Pei-Ling Yu, Navjot Kaur, and Bhabesh Dutta, University of Georgia, 2025
Choanephora fruit rot has recently emerged as a significant disease in pepper production in Georgia, raising new concerns for Georgia growers. Outbreaks in bell pepper fields highlight the need for increased awareness, updated management strategies, and further research to address this rapidly developing threat.
Signs and Symptoms
Choanephora fruit rot is caused by Choanephora spp., fungal pathogens that thrive in warm, humid, and wet environments, conditions that was prevalent in the months of June and July in Georgia. Symptoms often begin on senescing blossoms and spread rapidly to developing fruit. Infected fruits develop mushy, water-soaked lesions that quickly enlarge and cause fruit rot resulting in considerable losses (Figure 1).
Choanephora fruit rot can affect all above ground parts of the plant. In addition to fruit infection, stems and pedicels can also be affected. The disease can be easily recognized in the field when stem appears covered with dark, spore-bearing structures that resemble “hairy” growth under humid conditions (Figure 2).
Outbreak and Current Challenges
Pepper growers in Georgia have reported multiple outbreaks of Choanephora rot in summer (2025), despite the use of standard fungicide programs. Most of the labeled fungicides in pepper are ineffective in reducing the infection under field conditions. Information is limited in terms of the effectiveness of fungicides on Choanephora spp. Based on our experience in squash where this pathogen occurs sporadically, some of the fungicides in FRAC 3 and FRAC 11 should be effective. However, in pepper, the current scenario seems to be different. We hypothesize that either we are dealing with a new species or fungicide-resistant populations. Hence, determining the cause is essential to guide effective management recommendations.
Another challenge is the sporadic but severe nature of disease outbreaks. Because the pathogen depends on high humidity and prolonged wetness, weather patterns play a critical role. This makes disease incidence unpredictable and complicates timing of fungicide applications.
Management
At present, cultural practices are limited but can help reduce disease severity. Practices include crop rotation with non-host plants can help reduce soilborne inoculum and limit the persistence of Choanephora in the field. Removing infected plant debris after harvest is also important to minimize sources of the pathogen survival. Improving air circulation within the canopy by using wider row spacing can lower humidity around plants and make conditions less favorable for disease development. Finally, avoiding overhead irrigation is recommended, since this practice can facilitate the dispersal of spores from infected to healthy plants.
Chemical control has been inconsistent. While fungicides remain an important component of management, recent failures emphasize the need for resistance monitoring and evaluation of alternative products. At this stage, no single strategy provides reliable control, and integrated approaches will be necessary.
Ongoing Research and Future Directions
Researchers at the University of Georgia in Dutta Lab are actively investigating this emerging issue to support growers with data-driven recommendations. As part of these efforts, isolates of Choanephora are being collected from pepper fields across producing areas in Georgia, and their sensitivity to QoIs, DMIs, and SDHIs are being assessed. This work will help determine whether fungicide resistance is present and how widespread it may be.
Replicated field trials are also underway to evaluate the performance of both registered and experimental fungicides under natural conditions. These studies are expected to provide critical insights into which products could be most effective for managing Choanephora rot in commercial pepper production.
In order to address the identity of causal, Dutta Lab is using multilocus sequence analysis (MLSA) and whole-genome sequencing to characterize the species and species complexes (if any) in Georgia. These efforts will help clarify if the recent outbreaks are associated with new introductions of the pathogen or shifts within existing species.
In addition, a species-specific real-time PCR assay will also be developed. Once validated, this diagnostic tool will enable rapid and accurate detection of Choanephora species, which will allow growers and Extension specialists to make more timely management decisions.
Pei-Ling Yu and Navjot Kaur are Postdoctoral Research Associates, and Bhabesh Dutta is a Professor and Extension Vegetable Disease Specialist, all at the University of Georgia in Tifton.