Characterization of Alternaria Isolates from Brazilian Citrus Orchards by Fungicide Resistance Phenotype and Species

Alternaria brown spot (ABS), caused by Alternaria spp., is an important fungal disease of mandarins in several citrus-growing regions worldwide. In Brazil, ABS has become increasingly severe in Paraná (PR) state, which accounts for 14% of national mandarin production, with growers reporting failures to control in the field. Despite its relevance, no prior studies have assessed the prevalence of Alternaria species or their sensitivity to fungicides. This study aimed to: (i) identify Alternaria species through molecular analysis, (ii) assess the sensitivity of isolates from conventional, organic in transition, and organic production systems in PR to quinone outside inhibitors (QoIs) and demethylation inhibitors (DMIs) using discriminatory doses, (iii) detect the QoI-resistant allele G143A by PCR, and (iv) assess pathogenicity on ‘Murcott’ leaves. Multilocus phylogenetic analysis identified A. alternata (65.5%) as the predominant species, followed by A. longipes (27%) and A. arborescens (7.5%). High frequencies of resistance to azoxystrobin and pyraclostrobin (67%) and to tebuconazole (53%) and difenoconazole (19%) were detected. Resistant phenotypes were significantly more frequent in conventional systems (χ² = 27.7; P < 0.001). The G143A mutation was detected in QoI-resistant isolates, with higher frequencies in conventional (85.1%) than in organic in transition (50%) and organic systems (16.7%). All three species were pathogenic on leaves, with no differences in ABS severity. These findings provide the first detailed report of ABS-related Alternaria species and fungicide resistance in PR, highlighting the need for integrated resistance management to sustain effective ABS control.