Thesis (MSc)--Stellenbosch University, 2010. / ENGLISH ABSTRACT: Late blight caused by Phytophthora infestans on potato and tomato causes major economic losses worldwide. Until the 1980s, P. infestans populations outside its centre of origin (either central Mexico or the Andean region) only consisted of one mating type (A1), which prevented the pathogen from reproducing sexually. Pathogen populations outside the centre of origin most likely only consisted of a few genotypes prior to the 1980’s. Pan globally, these genotypes probably first consisted of genotype/s that had mitochondrial DNA (mtDNA) haplotype Ia, which was subsequently replaced by a mtDNA haplotype Ib genotype known as the US-1 lineage. This relative simple population structure of the pathogen changed almost worldwide in the late 1970s and early 1980s, when a second set of migrations took place from the centre of origin. These populations contained both A1 and A2 mating type isolates that consisted of several different genotypes, which were more virulent than the pre-1970s genotypes and resulted in the displacement of these genotypes almost worldwide. Some of the new genotypes were also resistant to metalaxyl, the fungicide that was most effective in controlling late blight. In Sub-Saharan Africa (SSA), the characteristics of P. infestans populations are not well documented in most countries except South Africa, Kenya and Uganda. Previous studies in SSA showed that populations were dominated by the US-1 lineage and its variants. The exceptions were reports of the presence of a few mtDNA haplotype Ia isolates in Rwanda and Ethiopia. The current study aimed to determine the population structure of P. infestans in eight selected SSA countries (Burundi, Kenya, Rwanda, Tanzania, Uganda, Malawi, Mozambique and South Africa), mainly on potato and on a limited scale on tomato and petunia, using ‘old’ markers (mating type determination, glucose-6-phosphate isomerase [Gpi] genotyping, mtDNA haplotyping, DNA fingerprinting with probe RG-57 and metalaxyl sensitivity). Populations were further also genotyped using seven recently published Simple Sequence Repeats (SSRs) markers. This information would help to define the population structure of P. infestans in SSA for the first time on a regional basis, and will also determine whether new migrations have taken place since the last characterization studies took place in 2001. A survey in the eight SSA countries yielded a total of 281 P. infestans isolates, mainly obtained from potato fields (Tanzania, Kenya, Uganda, Rwanda, Burundi, Malawi and South Africa), but also from tomato (Malawi, Mozambique and South Africa) and Petunia ´ hybrida (South Africa) that were characterized. Characterization of subsets of the isolates with the ‘old’ markers (176 isolates for mating type, 281 isolates for mtDNA, 70 isolates for [Gpi] and 49 isolates with restriction fragment length polymorphism analysis with probe RG-57), showed that most of the isolates belonged to the US-1 genotype or its variants (US-1.10 and US-1.11). The exception were isolates that belonged to genotype KE-1 (A1 mating type, mtDNA haplotype Ia, Gpi 90/100 and unique RG-57 genotype) that was identified in two fields in Kenya. Genotype KE-1, based on the ‘old’ marker data, is related to genotypes (RW-1 and RW-2) previously identified in Rwanda, and several Ecuadorean and European genotypes. Metalaxyl sensitivity testing of 64 isolates showed that metalaxyl resistant potato isolates were present in all the countries except Malawi, whereas all the tomato isolates were sensitive. Genotyping of 176 isolates with seven recently published simple sequence repeat (SSR) markers revealed a high number (79) of multi-locus genotypes (MLGs) in SSA. However, when locus D13, which was difficult to score, was excluded only 35 MLGs were identified. When locus D13 was excluded from analyses of molecular variance (AMOVA), (i) there was no significant genetic differentiation between populations from central-east Africa (Burundi, Kenya, Rwanda, Tanzania and Uganda), south-east Africa (Malawi and Mozambique) and South Africa, (ii) the KE-1 population was genetically differentiated (Fst = 0.33; P = 0.001) from the US-1 and US-1.10 populations and (iii) genetic differentiation between populations from potato and tomato was low (Fst = 0.07; P = 0.004). The study has expanded the worldwide genotypic database of P. infestans for SSA. Previously, no populations were characterized from Burundi, Malawi and Mozambique. The characterization work showed that migrations seem unlikely to have taken place in SSA, or if these did occur, it was on a very limited scale. The more severe epidemics in some SSA countries could be due to the presence of metalaxyl resistance. Furthermore, the occurrence of mutations or mitotic recombination might have resulted in more aggressive and/or better adapted genotypes, for example the US-1.10 lineage that was