Development of SNP Markers for the Identification of Commercial Korean Watermelon Cultivars Using Fluidigm Genotyping Analysis

Molecular markers based on simple sequence repeats (SSRs) from expressed sequence tags (ESTs) have been used to identify the registered commercial cultivars in watermelon (Citrullus lanatus). To characterize diversity in watermelon cultivars, molecular markers based on genome-wide single nucleotide polymorphisms (SNPs) are needed. Here, we used Fluidigm genotyping for the development of a core set of SNPs to differentiate Korean watermelon commercial cultivars. A candidate subset of SNPs was discovered by genotyping-by-sequencing using 48 F1 cultivars. The cultivars could be divided into three subpopulations with 97.5% similarity by unweighted pair group method with arithmetic mean (UPGMA) clustering based on 2,300 SNPs. After filtering loci with a high polymorphism information content (PIC), a subset of 238 SNPs was selected and analyzed in 92 F1 cultivars on the Fluidigm genotyping system. Among these, 141 polymorphic, bi-allelic SNPs were obtained. To evaluate genetic diversity in 92 cultivars, a principal component analysis (PCA) and hierarchical clustering analysis were performed. The first two axes of the PCA explained only 30.5% of the total variance; however, the 92 cultivars clustered into three subgroups with similar sizes. Approximately 90% of the subgroups remained unchanged in the UPGMA clustering analysis. In addition, when the subset of 141 SNPs was filtered with a threshold PIC of 0.36, a core set of 96 SNP markers were obtained, without identical clustering results. The core set of SNP markers can be used for the identification of commercial Korean watermelon cultivars and for the protection of proprietary rights for new cultivar development.