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Apple scab, caused by the ascomycete Venturia inaequalis (Cke.) Wint., is the most important fungal disease in many growing areas of Malus × domestica Borkh. Strong monogenic resistances originating from wild Malus species build an important basis for resistance breeding. Most of these scab resistances have been mapped, and associated molecular markers are available. Within the VINQUEST network (www.vinquest.ch), differential hosts carrying single resistance genes (R-genes) are monitored for resistance breakdown around the world. To date, most commercially available scab resistant cultivars carry the R-gene Rvi6 (Vf) originating from Malus floribunda 821. However, the pathogen has overcome Rvi6 in many areas of Europe and the USA. Therefore, new cultivars with durable resistance are urgently needed. Breeding for durable disease resistance against apple scab has been a major goal in the Agroscope apple breeding program for almost 40 years. For effective resistance breeding, methods of stacking multiple R-genes against apple scab were implemented, such as screening with artificial scab inoculation and accelerated introgression cycles, complemented by the use of marker-assisted selection (MAS). MAS proved to be a useful and very efficient tool to select genotypes with stacked R-genes against apple scab. Recently, MAS in apple has progressed from using sequence-characterized amplified regions (SCAR) and simple-sequence repeat (SSR) markers to more cost-effective single nucleotide polymorphism (SNP) markers. As part of the European FP7 Fruitbreedomics project, SNP markers for several scab resistances (Rvi2, Rvi4, Rvi5, Rvi6, Rvi11, Rvi12, Rvi15) were identified, and an outsourced genotyping pipeline was established. Since then, the marker set has been fine-tuned and extended to resistances against other diseases (e.g., fire blight, powdery mildew) and fruit quality traits. The ongoing implementation of the combination of MAS for R-genes against various diseases with genomic selection for quantitative traits related to fruit quality, yield, and growth characteristics is a promising approach for breeding.