only detected in the Western Cape Province of South Africa. The significance of the discovery of the KE-1 genotype in Kenya needs further investigation since it might (i) be an asexual descendent of genotypes (RW-1 and RW-2) that were previously reported in Rwanda in the 1980s, (ii) previously have gone undetected due to the small surveys that were conducted in SSA, (iii) be a new migrant from countries other than SSA or (iv) have been introduced in the very first introductions into Kenya prior to the 1970s. The SSR results from the survey will allow comparison of the SSA late blight populations with other populations worldwide through the EucaBlight database in future studies. / AFRIKAANSE OPSOMMING: Laatroes, veroorsaak deur Phytophthora infestans op aartappel en tamatie, veroorsaak groot ekonomiese verliese wêreldwyd. Phytophthora infestans populasies buite hul kern van oorsprong (óf sentraal Meksiko óf die Andes area), het tot die 1980’s slegs uit een paringstipe (A1) bestaan, wat verhoed het dat die patogeen geslagtelik vermeerder. Patogeenpopulasies buite die kern van oorsprong, het heel moontlik vóór die 1980’s slegs uit ‘n paar genotipes bestaan. Wêreldwyd, het hierdie genotipes moontlik aanvanklik uit genotipe(s) bestaan wat mitokondriale DNS (mtDNS) haplotipe Ia bevat het, wat later met ‘n mtDNS haplotipe Ib genotipe, bekend as die US-1 genotipe, vervang is. Hierdie relatiewe eenvoudige populasiestruktuur van die patogeen, het omtrent wêreldwyd in die láát 1970’s en vroeë 1980’s verander, toe ‘n tweede stel migrasies vanaf die patogeen se kern van oorsprong plaasgevind het. Hierdie populasies het beide A1 en A2 paringstipe isolate ingesluit, wat uit verskeie verskillende genotipes bestaan het, wat meer virulent as die vóór-1970’s genotipes was, en wat die verskuiwing van hierdie genotipes omtrent wêrelwyd tot gevolg gehad het. Sommige van die nuwe genotipes was ook weerstandbiedend teen metalaksiel, die fungisied wat mees effektief in die beheer van laatroes was. Die kenmerke van P. infestans populasies is nie goed in die meeste lande in Sub- Sahara Afrika (SSA) gedokumenteer nie, behalwe vir Suid-Afrika, Kenia en Uganda. Vorige studies in SSA het aangedui dat populasies deur die US-1 genotipe en sy variante gedomineer word. Die uitsonderings was aantekeninge oor die teenwoordigheid van ‘n paar mtDNS haplotipe Ia isolate in Rwanda en Etiopië. Die huidige studie was daarop gemik om die populasiestruktuur van P. infestans in agt geselekteerde SSA lande (Burundi, Kenia, Rwanda, Tanzanië, Uganda, Malawi, Mosambiek en Suid-Afrika), hoofsaaklik op aartappel en op ‘n beperkte skaal op tamatie en petunia, vas te stel, deur die gebruik van ‘ou’ merkers (paringstipe-bepaling, glukose-6-fosfaat isomerase [Gpi] genotipering, mtDNS haplotipering, DNS fingerafdrukke met RG-57 en metalaksielsensitiwiteit). Die genotipe van populasies is verder ook bepaal deur gebruik te maak van sewe onlangs-gepubliseerde “Simple Sequence Repeats (SSRs)” merkers. Hierdie inligting sal help om die populasiestruktuur van P. infestans in SSA vir die eerste keer op ‘n streeksbasis vas te stel, en sal ook bepaal of nuwe migrasies sedert die laaste karakteriseringstudies wat in 2001 uitgevoer is, plaasgevind het. ‘n Opname in die agt SSA lande, het ‘n totaal van 281 P. infestans isolate opgelewer, hoofsaaklik vanaf aartappellande (Tanzanië, Kenia, Uganda, Rwanda, Burundi, Malawi en Suid-Afrika), maar ook vanaf tamatie (Malawi, Mosambiek en Suid- Afrika) en Petunia ´ hybrida (Suid-Afrika) wat gekarakteriseer is. Karakterisering van geselekteerde isolate met die ‘ou’ merkers (176 isolate vir paringstipe, 281 isolate vir mtDNS, 70 isolate vir Gpi en 49 isolate met restriksiefragment-lengte-polimorfismeanalise met RG-57), het aangetoon dat die meeste van die isolate aan die US-1 genotipe of sy variante (US-1.10 en US-1.11) behoort het. Die uitsondering was isolate wat tot die genotipe KE-1 behoort het (A1 paringstipe, mtDNS haplotipe Ia, Gpi 90/100 en unieke RG-57 genotipe) wat in twee velde in Kenia geïdentifiseer is. Genotipe KE-1, gebaseer op die ‘ou’ merkerdata, is aan genotipes (RW-1 en RW-2) verwant, wat voorheen in Rwanda, en verskeie Ekwadoreaanse en Europese lande geïdentifiseer is. Metalaksielsensitiwiteitstoetsing van 64 isolate het aangetoon dat metalaksiel-weerstandbiedende aartappel-isolate in al die lande teenwoordig was, behalwe vir Malawi, terwyl al die tamatie-isolate sensitief was. Genotipering van 176 isolate met sewe onlangs gepubliseerde “Simple Sequence Repeat” (SSR) merkers, het ‘n hoë aantal (79) multilokus genotipes (MLGs) in SSA aangedui. Met die uitsluiting van lokus D13, wat moeilik was om te evalueer, is slegs 35 MLGs egter geïdentifiseer. Met die uitsluiting van lokus D13 uit die analise van molekulêre variansie (AMOVA), was (i) daar geen betekenisvolle genetiese differensiasie tussen populasies van sentraal-oos Afrika (Burundi, Kenia, Rwanda, Tanzanië en