Prevalence of Mutations Associated with QoIs, QiIs, QioSIs, and CAA Fungicide Resistance Within Plasmopara viticola in North America and a Tool to Detect CAA-Resistant Isolates.

Abstract

Grape downy mildew, caused by Plasmopara viticola, poses a significant threat to grape cultivation globally. Early detection of fungicide resistance is critical for effective management. This study aimed to assess the prevalence and distribution of mutations associated with resistance to quinone outside inhibitor (FRAC 11), quinone inside inhibitor (FRAC 21), carboxylic acid amide (CAA, FRAC 40), and quinone inside and outside inhibitor, stigmatellin binding mode (FRAC 45) fungicides in P. viticola populations in the eastern United States and Canada and to evaluate whether these mutations are linked to fungicide resistance correlated with specific P. viticola clades. A total of 658 P. viticola samples were collected from commercial vineyards across different states and years in the eastern United States and Canada and sequenced for the PvCesA3 and cytb genes and the internal transcribed spacer (ITS)1 region. The results showed that P. viticola clades aestivalis, vinifera, and riparia were prevalent in the eastern United States and Canada. Quinone outside inhibitor resistance was widespread, and the A-143 resistant genotype was prevalent in P. viticola clades aestivalis and vinifera. The G143A mutation did not show specificity based on clade differentiation. CAA resistance, associated with the G1105S mutation, was mainly identified in P. viticola clade aestivalis from Georgia, New York, and Ontario. G1105-S1105 mixed-genotype samples were observed in P. viticola clades vinifera and riparia from Wisconsin, Michigan, and New York. However, mutations associated with quinone inside and outside inhibitor and quinone inside inhibitor fungicides were not detected. A TaqMan probe-based assay was developed to detect the G1105S mutation in P. viticola conferring CAA fungicide resistance. The TaqMan assay demonstrated sensitivity at low DNA concentrations and specificity in distinguishing between sensitive and resistant genotypes. The assay accurately distinguished the G1105S mutation in leaf and air samples. This study provides insight into the geographic distribution of fungicide resistance in P. viticola populations and presents a reliable method for detecting CAA resistance in P. viticola. These findings can be utilized to implement effective fungicide resistance management strategies in viticulture.