Discovery of Genome-wide Single Nucleotide Polymorphisms using Next Generation Sequencing in Melon (Cucumis Melo L.)

The decreasing cost along with rapid progress in next generation sequencing (NGS) and related bioinformatics computing resources has facilitated large-scale discovery of SNPs in crop species. Melon (C. melo L.) is an economically important species (2n = 2x = 24) in the Cucurbitaceae family. It has been extensively studied as a model fruit for several biological characters such as fruit ripening and sex determination. In this study, the genomes of two melon varieties (P1 and P2) were sequenced using the HiSeq system. The 6.8 Gbp and 6.0 Gbp sequences were generated for P1 and P2, respectively and these sequences were used to identify single nucleotide polymorphisms (SNPs). By comparing with the melon reference genome assembly version 3.5.1, we detected 1,844,761 (P1) and 1,654,882 (P2) SNPs in both intergenic and genic regions. In addition, a total of 534,477 SNPs were detected between P1 and P2 varieties. Of these SNPs, a subset of 222 SNPs were randomly selected for validation and their primers were designed for high resolution melting (HRM) analysis. A total of 185 SNPs (83.33%) were validated and these SNPs were used to genotype additional 16 melon varieties. The SNPs from our study will be a useful resource for genome-wide association studies and breeder’s toolbox development.