The development of PM resistance melon lines is essential to combat this devastating disease. We investigated the inheritance pattern of resistance to PM against a widespread Korean race, race 5 and developed high throughput molecular markers for selecting resistant lines. In our bioassay after inoculation with P. xanthii race 5, the F1 populations from a cross between P. xanthii race 5-susceptbile (SCNU1154) and –resistant (PMR 5) lines were resistant, indicating the dominant nature of resistance to PM (Fig. 3 and Table 2). A phenotypic ratio of 3:1 (resistant: susceptible) was found in 137 F2 plants, indicating a monogenic trait of resistance to P. xanthii race 5 (Table S2). Various patterns of inheritance of resistance to powdery mildew in melon were previously identified including polygenic against race N1 (Kim et al. 2016b), partial-dominant against KN1 (Nou, IS. unpublished data), co-dominant against race 1, 2 and 5 (Yuste-Lisbona et al. 2011) and dominant against race 1, pxCh1 and KN2 (Fukino et al. 2008; Liu et al. 2010; Nou, IS. unpublished data). Development of markers, especially the high throughput ones, is essential for mass screening and speed breeding these days (Wanga et al. 2021; Watson et al. 2018; Thomson 2014). As to the markers for selecting resistant vs susceptible lines, several SSR markers including CMBR150 and CMBR111 (Fukino et al. 2008), CMN1-38 (Fukino et al. 2007), CMBR120 (Kim et al. 2016b) and TJ29 (Gonzalo et al. 2005); SRAP marker Pm-8 (Liu et al. 2010) and CAPs markers, CAPS-Dde I (Zhang et al. 2013), and PM2-CAPS and PM5-CAPS (Yuste-Lisbona et al. 2011) were linked with linked to PM resistance against specific races. These markers were mainly used to developed linkage map and are of low throughput. SNPs, these days, can easily be identified and SNPs linked with specific phenotypic expressions can be used for developing high throughput genotyping upon validation in diverse natural population and in developed segregating populations (Mammadov et al. 2012; He et al. 2014; Thomson 2014; Yang et al. 2015)
Based on the whole Genome Re-Sequencing of PM susceptible genotype, SCNU1154 and resistant genotypes, Edisto47, MR-1, and PMR5, we have identified the genome-wide SNPs, of which 112 SNPs and 12 InDels were observed in powdery mildew responsive chromosomes, chromosomes 2, 5 and 12 (Natarajan et al. 2016; Howlader et al. 2020). Among these, three polymorphic SNPs namely, SNPR5-119, SNPR5-120 and SNPR5-121 demonstrated race 5‑specific genetic variation in melon (Kim et al. 2016a; Kim et al. 2016b). Among these, three SNPs, namely, SNPR5_119, SNPR5_120, and SNPR5_121 on chromosome 12 (closely located to the SSR marker CMBR150) were later identified to be associated with the phenotypic variation against race 5-specific susceptible (SCNU1154, PMR45, WMR29, and Edisto47) and resistant (PI414723, PMR5, and MR1) lines in C. melo via derived cleaved amplified polymorphic sequence (dCAPS) assay, indicating their linkage with resistance against PM race-5 (Howlader et al. 2020). Here, we designed HRM markers and validated their genotyping efficacy in wide range of diverse natural population and the developed F2 segregating generations. Among these three markers, PMm-HRM-1 showed more than 90% accuracy in genotyping the resistance status of both natural and F2 segregating populations, opposed to only ∼80% accuracy of the other two markers, PMm-HRM-2 and PMm-HRM-3 in F2 population (Table S1). The SNPs, SNPR5-120 and SNPR5-121 are located in the intergenic region between the genes, MELO3C002316 and MELO3C002317. Whereas, SNPR5-119 is located in the intragenic region of the intron-less leucine-rich repeat (LRR) receptor-like protein kinase family gene, MELO3C002393 on chromosome 12 (Table 3). Plant R genes are mainly encoded nucleotide-binding site leucine-rich repeat (NBS-LRRs), LRR, receptor-like protein kinases (RLKs) and LRR-RLKs domains, all of which are involved in plant defense against pathogens (Ellis et al. 2000; Harris et al. 2013; Kourelis and Van Der Hoorn 2018; Brotman et al. 2013; Marone et al. 2013). The LRR domain provides pathogen recognition specificity (DeYoung and Innes 2006; Eitas and Dangl 2010). Moreover, the NBS-LRR domain in plant immune receptors relied on the LRR domain for perform many important roles (Padmanabhan et al. 2009), and mutations in the LRR domain may result in a susceptible phenotype. SNPR5-119 results in a missense mutation (Lysine → Glutamic acid) in the LRR region of MELO3C002393 indicating its potential role in eventual protein product and thereby, influencing the ability to confer resistance against race 5 (Fig. S4). Taken together, these findings suggest that the SNP maker, SNPR5-119 may play potential roles and can effectively be used in HRM assay to detect P. xanthii race 5 resistant and susceptible melon genotypes and hence, can be used as high throughput molecular markers in MAS Based breeding programs.