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Exploiting bacterial genomics to develop tools for effective pathogen monitoring in rice

Ricardo Oliva: International Rice Research Institute

<div>The recurrent emergence of highly aggressive clones of plant pathogens in agricultural ecosystems represents an important threat to food security. Bacterial blight, caused by <em>Xanthomonas oryzae</em> pv. <em>oryzae</em> (<em>Xoo</em>), is the most important bacterial disease of rice. At the population level, <em>Xoo</em> is usually composed of a number of phenotypic groups (races), which show R gene-specific interactions. Estimating the race composition of <em>Xoo</em> in the rice paddy is critical to design sustainable management strategies. In this work, we used bacterial genomics to develop DNA markers for effective surveillance of <em>Xoo</em> races in the Philippines archipelago. We first identified the evolutionary forces that shape contemporary groups during the last 40 years of <em>Xoo</em> outbreaks. Through comparative genomics on 100 highly informative strains, we identified six <em>Xoo</em> populations, which diverge before the colonization of the islands. The patterns of positive selection, recombination, and diversification of effector genes suggest that each population experienced a distinct adaptation process that led to the creation of modern races. Using this information, we developed single nucleotide polymorphism (SNP) markers that allow us to detect the pathogen groups in the rice leaf. We validated the robustness of SNP markers for three cropping seasons using a trapping system based on near-isogenic lines carrying different R genes, and demonstrated that real-time surveillance of <em>Xoo</em> is possible. In this scenario, we are proposing an interactive platform, called Pathotracker, which integrates early-season race diagnostics, modeling of weather patterns, and disease resistance profiles to accurately predict which variety should be used in the following season. The platform will allow us to manage bacterial blight epidemics in real-time and to define breeding priorities for the region.</div>