Exploiting Bacterial Genomics to Understand Host Specificity and Developing Tools for Effective Pathogen Monitoring in Rice Ecosystems

The emergence of highly aggressive clones of plant pathogens in agricultural ecosystems represents an important threat to food security. Bacterial leaf blight, caused by Xanthomonas oryzae pv. oryzae (Xoo), is the most important bacterial disease of rice. To establish a successful interaction with rice, Xoo relies on a highly conserved type III secretion system (T3SS). The bacteria use this “needle-like” structure to efficiently deliver type III effector (T3E) proteins inside host cell. Once translocated, effector proteins modulate immune responses or facilitate nutritional or virulence processes to benefit the pathogen. Increasing evidence suggest that T3E can activate defense response and play a major role in determining phenotypic linkage to host cultivar specificity. At population level, Knowledge on the distribution of phenotypic groups (races) may be critical to predict disease outcomes under particular scenario. For that reason, gaining insights into the variability of T3E repertoires and linked regions in Xoo communities and understanding host specificity factors will open the door for better and more efficient ways to deploy resistance genes in rice agro-ecosystems. Our group is using complementary approaches to analyze a large collection of Xoo representing different phenotypic groups.  Different shotgun sequencing strategies are used to disclose major determinants of host specificity and characterize overall diversity. In addition, we want to reduce genome complexity into unique regions suitable for marker development. Transcriptional profiling of contrasting phenotypic groups is underway and will provide further evidence to support monitoring activities