Uganda), suid-oos Afrika (Malawi en Mosambiek) en Suid-Afrika nie, (ii) die KE-1 populasie geneties (Fst = 0.33; P = 0.001) van die US-1 en US-1.10 populasies gedifferensieerd en (iii) genetiese differensiasie tussen populasies vanaf aartappel en tamatie laag (Fst = 0.07; P = 0.004). Die studie het die wêreldwye genotipe-databasis van P. infestans vir SSA uitgebrei. Voorheen is geen populasies vanuit Burundi, Malawi en Mosambiek gekarakteriseer nie. Die karakteriseringswerk het aangetoon dat die waarskynlikheid klein is dat migrasies in SSA plaasgevind het, of indien dit wel plaasgevind het, dit op ‘n baie beperkte skaal plaasgevind. Die meer ernstige epidemies in sommige SSA lande kan die gevolg wees van die teenwoordigheid van metalaksiel-weerstand. Die voorkoms van mutasies of mitotiese rekombinasie kon verder meer aggressiewe en/of beter aangepaste genotipes tot gevolg gehad het, byvoorbeeld die US-1.10 genotipe wat slegs in die Westelike Kaapprovinsie van Suid-Afrika waargeneem is. Die betekenis van die ontdekking van die KE-1 genotipe in Kenia benodig verdere ondersoek aangesien dit (i) ‘n ongeslagtelike afstammeling van genotipes (RW-1 en RW-2) mag wees wat voorheen in die 1980’s in Rwanda aangeteken is, (ii) voorheen nie waargeneem is nie weens die klein opnames wat in SSA uitgevoer is, (iii) ‘n nuwe genotipe van lande buite die SSA kan wees of (iv) ingebring is tydens die heel eerste inkoms in Kenia vóór die 1970’s. Die SSR resultate van die opname sal vergelykings tussen die SSA laatroespopulasies en ander populasies wêreldwyd toelaat, deur gebruik te maak van die EucaBlight databasis in toekomstige studies.

Graduation date: 1995

Thesis. (M. A. Agriculture (Agricultural Economics)) -- University of Limpopo, 2022 / Food security, poverty and hunger issues, as well as methods of addressing remain a concern for many South Africans. Smallholder farmers' agricultural production is seen as the key to simultaneously alleviating poverty and ensuring food security, especially in rural areas. The sweet potato crop is commonly produced by smallholder farmers in rural areas as a staple in many South African households with the potential to reduce hunger and poverty. Nevertheless, just like other crops, the sweet potato is impaired by external factors such as extreme weather conditions, insects, pests and diseases, thus threatening food security. The most destructive pest to sweet potatoes acknowledged in the literature is the sweet potato weevil (SPW), which can cause between 5-100% in areas where it is not controlled. While there are many SPW control measures Entomopathogenic Nematodes (EPNs) are emerging as one of the Integrated Pest Management (IPM) bio-control techniques that have shown promise in controlling SPW infestations in South Africa and globally. This study conducts a socio-economic analysis of smallholder sweet potato production and analyses the acceptability of EPNs as bio-control measures against the SPW in the Gauteng, Limpopo and North West Provinces of South Africa. This was done through an assessment of farmers‘ knowledge, attitudes, perception and practices (KAPP analysis), exploration of the acceptability of EPNs by farmers, determination of and factors influencing profitability and technical efficiency. Primary data was collected from 119 respondents who were selected through non-probability sampling techniques; purposive, census, and snowball. The analytical tools used to analyse the data were descriptive statistics, Gross Margin Analysis, Multiple linear regression model, Data Envelopment Analysis (DEA) and the Tobit regression model. From the results, an average knowledge score of 2.30 based on a 3–point Likert scale revealed that sweet potato farmers are knowledgeable of the SPW, the impacts and the control measures. Despite this level of knowledge, the farmers were impartial about the attitudes and perceptions regarding the SPW and the control measures. This was based on the findings of a 5-point Likert scale, which yielded average scores of 2.53 and 2.74, respectively. The study also revealed that the majority of the farmers prefer the use of indigenous and physical practices to control SPW. With regards to acceptance of the EPNs bio-control innovation towards control of the SPW, a mean Composite Index of Acceptancy (CIA) of 0.77 revealed the willingness of farmers to accept the EPNs as a bio-control measure. A Gross margin of R9 552.37 indicates that sweet potato farming is generally profitable, and this is influenced by socio-economic factors such as marital status, employment status, sweet potato output per cycle and access to machinery. On the other hand, while sweet potato farming was found to be profitable, the DEA score of 0.09 reveals that these farmers are technically inefficient. Their technical inefficiency is influenced by sweet potato output per cycle, gross margins, farm size, and access to credit, employment status, and chemical use. Based on these findings, the study recommends farmers‘ support through capacity development initiatives for the sweet potato farmers with regards to general economics of sweet potato production and marketing to maximise and sustain their revenue generation, as well as their general efficiency. In addition, increased training and awareness of the EPNs and their benefits as bio-control measures towards SPW infestation will work towards changing farmers‘ mindset with regard to SPW control measures. / Department of Social Innovation (DSI) and United States Agency for International Development (USAID)

