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京都大学 / 新制・課程博士 / 博士(農学) / 甲第24668号 / 農博第2551号 / 新制||農||1099(附属図書館) / 学位論文||R5||N5449(農学部図書室) / 京都大学大学院農学研究科応用生命科学専攻 / (主査)教授 小川 順, 教授 栗原 達夫, 教授 伊福 健太郎 / 学位規則第4条第1項該当 / Doctor of Agricultural Science / Kyoto University / DFAM

Tesis por compendio / [ES] La mejora de las especies cultivadas es un área dinámica, sujeta a las necesidades y requerimientos de los diferentes cultivos en cada momento y de las exigencias de productores y consumidores. Una limitación en este proceso de mejora es la diversidad genética existente en los cultivos, debido a cuellos de botella poblacionales, que hacen necesario el uso de especies silvestres. El tomate cultivado (Solanum lycopersicum var. lycopersicum, SLL) surgió a partir de Solanum lycopersicum var. cerasiforme (SLC) que a su vez fue pre-domesticada a partir de Solanum pimpinellifolium (SP). Pese al potencial para la mejora de estas especies, su uso está limitado en gran medida por la falta de información de las colecciones mantenidas en los bancos de germoplasma, principalmente en SLC. Para dar solución a este problema, se ha empleado una colección de germoplasma compuesta por 15 accesiones de SLL, procedentes de México; 27 de SP, procedentes de Perú y Ecuador y 121 de SLC, procedentes de Perú, Ecuador, México y Mesoamérica. Esta colección ha sido sometida a una extensa caracterización fenotípica y genética, lo que ha permitido identificar las regiones de genoma asociadas a caracteres fenotípicos mediante estudios de asociación del genoma completo (GWAS). Además, se han creado poblaciones segregantes F2 para cada una de las entradas de la colección a partir de los híbridos obtenidos con tres parentales diferentes, y estos cruces se han puesto a disposición de la comunidad científica. Este recurso permitirá el estudio del control genético de mutantes de interés en mejora. El estudio realizado con los datos morfológicos ha demostrado la presencia de una gradación morfológica continua entre los tres grupos taxonómicos, y ha permitido la identificación de una serie de caracteres que permiten la diferenciación entre grupos y también entre las distintas procedencias geográficas dentro de cada grupo taxonómico. Los diferentes polimorfismos de nucleótido único (SNPs) fueron anotados con base a la predicción de sus efectos en la secuencia codificantes mediante el programa SnpEff y se llevaron a cabo estudios de GWAS. El análisis genético reveló a Perú y Ecuador como las regiones con mayores niveles de diversidad, tanto en la especie SP como en SLC. Se observó una reducción en el número de variantes SNP en SLC México, que concuerda con la hipótesis de que Mesoamérica sea centro de domesticación y difusión del tomate cultivado. Por último, se constató el proceso de domesticación como la causa de la menor diversidad presente en la especie cultivada. Los estudios GWAS permitieron la identificación de correlaciones genotipo-fenotipo, revelando la asociación entre 107 SNPs y ocho caracteres cuantitativos y un total de 30 SNPs asociados a 7 caracteres cualitativos. Una parte de los SNPs detectados fueron localizados cerca de regiones genómicas ya asociadas con genes y QTLs, otra parte se localizaron en regiones con posibles genes candidatos anotados y el resto de SNPs detectados se corresponden a regiones no descritas previamente, lo que abre el camino a estudios para la detección de nuevos genes candidatos. En esta tesis se muestra la utilidad de la colección de familias segregantes mediante su uso en el estudio del control genético de la presencia y alta densidad de tricomas tipo IV en dos fondos genéticos diferentes, SLL x SP y SP x SLC. En ambos fondos se han detectado dos QTLs principales en los cromosomas 9 y 11. Además, se han detectado señales en los cromosomas 2, 5, 6, 7 y 8, en función de la familia segregante estudiada. Las regiones detectadas en los cromosomas 9 y 11 habían sido previamente descritas en otras especies por regular la densidad de este tipo de tricomas o los niveles de acilazúcares. En ambas regiones hay genes anotados que intervienen en el desarrollo de los tricomas o en la formación de acilazúcares, como aciltransferasas, glicosiltransferasas o los factores de transcripción MYB. / [CA] La millora de les espècies