Mycotoxin contamination in food is a serious concern for human and animal health. Today, we do not know how to detoxify food materials that are contaminated with mycotoxins in ways that retain their edibility. Therefore, avoiding mycotoxins from entering the food chain is an important approach. This needs early and easy identification, detection, and quantification of mycotoxinproducing fungi. The conventional methods for the identification, taxonomy, detection, and quantification of toxigenic fungi are challenging because they require a high level of expertise and a set of sophisticated equipment. 

The aim of current study was to use molecular-based approaches (as they are practical, rapid, and more reliable) to identify, classify, detect, and quantify mycotoxin-producing fungi including aflatoxin-producing Aspergillus and fumonisin- and trichothecene (TC)-producing Fusarium species. The results obtained from this study suggested that there are 2 main populations of F. graminearum in Europe. The population of the 3-acetyl-deoxynivalenol (3ADON) chemotype is dominant in northern Europe and it has probably recently been spreading from Finland to north-western Russia, while the population of the 15ADON chemotype is dominant in the central and southern Europe and it has been spreading to the Denmark and Norway. 

The results also suggested that the homogenization of the oat flour by milling with a 1 mm sieve is important for the reproducibility of deoxynivalenol (DON) and F. graminearum DNA levels, which is evident from a higher correlation between the DON and F. graminearum DNA levels in oat grain samples that were sieved after milling. In the thesis, the F. langsethiae isolate obtained from Iranian wheat was reidentified as F. sibiricum, and the identification was confirmed by IGS sequencing. This work reports the first record of F. sibiricum from Iran, outside northern Asia and Norway, and the first isolation of F. langsethiae (a European pathogen) from western Siberia. 

Large variations in the DON content and the amounts of F. graminearum DNA, and poor coefficient of determination (R2 ) between these were detected in oat grain when the RIDA®QUICK SCAN kit was used for DON content estimation. This study confirmed that the coefficient of determination was usually less when DNA or DON levels were estimated from oat flour that was not ground with 0.8 mm or 1 mm sieves. DON levels obtained with the Rida®Quick method were usually higher than those obtained with accredited GC-MS method in the Finnish oat, barley, and wheat samples. The homogenization of the oat flour by sieving is therefore likely to be connected to the variations in the DON detection. Also, it was suggested that the amounts of DON close to the legislative limits should be reconfirmed with accredited quantitative analyses. 

In addition, isolation, identification, detection, and quantification of Fusarium and Aspergillus isolates from Egypt and the Philippines maize, wheat, and soil samples were implemented in this thesis. A. parasiticus isolates, which produced higher amounts of aflatoxins, were only found in the Philippines.