Apple breeding programs are aimed at improving the agronomic and consumer traits of apples. While DNA-informed breeding doesn’t reduce the time between generations, it can enable the early elimination of undesirable seedlings, thus saving resources for the program. Combined with horticultural and biotechnological approaches to reduce generation times, DNA-informed breeding can enable the development of superior cultivars in an economically efficient way. In this chapter, we provide a brief overview of the development of genome sequencing technology, review the process of sequencing the apple genome and then consider how this information can be employed, both to develop new and better varieties of apple, and in the shorter term to improve current horticultural practices.