Construction of a genetic linkage map of watermelon (Citrullus lanatus) using CAPS and SSR markers and QTL analysis for fruit quality traits

• A watermelongenetic map was constructed using 125CAPS and SSR markers.
• Allof the CAPS markers were newly developed based on high-throughput re-sequencing data.
• Atotal of 10 QTLs were identified, 4 for fruit sugar content, and 6 for fruit shape.
• These QTLs will be useful for breeding to improve watermelon traits.

A genetic map of watermelon [Citrullus lanatus (Thunb.) Matsum. & Nakai] was constructed using an F2:3 segregating population consisting of 145 individuals, which were derived from a cross between a cultivated inbred line (garden female parent) from China and an American inbred line (LSW-177). The map contained 125 polymorphic markers, comprising 82 cleavage amplified polymorphic sequence (CAPS) markers and 43 simple sequence repeat (SSR) markers. The map contained 11 major and 3 minor linkage groups spanning a total length of 1,244.5 cM, with an average of 9.96 cM between markers. All of the CAPS markers were newly developed based on high-throughput re-sequencing data for the garden female parent and LSW-177. A quantitative trait locus (QTL) analysis was conducted using the composite interval mapping method to locate fruit sugar content and fruit shape traits. A total of 10 QTLs were identified; 4 for fruit sugar content and 6 for fruit shape. This map and QTL analysis will be useful for breeding to improve various economic traits in watermelon.