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An experiment was conducted to screen a germplasm panel comprising 331 Citrullus sp. accessions against Fon race 1 for identification of resistance and to validate a candidate QTL (Fon-1) region conferring resistance. The accessions were screened through artificial inoculation of spore suspension during the rainy season of 2017. A genotype with ≥67% survival at 28 days post-inoculation (DPI) was categorised as resistant. A total of 41 accessions were identified to possess resistance to Fon race 1. Of these, nine accessions were highly resistant (mean survival ≥90% at 28 DPI). The reactions of these accessions were also confirmed in another bioassay. These accessions need deployment in future watermelon breeding programmes. Six markers, located within the previously reported Fon-1 locus, were tested for their association with resistance and among them, InDel-4, located in the 5ʹ promoter region of an ABC Transporter protein, was found to be most significantly associated and explained maximum phenotypic variation, proving its relevance for marker-assisted introgression of resistance to Fon race 1 into elite commercial backgrounds of watermelon. [ABSTRACT FROM AUTHOR]