Development of powdery mildew race 5-specific SNP markers in Cucumis melo L. using whole-genome resequencing

Melon (Cucumis melo L.), belonging to the Cucurbitaceae family, is cultivated worldwide and is highly valued for its fruit quality. However, this important crop is negatively affected by several races of powdery mildew (PM) fungus, Podosphaera xanthii. Hence, exploration of PM race-specific resistant markers would be an effective strategy to develop race-specific melon cultivars. Young leaves from four melon genotypes, including susceptible SCNU1154 and race-specific-resistant Edisto47, PMR5, and MR1 lines, were sequenced by next-generation sequencing, specifically whole-genome resequencing (WGR), to detect race-specific single nucleotide polymorphism (SNP) markers. Including putative resistance gene (R-gene) SNPs, 168, 83, and 122 race 5-specific SNPs with the exact variation were identified on PM-related chromosome 2, 5, and 12, respectively, for distinguishing race-specific lines by comparing the WGR data in the C. melo genome. Based on proximity to the PM resistance quantitative trait loci (QTLs) in physical maps, 43, 37, and 48 SNPs were screened on chromosome 2, 5, and 12, respectively. Using a derived cleaved amplified polymorphic sequence (dCAPS) method, polymorphisms were only found in three SNPs (SNPR5_119, SNPR5_120, and SNPR5_121) out of 48 against race 5 on chromosome 12. Among these three, a putative R-gene, an NBS-LRR-type SNP, SNPR5_119, displayed similar genotypic and phenotypic variation to race 5-specific susceptible (SCNU1154, PMR45, WMR29, and Edisto47) and resistant (PI414723, PMR5, and MR1) lines in C. melo except for PI124112. Importantly, two other intergenic SNPs, SNPR5_120 and SNPR5_121, showed genotypic and phenotypic variation between susceptible and resistant lines tested. High-resolution melting (HRM) analysis was used to further validate the same expression patterns of SNPR5_120 as a dCAPS method in all lines tested. Therefore, the identified PM race 5-specific candidate markers described here might be useful for a marker-assisted selection breeding program in C. melo.