Assessment of Verticillium flax inoculum in agroecosystem soils using real-time PCR assay

Verticillium wilt, due to the soilborne fungus Verticillium dahliae, is a persistent disease affecting flax culture in Upper Normandy. This pathology has increased since the last decade, leading to yield losses for flax producers. In part due to the long survival of V. dahliae in soil and the difficulty of early diagnosis in affected plant, Verticillium flax wilt management remains problematic in the absence of efficient phytosanitary treatment. Pathogen avoidance and the reduction of soil inoculum through adapted cultural practices are the best alternatives to fight against Verticillium wilt. Therefore, the objective was here to optimize and validate a rapid and specific real-time PCR assay targeting the ribosomal DNA Internal Transcribed Spacers (ITS) to measure V. dahliae density in soil. This method was then used to assess and compare the pathogen density in fields from four diverse management systems: conventional, integrated with or without tillage, and organic. First, the real-time PCR assay provided sensitive and reliable quantification of V. dahliae in a range of artificially inoculated soils with known inoculum density. Then, this method was successfully applied in crop fields. Measured V. dahliae densities presented an intra-parcel heterogeneity, emphasizing the importance of an adapted sampling strategy to assess pathogen load in crop field. Furthermore, these densities appeared to be impacted by agricultural practices, particularly tillage. The influence of the previous crop on pathogen load had also to be considered with attention to manage efficiently this disease through crop rotation. Such knowledge of pathogen density in soils could provide critical information for stakeholders to identify infested fields and predict disease development. Molecular approach should be considered as a useful tool for Verticillium wilt management in flax culture.