Breeding new apple varieties is a costly and time-consuming endeavour, often selecting for consumer-preference traits at the expense of other traits of agronomic importance. However, combining both sustainable cultivation with market acceptability is a goal that if achieved would benefit growers, consumers and the environment. This chapter summarises the current status of apple breeding and genomics research, taking a forward look at the key factors that may improve the selection efficiency within apple breeding programmes to simultaneously enhance both resource-use efficiency traits and resilience to biotic and abiotic stress. The chapter discusses how coupling enhanced automated phenotyping, rapid cycling through generations, genome-assisted selection and genome editing using CRISPR-Cas9 would improve breeding programme productivity. Also covered are advances in genetic characterisation of key rootstock traits, for example, selection of traits which lead to reduction in inorganic nitrogen application, may result in more sustainable cultivation.