Thesis (PhD)--Stellenbosch University, 2012. / ENGLISH ABSTRACT: Potato virus Y (PVY) is responsible for considerable yield losses in the South African potato industry. The incidence of this virus has greatly increased over the past 20 years. In previous studies nonrecombinant strains of PVY, PVY N and PVY O, were detected in South African potatoes. In a recent study the occurrence of non-recombinant strains of PVY in South African potatoes was shown to have decreased while infection by more virulent recombinant strains, PVY NTN and PVY N-W, had increased dramatically. Infection of potato plants with PVY may cause stunted growth and mosaic or necrotic leaf symptoms which in turn can lead to a significant reduction in yield. Highly virulent recombinant PVY isolates as well as some of the non-recombinant strains may cause potato tuber necrotic ringspot disease (PTNRD) which may result in losses of 10% to total crop failure. For this reason investigation of infection by local recombinant isolates on local cultivars was important. To this end a representative number of isolates were selected for whole genome sequencing based on the relative occurrence of the various isolates in South Africa. A number of these sequenced isolates were subsequently used to infect local cultivars of potato in order to investigate the influence of genetic variation within the viral genome on symptom expression. In this study 27 South African isolates of PVY were sequenced through overlapping RT-PCR fragments. Seven of these isolates, six PVY NTN and one PVY N-W, were used to mechanically infect four local cultivars of potatoes under greenhouse conditions. The infected plants were monitored to establish the rate of systemic spread using a highly sensitive qRT-PCR and resulting tubers were visually screened for PTNRD. Highly variable recombinant isolates appear to be less virulent than the more conserved recombinant isolates possibly indicating molecular determinants for pathogenicity. For this reason the amino acid sequences of the South African isolates were compared to those of international isolates and scrutinized for variation and substitutions. Some South African isolates displayed amino acid substitutions unique to the specific isolate, making them unlike those found internationally. Substitution rates throughout the amino acid sequences differed greatly, with some isolates displaying hardly any changes whilst others varied a great deal from overseas isolates. Certain regions, many of which had specific functions, were more conserved than others. This study further investigated the recombination events within the PVY genome using reticulate phylogenetic analysis, molecular dating and network construction techniques. Unlike existing approaches, the one described in this study neither assumes an underlying strictly bifurcating species tree nor assumes prior knowledge of processes underlying deviations between individual gene trees. Through the use of the resulting robust time calibrated phylogeny, the patterns of diversification and recombination in PVY may be placed in the historical context of human cultivation of potatoes. Through the use of these techniques the study aimed to test whether diversification of the major strains of PVY and recombination between them occurred within the time frame of the domestication and modern cultivation of potatoes. From these analyses it can be deduced that recombinant strains of PVY were imported into South Africa. / AFRIKAANSE OPSOMMING: Aartappel virus Y (PVY) is verantwoordelik vir aansienlike opbrengs verliese in die Suid-Afrikaanse aartappelbedryf. Die voorkoms van die virus het grootliks toegeneem oor die afgelope 20 jaar. In vorige studies is nie-rekombinante rasse van PVY, PVY N en PVY O, gedokumenteer in Suid-Afrikaanse aartappels. 