Efficient Genetic Mapping and QTL Analysis in Watermelon

Watermelon is one of the important vegetable crops. It has been very hard to generate a high-dense genetic map, since the watermelon has narrow genetic diversity background and segregation distortions of molecular markers derived from RAPD, AFLP, and SSRs. Here we present efficient way to assemble genetic map and markers with Next-Generation Sequencing (NGS) coupled with Genotyping by Sequencing (GBS) in F2 generation. After cross between C. lanatus ssp. citroides (PI 189225) and C. lanatus ssp. lanatus (TS, Korean cultigen), 163 of F2 progenies were sequenced through Illumina's Hi-Seq GAII. Libraries for GBS for watermelon were constructed by ApeKI-digested watermelon genome. From sequence information of VCF, the genetic map of watermelon based on SNPs consisting of 11 linkage groups were pre-constructed using MstMap software. The SNPs were filtered and optimized by sequencing depth and physical bin for reordering scaffolds of physical map prior to construct more reliable genetic linkage map. Then all the reliable SNP loci were determined and compared to sequences of physical map. In addition, we determined QTLs and found two major loci corresponding to seed size of watermelon.