The characterization of the association of apple stem pitting virus with pear stony pit disease

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dc.contributor.advisorBester, Rachelleen_ZA
dc.contributor.advisorMaree, Hans, Jacoben_ZA
dc.contributor.authorBougard, Kayleighen_ZA
dc.contributor.otherStellenbosch University. Faculty of Agrisciences. Dept. of Genetics.en_ZA
dc.date.accessioned2023-03-01T11:39:47Z
dc.date.accessioned2023-10-26T13:47:58Z
dc.date.available2023-03-01T11:39:47Z
dc.date.available2023-10-26T13:47:58Z
dc.date.issued2023-04
dc.descriptionThesis (MScAgric)--Stellenbosch University, 2023. en_ZA
dc.description.abstractENGLISH 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.en_ZA
dc.description.abstractAFRIKAANSE OPSOMMING: Die algehele gesondheid van die vrugtebedryf is afhanklik van hoëgehalte plantmateriaal wat vry is van patogene en plae. Binne die plantverbeteringskema word vir verskeie virusse getoets voordat die voortplantingsmateriaal kommersiële boorde bereik. In die peer bedryf oor die laaste paar jaar was daar ‘n waarneming van gepitte en misvormde vrugte wat moontlik simptome van Peer-steenpitsiekte (PSPD) kan wees. Hierdie misvormde vrugte was die oorsaak vir 'n drastiese afname in oesopbrengste, en met hierdie pere wat nie bemarkbaar is nie, word ekonomiese verliese ook ervaar. Dit is bekend dat PSPD geassosieer word met appelstampitvirus (ASPV), 'n virus wat slegs deur voortplantingsmateriaal oorgedra word. Maar onlangs het plaaslike produsente bespiegel dat stinkbesievoeding die oorsaak vir hierdie misvormings kan wees. Daarom het hierdie projek ‘n simptoom opmeting van peerboorde ingesluit wat oor twee geografies streke in die Wes-Kaap, Suid-Afrika, versprei was. Blaarmonsters is geneem van ses verskillende peerboom kultivars. Om ASPV-assosiasie met die siekte te bepaal, is voorlopige tru-transkripsie polimerase ketting reaksie (RT-PKR)- toetsing uitgevoer, maar na hoë deurset volgorde bepaling (HTS)-viroom profiele saamgestel is, is daar geïdentifiseer dat daar 'n uiteenlopende variant van hierdie virus in Suid-Afrika teenwoordig is en die voorlopige bepaling was onvoldoende om dit vas te vang. 'n Nuwe RT- multipleks PKR (RT-mPKR) is dus tydens hierdie projek ontwikkel wat alle bekende ASPV- variante in Suid-Afrika kan opspoor. Die HTS-resultate het toegelaat vir die eerste vollengte genoomvolgorde van hierdie uiteenlopende variant (isolaat B173). Die HTS-viroom profiele het ook gelei tot die aanmelding van twee virusse, sitrusvirus A (CiVA), wat nog nie voorheen in pere in Suid-Afrika gevind is nie, en appelrubberige houtvirus 2 (ARWV2), wat nog nie voorheen in appel en of peer in Suid-Afrika gevind is nie. Die stinkbesievoedingsproef is op twee peerkultivars, ‘Forelle’ en ‘Rosemarie’, uitgevoer deur verskeie goggas in gaassakkies om peertrosse op vrugset stadium toe te sluit, en die vruggesondheid aan die einde van die seisoen te evalueer. Filogenetiese ontledings is uitgevoer, wat ASPV/apple green crinkle associated virus (AGCaV)-volgordes geëvalueer het om die verwantskappe met gasheer oorsprong, en ook of 'n onderskeid tussen die twee virusse gemaak kan word te bepaal. Die resultaat het nie ‘n duidelike onderskeiding verskaf nie. Die data wat in hierdie studie gegenereer is, het die behoefte beklemtoon om die fitosanitêre status van voortplantingsmateriaal te herevalueer om virusvrye peerboorde vir die toekoms te verseker. Beide die virus- en voedingskade is geïdentifiseer as potensiële bydraende faktore tot PSPD- agtige simptome. Die studie stel voor dat, met behoefte aan verdere bevestinging, dat ASPV- infeksie die oorsaak is vir resultate in peersimptome met meer gedefinieerde eksterne putte. Die boorde waar hierdie simptoom gevind is, het gelei tot 100% en 92% assosiasie met ASPV op onderskeidelik simptomatiese en asimptomatiese bome. Die boorde wat die minder gedefineerde pitsimptome toon, het ‘n laer assosiasie (56%) tot ASPV-infeksie gehad. Tans sal die beste praktyk aanbeveling vir siektebestuur insluit om ASPV-vrye plantmateriaal te plant en die teenwoordigheid van stinkbesies uit boorde uit te skakel.af_ZA
dc.description.versionMastersen_ZA
dc.format.extentx, 64 pages : illustrations (some color)en_ZA
dc.identifier.urihttps://scholar.sun.ac.za/handle/10019.1/128659
dc.language.isoen_ZAen_ZA
dc.publisherStellenbosch : Stellenbosch Universityen_ZA
dc.rights.holderStellenbosch Universityen_ZA
dc.subject.lcshApples -- Qualityen_ZA
dc.subject.lcshApples -- Diseases and pestsen_ZA
dc.subject.lcshFruit trade -- South Africa -- Quality controlen_ZA
dc.subject.lcshPear industry -- South Africa -- Western Capeen_ZA
dc.subject.lcshPear stony pit diseaseen_ZA
dc.subject.lcshPears -- Diseases and pestsen_ZA
dc.subject.lcshApple stem pitting virusen_ZA
dc.subject.lcshStinkbugsen_ZA
dc.subject.lcshTrees -- Phylogeny -- Molecular aspectsen_ZA
dc.subject.nameUCTDen_ZA
dc.titleThe characterization of the association of apple stem pitting virus with pear stony pit diseaseen_ZA
dc.typeThesisen_ZA
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