Exploring molecular markers and candidate genes responsible for watermelon dwarfism

Watermelon is an important crop of the Cucurbitaceae family and accounts for approximately 7% of global crop production. Cultivation of watermelon and other cucurbit crops requires a large cultivation area and intensive labor to remove the stem. The adoption of the watermelon dwarfism trait in cultivation is an economical alternative solution for farmers. Here, we identified the single-nucleotide polymorphism (SNP) associated with the dwarfism of watermelons in a breeding program. The SNP markers were genotyped with F2 progeny derived from a cross of ‘Caupat-dw’ (dwarf-type) and ‘Hs4450’ (wild-type) using bulked segregant analysis (BSA) of next-generation sequencing (NGS). The BSA-NGS analysis revealed that two candidate loci from 1.7 to 2.0 Mbp and 5.6 to 6.2 Mbp on chromosome (Chr) 9 were associated with dwarfism. We validated these SNPs in F2 progeny using a high-resolution melting assay. Based on the results, we identified a perfect cosegregation region of 1,872,994 to 1,866,655 bp on Chr 9. Within the candidate region, Cla015405 and Cla015406 , both of which are annotated as a gene of 2 - oxoglutarate - dependent dioxygenase , were found. The expression level of Cla015405 was upregulated in ‘Caupat-dw’ but not in ‘Hs4450’. There was no significant expression difference in Cla015406 . We found that Cla015405 has a 2-beta-dioxygenase (GA2ox) motif that when upregulated converts bioactive GAs to inactive GAs. Thus, Cla015405 located within the cosegregated region of the dwarf phenotype may play an important role in GA metabolism to induce dwarfism of ‘Caupat-dw’. In this study, we developed SNP markers tightly linked to dwarfism in watermelon, which will contribute to dwarf gene research and watermelon breeding programs.