Taqman qPCR Quantification and Community Analysis to Evaluate Toxigenic Fungi in Cereals.

Fusarium head blight (FHB) is an economically important plant disease. Some species produce mycotoxins that cause food safety concerns for both humans and animals. One especially important mycotoxin-producing fungus causing FHB is . However, species form a disease complex where different species co-occur in the infected cereals. Effective management strategies for FHB are needed. Development of the management tools requires information about the diversity and abundance of the whole community. Molecular quantification assays for detecting individual species and subgroups exist, but a method for the detection and quantification of the whole group is still lacking. In this study, a new TaqMan-based qPCR method (FusE) targeting the -specific elongation factor region () was developed for the detection and quantification of spp. The FusE method was proven as a sensitive method with a detection limit of 1 pg of DNA. abundance results from oat samples correlated significantly with deoxynivalenol (DON) toxin content. In addition, the whole community in Finnish oat samples was characterized with a new metabarcoding method. A shift from to in FHB-infected oats has been detected in Europe, and the results of this study confirm that. These new molecular methods can be applied in the assessment of the community and mycotoxin risk in cereals. Knowledge gained from the community analyses can be applied in developing and selecting effective management strategies for FHB.