The diversity and prevalence of Fusarium species and their chemotypes on wheat in the North-West and North of Iran was determined. Wheat in these areas is severely affected by Fusarium head blight, with Fusarium graminearum as prevalent species causing 96% of the infections in the North-West and 50% in the Northern provinces. Fungal isolates were identified based on morphological characters and sequences of the internal transcribed spacer region, and parts of translation elongation factor 1-? and RNA polymerase subunit II sequences. Phylogenetic and phylogeographic analyses show little haplotype variation between the F. graminearum strains collected from the different locations, but the isolates differ significantly in their trichothecene chemotypes as determined with a multilocus genotyping assay. F. graminearum strains producing 15-acetyldeoxynivalenol were abundant in Ardabil (North-West of Iran), while in Golestan province (North of Iran) at the other side of the Caspian Sea especially nivalenol producing strains and a variety of other Fusarium species were observed. Strains producing 3-acetyldeoxynivalenol were rarely found in both areas. This is the first detailed study on Fusarium infections in Iranian wheat, showing large differences in prevalent etiological agents and in mycotoxin chemotypes geographically.

Biosynthesis of trichothecenes requires the involvement of at least 15 genes, most of which have been targeted for PCR. Qualitative PCRs are used to assign chemotypes to individual isolates, e.g., the capacity to produce type A and/or type B trichothecenes. Many regions in the core cluster (consisting of 12 genes) including intergenic regions have been used as targets for PCR, but the most robust assays are targeted to the tri3 and tri12 genes. Quantitative PCRs, that work across trichothecene-producing members of the Fusarium head blight complex, are described along with procedures to quantify the amount of fungal biomass in wheat samples. These assays are directed to the chemotype(s) present in field samples and quantify the total fungal biomass of trichothecene-producing fungi, irrespective of their genetic identity.