Molecular Mapping and Candidate Gene Analysis for GA₃ Responsive Short Internode in Watermelon (Citrullus lanatus)

Plants with shorter internodes are suitable for high-density planting, lodging resistance and the preservation of land resources by improving yield per unit area. In this study, we identified a locus controlling the short internode trait in watermelon using Zhengzhouzigua (long internode) and Duan125 (short internode) as mapping parents. Genetic analysis indicated that F₁ plants were consistent with long internode plants, which indicates that the long internode was dominant over the short internode. The observed F₂ and BC₁ individuals fitted the expected phenotypic segregation ratios of 3:1 and 1:1, respectively. The locus was mapped on chromosome 9 using a bulked segregant analysis approach. The region was narrowed down to 8.525 kb having only one putative gene, Cla015407, flanking by CAPS90 and CAPS91 markers, which encodes gibberellin 3β-hydroxylase (GA 3β-hydroxylase). The sequence alignment of the candidate gene between both parents revealed a 13 bp deletion in the short internode parent, which resulted in a truncated protein. Before GA₃ application, significantly lower GA₃ content and shorter cell length were obtained in the short internode plants. However, the highest GA₃ content and significant increase in cell length were observed in the short internode plants after exogenous GA₃ application. In the short internode plants, the expression level of the Cla015407 was threefold lower than the long internode plants in the stem tissue. In general, our results suggested that Cla015407 might be the candidate gene responsible for the short internode phenotype in watermelon and the phenotype is responsive to exogenous GA₃ application.