Dynamic genomes and the evolution of bacterial host specificity

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Pests and pathogens pose a serious challenge to agriculture, collectively destroying ~25% of the world's five most important food crops (wheat, rice, corn, potato, soybean), which account for >48% of the global calorie intake. What determines if a particular pathogen will cause disease on a specific host? Where do newly emerged pathogens come from? How do pathogens 'jump' to a new host? Understanding how hosts and pathogens interact is not only important for protecting our food supply, but also provides an extraordinary system for studying fundamental questions related to pathogen effector function, and host immunity, pathogen ecology and evolution, and host-pathogen co-evolution. Our long-term objective is to protect crop plants from rapidly evolving bacterial pathogens. To achieve this goal we propose three objectives: 1. Study immunodiversity within & between host species by using a library of pathogen effectors to probe for immune responses in a collection of closely related wild and domesticated plant species. We are particularly interested in understanding how immunodiversity has been impacted by crop domestication. 2. Study interactions between effectors to determine how effector-effector interactions influence host-pathogen outcomes and the evolution of host specificity. This work will also provide insight into the variety of distinct ways that a pathogen can overcome the immune defenses of specific plant hosts. 3. Investigate the mechanism underlying host specificity by manipulating pathogen effector genes that are associated with host transitions. We will also develop models to predict infection outcomes using pathogen genomic data. This work will help us monitor new pathogen outbreaks and develop means to protect plants against emerging threats. This study will identify pathogen effectors and host resistance genes that govern the outcome of host-pathogen interactions, providing fundamental information on the mechanisms underlying the arms race and between crops and their pathogens, as well as develop new genetic resources for breeding resistant crops. We will better understand how the plant immune response changes over the course of crop domestication, providing knowledge into how this process impacts the maintenance of immunodiversity. We will characterize the range of ways that a pathogen can adapt to a host, providing new understanding of the evolution of novelty. We will develop models to predict pathogen host specificity, providing insight into the genetic structure of this complex trait and diagnostic methods that could be used for rapid in-field monitoring. All of these studies will better enable us to respond to the unrelenting challenge imposed by bacterial pathogens; a threat that will only increase as the consequences of global climate change become more immediate.