Assay development and marker validation for marker assisted selection of Fusarium oxysporum f. sp. niveum race 1 in watermelon

Fusarium wilt, Fusarium oxysporum f. sp. niveum (FON), of watermelon ( Citrullus lanatus ) is a fungal pathogen that causes significant yield losses in the US watermelon industry. FON damages watermelon through invasion of the root system and remains a difficult pathogen to manage due to its long-lasting survival spores which persist in the soil. Chemical control options for this pathogen are lacking, making development of genetic resistance the best option. There are four known races of FON (0, 1, 2, and 3) which are distinguished based on their pathogenicity of differential cultivars. Most modern cultivar releases have FON race 1 (FON-1) resistance, which has been mapped on the end of chromosome 1. Application of marker assisted selection (MAS) would improve the efficiency of FON-1 resistance breeding. In order to identify markers for selection in the FON-1 region, the QTL-seq method was utilized on an F 2 population segregating for FON-1 resistance. Single nucleotide polymorphism (SNP) markers in the region were developed into Kompetitive allele-specific PCR (KASP™) assays and tested for trait association on the segregating F 2:3 population. Marker validation was done using an F 2 population from a cross between FON-1 susceptible “New Hampshire Midget” and FON-1-resistant “Calhoun Gray.” Further validation on a panel of susceptible and resistant cultivars and Plant Introductions identified SNP marker UGA1_502161 as a useful marker for selection of FON-1 resistance from Calhoun Gray.