'n Onlangse studie het gevind dat die voorkoms van nie-rekombinante rasse van PVY in Suid- Afrikaanse aartappels aansienlik gedaal het terwyl infeksie deur virulente rekombinante rasse, PVY NTN en PVY N-W, dramaties toegeneem het. Infeksie van aartappelplante met PVY kan vertraagde groei en mosaïek- of nekrotiese blaarsimptome veroorsaak wat kan lei tot aansienlike vermindering in opbrengs. Hoogs virulente rekombinante PVY isolate, sowel as sommige nie-rekombinante rasse, kan aartappel nekrotiese ring simptome (PTNRD) veroorsaak wat verliese van 10% tot totale misoes tot gevolg kan hê. Om hierdie rede was die ondersoek van infeksie deur plaaslike rekombinante isolate op plaaslike kultivare belangrik. Vir hierdie doel is 'n verteenwoordigende aantal isolate gekies, gebaseer op die relatiewe voorkoms daarvan in Suid-Afrika, vir heelgenoom-volgordebepaling. Van die isolate is vervolgens gebruik om plaaslike kultivare te besmet ten einde die invloed van genetiese variasie binne die virale genoom op simptoom uitdrukking te ondersoek. In hierdie studie is 27 heelgenoomvolgordes van Suid-Afrikaanse PVY isolate bepaal deur oorvleuelende RT-PCR fragmente. Sewe van hierdie isolate, ses PVY NTN en een PVY N-W, is gebruik om vier plaaslike aartappel kultivare, gegroei onder kweekhuis kondisies, meganies te infekteer. Die geïnfekteerde plante is gemonitor om die tempo van sistemiese verspreiding vas te stel deur middel van 'n hoogs sensitiewe qRTPCR en knolle is visueel inspekteer vir PTNRD. Hoogs variante rekombinante isolate blyk om minder virulent te wees as die meer bewaarde rekombinante isolate wat dui op molekulêre determinante van patogenisiteit. Om hierdie rede is die aminosuurvolgordes van die Suid-Afrikaanse isolate vergelyk met die van internasionale isolate en ondersoek vir variasie en substitusies. Sommige Suid-Afrikaanse isolate vertoon aminosuur substitusies wat uniek is tot die spesifieke isolaat en maak hul dus anders as internasionale isolate. Die aantal aminosuursubstitusies in die volgordes verskil grootliks. In vergelyking met internasionale isolate toon sommige isolate skaars enige veranderinge terwyl ander ‘n aantal verskille toon. Sekere gebiede, waarvan baie spesifieke funksies het, was meer gekonserveerd as ander. Hierdie studie ondersoek ook rekombinasie gebeure binne die PVY genoom deur retikulêre filogenetiese analise, molekulêre datering en netwerk konstruksie tegnieke. In teenstelling met bestaande benaderinge, aanvaar die tegniek wat hier beskryf word nie ‘n streng bifurkeerende filogenie, wat onderliggende verdeel, of enige voorafgaande kennis van die prosesse onderliggend aan afwykings tussen individuele filogenieë nie. ‘n Robuuste, tyd gekalibreer filogenie kan diversifikasie patrone en rekombinasie van PVY plaas in die historiese konteks van menslike verbouing van aartappels. Deur gebruik te maak van hierdie tegnieke poog die studie om te toets of diversifikasie en rekombinasie van PVY rasse plaasgevind het binne die tydsbestek van die inburgering en moderne verbouing van aartappels. Van hierdie ontledinge word afgelei dat rekombinante rasse van PVY wat in Suid-Afrika voorkom, ingevoer is.

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.

Maize grey leaf spot (GLS), caused by Cercospora zeae-maydis, and potato late blight (LB), caused by Phytophthora infestans, are foliar diseases of maize and potato, two of the most widely grown crops in KwaZulu-Natal (KZN), after sugarcane and timber. Commercial maize in KZN accounts for just on 4.3% of the national maize crop. This is worth R563 million using an average of the yellow and white maize price for the 2001/02 season (at R1 332.87 ton(-1)). In 2003 KZN produced about 5% of the national potato crop (summer crop: 7531 300 10kg pockets from 2243 hectares). This equates to a gross value of R89.4 million based on an average price of R1 188 ton(-1) in 2001. Successful commercial production of maize and potatoes depends upon control of these diseases by translaminar fungicides with highly specific modes of action. This study extends an existing model available for timing of fungicide sprays for GLS and tests and compares two LB models for two calendar-based spray programmes. The study also evaluated the use of an early blight model which is caused by Alternaria solani, and over the single season of evaluation showed potential for use in KZN. For the GLS model it was found that a number of refinements are needed, e.g., the amount of infected maize stubble at planting and not the total amount of maize residue at planting. Based on two years' data, it was found that for the LB models there are no significant differences in levels of control between using a predicted fungicide programme and a calendar-based programme. The importance of knowing initial infection sites, and hence initial inoculum, was demonstrated. This led to the creation of a KZN LB incidence map, now being used to more accurately time the start of a preventative spray programme and to time the inclusion of systemic fungicides in the preventative spray programme. This study has contributed to the further development and expansion of the Automatic Weather Station Network (AWSN) at Cedara, which now comprises 15 automatic weather stations in KZN. The AWSN is currently used to aid farmers and advisers in decision-making regarding fungicide spray timing for GLS and LB. / Thesis (M.Sc.Agric.)-University of Natal, Pietermaritzburg, 2003.

