Genotyping by sequencing for SNP discovery and genetic mapping of resistance to race 1 of Fusarium oxysporum in watermelon

• 1024 SNPs generated through genotyping by sequencing will be useful in future genetic studies in watermelon.
• Qfon1 locus on chromosome 1 is a viable candidate for MAS against Fon race 1 in watermelon.
• The modified tray-dip method provides an important stride towards high-throughput precision phenotyping in watermelon.

Management of fusarium wilt caused by Fusarium oxysporum f. sp. niveum (Fon) (E.F. Sm.) W.C. Snyder & H.N. Han. in watermelon [Citrullus lanatus (Thunb.) Matsum. & Nakai] is largely dependent on cultivation of resistant cultivars. Application of marker-assisted selection (MAS) in conventional breeding programs can accelerate the release of new watermelon cultivars resistant to fusarium wilt. Towards developing tools for MAS, physical (1024 SNPs) and genetic (389 SNPs) maps were developed in the current study for an F2 population (n = 89; Calhoun Gray x Sugar Baby) segregating for resistance against Fon race 1 using the genotyping by sequencing platform. A modified tray-dip method was established for high-throughput phenotyping of the segregating F3 population. A major quantitative trait locus (QTL) accounting for up to 38.4% of the phenotypic variation in the F3 population was identified on chromosome 1 on both the physical and genetic maps in a region previously associated with Fon race 1 resistance. This resistance locus was consistently detected over five different time points and three different phenotypic screens, showing the reliability of the screening method in discriminating susceptible and resistant genotypes. Eight resistance genes were found within the confidence interval of the identified QTL. SNPs close to this QTL may be exploited in MAS for fusarium wilt resistance in breeding programs. This study confirms the resistance locus on chromosome 1 and demonstrates the use of a physical map for QTL detection in watermelon. The SNPs reported here will be useful for future genetic studies in watermelon.