Diagnosis and Assessment of Some Fungal Pathogens of Rice: Novel Methods Bring New Opportunities

Global food security depends to a substantial degree on the rice crop. Rice production is threatened by many pathogens, requiring a range of prevention and control strategies. These need to be integrated with efficient monitoring and detection. This chapter focuses on diagnostic tools developed for three of the most important rice pathogens: Pyricularia oryzae, the agent of rice blast; Bipolaris oryzae, the agent of rice brown spot; and Fusarium fujikuroi, the agent of bakanae disease. Accurate, effective, sensitive and specific diagnostic techniques are required to forecast and manage these diseases. Observation of symptoms in field crops is not always accurate. Serological and, especially, molecular techniques present advantages in terms of speed, specificity and ease of use. Whole-genome sequencing has revealed novel genomic regions and genes and can be used to distinguish between clonal lineages of pathogens. High-throughput sequencing applied to the aerial mycobiome of rice crops has revealed substantial biodiversity that can affect the airborne inoculum and may play a key role in survival and dispersal of fungal spores. The LAMP (Loop-mediated isothermal AMPlification) assay has been identified as a suitable solution for on-site detection. The application of LAMP combined with alkaline DNA extraction has an enormous potential to assess airborne and other inoculum. The use of molecular field testing is revolutionising disease diagnostics, giving results in a few hours. There are exciting prospects of further advances through machine learning. Improved detection should lead to better disease control and hence improved food security. However, pathogens are genetically dynamic so plant disease management will remain challenging.