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Approaches to effectively use pathogenomics for wheat crop protection against rusts

Guus Bakkeren: Agric & Agri Food Canada

<div>To improve our understanding of the globally important wheat rust pathogen, <em>Puccinia triticina</em> (<em>Pt</em>), we have sequenced 95 genomes of Canadian isolates and a variety of transcriptomes of interactions between specific races and Near-Isogenic Lines carrying specific leaf rust (<em>Lr</em>) resistance genes. Comparative analyses of high-resolution RNAseq datasets led to the identification of 700 effectors predicted to be secreted and expressed during host infection and <span>allowed us to discriminate between specific resistance responses triggered upon recognition by <em>Lr3</em> versus <em>Lr2a</em> with the latter revealing induction of a significant number of chloroplast-related genes. We were also able to visualize global gene expression reprogramming of a suite of 126 <em>Pt</em> effectors and wheat genes, and, using CytoScape, revealed gene co-expression networks possibly involved in disease or defense pathways. Transcription of some of the identified wheat genes is likely affected by some effectors having a nuclear localization. Fluorescent chimers of five <em>Pt</em> effectors, whose transcript levels were highly associated with wheat transcripts across various interactions, were found to be targeted to diverse plant organelles including the chloroplast in a heterologous <em>Nicotiana benthamiana</em> system. </span>A novel functional effector secretion assay was developed in a cereal-infecting <em>Ustilago</em> species to potentially assist <em>Lr</em> gene breeding, and essential fungal pathogenicity genes were targeted in a HIGS approach resulting in increased rust resistance in wheat. Examples will be presented to illustrate that generating genomic resources can drive research innovations for crop protection.</div>