Evaluation of pre-harvest fungicide treatments against Alternaria rot in California mandarins and occurrence of mutations associated with fungicide resistance

This study aimed to investigate the management of Alternaria rot in citrus by evaluating the efficacy of late-season fungicide programs in reducing latent infections and fruit drop. Furthermore, the occurrence of mutations conferring resistance to QoI and SDHI fungicides within an Alternaria population isolated from citrus was investigated. In field trials, high frequencies of Alternaria infections were observed on the stem end and stylar end of Satsuma and Shiranui mandarins, with a higher prevalence of stem-end infections. Fungicide treatments applied towards the end of the season effectively reduced the frequency of latent infections on the stem end, indicating that such infections occur during this period under specific conditions. While some fungicide treatments demonstrated efficacy in reducing fruit drop caused by Alternaria rot, the results varied across different orchards and years. Latent infections on fruits persisted at high frequencies in the majority of trials, highlighting the complex nature of disease management. Mutations associated with resistance against QoI and SDHI fungicides were identified within the Alternaria population affecting California citrus. Our study suggests the potential need for fungicide sprays at the onset of the season to reduce the frequency of Alternaria infections on the stem end and stylar end of fruits. However, the observed non-correlation or low correlation between latent infections and fruit drop indicates that latent infections alone cannot reliably predict fruit drop. Our findings indicate that pre-harvest fungicide treatments have inconsistent efficacy and are cost-effective only during unpredictable disease outbreaks. • Late-season fungicide programs reduced latent Alternaria infections on stems. • Resistance mutations to QoI and SDHI fungicides were identified in the Alternaria population. • Fungicide treatments had inconsistent effects on fruit drop across different orchards and years. • Targeting fungicide applications earlier in the season might improve overall disease control.