Thesis (MScAgric (Viticulture and Oenology))--University of Stellenbosch, 2010. / ENGLISH ABSTRACT: The table grape industry employ a wide range of viticultural management practices in order to produce the high quality grapes demanded by the export market. A common contributor to degrading the quality of table grapes is the occurrence of berry split, which not only has an unattractive visual effect, but also increases the berries’ susceptibility to infection by spoilage organisms. A number of environmental conditions such as rainfall and humidity, and/or agricultural practices, such as irrigation, and high density canopies, can lead to higher plant cell water content. This in turn, can increase the potential of berry split to occur. To date, the main method of berry split prevention has been the management of plant water status by; (i) regulating irrigation withdrawal times, and (ii) covering of canopies if rainfall is predicted prior to harvest. The aim of this study was to determine the effect that irrigation frequency, as induced by irrigation withdrawals; as well as boron (B) and calcium (Ca) treatments, applied as bunch directed sprays, have on pre- and post-harvest berry split. To this end, a newly released late ripening, white seedless cultivar, SoutherngrapeOne was chosen as a model cultivar as it has a high susceptibility to berry split. SoutherngrapeOne vines were subsequently subjected to a range of irrigation frequencies based on typical irrigation scheduling used in the table grape industry, which comprised of a low, medium and high frequency. The low frequency was duplicated in order to demonstrate the effect that a heavy irrigation, just before harvest may have on berry split. These treatments were further subdivided to investigate the effect that B and Ca may have on berry split. For the B treatment, four Solubor1 bunch directed sprays were applied from 8mm berry size to véraison. The Ca treatment consisted of Stopit R 2 and Caltrac R 3 bunch directed sprays applied over the same period. In addition, a combination of the B and Ca treatment were applied to investigate any possible interaction. To account for the effect of water as solvent in the B and Ca treatments, and the spraying effect, pure water as treatment was also evaluated. Control vines received no sprays. The applied irrigation treatments resulted in different plant water status conditions. Separate applications of B and Ca treatments resulted in a decrease of B and Ca content in the flesh respectively. The control and combination treatment, of B and Ca resulted in the same of B and Ca content in the flesh. Furthermore, none of the applied treatments resulted in an increase of either B or Ca content in the berry skin. It was found that the medium frequency irrigation resulted in the best irrigation strategy to prevent pre-harvest berry split. Surprisingly, all the subtreatments: B, Ca, and combination of B and Ca, resulted in an increased incidence of pre-harvest berry split when compared to the control group for the 2006/07 season. However, in the 2007/08 season only the B treatment resulted in an increase of pre-harvest berry split. Concerning post-cold-storage physiological disorders, Ca treatments appear to have reduced berry drop, but increased decay. In the 2006/07 season, the B treatment resulted in reduced post-cold-storage berry split, whereas Btreatment in the 2007/08 season had no effect. Both B and Ca should be considered as having the potential to increase the appearance of hairline cracking. Calcium treatment also led to an increase in decay which may have been as a result of the splitting it contributed to. Low frequency irrigation recieving irrigation before harvest was found to result in browner stems. Low irrigation frequencies decreased the cell size of the berry skin. The Ca treatment gave rise to thicker (weaker) cell walls, this morphological change may be responsible for the physiological disorders it caused. From these findings, it can be deduced that poorly managed irrigation, together with unnecessary application of B and/or Ca may result in an increase of berry split and other physiological disorders, with subsequent financial losses for the producer. / AFRIKAANSE OPSOMMING; Die tafeldruifindustrie maak gebruik van ’n wye reeks wingerdkundige praktyke ten einde die hoë gehalte druiwe te produseer wat die uitvoermark vereis. Korrelbars is ’n algemene verskynsel wat afbreek maak tot die gehalte van tafeldruiwe. Behalwe dat voorkoms van die druiwe benaadeel word, verhoog dit ook in vatbaarheid vir infeksie deur verrottingsveroorsakende swamme. Hoë reënval en humiditeit, sowel as wingerdkundige praktyke soos besproeiing en hoë lowerdigtheid, wat kan lei tot verhoogde waterstatus in plante, kan lei tot ’n toename in korrelbars. Daar word hoofsaaklik van twee metodes gebruik gemaak om korrelbars te beheer, naamlik die bestuur van plantwaterstatus deur; (i) beheer van besproeiingsontrekkingstye en (ii) bedekking van lowers indien reën voorspel word voor oestyd. Die doel van hierdie studie was om vas te stel wat die invloed van besproeiings frekwensies sowel as trosgerigte boor (B) en kalsium (Ca), spuitbehandelings, op voor- en na-oes korrelbars het. Die onlangs vrygestelde laat rypwordende, wit, pitlose kultivar, SoutherngrapeOne is gebruik, aangesien dit hoogs gevoelig is vir korrelbars. Stokke is aan verskillende besproeiings intervalle, soos tipies gebruiklik in die tafeldruifindustrie, blootgestel. Hierdie intervalle bestaan uit n’ lae, medium en hoë besproeiings frekwensie. Die lae besproeiings frekwensie is herhaal ten einde die invloed van besproeiing net voor oestyd op korrelbars te ondersoek. Die invloed van B- en Ca-behandeling op korrelbars is ook ondersoek. Vir die B-behandeling is vier Solubor1 trosgerigte spuite aangewend vanaf 8mm korrelgrootte tot deurslaan. Vir die Ca-behandeling is Stopit R 2 en Caltrac R 3 as trosgerigte spuite oor dieselfde tyd toegedien. Kombinasiebehandelings is ook aangewend om enige interaksie tussen B en Ca te ondersoek. Waterbehandelings is ook toegedien om die invloed van water as oplosmiddel van B- en Ca-behandelings sowel as die spuit-effek te ondersoek. Kontrole stokke is ook ingesluit en het geen spuitebehandeling ontvang nie. Die besproeiingsbehandelings het verskillende plantwater toestande tot gevolg gehad, B- en Ca-behandelings het gelei tot ’n afname in B- en Cainhoud in die vleis onderskeidelik. Die kombinasie en kontrole behandelings het eenderse hoeveelhede B en Ca in die vleis tot gevolg gehad. Geen van die aangewende behandelings gelei tot ’n toename in B- en Ca-inhoud in die dop nie. Die resultate toon dat medium besproeiings frekwensie die beste besproeiingsstrategie is om voor-oes korrelbars te voorkom. In vergelyking met die kontrole-behandeling in 2006/07, het B, Ca en die kombinasie van B en Ca, ’n toename in voor-oes korrelbars tot gevolg gehad. In die 2007/08 seisoen het slegs die B-toediening egter tot ’n toename in voor-oes korrelbars gelei. Kalsium behandelings het ’n afname in los-korrels, maar ’n verhoging in korrelbars tot gevolg gehad. In 2006/07, het B-toediening tot ’n afname in korrelbars na koelopberging gelei, maar in die 2007/08 seisoen het dit geen effek gehad nie. Beide B- en Ca-toediening het die potensiaal om haarlyn barste te veroorsaak. Kalsium toediening het bederf verhoog wat moontlik aan die hoër bars wat dit induseer toegeskryf kan word. Lae besproeiings frekwensie, het bruiner stingels veroorsaak, en ook gelei tot ’n afname van selgrootte in die dop. Die Ca-toediening het aanleiding gegee tot dikker selwande in die dop. Hierdie anatomiese veranderinge kan moontlik die rede wees vir die verhoging in fisiologise afwykings. Van hierdie bevindinge kan ons aflei dat swak bestuur van besproeiing, sowel as die onnodige aanwending van B en/of Ca, kan aanleiding gee tot ’n toename in korrelbars en ander fisiologiese afwykings, en dus finansiële verliese vir die produsent inhou.

