Development of Subgenome-Specific Markers for <i>FaRXf1</i> Conferring Resistance to Bacterial Angular Leaf Spot in Allo-Octoploid Strawberry

Bacterial angular leaf spot (ALS) caused by <i>Xanthomonas fragariae</i> has become increasingly problematic to strawberry producers and nurseries. The use of genetic resistance is the most effective way to manage ALS. In our previous study, the major locus, <i>FaRXf1</i>, was identified for resistance to ALS in the linkage group 6D (LG6D). In this study, we developed subgenome-specific markers tightly associated with <i>FaRXf1</i> and tested for their accuracy for high-throughput marker-assisted selection (HTP-MAS). Using the recently published octoploid reference genome sequence, we identified the location of <i>FaRXf1</i> on chromosome Fvb6–2. The sequences of IStraw90 Axiom® SNP markers for <i>FaRXf1</i> were used to design subgenome-specific high-resolution melting (HRM) markers. Two newly developed subgenome-specific HRM markers (Xf1HRM-8263 and Xf1HRM-8073) were consistent in their ability to correctly determine resistance and susceptibility of a total of 56 tested accessions. To validate the effectiveness of markers in HTP-MAS, we tested both CTAB purified DNA and NaOH crude extracts. The newly developed subgenome-specific marker Xf1HRM-8073 can be effectively used for the breeding of ALS resistance in cultivated strawberry.