The majority of the cultivated apple varieties are susceptible to the most common diseases, such as apple scab (Venturia inaequalis), powdery mildew (Podosphaera leucotricha), fire blight (Erwinia amylovora). As a result, modern dessert apple production in high-density, low-stem orchards requires a high number of applications of plant protection products throughout the season. Since the early 1990s, the apple breeding program at groscope in Switzerland has a strong focus on disease resistance breeding. Over the years, marker-assisted selection (MAS) has been successfully used to stack and combine resistance (R-) genes and QTLs for apple scab, powdery mildew, rosy apple aphid and fire blight.