Molecular Identification, Pathogenicity, and Fungicide Sensitivity of Sclerotinia spp. Isolates Associated with Sclerotinia Stem Rot in Rapeseed in Germany

(1) Background: Sclerotinia sclerotiorum is the main causal agent of Sclerotinia stem rot in rapeseed, while the related species S. subarctica has also been reported. However, its prevalence and impact in Germany remain unclear. Understanding the pathogenicity and fungicide sensitivity of Sclerotinia spp. is important for effective and sustainable disease management. (2) Methods: Isolates were collected from symptomatic rapeseed plants across Germany. Molecular identification was performed via ITS rRNA sequencing. Pathogenicity was assessed by stem inoculation of five rapeseed cultivars at the flowering stage. Fungicide sensitivity was tested in vitro against seven active substances, including azoles, boscalid, azoxystrobin, and fludioxonil. (3) Results: All isolates were identified as S. sclerotiorum; S. subarctica was not detected. Of the tested isolates, 23 showed low aggressiveness (relative lesion length < 15% of total plant length), 29 were moderately aggressive (15–20%), and 10 were highly aggressive (>20%). Azole fungicides were highly effective (EC50 < 1.6 μg a.s. mL−1), while reduced sensitivity was observed for boscalid, azoxystrobin, and fludioxonil (EC50 > 4.0). (4) Conclusions: This study provides insight into the molecular identity, pathogenicity, and fungicide sensitivity of Sclerotinia isolates. The observed variability in aggressiveness and mycelial growth to fungicide emphasize the need for integrated management strategies to ensure Sclerotinia stem rot control.