. Importantly, we also identified CA01g20110 encoding Thaumatin-like protein (GO: 0006952). Previous researches have reported that Thaumatin-like proteins (TLPs) are classified into PR (pathogenesis-related protein)-5 class protein, and TLP genes are upregulated in peanut (*Arachis hypogaea* L) with the treatment of the leaf spot pathogen, *Phaeoisariopsis personata* [85], as well as in wheat (*Triticum aestivum*) by leaf rust fungus, *Puccinia triticina* [86]. In addition, constitutive expression of *Arabidopsis* Thaumatin-like protein 1 (ATLP1) in potato are observed with reduced lesions and percent reductions in response to *Alternaria solani* and *Phytophthora infestans* [87], implying that TLPs are essential in diverse biotic response. Although we cannot completely rule out the effect of differential expression of other candidate genes in the list (Table 4) and minor QTL effects that were not detected on the BW resistance in the current study, it is our endeavor for future research to focus on the understanding of genetic mechanisms, such as

inheritance factors, as well as on functional analysis of the identified candidate genes in the resistance to *R. solanacearum*.
