Pathogenicity and Molecular Characterization of Colletotrichum kahawae Causing Coffee Berry Disease in Highland Plantations

Abstract

Coffee Berry Disease (CBD), caused by Colletotrichum kahawae, is one of the most devastating fungal diseases affecting Arabica coffee production in highland plantations, leading to severe yield losses and quality deterioration of berries. The pathogen primarily infects developing coffee fruits, resulting in dark sunken lesions, premature fruit drop, and complete crop failure under conducive environmental conditions. The present study was conducted to investigate the pathogenicity and molecular characterization of C. kahawae associated with Coffee Berry Disease in highland coffee-growing regions. Diseased coffee berries exhibiting typical CBD symptoms were collected from multiple plantations, and fungal isolates were obtained using standard isolation techniques on selective media. Morphological characterization was performed based on colony appearance, conidial shape, and growth characteristics, while molecular identification was carried out using polymerase chain reaction (PCR) amplification and sequencing of conserved genetic regions. Pathogenicity assays were conducted under controlled conditions by inoculating healthy coffee berries to confirm disease development and assess virulence levels among isolates. The results confirmed the consistent association of C. kahawae with Coffee Berry Disease symptoms across surveyed plantations. Considerable variation in pathogenicity was observed among isolates, with highly virulent strains causing rapid lesion development and extensive berry rot. Molecular analysis revealed high genetic similarity among isolates, with phylogenetic clustering closely related to known C. kahawae reference strains, confirming species identity. The study also highlighted the uniform pathogenic potential of isolates adapted to highland environmental conditions, indicating stable host–pathogen interactions. The findings provide important insights into the biology, genetic identity, and pathogenic variability of C. kahawae in coffee agroecosystems. This information is essential for developing effective disease management strategies, including the deployment of resistant varieties, improved cultural practices, and early detection systems to minimize losses in coffee production.