Characterization of a new Botrytis species and fungicide resistance in Botrytis cinerea from blackberry

Gray mold caused by the fungus Botrytis cinerea is the economically most important pre- and postharvest disease of blackberry. As part of a South Carolina fungicide resistance monitoring program, blackberry fruit were collected to survey for pathogenic fungi. Phylogenetic as well as morphological analysis indicated a new species, described as Botrytis caroliniana. A rapid method using polymerase chain reaction was developed to differentiate B. cinerea and B. caroliniana. A distribution and prevalence study indicated these two species co-existed in four out of six locations investigated. The control of gray mold in commercial fields largely relies on fungicide application. Therefore, survey was conducted to determine the occurrence and prevalence of fungicide resistance. The fungicide resistance profile was described in 198 B. cinerea isolates from blackberry. Of these isolates, 72% were resistant to thiophanate-methyl, 59% were resistant to pyraclostrobin, 56% were resistant to boscalid, 11% were resistant to fenhexamid, 10% were resistant to cyprodinil, 8.6% were resistant to iprodione, and 1% were resistant to fludioxonil. A statistical model revealed that multifungicide resistance patterns did not evolve randomly in populations. Resistance to thiopanate-methyl, pyraclostrobin, boscalid, and fenhexamid was based on target gene mutations, including E198A and E198V in β-tubulin, G143A in cytochrome b, H272Y and H272R in SdhB, and F412I in Erg27, respectively. In addition, a new genotype associated with fenhexamid resistance was found in one strain (i.e., Y408H and deletion of P298). Two levels of resistance, low resistance (LR) and moderate resistance (MR), to fludioxonil were found in three field isolates, and MR was caused by a previously described mutation (R632I) in transcription factor Mrr1. The LR and MR isolates were able to cause lesions and sporulated on detached fruit. The results obtained in this study contribute to our understanding of fungal biology and fungicide resistance development in gray mold fungi and are useful for improving resistance management practices.