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Unraveling historical shifts in Pseudoperonospora cubensis populations in the U.S. that resulted in the 2004 cucurbit downy mildew epidemic
Alamgir Rahman: NCSU; Lina Quesada-Ocampo: Department of Plant Pathology North Carolina State University; Emma Wallace: North Carolina State University; Jo Anne Crouch: Mycology and Nematology Genetic Diversity and Biology Laboratory, USDA-ARS; Frank Martin: USDA ARS
<div>The biotrophic oomycete pathogen <i>Pseudoperonospora cubensis</i> causes cucurbit downy mildew (CDM) on a plethora of Cucurbitaceae hosts. Following a devastating outbreak in 2004, CDM re-emerged as a major foliar disease on cucurbit crops in the United States (US). Prior to this outbreak, CDM was managed by host resistance in cucumber and fungicide applications in other cucurbits, both of which became ineffective or limited in efficacy. To investigate shifts in US <i>P. cubensis</i> populations that resulted in the 2004 epidemic we used mitochondrial genome sequencing and multilocus sequence analysis to examine more than 450 recent (post-2004) and 300 herbarium (pre-2004) samples. Our findings indicate that <i>P. cubensis</i> has two distinct clades with host specialization. Interestingly, Clade I was predominant before 2004 in the US regardless of cucurbit host, while samples collected after 2004 exhibited a mix of Clade I and II isolates with Clade II isolates being specialized on <i>Cucumis sativus</i>, <i>C. melo, </i>and <i>Cucurbita foetidissima</i>. Moreover, analysis of mitochondrial genomes allowed for development of a PCR marker that differentiates Clade I and Clade II, providing a means to assess crop infection risk by a particular isolate. We are expanding our investigation to determine the phylogenetic relationship among <i>P. cubensis</i> isolates from within and outside of US. Our findings will provide significant insight into population shifts that resulted in the 2004 CDM outbreak in the US.</div>

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