Dissertation (PhD)--University of Stellenbosch, 2003. / ENGLISH ABSTRACT: A survey was conducted in the Western Cape Province during the 1999/2000 and 2000/2001 seasons on mealybugs occurring in vineyards. P/anococcus ficus (Signoret) was the dominant mealybug in vineyards during this time. During this study P. ficus was recorded for the first time on roots of grapevines, which has far reaching implications for the control of this important vine leafroll virus vector as control actions were focused on above ground control. Other mealybugs presently recorded in local vineyards included Pseudococcus /ongispinus (Targioni) and Ferrisia ma/vastra (McDaniel). Pseudococcus viburni (Maskell) and Ps. so/ani Ferris were found on weeds in vineyards. Natural enemies of P. ficus recorded most frequently were species of Nephus predatory beetles, and the parasitaids Coccidoxenoides peregrinus (Timberlake), Anagyrus sp. and Leptomastix dacty/opii (Howard). Developmental studies on P. ficus and C. peregrinus indicated that the intrinsic rate of increase (rm) was similar, peaking at 25°C (rm = 0.169 for P. ficus; rm = 0.149 for C. peregrinus). The net replacement rate (Ra) was higher for P. ficus than for C. peregrinus at all five temperatures tested. The Ra for P. ficus reached a maximum at 21°C (308.87) and C. peregrinus at 25°C for C. peregrinus (69.94). The lower and upper thresholds for development of P. ficus were estimated at 16.59 and 35.61°C respectively. The lower threshold for development of C. peregrinus was 8.85°C. These parameters indicated that both insects were well adapted to temperatures in the Western Cape Province. The lower minimum threshold temperature of C. peregrinus in relation to that of P. ficus suggests that C. peregrinus should be more active during winter and early spring than P. ficus. A central systematic presence-absence sampling system was developed for P. ficus. Monitoring three different plant parts on the vine indicated that new growth areas on vines adjacent to the main stem could serve as an early warning system for pending P. ficus bunch infestations. Intervention should be planned when 2 % of the stems are infested with P. ficus when using this system. Seasonal population studies of P. ficus and its natural enemies showed that stem infestation by P. ficus reached peak levels during January in Robertson and Stellenbosch and during February in the Hex River Valley. Vine mealybugs colonised new growth early in the season, followed by the leaves and eventually the bunches towards the end of the season. High stem infestations early in the season resulted in high bunch infestation levels at harvest. A density dependent relationship was evident between P. ficus populations and parasitoid populations, suggesting that the parasitoids played a mayor role in the biological control of P. ficus populations. Biological control was however only achieved towards the end of the season when damage to the crop had already occurred. Mass releases of C. peregrinus on P. ficus populations were done in order to augment biological control as an alternative to chemical control. Between five and six releases of 20 000 C. peregrinus per release were done at monthly intervals in three grapegrowing areas. Mass released C. peregrinus controlled P. ficus adequately in the Hex River Valley. Control of P. ficus using this approach was no worse than using chemical control in Robertson and Stellenbosch. C. peregrinus is commercially available and can therefore be used as an alternative to chemical control by producers. Degree day estimation was used to predict development of P. ficus populations. This information was used as an input in a P. ficus pest management model. Data acquired from P. ficus and ant monitoring were used as components to construct a decision chart. This chart can be used by producers to optimise the control of P. ficus populations using either chemical control or mass releases of C. peregrinus. / AFRIKAANSE OPSOMMING: "n Studie is gedurende die 1999/2000 en 2000/2001 seisoene gedoen met die doelom die witluisspesies wat in wingerde voorkom, te identifiseer. Planococcus ficus (Signoret) is tans die dominante witluisspesie in wingerde in die Wes Kaap Provinsie. P. ficus kolonies is op wingerdwortels gevind. Dié bevinding kan verreikende gevolge hê vir die beheer van dié plaag as "n belangrike rolbladvirus vektor aangesien beheer tot dusver gefokus het op bogrondse gedeeltes. Ander witluisspesies wat in wingerde gevind is, sluit in Pseudococcus /ongispinus (Targioni) en Ferrisia malvastra (McDaniel). Pseudococcus vibumi (Maskell) en Ps. so/ani Ferris is op onkruide in wingerde gevind. Dominante natuurlike vyande van P. ficus sluit predatoriese kewertjies van verskeie Nephus spp. en die parasitoïede Coccidoxenoides peregrinus (Timberlake), Anagyrus sp. en Leptomastix dacty/opii (Howard) in. Ontwikkelingstudies op P. ficus en C. peregrinus het aangetoon dat die inhirente voortplantingstempo (rm) soortgelyk was vir beide insekte met "n maksimum by 25°C (0.169 vir P. ficus, 0.149 vir C. peregrinus). Die netto vervangingstempo (Ra) was in vergelyking met C. peregrinus hoër vir P. ficus by al vyf temperature getoets. Die Ra van P. ficus het "n maksimum bereik teen 21°C (308.87) en die van e. peregrinus by 25°C (69.94). Die teoretiese hoër en laer drempels vir ontwikkeling van P. ficus was onderskeidelik 16.59 en 35.61 oe. Die teoretiese laer drempelwaarde van ontwikkeling vir e. peregrinus was 8.85°e. Hierdie parameters dui aan dat beide insekte goed aangepas is by temperature in die Wes Kaap Provinsie. Die laer minimum drempel vir ontwikkeling van C. peregrinus in verhouding tot P. ficus impliseer dat C. peregrinus in die winter en vroeë lente meer aktief sal wees as P. ficus. 'n Sentrale sistematiese aan-afwesig moniteringsisteem met bekende vlakke van steekproefnemingsfout is ontwikkel in kommersiële wingerde vir P. ficus. Monitering van drie verskillende dele op die wingerdstok het aangedui dat die nuwe groei areas kan dien as 'n vroeë waarskuwing vir latere P. ficus trosinfestasies. Dié sisteem sal produsente in staat stelom te bepaal wanneer optrede noodsaaklik is. Daar word voorgestel dat optrede noodsaaklik is by 'n P. ficus besmettingsvlak van 2 % op die nuwe groei areas op stokke. Stambesmetting deur P. ficus het in Januarie piekvlakke bereik in Stellenbosch en Robertson, en in Februarie in die Hex Rivier Vallei. P. ficus koloniseer nuwe groei vroeg in die seisoen waarna blare en trosse aan die einde van die seisoen gekoloniseer word. Dié data dui aan dat P. ficus besmetting op nuwe groei vroeg in die seisoen 'n aanduiding kan gee van hoë trosbesmetting aan die einde van die seisoen. 