Browsing by Author "Basson, Elaine"

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    Incidence and epidemiology of apple core rot in the Western Cape of South Africa
    (Stellenbosch : Stellenbosch University, 2012-12) Basson, Elaine; Lennox, Cheryl L.; Stellenbosch University. Faculty of AgriSciences. Dept. of Plant Pathology.
    ENGLISH ABSTRACT: This study looked at the incidence, etiology and epidemiology of core rot of apples in orchards situated in the Western Cape, South Africa. Core rot is a post-harvest disease, with three symptoms, namely mouldy core (MC), dry core rot (DCR) and wet core rot (WCR). These symptoms are caused by various pathogenic fungi, including Alternaria and Penicillium. Although MC is not economically important, DCR and WCR are, as they affect the flesh of the fruit. Core rot occurs worldwide in susceptible apple cultivars such as ‘Starking’ and ‘Red Delicious’. These cultivars have a wider, open calyx tube which results in an open core area. In South Africa, core rot of apples are important post-harvest diseases and losses of between 5 and 12% occur in apple cultivars. An in depth literature search was done on core rot including literature on each core rot symptom, the genuses Alternaria and Penicillium, molecular identification and techniques, disease incidence and its economic importance, various inoculum sources, pathogenicity of core rot organisms and integrated management of core rot. This study included two research chapters, with seven objectives, namely, to 1, determine the incidence of core rot in apples from commercial orchards both pre- and post-harvest; 2, to identify the causal organisms associated with core rot symptoms; 3, to identify potential sources of inoculum of core rot pathogens and determine whether there is synergism between Alternaria and Tarsonemus mites associated with core rot; and 4, to determine whether the fungicide Bellis®, used a full bloom application, can be used to manage core rot in South Africa; 5, to identify the species of Alternaria and Penicillium sampled from core rot symptomatic fruit and inoculum sources (air, apple mummies and mites), using morphological and molecular methods; 6, to compare Penicillium species isolated from pre- and post-harvest WCR symptomatic fruit, using molecular species identification methods and 7, to compare and to select the most reliable pathogenicity test for use in future research. The total decay incidence for Ceres is considerably higher than the previous losses indicated in literature. Pre-harvest core rot, which was confirmed by previous studies, had a higher incidence of each core rot symptom than previously indicated. The two most frequently isolated causal organisms were Alternaria and Penicillium. Other organisms isolated and then identified from the symptoms were Fusarium, Cladosporium, Epicoccum, Ulocladium, Stemphylium, Phoma, Botryosphaeria, Botrytis, Trichoderma, Verticillium, Paecilomyces and Gliocladium. Three inoculum sources, air, mummies and mites, were regarded as potential sources of infection for core rot. During this study the sources of infection were verified and core rot causing organisms were isolated from these sources. Alternaria was isolated from air inoculum samples, but was not found on the other two sources. This dismissed the hypothesis that there was a possible synergism between Alternaria and Tarsonemus mites. Penicillium species were isolated from all three sources, more frequently from the mummies and mites. Bellis® was applied three times during the bloom period. The subsequent results showed a significant difference between the control and Bellis® treated treatments with the treated fruit having a significant higher incidence than the controlled fruit. No control was observed with this result and managing core rot with only Bellis® is not advisable. Alternaria species were identified using the following genetic loci, ITS, OPA1-3, 2-1 and 10-2 as well as endoPG. Isolates from pre- and post-harvest symptoms and air inoculum were identified using each of the genetic loci. Alternaria arborescens was one of the species that was identified. The other isolates obtained were A. alternata, A. tenuissima, A. gaisen, A. dumosa, A. turkisafria and A. perangusta. Separating combined species was not possible. Another molecular technique, ISSR, was used to identify Alternaria species. This technique, after multiple re-runs, did not give consistent results and species could not be identified. Penicillium species were identified using the genetic loci ITS for isolates collected from pre- and post-harvest symptoms and inoculum sources. Thirteen clades were identified, including the species P. ramulosum, P. sp. (aff. cecidicola), P. sp (aff. dendriticum), P. expansum, P. paneum, P. solitum, P. crustosum , P. brevicompactum, P. novae-zeelandiae, P. glabrum and P. rugulosum. Penicillium expansum and P. ramulosum had the highest distribution between the isolates. Pre- and post-harvest WCR isolates were identified using the partial beta-tubulin PCR-RFLP method, and comparing different banding-patterns. The species identified using this method were P. expansum, P. ramulosum, P. sp. (aff. cecidicola), P. sp (aff. dendriticum), P. rugulosum, P. chermesinum and P. glabrum. Penicillium ramulosum and P. expansum had the highest incidence with P. ramulosum occurring more frequently pre-harvest than post-harvest and P. expansum occurring more frequently post-harvest. Five methods, previously published, were compared to select the most reliable pathogenicity test. The methods included surface wounding of an apple with colonised toothpicks, surface wound inoculated with a pipette, inoculation of an open mesoderm core cavity, deep and non-wounding of apple fruit with colonised toothpicks. The surface wounding with a colonised toothpick gave the most reliable results and can be used in industry as a pathogenicity test for Alternaria in apples. This study contributed to our understanding on the incidence and etiology of core rot in the Western Cape as well as in identifying inoculum sources from where infection can take place in the orchard. The results for the fungicide trial were not as anticipated and more research is required on selecting fungicides for the control of core rot in South African orchards. Although molecular techniques reduce the time in identifying fungal species, it is costly and mistakes can occur due to contamination. Identification of species can be incorrect when using a Genbank as the sequence information may be incorrect. Molecular techniques, though a good tool in identifying species, should be combined with morphological characteristics to ensure more accurate results.
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    Morphological and molecular identification of fungi associated with South African apple core rot
    (Springer, 2018) Basson, Elaine; Meitz-Hopkins, Julia C.; Lennox, Cheryl L.
    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.