Fine mapping a ClGS gene controlling dark-green stripe rind in watermelon

The stripe pattern is an important agronomic trait in watermelon, which determines the fruit rind pattern and consumer choice. However, the genes controlling these traits are still largely unknown. In the present study, a dark-green stripe inbred line WT2 and a netted stripe inbred line WM204 were used for genetic analysis, which revealed that the dark-green stripe is controlled by a single dominant gene ClGS. By bulked-segregant analysis (BSA), the ClGS was primarily mapped on watermelon chromosome 6 by using F2 plants developed from a cross between WT2 and WM204. Next-generation sequencing-aided marker discovery and a large mapping population consisting of 1206 F2 plants was used for fine mapping of the ClGS gene, and it was further mapped into a 107 kb candidate region. There were 11 genes predicated in this candidate region and 10 of them were differentially expressed in the 1-DAP fruit rind between two parental lines. Furthermore, 64 SNPs and 3 Indels were detected in the CDS region of these candidate genes. To further confirm the candidate gene of ClGS, we investigated the sequence variations among 74 re-sequenced natural watermelon accessions by in silico bulk segregant analysis. A 3-bp insertion was identified in all the non-dark green stripe watermelon accession group, which was located on the 8th exon of Cla019205. A Indel marker developed harboring the insertion showed co-segregation with the phenotype in the F2 mapping population, and it was also in completely agreement with another 25 watermelon accessions by electrophoretic analysis. These evidences suggested Cla019205 is probably the candidate gene controlling dark-green stripe in watermelon. The results of this study will be helpful for better understanding of the stripe formation and marker-assisted selection in watermelon.