Genomics-Informed Multiplex PCR Scheme for Rapid Identification of Rice-Associated Bacteria of the Genus .

The genus forms a complex of more than 25 species, among which several cause diseases of various crop plants, including rice. Notably, strains of and have been repeatedly reported to cause bacterial leaf blight of rice, whereas other authors have observed that can also cause bacterial leaf blight of rice. The contribution of these and perhaps other species of to plant diseases and yield losses of crop plants is currently not well documented, partly due to the lack of efficient diagnostic tools. Using 32 whole-genome sequences of the three major plant-pathogenic spp., a set of PCR primers that detect each of the three species , , and was designed. A multiplex PCR scheme which can distinguish these three species and also detects members of other spp. was further developed. Upon validation on a set of reference strains, 607 suspected strains that were isolated from rice leaves or seed originating from 11 African countries were screened. In total, 41 strains from 8 countries, 79 strains from 9 countries, 269 strains from 9 countries, and 218 unresolved strains from 10 countries were identified. The PCR protocol allowed detection of bacteria grown in vitro, in planta, and in rice seed. The detection threshold was estimated as total genomic DNA at 0.5 ng/µl and heated cells at 1 × 10 CFU/ml. This new molecular diagnostic tool will help to accurately diagnose major plant-pathogenic species of . Due to its robustness, specificity, sensitivity, and cost efficiency, it will be very useful for plant protection services and for the epidemiological surveillance of these important crop-threatening bacteria.