As the world population increases, there is a need to produce more food in limited land space. There is a strong need to optimize food production while reducing space, cost and food waste. This can be achieved with high density plantings, automated harvesting and food with longer shelf life. Apples are one of the most widely grown foods in the world and contain necessary nutrients. Apple trees have distinct, naturally occurring growth habits that include standard, weeping and columnar. Understanding the genetic mechanisms behind these growth habits can lead to more trees planted per acre and mechanized harvesting. In this dissertation, weeping (W) was mapped to chromosome 13 and MdLazy1 was identified as a strong candidate gene underlying the weeping growth habit. Genetic mapping within a segregating columnar population revealed two recessive repressors regions of the columnar growth habit. Apple fruit are stored in cold storage after harvest allowing them to be available year round for consumption. A major problem with fruit storage is the softening of fruit over time and a decrease in quality. In this dissertation, alleles of two ethylene synthesis genes MdACS1 and MdACS3a were identified in 952 cultivars. Post-harvest storage studied on 131 cultivars combined with allelic genotypes revealed beneficial allelic combinations of the two genes that reduced fruit soften. Research conducted and summarized in this dissertation addresses apple tree architecture and fruit quality. The genetic regions identified, makers analyzed, markers created and genes characterized increase understanding of genetic mechanisms underlying weeping and columnar growth habit and fruit softening. This research helps address solutions to optimize food production, while also providing fruit breeder’s information that can be utilized when creating new superior apple cultivars.