cultivades és una àrea dinàmica, subjecta a les necessitats i requeriments dels diferents cultius a cada moment i de les exigències de productors i consumidors. Una limitació en aquest procés de millora és la diversitat genètica existent en els cultius a causa de diversos colls de botella poblacionals durant la seua domesticació. En aquests casos, les espècies silvestres emparentades revisten un especial interés, podent-se utilitzar com a font de al·lels en la millora genètica. Aquesta circumstància es dona en el cas de la tomaca cultivada (Solanum lycopersicum var. lycopersicum, SLL). Aquesta espècie va sorgir a partir de Solanum lycopersicum var. cerasiforme (SLC), que al seu torn va ser pre-domesticada a partir de Solanum pimpinellifolium (SP). Pese al potencial per a la millora d'aquestes espècies, el seu ús està limitat en gran manera per la falta d'informació de les col·leccions mantingudes en els bancs de germoplasma, principalment SLC. Per a aconseguir l'objectiu anteriorment exposat s'ha emprat una col·lecció de germoplasma composta per 15 accessions de SLL, procedents de Mèxic; 27 de SP, procedents del Perú i l'Equador i 121 de SLC, procedents del Perú, l'Equador, Mèxic i Mesoamèrica. Aquesta col·lecció ha sigut sotmesa a una extensa caracterització fenotípica i genètica, la qual cosa ha permés identificar les regions de genoma associades a caràcters fenotípics mitjançant estudis d'associació del genoma complet (GWAS). A més, s'han creat poblacions segregants F2 per a cadascuna de les entrades de la col·lecció creuant-les amb tres parentals diferents, i aquests creus s'han posat a la disposició de la comunitat científica. Aquest recurs permetrà l'estudi del control genètic de mutants d'interés en millora. Aquesta utilitat s'explora en l'últim capítol de la tesi, on s'estudia el control genètic de la densitat de tricomas en una accessió de l'espècie SP, característica d'interés per conferir resistència a artròpodes. L'estudi realitzat amb les dades morfològiques ha demostrat la presència d'una gradació morfològica contínua entre els tres grups taxonòmics, i ha permés la identificació d'una sèrie de caràcters que permeten la diferenciació entre grups i també entre les diferents procedències geogràfiques dins de cada grup taxonòmic. Els diferents polimorfismes de nucleòtid únic (SNPs) van ser anotats en base a la predicció del seu efecte en la sequència codificant mitjançant el programa SnpEff i es van dur a terme estudis de GWAS. L'anàlisi genètica va revelar al Perú i l'Equador com les regions amb majors nivells de diversitat, tant en l'espècie SP com en SLC. Es va observar una reducció en el nombre de variants SNP en SLC Mèxic, que concorda amb la hipòtesi que Mesoamèrica siga centre de domesticació i difusió de la tomaca cultivada. Finalment, es va constatar el procés de domesticació com la causa de la menor diversitat present en l'espècie cultivada. Els estudis GWAS van permetre la identificació de correlacions genotipe-fenotip, revelant l'associació entre 107 SNPs i huit caràcters quantitatius i un total de 30 SNPs associats a 7 caràcters qualitatius. Una part dels SNPs detectats van ser localitzats prop de regions genòmiques associades amb gens i QTLs o en regions amb possibles gens candidats anotats y la resta de SNPs detectats es corresponen amb regions no descrites prèviament el que obri el camí a estudis per a la detecció de nous gens candidats. La utilitat d'aquestes famílies F2 es demostra en l'últim capítol d'aquesta tesi mitjançant l'estudi de la base genètica de la densitat de tricomas tipus IV. S'estudia el control genètic de la presència i alta densitat de tricomas tipus IV en dos fons genètics diferents, SLL x SP i SP x SLC. En tots dos fons s'han detectat dos QTLs principals en els cromosomes 9 i 11. A més, s'han detectat senyals en els cromosomes 2, 5, 6, 7 i 8, en funció de la família segregant estudiada. Les regions detectades en els cromosomes 9 i 11 havien sigut prèviament descrites en altres espècies per regular la densitat d'aquests tricomas o els nivells de acilazúcares. En totes dues regions hi ha gens anotats que intervenen en el desenvolupament dels tricomas o en la formació de acilsucres, com aciltransferases, glicosiltransferases o els factors de transcripció MYB. / [EN] The