'n Digtheidsafhanklike verwantskap was waarneembaar tussen P. ficus plaagpopulasies en parasitoïed populasies. Dié verwantskap dui aan dat parasitoïede die belangrikste rol speel in biologiese beheer van P. ficus populasies. Biologiese beheer van witluis is egter eers aan die einde van die seisoen bereik toe die oes reeds beskadig was. Massavrylatings van C. peregrinus is in P. ficus besmette blokke gedoen om biologiese beheer aan te help en sodoende as alternatief tot chemiese beheer te dien. Tussen vyf en ses vrylatings met 20 000 C. peregrinus is een keer per maand gedurende die seisoen gedoen. Die vrygelate C. peregrinus het P. ficus populasies voldoende beheer in die Hex Rivier Vallei. Beheer van P. ficus deur massavrylatings van C. peregrinus was soortgelyk as chemiese beheer in Robertson en Stellenbosch. C. peregrinus is kommersieel beskikbaar en kan om hierdie rede as alternatief tot chemiese beheer gebruik word. Graaddag bepaling is gebruik om die ontwikkeling van P. ficus populasies te voorspel. Hierdie inligting is gebruik as 'n verdere hulpmiddel in die P. ficus plaagbeheermodel. Inligting verkry vanuit P. ficus en mier monitering is gebruik as komponente in die opstel van 'n besluitnemingstabel. Hierdie tabel kan gebruik word deur produsente om beheer van P. ficus plaagpopulasies te optimaliseer deur chemiese beheer of massavrylatings van C. peregrinus.

Thesis (MSc)--Stellenbosch University, 2003. / ENGLISH ABSTRACT: Paecilomyces Ii/acinus, ras 251 (geregistreer in terme van wet 36 van 1947 as Suid-Afrika se eerste natuurlike nematisiede en kommersieel beskikbaar as PI Plus) is as biologiese beheer agent getoets by aartappels en in geïntegreerde beheer programme by sitrus en wingerd teen respektiewelik Me/oidogyne species, Ty/enchu/us semipenetrans en verskeie ektoparasitiese nematodes. Die swam toon belofte vir die beheer van hierdie nematodes en het terselfdertyd nie 'n nadelige effek op nie-teiken, voordelige organismes in die grond nie. Veral in kombinasie met chemiese middels, as deel van geïntegreerde programme, kan dit lei tot verminderde gebruik van hoogs toksiese middels en dus meer omgewingsvriendelike landboupraktyke. Biological control of plant parasitic nematodes on potatoes, citrus and grapevine with the fungus, Paecilomyces liIacinus. Paecilomyces liIacinus, race 251 (registered in terms of act 36 of 1947 as South Africa's first natural nematicide, commercially available as PI Plus) was tested as a biological control agent on potatoes and in integrated control programs on citrus and grapevine against Me/oidogyne species, Ty/enchu/us semipenetrans and various ectoparasitic nematodes respectively. The fungus shows promise for the control of these nematodes, without having a harmful effect on non-target, beneficial organisms in the soil. Especially in combination with chemical products, as part of integrated programs, this can lead to less use of highly toxic compounds and thus to more environmentally friendly agricultural practices. / AFRIKAANSE OPSOMMING: Sedert die ontdekking van die swam, Paeci/omyces Ii/acinus (Thom.) Samson as 'n effektiewe eierparasiet van Meloidogyne incognita acrita en Globodera pal/ida (Jatala et al., 1979) het verdere veldproewe in Peru tot die effektiewe beheer van M. incognita en Tylenchulus semipenetrans gelei. Na verskeie suksesse in Peru is die swam onder verskillende klimaat- en grondkondisies in verskeie ander lande beproef. Die sukses behaal in die Filippyne het gelei tot die kommersiële produksie van die swam onder die handelsnaam Biocon. Anders as met chemiese middels vind die werking van biologiese agente stadig oor tyd plaas. Biologiese beheer sal nie chemiese beheer sonder meer kan vervang nie. Dit behoort egter deel te vorm van geïntegreerde nematode bestuur. Inkorporering van die natuurlike organismes, die oordeelkundige gebruik van chemiese nematisiedes, moontlik in kombinasie met die biobeheer agente, weerstand, en ander kulturele praktyke moet ernstig oorweeg word as ons hoop om die steeds groeiende wêreldbevolking te voed (Jatala, 1986). Paecilomyces liIacinus, ras 251, Suid-Afrika se eerste geregistreerde natuurlike nematisiede, kommersieel beskikbaar as PI Plus, is in die Olifantsrivier besproeiingsgebied geëvalueer vir die bestuur van ekonomies belangrike plantparasitiese nematodes by aartappels, sitrus en wingerd. Hierdie gewasse is belangrike bedryfstakke van die streek en is onderhewig aan skade deur nematodes wat die opbrengs nadelig beïnvloed. Chemiese beheer bied slegs 'n korttermyn oplossing vir nematode probleme en skadelike getalle word in 'n kort tyd weer opgebou. Boonop lei dié hoogs toksiese middels tot agteruitgang van die omgewing en sy waterbronne. Die toenemende besorgdheid hieroor en die groot potensiaal van biologiese beheer agente (Jatala, 1986) was die hoofrede vir die werk waaroor hier gerapporteer word.

Downy mildew, caused by the biotrophic Oomycete Plasmopara viticola, is one of the most important diseases of grapevines world wide. It is particularly destructive in temperate viticultural regions that experience warm wet conditions during the vegetative growth of the vine (Wong et al., 2001). The disease is not normally a problem in mediterranean climates where the growing season tends to be hot and dry (Mullins et al., 1992; Sivasithamparam, 1993). Grape downy mildew is however a major disease in Australian viticulture (McLean et al., 1984; Magarey et al., 1991). Grape downy mildew was first reported in Europe in 1878 (Viennot-Bourgin, 1981). In Australia, it was recorded for the first time in 1917 at Rutherglen in Victoria (Vic) (de Castella, 1917). The first recorded outbreak of the disease in Western Australia (WA) occurred in 1997 in a small planting of vines in the far north of the state. In the subsequent year, it was detected in widespread commercial viticulture in the Swan Valley production area, near Perth (McKirdy et al., 1999). The pathogen has since been found in all grape growing regions of WA. Since its introduction into European vineyards in the 1880?s, P. viticola has become one of the world?s most investigated grapevine pathogens. Many aspects its basic biology however remain unknown (Wong et al., 2001). Due to the recent detection of P. viticola in WA, little is known of the nature of strains of the pathogen in the state and their response to local environmental conditions. Much of the research concerning the influence of environmental factors on the development of P. viticola has been conducted in Europe e.g. parts of France and Germany. Due to significant differences in climatic conditions and a shorter selection time on the pathogen in WA, much of the information described in European studies may not be directly applicable to the grape downy mildew disease situation in WA. The focus of this thesis was to examine epidemiological aspects of P. viticola in the mediterranean climate of WA. The environmental conditions that could favour the development of epidemics by strains of the pathogen that have been detected in the state were determined. The existence of P. viticola ecotypes and genetic variation among strains from WA and the Eastern states of Australia was also investigated.

