Region-Wide Evaluation of QoI and SDHI Resistance in Alternaria Populations from California Pistachio Orchards Using Real-Time PCR

Alternaria late blight (ALB), caused by Alternaria spp., is one of the most prevalent and economically important diseases affecting pistachio production in California. Fungicide applications remain the primary strategy to control ALB. The fungicides Quinone outside Inhibitors (QoI) and Succinate Dehydrogenase Inhibitors (SDHI) are widely used in California. This study established two duplex real-time quantitative PCR (qPCR) approaches to determine the proportions of the mutant genotype G143A in the pathogen mitochondrial cytochrome b (cytb) gene (P _G143A ) and the mutant genotype H134R in the succinate dehydrogenase subunit C (sdhC) gene (P _H134R ). Specific primers and probes were designed to target the mutant and wild type genotypes associated with QoI and SDHI resistance. Strong correlations between the known proportions of mutant DNA in the prepared mixtures and the proportions estimated by qPCR demonstrated that the assays were suitable for quantifying QoI and SDHI resistance-associated genotypes. Multi-year surveys for fungicide resistance in pistachio orchards at a region-wide scale in California were conducted. Leaf samples collected from 2021 to 2023 were processed with the SYBR Green I technique and those collected from 2024 to 2025 were processed with the TaqMan technique in qPCR. A total of 195 and 182 samples were used for quantification of resistance levels to QoI and SDHI, respectively. Survey results demonstrated that 17.9 and 65.6% samples showed high and very high resistance levels to QoI, respectively. For SDHI, the very high resistance category represented the largest proportion of samples (45%) and was significantly greater than the other categories.