improvement of cultivated species is a dynamic field, subject to the needs and requirements of the different crops at different moments as well as to the demands of producers and consumers. A limitation in this improvement process is the amount of genetic diversity available for breeding purposes because of population bottlenecks during their domestication. This circumstance occurs in the case of cultivated tomatoes (Solanum lycopersicum var. lycopersicum, SLL) which evolved from Solanum lycopersicum var. cerasiforme (SLC), which was pre-domesticated from Solanum pimpinellifolium (SP). Despite these species have been used for tomato breeding, their use is still limited due to the lack of detailed information about the collections that are kept in genebanks. With the aim of solve this problem, a germplasm collection has undergone an extensive morphological and genetic characterization. This collection comprises a wide range of geographical origins: includes 15 SLL accessions from Mexico; 27 SP accession from Peru and Ecuador and 121 SLC accessions from Peru, Ecuador, Mesoamerica, and Mexico. Genome-wide association studies (GWAS) were performed to detect genomic candidate regions associated with each agronomic trait. Furthermore, a collection of segregating populations has been developed by crossing the whole collection with a representative accession for each of the three species (SLL, SLC and SP). These populations are available to the scientific community and could be very useful to speed up the validation of candidate genes or to study the genetic control of mutants. This last approach will be explored in the last chapter of this thesis, where the genetic control of density of type IV trichomes is studied. The study carried out with morphological data has demonstrated the presence of a phenotypic variation between our three species. The analysis has allowed the identification of characters which differentiate between species and between different geographical origin within each species. The identified SNPs were annotated, and their putative impacts were predicted by using SnpEff. The lowest number of variants was detected in SLL grups and the highest number of variants was detected in SP. SLC had a variation between SLL and SP, with lower levels in SLC Mexico. This fact agrees with the hypothesis for the domestication and diffusion of cultivated tomato in Mesoamerica. Additionally, GWAS analysis was carried out with this genetic data and revealed significant associations between 107 SNPs and 8 quantitative traits and a total of 30 SNPs associated with 7 qualitative traits. This analysis has allowed the identification of known genomic regions such as the associations between fruit weight and fw2.2 or fw9.2. However, regions with possible novel genes have also been detected such as the case of yellow fruit. These results reinforce the potential of our collection for breeding programmes. The usefulness of F2 populations have been used to determine the genetic control of density of type IV trichomes. During the characterization of this collection, a SP accession (BGV016047) with a high density of type IV trichomes was detected. These trichomes have been described to accumulate different types of chemical substances related to pest resistance. This thesis shows that this character is influenced by environmental factors such as plant and leave age. On the other hand, the genetic control of this character has been studied in two different genetic backgrounds, SLL x SP and SP x SLC. Two main QTLs have been detected in both families, on chromosome 9 and 11. In addition, the different F2 populations have revealed that this character could be under the control of other QTLs on chromosomes 2, 5, 6, 7 and 8. / This research was supported by the National Natural Science Foundation of USA Varitome project (NSF IOS 1564366). / Mata Nicolás, E. (2021). Utilización de una colección de germoplasma de tomate para la identificación de genes de interés [Tesis doctoral]. Universitat Politècnica de València. https://doi.org/10.4995/Thesis/10251/172639 / Compendio

