Development of A Novel Multiplex TaqMan Probe qPCR Assay Distinguishing Dikaryotic ITS rDNA Types of Sclerotium rolfsii (=Agroathelia rolfsii) and S. delphinii

Sclerotium rolfsii (=Agroathelia rolfsii) and S. delphinii are globally ubiquitous and prevalent soil-borne pathogens. These species are distinguishable by the morphology of their sclerotia formed on artificial media. However, this distinction requires prior pure isolation, complicating direct identification from diseased plants or soil samples. Additionally, each species contains two distinct ITS ribosomal DNA types in a dikaryotic cell, further complicating their identification through sequence analysis. To address this issue, we developed a novel multiplex qPCR method utilizing TaqMan probes and primers. This method specifically targets the two ITS types unique to each species, effectively distinguishing between these pathogens and differentiating them from non-target soil-borne fungal and oomycete pathogens. Its efficiency and sensitivity were confirmed through their detections in artificially inoculated plants and soil samples. Our multiplex qPCR technique offers a precise and reliable approach for the simultaneous detection and differentiation of S. rolfsii and S. delphinii, significantly improving disease surveillance and facilitating timely, effective disease management.