Genetic Mapping of a Candidate Gene ClIS Controlling Intermittent Stripe Rind in Watermelon

Rind pattern is one of the most important appearance qualities of watermelon, and the mining of different genes controlling rind pattern can enrich the variety of consumer choices. In this study, a unique intermittent rind stripe was identified in the inbred watermelon line WT20. The WT20 was crossed with a green stripe inbred line, WCZ, to construct F2 and BC1 segregating populations and to analyze the genetic characterization of watermelon stripe. Genetic analysis showed that the intermittent stripe was a qualitative trait and controlled by a single dominant gene, ClIS. Fine mapping based on linkage analysis showed that the ClIS gene was located on the 160 Kb regions between 25.92 Mb and 26.08 Mb on watermelon chromosome 6. Furthermore, another inbred watermelon line with intermittent stripe, FG, was re-sequenced and aligned on the region of 160 Kb. Interestingly, only two SNP variants (T/C, A/T) were present in both WT20 and FG inbred lines at the same time. The two SNPs are located in 25,961,768 bp (T/C) and 25,961,773 bp (A/T) of watermelon chromosome 6, which is located in the promoter region of Cla019202. We speculate that Cla019202 is the candidate gene of ClIS which controls the intermittent stripe in watermelon. In a previous study, the candidate gene ClGS was proved to control dark green stripe in watermelon. According to the verification of the two genes ClIS and ClGS in 75 watermelon germplasm resources, we further speculate that the ClGS gene may regulate the color of watermelon stripe, while the ClIS gene regulates the continuity of watermelon stripe. The study provides a good entry point for studying the formation of watermelon rind patterns, as well as providing foundation insights into the breeding of special appearance quality in watermelon.