Resistance in Alternaria alternata to SDHI Fungicides Causes Rare Disease Outbreak in Peach Orchards

Alternaria rot, caused by Alternaria alternata, was observed in commercial peach orchards in South Carolina. Single-spore isolates formed two phenotypically different culture morphologies on two artificial media. Isolates highly resistant (HR) to boscalid were also HR to penthiopyrad. Among isolates HR and medium resistant (MR) to boscalid and penthiopyrad, we detected isolates that were MR to fluopyram and HR to fluxapyroxad. Sequence analysis of succinate dehydrogenase (sdh) genes sdhB, sdhC, and sdhD revealed that resistant phenotypes were associated with point mutations leading to amino acid substitutions. In particular, H277Y/R in the SDHB and H134R in SDHC were consistently associated with the boscalid HR phenotype. The highest effective concentration that inhibits growth by 50% (EC50) values to penthiopyrad were conferred by H134R and D123E, whereas H134R conferred low resistance and MR to fluxapyroxad. A previously undescribed mutation, G79R, was identified in our collection conferring HR to both boscalid and penthiopyrad. The point mutations associated with highest EC50 values to all four FRAC 7 fungicides were H277L and H134R. The outbreak of Alternaria rot demonstrates that fungicide programs containing medium to high-risk fungicides may promote disease outbreaks by secondary pathogens that typically are outcompeted or controlled effectively, while still controlling the primary target disease.