Alternaria leaf petiole and stem blight is an important disease of sweetpotato (Ipomoea batatas (L.) Lam.) causing yield losses in both landraces and improved cultivars. The most important species causing economic yield loss in Uganda are Alternaria bataticola and A. alternate with A. bataticola the most aggressive and widely distributed. The study was conducted to: i) establish farmer-preferred sweet potato attributes, production constraints and Alternaria leaf petiole and stem blight awareness; ii) evaluate Ugandan sweet potato germplasm for Alternaria leaf petiole and stem blight resistance; iii) determine the mode of inheritance of resistance to Alternaria leaf petiole and stem blight and storage root yield components of sweet potato through estimation of the general combining ability (GCA) of the parents and the specific combining ability (SCA) of the parents for each cross; and iv) determine the adaptability and farmer acceptability of selected F1 genotypes across environments. The participatory rural appraisal was conducted to establish farmer preferences and production constraints revealed that farmer preferred sweet-potato traits were high yield, sweetness (taste), early maturity, high dry mass, resistance to pests and diseases, and in-field root storability after maturity. A majority of the farmers considered Alternaria leaf petiole and stem blight a serious production constraint causing yield loss of over 50%. The main control measures against the disease were roguing of infected plants, spraying with fungicides, use of healthy planting materials and planting resistant genotypes. Thirty sweet potato land races and improved cultivars were evaluated for Alternaria blight severity; yield, dry mass, harvest index, sweetpotato weevil (Cylas spp.) damage and sweetpotato virus disease at two sites (Namulonge and Kachwekano) over three seasons (2010B, 2011A, 2011B) under Alternaria inoculum and fungicide spray treatments. Landrace Shock was more resistant to Alternaria blight than Tanzania, the resistant check. Genotypes NASPOT 1, NASPOT 7, New Kawogo and Dimbuka were the most susceptible. Thirty two F1 families were generated from 16 parents in two sets in a North Carolina II mating scheme. The families were evaluated at two sites using a 5 x 7 row-column design with two replications. There were significant (P<0.05) differences among the families in Alternaria blight severity. Both GCA and SCA mean squares (MS) for Alternaria blight were highly significant (P<0.001) but the predominance of GCA sum of squares (SS) for Alternaria blight at 67.4% of the treatment SS versus 32.6% for SCA SS indicated that additive effects were more important than the non-additive effects in controlling this trait. For the yield components, the GCA MS were significant (P<0.05) and accounted for more than 60% of the treatment SS except for percentage dry mass composition where SCA SS accounted for 53.0% of the treatment SS implying that non-additive genetic effects were slightly more important than additive for this trait. Some parents that had desirable high, negative GCA effects for Alternaria blight produced families with undesirable positive SCA effects and the reverse was also true. This implied that the best parents should not be chosen based on GCA effects alone but also on SCA effects of their best crosses. The promising F1 genotypes selected from previously evaluated crosses together with one Alternaria blight resistant check (Tanzania) and one susceptible check (NASPOT 1) were evaluated at three sites (Namulonge, Kachwekano and Serere) using a randomised complete block design with three replications. Scientists and farmers evaluated the agronomic performance and also quality traits of the genotypes before and at harvest. Genotypes G14, G16, G24, G29, G49, G59 and G69 were the most stable across the sites for low Alternaria blight severity and can, therefore, be recommended for further evaluation under both low and high disease pressure areas. Genotypes G67, G13, G14, G24, G29 and G53 were the most high yielding and stable across the sites and were therefore the most widely adapted. In the participatory selection, before harvest and at harvest, Spearman’s rank correlation of the scientists and farmers’ mean ranking of the genotypes at each site was positive and significant. This indicated that the scientists in the study were capable of selecting for farmer preferred traits. / Thesis (Ph.D.)-University of KwaZulu-Natal, Pietermaritzburg, 2012.

