Quantification of Botrytis cinerea airborne conidia in blackberry and raspberry greenhouses and rain covers by qPCR and its latent presence in flowers and fruits

The rapid expansion of blackberry and raspberry cultivation has been challenged by Botrytis cinerea, the fungal pathogen causing gray mold, which causes severe crop losses and remains a persistent threat to growers. Despite its economic importance in berry production, current monitoring and management strategies remain limited. Calendar-based fungicide use, rather than risk-based approaches, promotes excessive chemical use and accelerates fungicide resistance in B. cinerea. Its complex disease cycle complicates infection risk prediction and timely intervention, highlighting the need for precise monitoring tools and integrated strategies that optimize fungicide efficacy while incorporating alternative control measures. This study evaluates the relationship between airborne Botrytis conidia, latent infections, and environmental factors, such as temperature and humidity, in blackberry and raspberry crops under greenhouse and rain-covered systems. Using a sensitive method based on a rotating-arm spore trap combined with qPCR, we monitored airborne spore levels, and assessed latent infections on floral and fruit tissues over two cultivation periods. Our results indicate that greenhouse environments exhibit lower spore concentrations and latent infection rates than rain-covered systems. However, raspberry greenhouses displayed higher spore levels and latent infection rates than blackberry greenhouses. In rain-covered systems, a strong positive correlation was observed between spore concentrations, relative humidity, and latent infections, suggesting the predictive utility of spore monitoring in managing Botrytis outbreaks. In contrast, greenhouse environments showed weaker correlations, possibly due to restricted air circulation and stable microclimates limiting spore dispersal. This study provides insights into fungal epidemiology and supports more targeted, sustainable disease management strategies in berry crops.