Droplet Digital PCR: A New Molecular Method to Detect G1105S/V Mutations in Plasmopara viticola CesA3 Gene

<i>Plasmopara viticola</i> is the causal agent of Grapevine Downy Mildew (GDM), which is a devastating disease of grapevines in humid temperate regions. The most employed method for protecting grapevines against GDM is the application of chemical fungicides. In Spain, Carboxylic Acid Amides (CAAs) are a fungicide group currently utilized in GDM control. In <i>P. viticola</i>, resistance to CAAs is conferred by G1105S and G1105V mutations in the <i>CesA3</i> gene. Droplet digital polymerase chain reaction (ddPCR) is an innovative technique that combines PCR and droplet microfluidics to disperse the sample into thousands of water-in-oil droplets in which an amplification reaction is individually performed. In this study, we set up a ddPCR protocol to quantify S1105 and V1105 mutations conferring resistance to CAAs in <i>P. viticola</i>. The optimal PCR conditions were established, and the sensitivity and precision of the protocol were assessed. Four <i>P. viticola</i> populations coming from commercial vineyards in northern Spain were analyzed, and different allele frequencies were found in the analyzed samples corresponding to the different fungicide management strategies, ranging from 7.72% to 100%. Knowing the level of mutated alleles allows for designing resistance management strategies suited for each location. This suggests that similar ddPCR assays could be developed for studying mutations implicated in fungicide resistance in other fungicide groups and plant pathogens.