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

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To better understand how Z. tritici causes STB disease, we developed a high-throughput UV mutagenesis and in planta gain-of-virulence (GoV) screen to identify effectors involved in gene-for-gene interactions with their corresponding wheat R-genes. As a proof of concept, we used the known gene-for-gene interaction between the Z. tritici effector AvrStb6 and the corresponding wheat R-gene Stb6. This method allowed us to rapidly and precisely identify SNPs or deletions of AvrStb6 that underpinned GoV on Stb6-containing wheat. We will use this new method, in conjunction with QTL mapping, to identify effectors that are recognised by four major resistances used in commercial wheat breeding. To do this, we will make use of large Z. tritici isolate collections and wheat near-isogenic lines (NILs) for each resistance provided by the breeding industry. These complementary approaches offer risk mitigation and we anticipate this will allow us to converge on the same candidate effectors. These genes' role in avirulence will be subsequently validated through generation of gene deletion and complementation strains. In addition, we will develop an amplicon-based next generation sequencing pipeline to categorise the different alleles of these effectors present in the current UK fungal population. Aligned with virulence testing on the wheat NILs for each resistance, this will allow us to identify the specific mutations in each gene that lead to loss of recognition by the corresponding R-gene and thus gain of virulence. Finally, taking amplicon sequencing data generated from strains recovered from defined wheat growing regions, we will develop a NextStrain-like interface for the sharing of sequence information related to the effectors identified in this study and two others identified in previous studies. This will be the beginning of a community resource to monitor the emergence of resistance-breaking Z. tritici isolates in the field in space and time.