The potato tuber moth, Phthorimaea operculella (Zeller), is a major pest of potato crops worldwide causing significant damage to both field and stored tubers. The current control method in South Africa involves chemical insecticides, however, there is growing concern on the health and environmental risks of their use. The development of novel biopesticide based control methods may offer a potential solution for the future of insecticides. In this study a baculovirus was successfully isolated from a laboratory population of P. operculella. Transmission electron micrographs revealed granulovirus-like particles. DNA was extracted from recovered occlusion bodies and used for the PCR amplification of the lef-8, lef-9, granulin and egt genes. Sequence data was obtained and submitted to BLAST identifying the virus as a South African isolate of Phthorimaea operculella granulovirus (PhopGV-SA). Phylogenetic analysis of the lef-8, lef-9 and granulin amino acid sequences grouped the South African isolate with PhopGV-1346. Comparison of egt sequence data identified PhopGV-SA as a type II egt gene. A phylogenetic analysis of egt amino acid sequences grouped all type II genes, including PhopGV-SA, into a separate clade from types I, III, IV and V. These findings suggest that type II may represent the prototype structure for this gene with the evolution of types I, III and IV a result of large internal deletion events and subsequent divergence. PhopGV-SA was also shown to be genetically more similar to South American isolates (i.e. PhopGV-CHI or PhopGV-INDO) than it is to other African isolates, suggesting that the South African isolate originated from South America. Restriction endonuclease profiles of PhopGV-SA were similar to those of PhopGV-1346 and PhopGV-JLZ9f for the enzymes BamHI, HindIII, NruI and NdeI. A preliminary full genome sequence for PhopGV-SA was determined and compared to PhopGV-136 with some gene variation observed (i.e. odv-e66 and vp91/p95). The biological activity of PhopGV-SA against P. operculella neonate larvae was evaluated with an estimated LC₅₀ of 1.87×10⁸ OBs.ml⁻¹ being determined. This study therefore reports the characterisation of a novel South African PhopGV isolate which could potentially be developed into a biopesticide for the control of P. operculella.

Thesis (M. Sc. (Plant Protection)) -- University of Limpopo, 2021 / Worldwide, root-knot (Meloidogyne species) nematodes are considered to be the most important and damaging genus in crop husbandry. The existence of a wide host range, over 2000 plants, and several biological races, makes the management of this nematode genus difficult with nematode-resistant crop Hybrid Sorghum Sudan grass (Sorghum bicolor × Sorghum Sundanese) has been classified as being resistant to certain Meloidogyne species and races, with a wide range of uses in crop rotation intended to manage nematode population densities. However, due to the ability of nematodes to enter chemiobiosis when gradually exposed to chemicals, this hybrid might not be effective in managing nematode population densities for the subsequent highly susceptible sweet potato (Ipomoea batatas L.) cultivars. The objective of the study was to determine whether hybrid Sorghum-Sudan grass would suppress M. javanica (Trial 1), M. incognita race 2 (Trial 2) and M. incognita race 4 (Trial 3) population densities, allowing a nematode susceptible sweet potato cv. ′Beauregard′ as successor crop to be cultivated without suffering nematode damage. The hybrid Sorghum-Sudan grass study was conducted under greenhouse conditions, with seven inoculation levels, namely, 0; 5; 25; 125; 625; 3 125 and 15 625 eggs and second-stage juveniles (J2) of each nematode species or race, arranged in randomised complete block design, with six replications and validated in time. Plant growth, foliar nutrient elements and nematodes were collected at 56 days after inoculation and prepared for analysis using standard methods. The reproductive factor (RF) at all levels was zero, whereas nematode inoculation at all levels did not have any effect on plant growth of the hybrid Sorghum-Sudan grass. However, the nematode levels affected the accumulation of nutrient elements and the quality of forage. After cultivating the susceptible sweet potato cultivar in pots xxx previously with hybrid Sorghum-Sudan grass at increasing levels of M. javanica alone, that is in Trial 1, similar results were observed with respect to RF and lack of nematode damage to plant growth. Consequently, the hybrid was suitable for use in crop rotation with sweet potato for the purpose of managing nematode population densities of thermophilic Meloidogyne species and/or races. / National Research Foundation of South Africa (NRF) and the Agricultural Research Council (ARC)

