Identification of Candidate Genes at Rvi19 and Rvi20, Two Apple Scab Resistance Loci in the ‘Honeycrisp’ Apple (Malus x domestica)

Two apple scab resistance gene loci have been identified in the apple (Malus x domestica) cultivar Honeycrisp.  Apple scab, caused by Venturia inaequalis, is the most economically important disease affecting apple.  Novel resistance loci were mapped in seedling families when inoculated with single spore isolates in the greenhouse.  These resistance gene loci, Rvi19 and Rvi20, map to linkage groups 1 and 15 respectively.  Haplotypes defined by SSR markers and SNPs that flank the loci have been developed to provide breeders with reliable tools for marker assisted selection.  The Rvi19 haplotype spans 2.3 Mb which is ~12.6 cM in a ‘Honeycrisp’ x ‘Twin Bee Gala’ linkage map (n=125) utilized in mapping the resistance loci. This haplotype includes the well characterized Rvi6 locus (Vf).  The gbrowser available at the Genome Database for Rosaceae (GDR; www.rosaceae.org) was used for comparative mapping of the physical and genetic positions of these loci as well as for identifying candidate genes.  The Rvi19 haplotype consists of 263 consensus genes, 14 of which contain a leucine rich repeat region (LRR), a motif common in R genes. The Rvi20 haplotype spans 3.2 Mb which is ~10.1 cM.  In the Rvi20 haplotype, 460 consensus genes were identified with 14 containing the signature LRR, making these genes prime candidates for the R gene at this locus.  The gene ontologies of the consensus genes for each haplotype were evaluated to characterize these regions.