Introgression of genes from the 25 to 33 species of apple provides the opportunity for unique traits in genetic improvement, such as disease resistance, increased antioxidants, unique phenolic compounds, and interesting flavor profiles and tannins. However, the use of wild species has been relatively limited, so the understanding of the inheritance and control of these traits are also limited. Introgression of wild species also offers the opportunity to understand the control of traits that are mostly fixed in the domesticated gene pool, because of domestication or later intentional breeding. However, the primary challenge with introgression is that fruit of wild species are often much smaller, with inferior fruit quality, potentially requiring generations of modified backcrossing for quality. New cultivars must be an improvement over what is currently on the market. This includes disease resistance, distinctive qualities, new flavor profiles, enhanced nutrition, long storage, or superior processing ability. In this project polygenic controls of economically important traits such as fruit acidity, fruit size and shape, phenolic concentrations as well physiological controls of fruit storage were found from an interspecific population with M. prunifolia (PI 589816) as a parent. Evidence was found for a more complicated control of acidity in apple than currently described including transcription factors identified on chromosome 8 in previously identified regions. Genetic controls of fruit quality traits such as fruit size and phenolic concentration were identified and confirmed from previous studies. Genetic associations for fruit storage time and the associated pathways of senescence and ethylene biosynthesis in a unique background were found. Together this research discusses the potential usefulness of M. prunifolia (PI 589816) as a breeding parent, as well as importantly adding context to the traits that have been selected upon during domestication, and considerations for apple breeders when pursuing interspecific solutions in apple breeding.