Morphological and molecular identification of fungi associated with South African apple core rot

Core rot is a major contributor to postharvest losses in apples worldwide. Pathogens most commonly associated with the disease are Alternaria spp. and Penicillium spp. Although both genera show specific morphological characteristics, they can be difficult to identify to species level. In this study, Alternaria spp. (49) and Penicillium spp. isolates (97), associated with pre- and post-harvest apple core rot-symptoms and isolates from potential inoculum sources were identified using molecular methods. Initially, dry core rot causing Alternaria spp. were identified morphologically in an average of 70% of infected fruit pre-harvest and 32% postharvest. Furthermore, 78% of mouldy core rot causing pathogens were identified as Alternaria spp. preharvest and 40% postharvest. Wet core rot was associated with Penicillium spp. in 64% of cases preharvest and 36% postharvest. Species identity of a selection of samples was confirmed using the endopolygalacturonase (endo-PG) gene, the ITS region, and the anonymous genomic regions (OPA1-3, 2-1), which resulted in the identification of A. alternata, A. arborescens, A. dumosa, A. eureka and A. tenuissima. Penicillium species were identified through ITS sequencing and partial beta-tubulin polymerase chain reaction - random fragment length polymorphisms (PCR-RFLP) for the samples collected from wet core rot symptoms. Phylogenetic analyses separated the Alternaria spp. into five clades, including three separate clades for A. alternata, A. tenuissima and A. arborescens, respectively. This is the first report of A. eureka and P. polonicum as potential core rot pathogens. Phylogenetic analysis identified Penicillium ramulosum and P. expansum as the most commonly occurring species associated with WCR symptoms.