Information from some recently published studies using molecular methods to identify plant pathogenic fungi from culture is summarized in Table 1. Many of these studies were designed to develop methods to distinguish between closely related taxa within a single genus or species for which morphological or physiological characters overlap or take too long to develop.
There are several advantages in isolating the fungus of interest in culture before conducting molecular identifications. First, one knows immediately whether or not the pathogen is viable in the plant. Second, working with pure cultures lessens the possibility of errors such as accidentally creating a PCR product from the wrong fungus. There are also disadvantages to this approach. First, it takes longer time because the pathogen must be isolated before it is analyzed. Second, some true (obligate) pathogens cannot be cultured in the laboratory. Finally, metabolites such as mycotoxins may remain in the crop even after the fungus dies and these may be missed if no viable fungus is present.
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