Browsing by Author "Bougard, Kayleigh"

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    The characterization of the association of apple stem pitting virus with pear stony pit disease
    (Stellenbosch : Stellenbosch University, 2023-04) Bougard, Kayleigh; Bester, Rachelle; Maree, Hans, Jacob; Stellenbosch University. Faculty of Agrisciences. Dept. of Genetics.
    ENGLISH ABSTRACT: The overall health of the fruit industry is reliant on high-quality planting material that is free of pathogens and pests. Within the plant improvement scheme, several viruses are tested for before the propagation material may enter commercial orchards. In the pear industry, there have been observations over the last few years of pitted and deformed fruits, possible symptoms of Pear stony pit disease (PSPD). In affected orchards these deformed fruits have been the cause for a drastic decrease in crop yield each season, and with these pears being unmarketable, economic loses are also experienced. PSPD is known to be associated with apple stem pitting virus (ASPV), a virus that is only transmitted via propagation material. But recently, local producers have hypothesized that stink bug feeding may be the cause for these deformities. Therefore, this project included surveying pear orchards distributed over two geographically distinct regions in the Western Cape, South Africa. Leaf samples were harvested from pear trees, covering six different cultivars. To determine the association of ASPV with the disease, preliminary reverse transcription polymerase chain reaction (RT-PCR) testing was performed but after high throughput sequencing (HTS) virome profiling, it was identified that there is a divergent variant of this virus present in South Africa and the preliminary assay was insufficient to capture it. A new multiplex RT-PCR (RT-mPCR) was therefore developed during this project which can detect all known ASPV variants present in South Africa. The HTS results allowed for the first full-length genome sequence of this divergent variant (Isolate B173). Virome profiling also allowed for the reporting of two viruses, citrus virus A, which has not been found on pears in South Africa before, and apple rubbery wood virus 2, which has not been found on apples and or pears in South Africa before. A stink bug feeding trial was performed on two pear cultivars, ‘Forelle’ and ‘Rosemarie’, by enclosing several bugs in mesh bags around pear clusters from fruit set, and the fruit health was evaluated at the end of the season. Phylogenetic analyses were performed, evaluating ASPV/apple green crinkle associated virus (AGCaV) sequences to determine the relationships of host, origin, and also whether a distinction can be made between these two viruses. The result did not provide a clear distinction between these viruses sequences. The data generated in this study highlighted the need to re-evaluate the phytosanitary status of propagation material to ensure virus free pear orchards for the future. Both the virus and feeding damage was identified as potential contributing factors to PSPD-like symptoms. The study suggests, with need for further confirmation, that ASPV infection results in pear symptoms with more defined external pits. The orchards where this symptom was found resulted in 100% and 92% association with ASPV on symptomatic and asymptomatic trees, respectively. The orchards exhibiting the less defined pitted symptoms had a lower association (56%) to ASPV infection. Therefore, currently, the best practice recommendation for symptom management will include to plant ASPV free plant material and to eliminate stink bugs from orchards.