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Tilletia controversa  causing dwarf bunt of wheat is a quarantine pathogen in several countries. Therefore, its specific detection is of great phytosanitary importance. Genomic regions routinely used for phylogenetic inferences lack suitable polymorphisms for the development of species-specific markers. We therefore compared 21 genomes of six  Tilletia  species to identify DNA regions that were unique and conserved in all  T. controversa  isolates and had no or limited homology to other  Tilletia  species. A loop-mediated isothermal amplification (LAMP) assay for  T. controversa  was developed based on one of these DNA regions. The specificity of the assay was verified using 223 fungal samples comprising 43 fungal species including 11  Tilletia  species, in particular 39 specimens of  T. controversa,  92 of  T. caries  and 40 of  T. laevis , respectively. The assay specifically amplified genomic DNA of  T. controversa  from pure cultures and teliospores. Only  Tilletia trabutii  generated false positive signals. The detection limit of the LAMP assay was 5 pg of genomic DNA per reaction. A test performance study that included five laboratories in Germany resulted in 100% sensitivity and 97.7% specificity of the assay. Genomic regions, specific to common bunt ( Tilletia caries  and  Tilletia laevis  together) are also provided.

Development of a loop-mediated isothermal amplification assay for the detection of Tilletia controversa based on genome comparison