There is a considerable demand for crop improvement, especially considering the growing population, continuing climatic fluctuations, and rapidly evolving plant pests and pathogens. Crop wild relatives hold great potential in providing beneficial alleles for crop improvement. Wild soybean, Glycine soja (Siebold & Zucc.), the wild ancestor to the domesticated soybean (Glycine max (L.) Merr.), harbors a high level of genetic variation. Research on G. soja has been largely devoted to understanding the domestication history of the soybean, while little effort has been made to explore its genetic diversity for crop improvement. In this dissertation, genomic dissection of agronomically important complex trait variation in G. soja was carried out in order to determine the potentially novel genetic architecture of traits of interest, and to better understand the use of crop wild relatives for crop improvement. The genetic background of quantitative traits: early vigor, Soybean Cyst Nematode (SCN) resistance and the effects of abiotic and biotic combination stresses (drought and SCN) on gene regulation was investigated. These findings have the potential to enhance the cultivated soybean with cutting edge biotechnologies (genetic modification, gene editing) and promote the exploration and use of wild resources for crop improvement in order to meet future food requirements.