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

Abstract

Fusarium head blight (FHB) is an economically important plant disease. Some <i>Fusarium</i> species produce mycotoxins that cause food safety concerns for both humans and animals. One especially important mycotoxin-producing fungus causing FHB is <i>Fusarium graminearum</i>. However, <i>Fusarium</i> species form a disease complex where different <i>Fusarium</i> 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 <i>Fusarium</i> community. Molecular quantification assays for detecting individual <i>Fusarium</i> species and subgroups exist, but a method for the detection and quantification of the whole <i>Fusarium</i> group is still lacking. In this study, a new TaqMan-based qPCR method (FusE) targeting the <i>Fusarium</i>-specific elongation factor region (<i>EF1α</i>) was developed for the detection and quantification of <i>Fusarium</i> spp. The FusE method was proven as a sensitive method with a detection limit of 1 pg of <i>Fusarium</i> DNA. <i>Fusarium</i> abundance results from oat samples correlated significantly with deoxynivalenol (DON) toxin content. In addition, the whole <i>Fusarium</i> community in Finnish oat samples was characterized with a new metabarcoding method. A shift from <i>F. culmorum</i> to <i>F. graminearum</i> 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 <i>Fusarium</i> community and mycotoxin risk in cereals. Knowledge gained from the <i>Fusarium</i> community analyses can be applied in developing and selecting effective management strategies for FHB.