Effective Genome-Wide SNP Detection and Genotyping for Constructing a High-Dense Genetic Linkage Map of Watermelon (Citrullus ianatus (Thunb.) Matsum & Nakai )

Watermelon is one of important agricultural crops. As the watermelon breeding goes with many genes and narrow genetic diversity background, it has been very hard to find proper markers for developing new watermelon cultivar. Here we present efficient way to assemble genetic map and markers with Next-Generation Sequencing (NGS) coupled with Genotyping by Sequencing (GBS). We use ApeKI as a restriction enzyme, which recognizes 5 bases and has methylation sensitivity. After cross between C. lanatus ssp. citroides (PI 189225) and C. lanatus ssp. lanatus (TS, Korean cultigen), 165 of F2 progenies were sequenced through NGS. Sequence information was analized to find SNP informations yielding 2614 Single-Nucleotide Polymorphisms (SNPs) with 1102 genetic bins. After filtered by SMOOTH algorithms to remove sequencing errors and double recombinants, final genetic map was contructed with 8889 SNP-based markers and 2705 genetic bins which have 2553 cM  in map length with an average inter-marker distance of 0.237 cM. In conclusion, high-dense genetic map built from 165 watermelon of F2 population via GBS and resulting 8889 SNP markers would be utilized in mapping and breeding.