Mapping and Identification of Disease Resistance Candidate Genes in Three Malus Populations Using SSRs, DArTs and Infinium SNP Markers and Illumina Sequencing Technology

Apple scab and powdery mildew are a major concern in apple production. Control of these diseases by the development of varieties with durable disease resistance is an efficient and environmentally friendly solution. Therefore, the identification and mapping of resistance genes is of paramount importance for gene pyramiding. In this study, mapping of Quantitative Trait Loci (QTLs) for apple scab and powdery mildew was performed on progeny of three mapping populations. Putative QTLs were detected for the study populations: 10 for ‘Mildew Resistant’ x ‘Golden Delicious’, 8 Malus platycarpa x ‘Mildew Resistant’ and 7 for ‘Russian Seedling’ x ‘Golden Delicious’ “divefor the two diseases. Two QTLs for apple scab detected on LG 02 of the ‘Russian Seedling’ x ‘Golden Delicious’ cross, coincided with loci previously identified as encoding apple scab resistance genes Vh2 and Vh4 on ‘Russian apple’. Re-sequencing of ‘Russian Seedling’ led to candidate gene identification in the Vh2 and Vh4 regions. The Vh2 region had eight disease resistance related sequences and three putative CC-NBS-LRR resistance protein domains, whereas Vh4 region revealed seven disease resistance related genes and two HcrVf2-like gene sequences. Species phylogenetic analysis was performed on data from the Infinium 8K SNPs and aligned mitochondrial genomes indicated ‘Russian Seedling’ and M. sieversii as being closely related and were genetically divergent from the commercial cultivars. Identification of these markers, which are closely associated with apple scab and powdery mildew resistance, will add in the implementation of MAB in the apple-breeding program in South Africa.