Fine-mapping of a major quantitative trait locus Qdff3-1 controlling flowering time in watermelon

Flowering time is crucial in watermelon (Citrullus lanatus) production as it determines time of fruit set. Early flowering is desirable because it enables crops to escape biotic and abiotic stresses that are intensified by long production cycles. Production of seedless watermelon is also reliant on synchronized flowering of diploid pollenizers and the triploid watermelon cultivars. Utilizing marker-assisted selection (MAS) of flowering time in watermelon breeding would potentially aid in selection for early flowering, which would shorten the production time. A major quantitative trait locus Qdff3-1 (12-17 Mb) associated with days to female flower (R-2 = 50%) was previously identified on chromosome 3 of watermelon. In this study, we validated the Qdff3-1 locus using QTL-seq. To determine more precisely the interval of Qdff3-1 and the candidate gene controlling flowering time, SNP markers were identified in the region and Kompetitive Allele Specific PCR (KASP) assays were developed for high-throughput genotyping. Markers were tested for trait association on the mapping population, recombinant F-2:3 populations, and a panel of differential cultivars. In the KBS x NHM genetic background the QTL was delineated to a 1.13-Mb region, flanked by markers UGA3_14537958 and NW0248748. This region includes the FT and a protein phosphatase 2C (PP2C) gene. Genotyping the regions of interest in a panel of genetically diverse cultivars suggests that genetic control of flowering time in watermelon is dependent on the genetic background. These results lay the foundation for a greater understanding of flowering mechanisms in watermelon and improved breeding strategies for this trait.