Thesis (MSc (Genetics))--University of Stellenbosch, 2010. / Includes bibliography. / Title page: Dept. of Genetics, Faculty of Science / ENGLISH ABSTRACT: Next-generation sequencing technologies are increasingly used in metagenomic studies, largely due to the high sequence data throughput capacity and unbiased approach in determining the genetic composition of an unknown environmental sample. This study investigated the applicability of the Illumina next-generation sequencing platform for metagenomic sequencing of grapevine viruses to provide the first complete viral profile, or virome, of a diseased vineyard. Leaf material was harvested from 44 randomly selected vines in a leafroll-diseased vineyard in South Africa. Sample material was pooled and double-stranded RNA extracted. The dsRNA was sequenced as a paired-end sequencing run using the Illumina sequencing-by-synthesis technique, and more than 19 million sequence reads, equivalent to approximately 837 megabases of metagenomic sequence data, were obtained. Of these data, approximately 400 megabases could be assembled into 449 scaffolds, using the de novo assembler Velvet. These scaffolds were subjected to BLAST searches against the NCBI databases and top hit scores were used for virus identification. Based on the BLAST results, suitable sequences were selected from the NCBI database and used as reference sequence in MAQ mapping assemblies. The bioinformatic analyses allowed for the determination of the virus species present, the most prominent variants, and the relative abundance of each. Four known grapevine viral pathogens were identified. Grapevine leafroll-associated virus 3, representing 59% of the analyzed short read sequence data, was identified as the most prominent virus species. Three variants of this virus were detected: GP18 was the most abundant, followed by a minor Cl766/NY1 variant and a potential novel grapevine leafroll-associated ampelovirus. A single Grapevine rupestris stem pitting ]associated virus variant, similar to SG1, and a Grapevine virus A variant, a member of molecular group III, were identified. This study is also the first to report the presence of Grapevine virus E (GVE) in South African vineyards. Grapevine virus E was further genetically characterized and the genome sequence of GVE isolate SA94 determined. The GVE SA94 genome sequence, 7568 nucleotides in length, is the first complete genome sequence for the virus species. The genome organization of GVE SA94 is typical of vitiviruses, but in contrast to other RNA viruses, the AlkB domain is located within the helicase domain in open reading frame 1 (ORF 1). Grapevine virus E SA94 shares nearly 100% nucleotide identity with the Japanese TvP15 isolate and GVE 3404, a de novo scaffold generated from the metagenomic sequence data. Bioinformatic analysis of metagenomic sequence data further revealed the presence of three fungus-infecting viral families, Chrysoviridae, Totiviridae and the unclassified dsRNA virus, Fusarium graminearum dsRNA mycovirus 4. A virus from the family Chrysoviridae, similar to Penicillium chrysogenum virus, was the second most abundant virus detected. We demonstrated the successful application of a short read sequencing technology, such as the Illumina platform, for viral profiling of an infected vineyard. To our knowledge this is the first application of the Illumina technology for this purpose. / AFRIKAANSE OPSOMMING: Volgende-generasie tegnologie om basis volgordes van nukleiensure te bepaal, word al meer gebruik in metagenomiese studies. Dit is veral weens die hoe data-omset kapasiteit en onbevooroordeelde aanslag in die bepaling van die genetiese samestelling van onbekende omgewingsmonsters. Hierdie studie het die aanwending van die Illumina volgende-generasie volgorde-bepalingsplatform in 'n metagenomiese studie van wingerdvirusse, ondersoek. Dit het ten doel gehad om die eerste volledige virus profiel, of viroom, van 'n geinfekteerde wingerd saam te stel. Blaarmateriaal is verkry vanaf 44 lukraak-gekose wingerdstokke in 'n rolblad-geinfekteerde wingerd in Suid-Afrika. Monster materiaal is saamgevoeg en dubbelstring-RNS geekstraheer. Die dubbelstring-RNS is onderwerp aan gepaarde-ent volgorde-bepaling deur gebruik te maak van die Illumina volgorde-bepaling-deur-sintese tegniek. Meer as 19 miljoen volgorde reekse, ekwivalent aan ongeveer 837 megabasisse volgorde data, is verkry. Van hierdie data kon ongeveer 400 megabasisse saamgevoeg word in 449 konstrukte ("scaffolds"), deur gebruik te maak van die de novo samesteller Velvet. Hierdie konstrukte is onderwerp aan BLAST soektogte teen die NCBI databasisse en die hoogste trefslag-telling is gebruik vir virus identifikasie. Op grond van die "BLAST" resultate is geskikte volgordes geselekteer vanaf die NCBI databasis en gebruik as verwysingvolgordes in MAQ kartering-analises. Met die bioinfomatika analises kon die virus spesies teenwoordig, asook die mees prominente variante en relatiewe voorkoms van elk, bepaal word. Vier bekende virus wingerdpatogene is geidentifiseer. Grapevine leafroll-associated virus 3, verteenwoordig deur 59% van die geanaliseerde kort-reeks volgorde data, is identifiseer as die mees prominente virus spesie. Drie variante van die virus is in die wingerdmonster opgespoor: GP18 kom die mees algemeen voor, gevolg deur 'n CL-766/NY1 variant en 'n potensiele nuwe wingerd rolblad-geassosieerde ampelovirus. 'n Enkele Grapevine rupestris stem pitting-associated virus variant, soortgelyk aan SG1, en 'n Grapevine virus A variant, 'n lid van molekulere groep III, is geidentifiseer. Hierdie studie is ook die eerste om die teenwoordigheid van Grapevine virus E (GVE) in Suid-Afrikaanse wingerde te rapporteer. Grapevine virus E is verder geneties gekarakteriseer en die genoomvolgorde van GVE isolaat SA94 is bepaal. Die GVE SA94 genoomvolgorde, 7568 nukleotiede lank, is die eerste volledige genoomvolgorde vir hierdie virus spesie. Die genoomorganisasie is tipies van vitivirusse, maar in kontras met ander RNA virusse is die AlkB domein binne-in die helikase domein van oopleesraam 1 (ORF 1) geleë. Grapevine virus E SA94 deel byna 100% nukleotied identiteit met die Japannese TvP15 isolaat en GVE 3404, 'n de novo konstruk gegenereer vanaf die metagenomiese volgorde data. Bioinformatika analises van die metagenomiese volgorde data het verder die teenwoordigheid van drie swam-infekterende virus families, die Chrysoviridae, Totiviridae en ongeklassifiseerde dubbelstring-RNS virus, Fusarium graminearum dsRNA mycovirus 4, aangetoon. 'n Virus van die Chrysoviridae familie, soortgelyk aan Penicillium chrysogenum virus, het die tweede meeste voorgekom in die wingerd monster. Hierdie studie demonstreer die suksesvolle toepassing van 'n kort reeks volgorde-bepalingstegnologie soos die Illumina platform, vir die opstel van 'n virusprofiel van 'n geinfekteerde wingerd. Sover ons kennis strek is hierdie die eerste aanwending van die Illumina tegnologie vir hierdie doel.

