Fungi include a vast diversity of microbes that are abundantly present on earth. Phytopathogenic fungi are the disease-causing agents in plants and aggravating the substantial yield losses around the globe. Fungal pathogens are among the microbes which infecting a broad host range of plants. They may be obligate parasites (require a living host for their growth and reproduction) or may be saprophytic (do not have the requirement of a living host for their growth and reproduction). Fungal isolates of different species are differentiated based on their morphology, pathogenesis, host plants, and potential to produce stable vegetative heterokaryons by the fusion of genetically diverse strains of fungi.
Recent advances in molecular biology have made it possible to decipher the whole genome of fungi. However, accurate detection and identification of Phytopathogens are among the most crucial strategies for initiating preventive measures to control plant diseases. Early detection of the pathogens in seeds and propagated materials are of great importance for avoiding the epidemic situation. Hence, the availability of accurate, rapid, and sensitive tools for detecting fungal pathogens is indispensable for disease control. Identification of fungi based on cultural characteristics and morphology is the conventional approach, which relies on comprehensive knowledge of classical taxonomy. This traditional way of fungal identification also has limitations of inaccurate quantification of fungal pathogens, intricacy in the precise identification of some fungal species that are difficult to culture under in vitro condition, and cryptic species.
These restrictions have directed to the development of molecular tools with enhanced accuracy and reliability. Numerous molecular approaches have been in practice for the identification, detection, and quantification of phytofungi. The application of molecular tools facilitates unraveling the taxonomy, genetic variability, and identification of new fungi with more accuracy and sensitivity, leading to controlling plant diseases. Hence, in this manual, the broadly practiced molecular tools for detecting Phytofungi will be explained. For an unequivocal description of these molecular tools, here they are categorized into two schemes. Scheme 1 will deal with the PCR based molecular tools; however, scheme 2 will deal with the nucleic acid probes and arrays based molecular tools to detect Phytofungi.