Verification of the effectiveness of SCAR (sequence characterized amplified region) primers for the identification of Polish strains of Fusarium culmorum and their potential ability to produce B-trichothecenes and zearalenone

Rapid and sensitive methods to detect Fusarium culmorum and trichothecene and zearalenone producing strains in food and feed are valuable in predicting potential contamination. In this study the effectiveness of primers, recommended in the literature, for species identification of F. culmorum and basic genes encoding for mycotoxin production was tested. A total of 68 isolates of F. culmorum were collected from cereals and potato between 2005 and 2008 from different Polish provinces. It was shown that from among the four primer pairs enabling the identification of F. culmorum, and therefore also to establish its presence in the material, only primers Fc01F/Fc01R seem to be fully effective in the case of Polish strains. Determination of material contamination by F. culmorum, however, is only a first step in determining food safety. It is also extremely important to identify genes encoding the potential ability to produce mycotoxins. It was shown that three pairs of primers (tox5-1/tox5-2, HATriF/HATriR and Tri5F/Tri5R) enable a fully effective identification of the presence of the Tri5 gene responsible for producing trichothecenes. Determination of the DON-chemotype, and thus identification of the strains of F. culmorum potentially producing deoxynivalenol, is enabled equally by MinusTri7F/MinusTri7F, Tri7F/Tri7DON and Tri13F/Tri13DONR. However, a determination of the NIV-chemotype, and thus identification of the strains potentially producing nivalenol, is enabled by Tri7F/Tri7R, Tri7F/Tri7NIV and Tri13NIVF/Tri13R. The potential ability of isolates to produce ZEA can be determined to the same degree in assay with PKS4-PS.1/PKS4-PS.2 and F1/R1.

Research highlights
► Primers Fc01F/Fc01R are fully effective in species-specific determination of F. culmorum;
► tox5-1/tox5-2, HATriF/HATriR and Tri5F/Tri5R enable identification of the Tri5 gene;
► DON-chemotype identification is enabled by MinusTri7F/MinusTri7F, Tri7F/Tri7DON and Tri13F/Tri13DONR, Tri303F/Tri303R;
► NIV-chemotype determination is enabled by Tri7F/Tri7R, Tri7F/Tri7NIV and Tri13NIVF/Tri13R;
► the ability to produce ZEA can be determined with PKS4-PS.1/PKS4-PS.2 and F1/R1.