Sweet potato (Ipomoea batatas Lam.) is ranked as the seventh most important food crop in the world and its large biomass and nutrient production give it a unique role in famine relief. However, multiple virus infection is the main disease limiting factor in sweet potato production worldwide. The main objective of this research project was to develop a transgenic sweet potato cultivar with broad virus resistance in South Africa (SA). A review of current literature assembled background information pertaining to the origin, distribution and importance of the sweet potato crop; viruses and complexes infecting sweet potato; and the strategies used in sweet potato virus detection and control. A survey to determine the occurrence and distribution of viruses infecting sweet potato (Ipomoea batatas Lam.) was conducted in major sweet potato-growing areas in KwaZulu-Natal (KZN). A total of 84 symptomatic vine samples were collected and graft inoculated onto universal indicator plants, Ipomoea setosa Ker. and Ipomoea nil Lam. Six weeks post inoculation, typical sweet potato virus-like symptoms of chlorotic flecking, severe leaf deformation, stunting, chlorotic mosaic, and distinct interveinal chlorotic patterns were observed on indicator plants. Under the transmission electron microscope (TEM), negatively stained preparations of crude leaf sap and ultra-thin sections from symptomatic grafted I.setosa plants revealed the presence of elongated flexuous particles and pinwheel type inclusions bodies‟ that are characteristic to the cytopathology of Potyviruses. Symptomatic leaf samples from graft-inoculated I. setosa and I. nil were assayed for Sweet potato feathery mottle virus (SPFMV), Sweet potato mild mottle virus (SPMMV), Sweet potato chlorotic stunt virus (SPCSV), Sweet potato chlorotic fleck virus (SPCFV), Sweet potato virus G (SPVG), Sweet potato mild speckling virus (SPMSV), Sweet potato caulimo-like virus (SPCaLV), Sweet potato latent virus (SPLV), Cucumber mosaic virus (CMV), and Sweet potato C-6 virus (C-6) using the nitrocellulose membrane enzyme-linked immunosorbent assay (NCM-ELISA). The majority of leaf samples (52%) tested positive for virus disease and showed the occurrence of SPFMV, SPMMV, SPCSV, SPCFV, SPVG, SPMSV, and SPCaLV. Of these 7 viruses, the most frequently detected were SPFMV (39%), SPVG (30%), followed by SPCSV (13%) and SPMMV (12%). SPCaLV and SPCFV at 10% and SPMSV at 7% were found exclusively in samples collected from one area. SPFMV, SPVG, SPCSV, and SPMMV were identified as the most prevalent viruses infecting sweet potato in KZN. The genetic variability of the three major viruses infecting sweet potato (Ipomoea batatas Lam.) in KZN was determined in this study. A total of 16 virus isolates originating from three different locations (Umbumbulu, Umfume and Umphambanyomi River) in KZN were analyzed. These comprised of 10 isolates of Sweet potato feathery mottle virus (SPFMV), five isolates of Sweet potato virus G (SPVG) and one isolate of Sweet potato chlorotic stunt virus (SPCSV). The phylogenetic relationships of the SPFMV, SPVG and SPCSV isolates from KZN relative to isolates occurring in SA and different parts of the world were assessed. The division of SPFMV into four genetic groups (strains) according to the phylogenetic analysis of coat protein encoding sequences revealed mixed infections of the O (ordinary) and C (common) strains in sweet potato crops from KZN. All SPFMV isolates showed close lineage with isolates from South America, East Asia and Africa. The SPVG isolates showed high relatedness to each other and close lineage with other isolates, especially those from China and Egypt. Analysis of the partial sequence of the Heat shock protein 70 homologue (Hsp70h) gene indicated that the SPCSV isolate from KZN belongs to the West African (WA) strain group of SPCSV and showed close relatedness to an isolate from Argentina. The knowledge of specific viral diversity is essential in developing effective control measures against sweet potato viruses in KZN. Multiple virus infections of Sweet potato feathery mottle virus (SPFMV), Sweet potato chlorotic stunt virus (SPCSV), Sweet potato virus G (SPVG) and Sweet potato mild mottle virus (SPMMV) cause a devastating synergistic disease complex of sweet potato (Ipomoea batatas Lam.) in KZN. In order to address the problem of the multiplicity and synergism of sweet potato viruses in KZN, this study aimed to develop transgenic sweet potato cv. Blesbok with broad virus resistance. An efficient and reproducible plant regeneration protocol for sweet potato (Ipomoea batatas Lam.) cultivar Blesbok was also developed in this study. The effect of different hormone combinations and type of explants on shoot regeneration was evaluated in order to optimize the regeneration protocol. Coat protein (CP) gene segments of SPFMV, SPCSV, SPVG and SPMMV were fused to a silencer DNA, the middle half of the nucleocapsid (N) gene of Tomato spotted wilt virus (TSWV) and used as a chimeric transgene in a sense orientation to induce gene silencing in the transgenic sweet potato. Transformation of apical tips of sweet potato cv. Blesbok was achieved by using Agrobacterium tumefaciens strain LBA4404 harboring a modified binary vector pGA482G carrying the plant expressible neomycin phosphotransferase ll gene (nptll), the bacterial gentamycin-(3)-N-acetyl-transferase gene and the expression cassette. A total of 24 putative transgenic plants were produced from the transformed apical tips via de novo organogenesis and regeneration into plants under 50mg/L kanamycin and 200 mg/L carbenicillin selection. Polymerase chain reaction (PCR) and Southern blot analyses showed that six of the 24 putative transgenic plants were transgenic with two insertion loci and that all plants were derived from the same transgenic event. The six transgenic sweet potato plants were challenged by graft inoculation with SPFMV, SPCSV, SPVG and SPMMV- infected Ipomoea setosa Ker. Although virus presence was detected using NCM-ELISA, all transgenic plants displayed delayed and milder symptoms, of chlorosis and mottle of lower leaves when compared to the untransformed control plants. These results warrant further investigation under field conditions. / Thesis (Ph.D.)-University of KwaZulu-Natal, Pietermaritzburg, 2013.