Rimsulfuron {N-[[ 4,6-dimethoxy-2-pyrimidinal)amino ]carbonyl]-3-( ethylsulfonyl)-2-pyridinesulfonamide} is a new sulfonylurea herbicide under development by E.I. Dupont de· Nemours & Company Inc. for preemergence and postemergence grass and broadleaf weed control in Solanaceous vegetable crops. The efficacy and selectivity of rimsulfuron were determined in potatoes, transplanted tomatoes, and transplanted peppers in field studies in 1991, 1992, and 1993. Treatments included rimsulfuron and metribuzin alone and in combination in potatoes and tomatoes, rimsulfuron alone in peppers, and sequential applications of rimsulfuron in tomatoes and peppers. Application timings included preemergence and postemergence in potatoes, while only post-transplant applications were evaluated in tomatoes and peppers. Preemergence applications of rimsulfuron controlled weeds if rainfall was received within a few days following application. Control was often greater in potatoes and tomatoes than in peppers. These differences likely relate to more frequent rainfall events in potatoes and tomatoes than in the later-planted peppers. / Master of Science

The demand for biodegradable packaging materials as an alternative to synthetic ones to reduce environmental cost has seen an increase in recent years. In addition, functionalizing the packaging film to provide specific advantages like antimicrobial properties has yet to be explored thoroughly. This study considers adding antimicrobial agents to improve the quality and safety of actively packaged fresh produce using an antimicrobial enzyme (lysozyme) immobilized on a biopolymer based packaging film (corn-zein). The developed packaging material is aimed as an active biodegradable packaging to reduce bacterial contamination on the surface of fresh organic produce, specifically tomatoes. The study uses glutaraldehyde and glyoxal as binding agents to immobilize the enzyme on the packaging film. The effect of concentration of glutaraldehyde and glyoxal on the controlled release of the enzyme was studied. Concentrations of 0.1 and 0.2 g/g lysozyme: cross linking agent had controlled release properties. However, concentrations of 0 or 0.05 are about 20-30% more effective at inactivating bacteria. Antimicrobial activity in the constructed zein films are also tested against selected pathogens (Salmonella Newport and Listeria monocytogenes). Developed zein based film is tested against inoculated tomatoes to determine the efficacy of the films in reducing the pathogen population. The inoculated tomatoes are stored at room temperature over a storage period of one week. The film was able to reduce Listeria monocytogenes population by three logs but was unable to reduce the population of Salmonella Newport. / Master of Science

Host range and symptomatology of peanut stunt virus (PSV), cucumber mosaic virus (CMV), the Blencowe isolate of tomato aspermy virus (TAV-B) and a chrysanthemum virus (CV-L) varies on selected hosts. In sucrose density-gradient centrifugation each virus has a sedimentation rate of approximately 100s. Purified preparations of PSV and CV-L are homogenous and stable while CMV and TAV-B aggregate and lose infectivity. In acrylamide gel electrophoresis, all the viruses move as a single component with CMV migrating faster than the other three. Formaldehyde-stabilization of PSV and CMV did not increase the titer of immune sera. Classical microprecipitin and gel diffusion tests were unsatisfactory because of nonspecific precipitation and antibodies to normal host antigens. Analysis of incubated homologous and heterologous virus-antibody mixtures by density-gradient centrifugation detected specific precipitation with surface antigenic sites on the virions. In reciprocal tests, CMV and CV-L show no serological relationship. CV-L and TAV-B react reciprocally and are strains. CMV antiserum reacts with TAV-B, but not conversely. PSV reacts reciprocally with the other three viruses, and thus is related at the strain level to all three. Of the viruses compared, PSV appears to be most like the hypothetical parent strain of the CMV group, since it possesses antigenic sites in common to at least three members of the group. / Master of Science

