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Development of assays for the detection and genotyping of regulated plant pathogens using genomic information for identification of molecular markers.

Guillaume J. Bilodeau: Canadian Food Inspection Agency

<div>Engaging in global trade necessitates the implementation of governmental regulations to restrict the movement of organisms on infected plant commodities. These regulations rely heavily on accurate plant disease diagnostics, which can be challenging for fungi/oomycetes that are difficult to isolate and/ differentiate from closely related species. We are developing tools for the identification and genotyping of regulated organisms that will improve these diagnostic efforts. Next-generation sequencing (NGS) can generate sufficient genomic data to help providing answers to biological questions and to identify markers for the development of diagnostic assays. These DNA-based tools are contributing to the genomic toolbox to assess the genetic diversity from the species to the intra-lineage level. The tools we have developed with NGS data included qPCR microsatellite assays, SNPs markers, and AmpliSeq technology to sequence a subset of genes or regions of the genome. These will be presented, using organisms from forestry and agriculture that are included in our regulatory work. Identification assays have been developed using genomic strategies targeting <em>Lachnellula willkommii</em>, European Larch Canker; <em>Phytophthora ramorum,</em> Sudden Oak Death; and <em>Fusarium sporotrichioides</em> in peas, among others. The approach taken to obtain markers by using genomic data and the identification of unique regions will be presented with information regarding assay specificity and sensitivity.</div>