Development of SNP markers and validation assays in commercial Korean melon cultivars, using Genotyping-by-sequencing and Fluidigm analyses

•Detection of genome-wide highly efficient SNPs in melon using Genotyping-by-sequencing (GBS).•Genome-wide SNP Markers development and validation design in melon with 95.83 % of validation ratio via high-throughput Fluidigm system.•The estimates of PIC showed 97.28 % more than 0.3 of PIC.•UPGMA analysis using 184 SNPs demonstrated genetic differentiation among commercial melon cultivars.•SNP markers reported here will be a valuable tool for cultivar identification, genetic diversity and marker-trait association studies in melon. Melon is an important horticultural crop across the globe, which consisted of several subspecies. Single nucleotide polymorphisms (SNPs) are the most preferred molecular markers in genetic diversity and genomic studies. Recently, Genotyping-by-sequencing (GBS) has produced sequences that detect genome-wide distribution of these SNP markers. In this study, we identified genome-wide highly efficient SNP markers to differentiate the cultivars of the melon using GBS. Here we detected 9018 SNPs by the analysis of 48 commercialized Korean melon cultivars, which released by various seed companies in South Korea. Further, precise filtering resulted in 5644 high-quality SNPs. Of these, 5293 SNPs and 351 were identified in the genic region and intergenic region, respectively. A total of 192 SNPs were identified as putative SNPs, on the basis of high polymorphism information content (PIC) and physical distance. These SNPs were further analyzed to distinguish 95 commercial melon cultivars via high-throughput Fluidigm system, thus revealed 95.83 % (184 SNPs) of validation ratio. The summary of SNP genotyping revealed estimates of PIC ranged from 0.02 to 0.53 and 179 SNPs (97.28 %) showed more than 0.3 of PIC. This is the first study in melon to develop and validate genome-wide SNP markers using GBS and Fluidigm platform, respectively. The SNP markers reported in this study will be a valuable tool for cultivar identification, genetic diversity, and marker-trait association studies in melon.