Mapping and identification of disease resistance candidate genes in three Malus populations

Apple scab and powdery mildew are a major concern for apple breeders and producers. Control of these apple diseases by the development of varieties with durable disease resistance is the most efficient and environmentally friendly way. Therefore, the gene-pyramiding route for the development of apple varieties with durable disease resistances requires a supply of a diverse resistance gene pool. The identification and mapping of these genes is therefore of paramount importance. In this study genetic mapping of Quantitative Trait Loci (QTLs) for apple scab and powdery mildew was performed on progeny of three mapping populations (‘Mildew Resistant’ x ‘Golden Delicious’, ‘Russian Seedling’ x ‘Golden Delicious’ and Malus platycarpa x ‘Mildew Resistant’). Three marker systems were used and these were Simple Sequence Repeats (SSRs), Diversity Arrays Technology (DArTs) and Single Nucleotide Polymorphisms (SNPs) markers. A total of 17 putative QTLs were detected for the ‘Mildew Resistant’ x ‘Golden Delicious’ population, 10 for the Malus platycarpa x ‘Mildew Resistant’ population and nine for the ‘Russian Seedling’ x ‘Golden Delicious’ populations for the three diseases. Two putative QTLs for apple scab detected on LG 02 of the ‘Russian Seedling’ x ‘Golden Delicious’ coincided with loci previously identified as encoding two apple scab resistance genes Vh2 and Vh4 on ‘Russian apple’. SNP markers R_8936738_Lg2 and R_32981524_Lg2 were strongly linked to the Vh4 and Vh2 QTL regions respectively. The analysis of chromosome two led to the identification of two candidate genes for the Vh4 locus and a cluster of ABC (PDR) for Vh2.