Genetic diversity is an important component to ongoing plant breeding. Understanding where it exists and what it comes from can influence the ability to search and detect valuable agronomic traits in the future. In this thesis I explore three avenues surrounding this topic. In the first chapter I explore the current literature and knowledge of structural variation, such as deletions and duplications, documented in the soybean germplasm. In the next chapter I describe detecting these unique genetic variants in a subset of 41 soybean breeding lines and interesting patterns shaping their frequencies. In the third chapter I explore the frequency at which these genetic variants are induced in fast neutron mutagenesis or plant genetic transformation and tissue culture. Finally, in my last chapter I explore the USDA germplasm diversity to analyze patterns of local adaptation and environmental association in Glycine soja, soybean’s crop wild relative.