Identification, pathogenicity, and fungicide sensitivity of Colletotrichum isolates obtained from different asymptomatic organs of apple trees

Colletotrichum spp. are the causal agents of Glomerella leaf spot, Colletotrichum fruit spot, and bitter rot in apple orchards in Brazil. These species can asymptomatically colonize different plant tissues and remain within them until environmental conditions become favorable for their development, forming populations that are still poorly understood. Therefore, this study aimed to identify Colletotrichum species obtained from asymptomatic apple tissues, evaluate their pathogenicity, and determine their sensitivity to the fungicides trifloxystrobin (QoI, FRAC 11), fluxapyroxad (SDHI, FRAC 7), thiophanate-methyl (MBC, FRAC 1), tebuconazole (DMI, FRAC 3), and mancozeb (dithiocarbamate, FRAC M03). Isolates were obtained from leaves, flowers, green fruits, and mummified fruits collected from three orchards with low, intermediate, and high frequencies of fungicide applications. Five Colletotrichum species were identified: C. chrysophilum , C. fructicola , C. nymphaeae , C. cf. melonis , and C. karstii . In pathogenicity tests, 93% of the isolates were pathogenic on fruits, 58% on leaves, and 6.7% were non-pathogenic. All isolates were sensitive to mancozeb. The isolates exhibited low sensitivity to fluxapyroxad regardless of the orchard of origin, while mycelial growth inhibition by tebuconazole ranged from 0 to 60%. Isolates collected from orchards with a high frequency of fungicide applications showed reduced sensitivity to thiophanate-methyl and trifloxystrobin, associated with the E198A mutation in the β-tubulin gene and the G143A mutation in the cytb gene, respectively. Colletotrichum populations obtained from asymptomatic tissues, belonging to the major species complexes associated with apple diseases, may act as sources of inoculum for pathogenic isolates with reduced fungicide sensitivity, highlighting the importance of monitoring these populations and promoting the rational use of fungicides in apple disease management.