Characterizing the dynamics of virulence and fungicide resistance of Phytophthora capsici in Michigan vegetable fields reveals loci associated with virulence

Abstract

The oomycete, Phytophthora capsici, is a destructive pathogen infecting more than 50 plant species and is one of the most serious threats to cucurbit production. Phytophthora blight can affect all plant stages, fungicides and cultural controls are used to limit losses. Pathogen virulence and fungicide resistance can provide insights into pathogenic mechanisms and inform effective management practices. In this study, we assessed virulence, mefenoxam sensitivity and genetic diversity of nine P. capsici populations collected from Cucurbitaceae, Solanaceae, and Fabaceae host families in Michigan from 2002 to 2016. We developed 992 simple sequence repeats (SSRs) in the P. capsici genome and identified 60 SSRs located within or close to RXLR-class (Arginine-any amino acid-Leucine-Arginine) effectors and 29 SSRs within or close to effector CRN (CRinkling and Necrosis) family protein, which represent 62 RXLR and 34 putative CRNs. Population structure analysis shows that mefenoxam resistance was not associated with the year of collection, host type, or location, but there were significant differences in virulence among the populations. Using the general linear model and mixed linear model-based association analyses with all effector-related SSRs, we identified four SSRs significantly associated with at least one of the virulence-related parameters. Of these SSRs, one (Pce_SC18) was in a predicted CRN effector and had high identity with the putative PhCRN37 effector in a related pathogen Plasmopara halstedii which can be further verified for virulence identification in P. capsici.