Molecular Markers and Marker-Assisted Selection Provide Genetic Insights for Identifying Key Quantitative Trait Locus for Watermelon Rind Thickness

Rind thickness (RT) is an important agronomic trait in watermelon [<i>Citrullus lanatus</i> (Thunb.) Mansf.] and affects watermelon storability. However, genetic studies on this trait, as well as gene regulation studies, are scarce and of limited production significance. We constructed a temporary F₂ generation using the highly differentiated thick-rind watermelon 'XiaoXiGua-4' and the thin-rind watermelon 'DuanMan' as parents and localized the <i>Cla97C02G044120</i> gene, which controls the thickness of watermelon rind, to the intervals of chromosome 2, CL2-32303995 and CL2-32316840, through 2 years of genetic analysis. No exonic mutations were found in this gene, but two promoter mutations resulted in changes in the promoter progenitor. Fluorescence quantitative PCR analysis revealed highly significant differences in expression at 1 d and 28 d, and the expression was significantly lower in thick-skinned watermelon varieties. Marker-assisted selection (MAS) for this trait was performed using the Caps marker CL2-32303995 and the InDel marker CL2-32316840, which not only verified the stability of the localization interval but also distinguished thick rind from thin rind. These results can be used for germplasm resource screening and have strong breeding significance.