Development of two loop-mediated isothermal amplification (LAMP) Genomics-informed diagnostic protocol for rapid detection of Pantoea species from rice

ABSTRACT Pantoea spp was recently reported as also responsible for rice bacterial blight disease and grain discoloration in Sub-Saharan Africa. Thus, measures need to be taken to limit the pathogen's dispersion and robust diagnostic tools are also required for rapid and cheap diagnosis in the field as well as for routine seed certification or control. Therefore, several diagnostic tools such as simplex and multiplex PCR schemes and a semi-selective medium have been developed and are being used. However, the use of these tools is time-consuming, expensive and therefore limited to laboratories that can afford the chemicals. We have therefore developed two isothermal loop amplification (LAMP) protocols, one of which detects all Pantoea in the genus and the other one which is specific to P. ananatis. • The novel LAMP assays allow rapid and sensitive detection of these bacteria. • They will be help plant protection services in routine field and laboratory tests especially for monitoring the phytosanitary status of rice seeds.