Sclerotinia stem rot (SSR), caused by Sclerotinia sclerotiorum, ranks among the most damaging diseases in U.S. soybean production, responsible for losses exceeding 200 million bushels between 2015 and 2019. In Minnesota alone, losses were valued at more than $330 million. The pathogen has a broad host range and produces long lived sclerotia making managing the disease particularly challenging. Fungicides can provide control, but their effectiveness is limited by timing, cost, and environmental conditions. While partial genetic resistance has been identified, the role of soybean shoot architecture, upright versus bushy growth habits, in shaping the microclimate and influencing SSR development remains poorly understood. Shoot architecture is a key determinant of the canopy microclimate, which in turn is critical for pathogen establishment and disease progression. Thus, studying architectural effects on SSR could provide new opportunities in developing effective management and breeding strategies.

To investigate the role of architecture in SSR development, we are comparing the commercial soybean varieties broadly categorized as “upright” or “bushy.” Field trials were established in randomized complete block designs with replicated plots. Architectural traits such as canopy coverage, branch angle, petiole slope and leaf shape were quantified using imaging and high throughput drone based methods. Sclerotia were introduced into the field, and an irrigation system was employed to promote disease. SSR severity was scored on a standardized 0–3 scale, while sclerotia depots were deployed to monitor germination and apothecia production under different canopy types. Additional trials were also employed to compare fungicide efficacy across architectures. Finally, a legacy panel of soybean lines (1940s–2000s) was screened to assess whether changes in shoot architecture associated with soybean breeding have also been accompanied by changes in SSR resistance.