Plant diseases remain a major obstruction to meeting the world’s increased demand for soybean oil and protein. Reducing the losses caused by diseases in order to improve crop production is a high priority for agricultural research. The need for novel strategies for plant disease control cannot be overstated. In the present study, selected defense-related genes were silenced and/or overexpressed in soybean using a virus-based vector and the resultant plants were tested for their responses to pathogens. The first part of the study focused on Rps1k (Resistance to Phytophthora sojae) gene. The two conserved domains encoding ‘P-Loop NTPase’ and ‘PLN03210’ of Rps1k were independently overexpressed. Stem inoculation assays for the overexpressing plants showed significant resistance to virulent races; 90% standing plants compared to 10% in controls. Lesion length was greatly restricted only in case of plants overexpressing ‘PLN03210’. Simultaneous silencing of Rps1k-1 and Rps1k-2 resulted in remarkable susceptibility to avirulent races when tested by a detached-leaf assay. The second part of the study entailed silencing/overexpression of the chlorophyllase genes GmCLH1 and GmCLH2 and testing the responses of the silenced/overexpressing plants to the sudden death pathogen Fusarium virguliforme. Four weeks post root inoculation, GmCLH2-silenced plants showed enhanced resistance while the GmCLH2-overexpressing plants exhibited markedly increased susceptibility when compared to empty vector control. RT-PCR assay of PR genes revealed elevated expression of PR2 and PR4 in GmCLH2-silenced plants. In the third part of the study, soybean plants silenced for a leucine-rich repeat receptor-like kinase (GmRLK3) gene were examined for their responses to different pathogens. Silencing of GmRLK3 enhanced susceptibility to infection with Alternaria tenuissima or Sclerotinia sclerotiorum as revealed by rapid disease progress on treated leaves. Surprisingly, silencing of GmRLK3 in known susceptible soybean cultivars rendered the silenced plants resistant to P. sojae. The ensuing partial resistance to P. sojae was consistent with results of RT-PCR assays that showed a significant increase in the transcript level of the osmotin-encoding gene (PR5a) in the GmRLK3-silenced plants. PR5a is considered a marker for systemic acquired resistance.