The tools of molecular evolutionary biology and genomics are making it possible to use genetic variation in pathogens and hosts to prevent and treat plant pathogenic fungi. There is a wide range of molecular features that can be used as markers at the population level for studying plant pathogenic fungi. The different markers will often reflect different levels of variation within and between plant pathogenic taxa, and may also reflect changes resulting from meiosis and recombination. It is therefore possible to study the spread and dynamics of fungal populations on crop plants, and to determine the role of populations of the same fungus occurring on secondary hosts, in the soil or on debris. Molecular markers can also be used to determine the genetic integrity of host or variety specific groups, and can provide information on differences between pathogenic races. This information is fundamental to understanding the spread of fungal plant diseases, and is important in developing disease control strategies. The choice of marker will depend on the particular fungus under study, and the correct choice of markers may also provide information as to the role of spores or particular mating types in epidemiology. Variation in fungal pathogen genotype is the basis for developing methods to identify these pathogens using PCR. Recently, strains/species specific molecular markers/primers have been developed for several plant pathogenic fungi. There is unfortunately no single marker system that can be guaranteed to provide the desired level of discrimination for all fungi, and some initial screening of different methodologies may be required before a full study can be initiated.

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