SeptPROTECT: Rapid effector discovery to protect wheat from Septoria tritici blotch disease

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Plants are under continual attack from pathogens in their environment. This is a huge problem in agriculture, where plant health and productivity are crucial for ensuring the food supply.Plants protect themselves from disease with an immune system that detects and blocks invading microbes. However, microbial pathogens are continually evolving to suppress this immune system. One set of tools that pathogens use to evade the plant immune system are small, secreted proteins known as effectors. Plants can regain the upper hand by evolving disease resistance genes that detect pathogen effectors and initiate activation of immune responses.Zymoseptoria tritici is a fungus that causes Septoria tritici blotch disease of wheat plants, a major problem for farmers in the UK. Currently farmers rely on plant resistance genes that serve to recognise the fungus and limit disease development on the leaf. This fungus, however, evolves rapidly and escapes from the recognition and control provided by plant resistance genes. While we currently do not know how the fungus evades plant resistance genes, we hypothesise that the mutation or deletion of fungal effectors is one key way in which this pathogen evades recognition. A critical knowledge gap is that we do not know the identity of the effectors that are recognised by plant resistance proteins. Therefore, it is currently impossible for us to know or predict which changes in the pathogen are a threat to wheat.Identification of Z. tritici effectors has previously been challenging as this fungus is highly diverse, and there are many differences in DNA sequences between different strains. We have developed a simple but powerful method for the identification of fungal effectors recognised by corresponding wheat resistance genes. Here we will apply this new method to identify the fungal effectors recognised by four different resistance genes currently used in commercial UK wheat breeding programmes.The second goal of the project is to identify specific changes that occur in these effectors that enable them to escape recognition by wheat resistance genes. To do this, we will examine the sequence diversity found in fungal effector genes in hundreds of different strains collected directly from UK wheat fields. We will combine this sequence diversity information with knowledge of which strains are able to cause disease on wheat varieties carrying specific resistance genes. Together, this information will enable us to test and conclude which evolutionary changes in the effector genes allow the fungus to "gain virulence" on particular wheat varieties.The final goal of the project is to develop a system whereby information on the presence and frequency of Z. tritici strains able to overcome specific disease resistance genes can rapidly be made publicly available. We will do this by implementing a system similar to that developed for tracking evolution of the SARS-CoV-2 virus during the COVID pandemic. Similar tracking systems exists for other plant pathogens, but not for Z. tritici despite its agronomic importance. In the future, this system may allow us to accurately track the gain of virulence mutations in the fungal population across a large geographical area. The benefit of this is that specific wheat varieties could then be chosen to be grown in certain areas, as they were predicted to be most resistant against the local pathogen population.