DArT and SSR markers are linked with a strong QTL for resistance to fire blight in the apple wild species Malus fusca.

The most important bacterial disease affecting pome fruit is fire blight caused by Erwinia amylovora. Antibiotics treatment is the only reliable control measure for this devastating disease, yet their use is strictly regulated if not completely banned in many European countries due to environmental and sustainable issues. Since resistance can be genetically determined, planting of fire blight-resistant cultivars seems to be a highly probable approach. In this study, we explored a segregating population derived from a cross between the apple wild species Malus fusca and the Malus x domestica cultivar ‘Idared’. The mapping population was artificially inoculated with Erwinia amylovora strain Ea222_JKI at a concentration of 109 cfu/ml in 3 different years. A new library of DArT clones was constructed using the complexity reduction method that identified 1080 DArT markers after images were processed using DArTsoft. SSR markers were sourced from literature and used to genotype the population. The averages of percentage lesion length (PLL) of all replicates of each genotype were used as numerical traits for statistical analysis. A Kruskal-Wallis analysis, used to determine marker-phenotype association revealed one linkage group containing DArT markers significantly linked to fire blight resistance. To determine the corresponding linkage group, the DArT markers were sequenced and sequences aligned to the ‘Golden Delicious’ reference genome. SSR markers were developed from the ‘Golden Delicious’ genome to replace highly significant DArT markers and to determine the QTL region. Interval mapping revealed a strong QTL on LG10 explaining about 65% of the phenotypic variation. Through genome walking approach aimed at determining the resistance region, additional SSR markers have been developed and mapped