Thesis (MScAgric)--University of Stellenbosch, 2004. / ENGLISH ABSTRACT: Soilborne diseases of grapevines represent a complex problem with limited information available, both locally and internationally. Previous research in South Africa indicated that Phytophthora and Pythium spp. were the most widespread and devastating pathogens in grapevine nurseries and vineyards in the Western Cape province. The local grapevine industry is currently expanding; new cultivars, methods and agricultural chemicals are being used which can affect soilborne pathogens. It has therefore become necessary to reassess the status of soilborne pathogens in nurseries, since information in this regard is crucial for the development of disease management practices for the expanding local grapevine industry. Soilborne fungal genera associated with roots and crowns of declining nursery grapevines were assessed in surveys conducted at three different grapevine nurseries in the Western Cape province. Cylindrocarpon, Fusarium, Pythium, and Rhizoctonia spp. were consistently isolated from roots and crowns of declining nursery grapevines. Cylindrocladiella spp. and Phytophthora cinnamomi were infrequently isolated from diseased roots, crowns and soil whereas Pythium spp. were abundant in most of the soils. Results suggest that the status of soilborne fungal pathogens in grapevine nurseries in the Western Cape province has changed over the last 30 years. The DNA phylogeny and pathogenicity of the isolates of Cylindrocladiella were determined. Four species of Cylindrocladiella occur on grapevines in South Africa, namely C. lageniformis, C. parva, C. peruviana, as well as a new species, described in this study as C. viticola, which forms part of the C. infestans species complex. Pathogenicity trials were inconclusive. Ten Fusarium spp. were isolated from roots and crowns of declining nursery grapevines, namely F. acuminatum, F. anthophilum, F. chlamydosporum, F. equiseti, F. nygamai, F. oxysporum, F. proliferatum, F. scirpi, F. semitectum and F. solani. The dominant species was F. oxysporum, followed by F. proliferatum and F. solani. In pathogenicity trials F. oxysporum and F. solani significantly reduced root volume, root dry mass, length of new shoots, stem diameter and number of leaves, but increased the percentage of chlorotic leaves and root rot severity. Fusarium proliferatum also caused a significant reduction in new shoot growth, number of leaves and increased root rot severity compared to the controls. Fusarium so/ani seems to be more virulent than F. oxysporum, followed by F. pro/iferatum. This is the first report of F. oxysporum, F. pro/iferatum and F. so/ani as pathogens of grapevines in South Africa, and the first report of F. proliferatum as a pathogen of grapevines in the world. Phytophthora cinnamomi was isolated at low frequencies from declined grapevines, although present in the rhizosphere soil. It is possible that the extensive use of downy mildew chemicals in grapevine nurseries may protect grapevines from infection by P. cinnamomi. The effect of chemicals used to combat downy mildew on Phytophthora root rot of nursery grapevines was evaluated in a glasshouse. There was very little discernable effect of the chemicals tested relative to the control plants for the parameters measured and it was concluded that the inoculation technique needed refinement. However, plants treated with phosphorous acid tended to be taller and have more leaves, greater stem diameter and root volume than controls or plants treated with the other chemicals. The data obtained in this study are not conclusive, but indicated certain trends that more glasshouse trials and field trials would resolve. Results presented in this thesis indicate that a major shift has occurred in the status of soilborne fungi associated with roots and crowns of grapevines in nurseries in the Western Cape since the 1970s when Phytophthora and Pythium were predominant. The prevalence and role of soilborne fungi need to be determined so that new appropriate disease management strategies can be developed to limit losses in grapevine nurseries and ensure the sustainable production of healthy plants for the grapevine industry. / AFRIKAANSE OPSOMMING: 'N ONDERSOEK NA GRONDGEDRAAGDE SWAMME GEASSOSIEER MET WORTELS EN KRONE VAN WINGERD IN KWEKERYE Grondgedraagde siektes van wingerd is 'n komplekse probleem waaroor min inligting, beide plaaslik en internasionaal, beskikbaar is. Vorige navorsing in Suid-Afrika het aangedui dat swamme van die genera Phytophthora en Pythium die mees algemene en vernietigende grondgedraagde patogene in kwekerye en wingerde in die Wes-Kaap provinsie is. Die plaaslike wingerdbedryf brei huidiglik uit; nuwe kultivars, metodes en landbouchemikalieë word gebruik wat 'n invloed kan hê op grondgedraagde patogene. Gevolglik het dit noodsaaklik geword om die status van grondgedraagde patogene in wingerdkwekerye weer te bepaal, aangesien inligting in hierdie verband noodsaaklik is vir die ontwikkeling van siekte bestuurspraktyke vir die ontwikkelende plaaslike wingerdbedryf. Grondgedraagde swamgenera geassosieer met wortels en krone van terugsterwende wingerd in kwekerye is bepaal in opnames wat by drie verskillende wingerdkwekerye in die Wes-Kaap provinsie uitgevoer is. Cylindrocarpon, Fusarium, Pythium, en Rhizoctonia spp. is konstant vanuit wortels en krone van terugsterwende wingerdplante in kwekery geïsoleer, Cylindrocladiella spp. en Phytophthora cinnamomi is ongereeld vanuit siek wortels, krone en grond geïsoleer, terwyl Pythium spp. algemeen in meeste gronde voorgekom het. Resultate dui daarop dat die status van grondgedraagde swampatogene in wingerdkwekerye in die Wes- Kaap provinsie oor die laaste 30 jaar verander het. Die DNA filogenie en patogenisiteit van die isolate van Cylindrocladiella is bepaal. Vier spesies van Cylindrocladiella kom voor op wingerd in Suid-Afrika, naamlik C. lageniformis, C. parva, C. peruviana, sowel as 'n nuwe spesie, wat in hierdie studie as C. viticola aangedui is en wat deel is van die C. infestans spesie kompleks. Patogenisiteits proewe was onvoldoende om die patogeniese status van die swam me te bepaal. Tien Fusarium spp. is vanuit wortels en krone van terugsterwende wingerdplante in kwekery geïsoleer, naamlik F. acuminatum, F. anthophilum, F. chlamydosporum, F. equiseti, F. nygamai, F. oxysporum, F. proliferatum, F. scirpi, F. semitectum en F. solani. Die dominante spesies was F. oxysporum, gevolg deur F. proliferatum en F. solani. In pathogenisteitsproewe het F. oxysporum en F. solani gelei tot 'n betekenisvolle laer wortelvolume, droë massa van wortels, lengte en droë massa van nuwe groei en aantal