For the development of species specific markers you have to go through transcroptome sequencing of your research sample so that various SSR markers can be developed by marker development tools . These markers when applied will yield co-dominant type of expression.
To develop SSR marker is difficult way and their is a simple one. The simple one you need to search about your fungal pathogens (genetic diversity using SSR markers or genetic map). I tink you will find several groups work on these area