DNA-based detection of the bacterial blight agent in hazelnut, Xanthomonas arboricola pv corylina from plant tissues

Hazelnut (Corylus avellana L.), a crop of significant economic value, is threatened by bacterial blight disease caused by the pathogen Xanthomonas arboricola pv. corylina (Xac). This disease negatively impacts the sustainability of hazelnut agriculture by causing severe losses, especially in young orchards. This study aimed to isolate Xac from Turkish hazelnut regions, identify them using classical and molecular methods, determine their genetic and pathogenic characteristics, develop a reliable qPCR method for rapid detection, and evaluate the reactions of common hazelnut varieties to Xac. Isolates obtained from samples collected in hazelnut production areas were identified using classical and molecular methods. The genetic fingerprints of the isolates were determined by SCoT analysis, and their pathogenicity was confirmed on a susceptible hazelnut variety. For the rapid and quantitative detection of Xac, novel primers targeting the gyrB gene region were designed and synthesized, and a SYBR Green I-based real-time PCR (qPCR) method was developed and comprehensively validated. Finally, the reactions of 10 different hazelnut varieties to Xac were examined under controlled conditions. As a result of the studies, 28 isolates were identified as Xac, and all were found to be pathogenic on hazelnut. SCoT analysis was evaluated as a useful tool for grouping the isolates. The developed and validated qPCR method was proven to be capable of specifically and sensitively detecting Xac at the femtogram level, enabling quantitative analysis. In the hazelnut variety reaction trials, significant differences in susceptibility to Xac were found among the tested varieties; the 'Karafındık' variety exhibited a less susceptible reaction, whereas some varieties like 'Kalınkara' showed high disease severity. This study provides significant contributions to understanding the Xac populations in Turkey, developing reliable molecular tools for the accurate and rapid diagnosis of the disease, and identifying potentially tolerant genotypes in the fight against hazelnut bacterial blight. The findings and developed methodologies will constitute a foundation for creating integrated disease management strategies, hazelnut breeding programs, and future research.