blare, maar het die persentasie chlorotiese blare en graad van wortelvrot verhoog. Fusarium proliferatum het ook gelei tot 'n betekenisvolle afname in lengte en massa van nuwe groei, aantal blare en 'n verhoogde graad van wortelvrot in vergelyking met die kontrole behandelings. Dit wil voorkom asof Fusarium solani meer virulent is as F. oxysporum, gevolg deur F. proliferatum. Hierdie is die eerste aanmelding van F. oxysporum, F. proliferatum en F. solani as patogene van wingerd in Suid-Afrika, en die eerste aanmelding van F. proliferatum as 'n patogeen van wingerd in die wêreld. Phytophthora cinnamomi is konstant teen lae frekwensies vanuit terugsterwende wingerd in kwekerye geïsoleer, alhoewel dit in risosfeer gronde teenwoordig was. Dit is moontlik dat die ekstensiewe gebruik van chemikalieë teen donsskimmel in wingerdkwekerye die wingerdplante kan beskerm teen infeksie deur P. cinnamomi. Die effek van chemikalieë wat gebruik word teen donsskimmel op Phytophthora wortelverrotting van wingerd in kwekerye, is 'n glashuis geëvalueer. Die chemikalieë wat gestoets is, het vir die gemete parameters, tot baie min onderskeibare effek gelei relatief tot die kontrole plante, en daar is afgelei dat die inokulasie tegniek verbetering benodig. Plante wat met fosforiensuur behandel is, het egter geneig om langer te wees met meer blare, 'n groter stamdeursnee en wortelvolume as kontrole plante of plante behandel met ander chemikalieë. Data verkry vanuit die hierdie studie was onvoldoende, maar sekere neigings is aangedui wat deur verdere glashuis- en veldproewe verklaar sal word. Resultate wat in hierdie tesis weergegee is, het aangedui dat 'n algehele verskuiwing in die status van grondgedraagde swamme geassosieer met wortels en krone van wingerd in kwekerye vanaf die 1970s, toe Phytophthora en Pythium die dominante genera was, plaasgevind het. Die voorkoms en rol van grondgedraagde swamme moet bepaal word, sodat nuwe voldoende siektebestuurspraktyke ontwikkel kan word om verliese in wingerdkwekerye te beperk en sodoende die volhoubare produksie van gesonde plante vir die wingerdbedryf te verseker.

Thesis (PhD (Genetics))--University of Stellenbosch, 2010. / Includes bibliography. / Title page: Dept. of Genetics, Faculty of Science / ENGLISH ABSTRACT: Grapevine leafroll-associated virus 3 (GLRaV-3) is the type strain for the genus Ampelovirus, family Closteroviridae. There has been only one report that claimed the complete nucleotide sequence of GLRaV-3 (isolate NY-1, AF037268). Here we report the complete sequence of the South African GLRaV-3, isolate GP18 (EU259806) and show a significantly extended 5’ end. We used RLM-RACE to determine the 5’ end of GP18 and found the 5’ UTR to be 737 nt compared to 158 nt in the NY-1 sequence. This extended UTR was found in all other South African isolates of GLRaV-3 that were tested. In two collaborative studies the existence of the extended 5’ UTR was confirmed and further investigated. In the first study (Coetzee et al., 2010), metagenomic data generated by next generation sequencing (Illumina Genome Analyzer II) was analysed for GLRaV-3 specific sequences. Sequences similar to the GP18 isolate confirmed the sequence of the extended 5’ UTR. In the second study (Jooste et al., 2010), three genetic variants were identified and their respective 5’ UTRs studied. Great diversity was observed between the 5’ UTRs of the different genetic variants, however within a variant the 5’ UTR was found to be highly conserved. Grapevine leafroll-associated virus 3 is a positive sense, single stranded RNA virus that has been shown, like other closteroviruses, to produce subgenomic (sg) RNAs during replication. These sgRNAs are deployed for the expression of the ORFs on the 3’ half of the genome. In this study a dsRNA blot confirmed the presence of three, 3’ coterminal sgRNAs species [sgRNA(ORF3/4), sgRNA(ORF5) and sgRNA(ORF6)] in GLRaV-3-infected plant material when using a probe directed at the coat protein gene. The specific 5’ terminal nucleotides for these sgRNAs as well as four additional sgRNAs [sgRNA(ORF7), sgRNA(ORF8), sgRNA(ORF9) and sgRNA(ORF10-12)] were determined by RLM-RACE for GLRaV-3 isolate GP18. The construction of a GLRaV-3 mini-replicon, analogous to RNA1 of Lettuce infectious yellows virus, for the evaluation of putative sg-promoters is also described. / AFRIKAANSE OPSOMMING: Grapevine leafroll-associated virus 3 (GLRaV-3) is ‘n lid van die Closteroviridae familie en die hooflid vir die genus Ampelovirus. Tot dusver was daar net een studie wat die volledige nukleïensuurvolgorde van GLRaV-3 gerapporteer het (isolaat NY-1, AF037268). In hierdie studie rapporteer ons die volledige volgorde van ‘n Suid-Afrikaanse GLRaV-3, isolaat nl. GP18 (EU259806) wat noemenswaardig langer is aan die 5’ kant. RLM-RACE is gebruik om die 5’ eindpunt van GP18 te bepaal en daar is gevind dat die 5’ ongetransleerde streek (UTR) 737 nt lank is in vergelyking met die 158 nt van die NY-1 volgorde. Die verlengde 5’ UTR is gevind in alle Suid-Afrikaanse monsters wat getoets is. Die verlengde 5’ UTR is bevestig en verder bestudeer tydens twee samewerkingsprojekte. In die eerste studie (Coetzee et al., 2010), is metagenomiese data gegenereer deur volgende-generasie volgordebepaling (Illumina Genome Analyzer II) en geanaliseer vir GLRaV-3 spesifieke volgordes. Volgordes soortgelyk aan die GP18 isolaat het die verlengde 5’ UTR volgorde bevestig. In die tweede studie (Jooste et al., 2010), is drie genetiese variante van GLRaV-3 geidentifiseer en hulle onderskeie 5’ UTR volgordes bepaal en bestudeer. Daar is groot diversiteit tussen die 5’ UTRs van die verskillende genetiese variante gevind, maar tussen isolate van dieselfde variant is die volgordes gekonserveerd. Grapevine leafroll-associated virus 3 is ‘n positiewe-sin, enkelstring RNA virus wat al voorheen bewys is om, soos ander closterovirusse, subgenomiese (sg) RNAs te produseer tydens replisering. Hierdie sgRNAs word ingespan vir die uitdrukking van die ORFs op die 3’ helfte van die virusgenoom. In hierdie studie is ‘n dsRNA klad gebruik om die voorkoms van 3’ ko-terminale sgRNAs [sgRNA(ORF3/4), sgRNA(ORF5) and sgRNA(ORF6)] te bevestig in GLRaV-3 geinfekteerde plantmateriaal deur gebruik te maak van ‘n peiler teen die kapsiedproteïengeen. Die spesifieke 5’ terminale nukleotiedes vir hierdie sgRNAs sowel as vier additionele sgRNAs [sgRNA(ORF7), sgRNA(ORF8), sgRNA(ORF9) and sgRNA(ORF10-12)] is bepaal deur gebruik te maak van RLM-RACE op die GLRaV-3 isolaat GP18. Die konstruksie van ‘n GLRaV-3 mini-repliserings konstruk, analoog aan die RNA1 van Lettuce infectious yellows virus, vir die evaluasie van moontlike sg-promotors word ook beskryf.

