Genome-wide sequence variation in watermelon inbred lines and its implication for marker-assisted breeding

Watermelon is an economically important member of the Cucurbitaceae family. Cultivated watermelons (C. lanatus ssp. lanatus) have diverse fruit-related traits such as size, shape, color of flesh and skin, and the striped rind pattern. In this study, the whole genomes of 19 inbred watermelon lines were resequenced and genome-wide sequence variations were analyzed for the development of markers for MABC (marker-assisted backcross). Based on the single nucleotide polymorphisms (SNPs) and insertion/deletion (InDel) detected, we evaluated the distribution of genome-wide diversity, genetic relationship, cultivar type-specific allele abundance, and sequence divergence at quantitative trait loci (QTLs). For MABC, a total of 1,374 SNPs were selected at intervals of 0.5 Mb based on the Polymorphism Information Content (PIC) value. Principal components analysis (PCA) of the 19 cultivars was based on 1,374 SNPs to classify them into three major groups, which indicated a clear grouping pattern between Crimson-type and Jubilee-type watermelons. In addition, a set of SNPs (259) that discriminated Crimson-type cultivars from the non-Crimson-type were also selected. For the verification of SNPs, 26 cleavage amplified polymorphic sequence (CAPS) markers were designed based on the SNPs and used to genotype 11 cultivars, which resulted in high agreement rates above 0.8 for most of the markers. Our study uncovers the genetic diversity underlying cultivated watermelon species and provides genetic information useful for the development of molecular markers for marker-assisted breeding (MAB) strategies.