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The bioSAFE project: developing tools for the genomic biosurveillance of forest invasive alien pathogens in Canada

Louis Bernier: Université Laval, Centre d'Étude de la Forêt (CEF)

<div>The capacity of forests to provide long-term fibre supply and ecosystem services is threatened by the introduction of Forest Invasive Alien Species (FIAS). The bioSAFE project is developing a biosurveillance pipeline to generate genomic tools that will facilitate biosurveillance to increase preparedness and facilitate early action against FIAS. Dutch Elm Disease [DED] and Sudden Oak Death [SOD] are used as model pathosystems for developing accurate means of detection, identifying pathways of spread, and predicting fitness and outbreak-related epidemiological traits that affect the extent of outbreaks. Ongoing research on DED and SOD includes: 1) comparing whole genomes of the pathogens and their relatives for population genomic studies, 2) identifying genes contributing to parasitic fitness and invasiveness using transcriptomics, 3) genome-wide association studies, 4) quantitative trait locus analysis of progeny from controlled sexual crosses, and 5) developing efficient gene knockdown/knockout protocols for functional validation of candidate genes. Recent results include the assessment of global genomic diversity in pathogen populations, production of knockdown mutants of DED fungi, and development of a target-enrichment panel for <em>Phytophthora</em> spp. The bioSAFE project promises to generate transformative changes to address the challenges of biosurveillance of FIAS by speeding up and improving decision-making to inform FIAS mitigation and management.</div>