Thesis (MScAgric (Conservation Ecology and Entomology)--University of Stellenbosch, 2005. / The South African table grape industry exports approximately 60% of the table grapes produced. A major threat to the export of these grapes is the phytosanitary risk that insect pests pose. This study was conducted in the Hex River Valley, South Africa’s main table grape producing area. The aim of this study was to reduce the number of phytosanitary rejections from insects on table grapes from the Hex River Valley. Thus the main objectives of the study were to identify the most important phytosanitary pests in the Hex River Valley; the determination of their presence in the vineyards with possible means to control them; and to assess the possibility of using postharvest quarantine treatments in the Western Cape. Further aims were to determine the effect of different colour harvesting crates on the phytosanitary pests and whether the phytosanitary pests infested the grapes via packhouses. The most important phytosanitary pests of table grapes of the Hex River Valley are in order of importance: Phlyctinus callosus (Schonherr) (Coleoptera: Curculionidae), Epichoristodes acerbella Walker (Lepidoptera: Tortricidae), Planococcus ficus (Signoret) (Hemiptera: Pseudococcidae), Ceratitis capitata (Wiedemann) (Diptera: Tephritidae), Gonocephalum simplex Fabricius (Coleoptera: Tenebrionidae) and Dysdercus fasciatus Signoret (Hemiptera: Pyrrhocoridae). 12.71% of rejections were from species that were not identified, while a further 33% of the rejections were possibly identified incorrectly. Phytosanitary control of P. callosus appeared to be far more effective using Plantex® than pesticides. Weather conditions appeared to affect the abundance of P. callosus, especially warm weather, while bunches harboured less P. callosus later in the day. Control of E. acerbella with DiPel® (Bacillus thuringiensis var. kurstaki) appeared to at least reduce the population within the vineyards, and so its use is recommended. P. ficus is a non-actionable species for the USA market and is not listed as a phytosanitary pest for the Israeli market and so should not be causing any phytosanitary rejections. C. capitata appeared to be successfully controlled by the fruit fly sterile release program and the cold sterilisation it currently undergoes. G. simplex caused few rejections. It is still unclear where this pest infests the grapes, as it was found in both the field and in the packhouses. D. fasciatus occurrence on grapes was probably accidental. It was shown that picking during the early and late parts of the day, when this species was less active, reduced its occurrence in bunches. Gryllus bimaculatus (De Geer) (Orthoptera: Gryllidae), although not reported as a reason for rejections in table grapes for the past two years, was an actionable species that was present in large numbers in the Hex River Valley. There was a strong correlation between increasing quantities of pesticides and higher abundances of G. bimaculatus. It appeared to be an indicator of the overuse of pesticides. Results of this study showed that infestation by the phytosanitary pests came from neighbouring vineyards. The creation of barriers to prevent the movement of these pests between vineyards is suggested. Methyl bromide is the most commonly used postharvest quarantine treatment. Owing to the ozone-depleting properties of methyl bromide, it is scheduled to be outlawed in many countries from 2005. Alternative postharvest treatments are irradiation, extreme temperatures, forced air, vapour-heat treatments and the use of controlled atmospheres. Irradiation treatments appeared to control the pests at doses that do not damage the grapes. Controlled atmosphere treatments also have a high probability of success, although more research is required on this treatment. Low temperature treatments are relatively cheap as most exported fruit already undergoes cold storage, and appears to control species in the families Pseudococcidae and Tephritidae, although further research is required for the other pest. Colour or location of the harvesting crates in the vineyards appeared not to influence the number of phytosanitary pests collected, as they were not attracted to these crates.

