<i>Colletotrichum</i> Species Causing Glomerella Leaf Spot and Bitter Rot of Apple in Georgia and Their Resistance to QoI Fungicides

Glomerella leaf spot (GLS) and bitter rot, caused by Colletotrichum species, are two of the most economically damaging diseases of apple (Malus domestica) in the southeastern USA. However, the causal species and their resistance to fungicides have not been well established in Georgia. We surveyed nine orchards in the Georgia apple-growing region in 2023 to identify the Colletotrichum species responsible for these two diseases and to assess their resistance to QoI fungicides. A total of 252 isolates were identified to species, revealing that bitter rot was caused by C. chrysophilum, C. fioriniae, C. fructicola, and C. siamense, with frequencies varying by orchard. In contrast, GLS was dominated by C. fructicola (86%) and, in some orchards, by C. chrysophilum. Sequencing of the cytochrome b (cytb) gene showed that the G143A mutation, which confers complete QoI resistance, was present in all species, but was especially common in C. fructicola (96%) and C. siamense (63%). Several isolates were heteroplasmic for cytb intron variants as well as for G143A, which could only be detected using multiple, genotype-specific primer sets for each isolate, emphasizing that careful detection is required in future studies. Mycelium inhibition assays confirmed that G143A conferred resistance in vitro, as most G143A isolates (98.8%) were classified as resistant using a discriminatory dose of pyraclostrobin while most wild-type isolates (97.7%) remained sensitive. Overall, these findings indicate that QoI fungicides are unlikely to control GLS in Georgia and will be ineffective for bitter rot at many locations.