Use of Quantitative PCR Detection Methods to Study Biocontrol Agents and Phytopathogenic Fungi and Oomycetes in Environmental Samples

Quantitative polymerase chain reaction (qPCR) is a versatile technique forthe accurate, sensitive, reliable and high-throughput detection and quantificationof target DNA in various environmental samples, and in recentyears, it has greatly contributed to the advancement of knowledge in theplant pathology field. Indeed, this technique is ideal to evaluate inoculumthreshold levels and to study the epidemiology, biology and ecology ofphytopathogenic fungi and oomycetes, thus opening up new researchopportunities to investigate host–pathogen interactions and to addresstasks related to quarantine, eradication and biosecurity. Moreover, it canbe a useful tool in breeding programs. The present review analyses themost relevant applications of qPCR for the detection and quantification offilamentous fungi and oomycetes within host tissues and in soil, air andwater, along with brief paragraphs focusing on new application fields suchas the detection and quantification of mycotoxigenic fungi and biocontrolagents. The high potentiality of qPCR for present and future applicationsis highlighted together with a critical analysis of major drawbacks thatneed to be corrected to definitively confirm it as a preferential routinequantitative detection method.