Thesis (MSc (Genetics))--Stellenbosch University, 2008. / South Africa is one of the top ten wine producing countries in the world. The South African wine industry contributes approximately R16.3 billion to South Africa’s annual gross domestic product with 42.8% of wine being exported. To compete with the top wine producing countries and to ensure a viable export market, South Africa needs to ensure that healthy, virus free propagation material is produced and sold. One of the viruses that need to be tested for is Grapevine fanleaf virus (GFLV). Grapevine fanleaf virus causes degeneration and malformation of berries, leaves and canes and is responsible for significant economic losses by reducing crop yields by as much as 80%, reducing the longevity of the vines and affecting fruit quality. It is widespread in the Breede River Valley of the Western Cape where the nematode vector, Xiphinema index, is prevalent. The Breede River Valley contributes approximately 30% of the total production of the local wine industry, and severe losses in this region could threaten the viticulture. The Plant Improvement Act states that all propagation material sold must be tested for GFLV by a reputable scientific technique. The technique commonly used in South Africa is the Double Antibody Sandwich - Enzyme-linked Immunosorbent Assay (DAS-ELISA) and the kits are imported from Europe at a significant cost to the South African viticulture industry. The objective of this study was to produce a reliable and sensitive diagnostic assay specific for the South African strains of GFLV. This project aimed to develop and optimize a DAS-ELISA, by using recombinant DNA technology to produce antibodies against bacterially expressed viral coat protein. Total RNA was extracted from GFLV infected grapevine material and the viral coat protein (CP) amplified. The CP was cloned into the pGex-6P-2 expression vector, fusing a Glutathione STransferase (GST) partner to the viral coat protein enhancing solubility and protein purification. Insufficient amounts of the soluble protein were expressed and purified, preventing the production of antibodies and thus the development of the DAS-ELISA. An alternative diagnostic rapid-direct-one-tube-RT-PCR assay was developed. This rapid-directone- tube-RT-PCR assay was compared to commercially available DAS-ELISA and ImmunoStrip tests (Agdia) to assess the reliability, sensitivity and specificity of the rapid-direct-one-tube-RTPCR assay. Twelve GFLV isolates from South Africa were sequenced to investigate the variability between the isolates as well as the variability between the South African isolates and GFLV sequences available in Genbank. Sequence identities between clones from different GFLV isolates from South Africa were between 86-99% and 94-99% at the nucleotide and amino acid levels, respectively. Phylogenetic analysis based on the coat protein gene sequences showed that the South African isolates form two distinct clades or sub-populations. No significant correlation was found between geographical origin and symptoms, nor between geographical origin and sequence variability or between grapevine cultivar and symptom expression. Of the 23 samples tested with all three tests, 21 tested positive with rapid-direct-one-tube-RT-PCR, 19 with the ImmunoStrips and 17 with an imported DAS-ELISA kit (Agdia). Rapid-direct-one-tube-RT-PCR was found to be the most reliable technique for GFLV detection. Although the establishment of a DAS-ELISA directed to the South African strain(s) of GFLV was not successful, an alternative PCR based diagnostic system was developed, and proved to be sensitive and reliable. RT-PCR based diagnostic assays are generally accepted to be more sensitive than DAS-ELISA, but the latter is still used as the diagnostic assay of choice for routine testing due to ease of use. This rapid-direct-one-tube-RT-PCR assay is a rapid, sensitive and reliable diagnostic test, reducing the prevalence of false negatives, contributing to a virus free viticulture industry. The rapid-direct-one-tube-RT-PCR assay is as easy to use as DAS-ELISA, faster and can be performed by semi skilled workers, thus providing all the advantages associated with DAS-ELISA.

Thesis (MSc (Genetics))--University of Stellenbosch, 2010. / Includes bibliography. / ENGLISH ABSTRACT: The first aim of this study was to reliably and rapidly detect Grapevine rupestris stem pittingassociated virus (GRSPaV) in grapevine. This was achieved by screening 94 grapevines using crude plant extracts in both quantitative and conventional reverse transcription polymerase chain reaction (RT-PCR). The second aim was to establish a technique capable of differentiating GRSPaV sequence variants. The application of this technique is for the largescale screening of diseased vines to associate sequence variants of GRSPaV with disease symptoms. Nested quantitative polymerase chain reaction and high resolution melting assays (qPCR-HRM) were developed for three regions of the GRSPaV genome (coat protein, RNAdependant RNA-polymerase and triple gene block movement protein). The qPCR-HRM technique using the high saturation dye, EvaGreen™, and the Rotor-Gene™ 6000 analyzer was validated with a panel of sixteen sequence-characterized viral isolates. Diluted RT-PCR products and cloned cDNA gave the most consistent amplification plots and dissociation profiles. RT-PCR products generated from total RNA extracts were used as template for qPCR-HRM assays and for direct sequencing of sixteen samples in the three aforementioned regions. The average amplification efficiency for qPCR was 1.52±0.04. Auto-calling of userdefine genotypes was performed at a confidence interval of 70%. Phylogenetic analysis of the three regions of the GRSPaV genome was performed with published GenBank sequences to confirm the HRM data. The dominant sequence variants found in the South African sample set radiated with Group II, reference full-length variant GRSPaV-SG1. GRSPaV-infected samples can in future be subjected to qPCR-HRM assays developed during this study. This can be performed to establish similarity to known genotypes and therefore phylogenetic groups. Mixed infection of sequence variants and quasi-species were a common occurrence. The assay will be useful in establishing correlation of specific genotypes to different phenotypical expression of viral disease. This could provide insight into the etiology of diseases associated with GRSPaV. / AFRIKAANSE OPSOMMING: Die eerste doel van hierdie studie was om die virus wat met Rupestris-stamverpitting (Grapevine rupestris stem pitting-associated virus of “GRSPaV”) in wingerd verbind is, vinnig en betroubaar op te spoor. Dit is bereik deur 94 wingerdstokke vir die teenwoordigheid van die virus te toets met beide kwantitatiewe en konvensionele trutranskripsie polimerase kettingreaksies (RT - PCR) vanaf ongesuiwerde plant-ekstraksies. Die tweede doel was die daarstelling van ’n tegniek om onderskeid te tref tussen variante van GRSPaV met verskillende nukleotiedvolgordes. Hierdie tegniek kan op groot skaal gebruik word om ge-affekteerde wingerdstokke te toets om sodoende siektesimptome met spesifieke variante van GRSPaV te verbind. Ge-neste kwantitatiewe polimerase-kettingreaksies (qPCR) en hoë-resolusie smelt-analises (HRM) is ontwikkel vir drie streke van die GRSPaV-genoom (mantelproteïen, RNS-afhanklike RNS-polimerase en trippelgeenblok bewegingsproteïen). Die tegniek van qPCR-HRM met die hoë-versadingingskleurstof EvaGreen™ en die Rotor- Gene™ 6000 ontleder se geldigheid is bevestig deur vergelyking met ’n paneel van sestien virus-isolate waarvan die volgorde reeds bepaal is. Verdunde RT-PCR-produkte en gekloneerde DNS het die mees konsekwente amplifikasie-uitstipping en dissosiasieprofiele opgelewer. RT-PCR-produkte wat vanuit totale RNS-ekstrakte verkry is, is as templaat vir qPCR-HRM-analises gebruik. Dieselfde produkte is ook gebruik, om die volgorde van sestien monsters in drie streke direk te bepaal. Die gemiddelde amplifikasiedoeltreffendheid van die qPCR was 1.52±0.04. Gebruiker-gedefinieerde genotipes is deur middel van outooproeping teen ’n vertroue-interval van 70% uitgevoer. Filogenetiese analises vir drie streke van die GRSPaV-genoom is uitgevoer met gepubliseerde GenBank-volgordes om die HRMdata te bevestig. Die dominante volgorde-variante in die stel Suid-Afrikaanse monsters het ooreengestem met Groep II, vollengte-verwysingsvariant GRSPaV-SG1. Monsters wat met GRSPaV besmet is kan in die toekoms onderwerp word aan die qPCR-HRM-analises wat in hierdie studie ontwikkel is. Dit kan uitgevoer word om ooreenkomste met bekende genotipes te bepaal, en dus ook met filogenetiese groepe. Die besmetting van plante met meer as een volgorde-variant het algemeen voorgekom. Die kwasi-spesies populasie-struktuur van die virus het ook gedurig na vore gekom. Die toets sal nuttig wees in die bepaling van korrelasies tussen spesifieke genotipes en verskillende fenotipiese voorkomste van virussiektes. Dit kan insig verleen in die etiologie van siektes wat met GRSPaV verbind word.