Submitted in fulfilment of the requirements for the degree of Master of Applied Science in Food Science and Technology, Durban University of Technology, 2015. / Listeria monocytogenes have been implicated as a public health concern worldwide. The study explored the survival of non-adapted, heat adapted and chlorine adapted L. monocytogenes on tomatoes; as well as the survival of non-adapted, heat adapted and chlorine adapted biofilms after exposure to sodium dodecyl sulphate (SDS), levulinc acid, sodium hypochlorite solution. Contact time of 1, 3 and 5 minutes was used. The survival of L. monocytogenes was monitored at 0, 24, 48 and 72 hours. The sanitizers were used individually or combined as follows; 1% sodium dodecyl sulphate individually; 0.5% levulinic acid individually; 200 ppm sodium hypochlorite solution individually and 0.5% levulinic acid/0.05% sodium dodecyl sulphate in combination (mixture). The samples were kept at 4 °C throughout the period of assessment. The effect of these sanitizers on pH, total soluble solids (TSS) and titratable acidity (TA) was also determined. Furthermore, the attachment of L. monocytogenes on tomatoes was investigated using a scanning electron microscope. Highest log reduction of non-adapted L. monocytogenes were observed on tomatoes treated with 1% SDS and least log reduction was achieved when tomatoes were treated with sodium hypochlorite solution. Though the log reduction achieved by 0.5% levulinic acid was higher that sodium hypochlorite solution, it was lower than log reduction achieved when 0.05% SDS / 0.5% levulinic acid mixture was used for all contact times. Using non-adapted L. monocytogenes, SDS was able to destroy all L. monocytogenes at 1, 3 and 5 minutes contact time. The trend was the same when heat adapted and chlorine adapted L. monocytogenes were used. There was no significant log reduction observed with biofilms. More favourable results were observed as contact time was increased from 1 to 5 minutes. Though there was a decrease in surviving bacteria from 1 to 3 minutes contact time, this decrease was not significant. The study investigated if exposure to sanitizer has an effect on pH, titratable acidity (TA) and total soluble solids (TSS) of the tomatoes. It was revealed that levulinic acid and mixture can have detrimental effect on pH, TA and TSS of tomatoes. The TA and TSS of samples treated with levulinic acid and mixture varied significantly (P ≤ 0.05) compared to the control sample. Although the TA and TSS of samples treated with SDS and sodium hypochlorite solution were different from the control, the differences were not significant. As much as sanitizers have the potential to reduce the bacterial population in fresh produce they may not completely destroy pathogens. Chlorine based sanitizers such as sodium hypochlorite though frequently used in the fresh produce industry, are not the best sanitizer to be used against food borne pathogens. Other sanitizers such as SDS used alone or in combination with another sanitizer can achieve better results than the widely used sodium hypochlorite solution as observed in this study. Stress adapted pathogens become less responsive to sanitizers during subsequent treatments. Through this research, it was established that biofilms are resistant to sanitizers. Though application of sanitizers in fresh produce is cheaper and simpler to apply, there is need to monitor varying concentrations of sanitizers, contact time and minimise contact with sub-surfaces as this could lead to sensory quality losses.

M. Tech. Agriculture / Tomatoes (Solanum lycopersicum) and sweet or bell peppers (Capsicum annuum L.) belong to the Solanaceae family. They constitute an excellent source of phenolic (flavonoids), vitamin C (ascorbic acid) and carotenoids (especially lycopene, b- carotene, a precursor of vitamin A), known as antioxidants. The aim of this study was to investigate the influence of photo-selective nets (ChromatiNet™) (red, pearl and yellow) with 40% shading on postharvest fruit quality parameters (Soluble solids content, Titratable acidity, fruit mass and firmness), bioactive compounds (ascorbic acid, total phenols, flavonoid, lycopene, b-carotene contents), antioxidant scavenging activity, odour active aroma compounds and the sensory quality of three indeterminate sweet pepper cultivars HTSP-5 (green), HTSP-3 (red) and Celaya (yellow) and three tomato cultivars (AlfaV, Irit, and SCX 248). A commercial black net (control) with 25% shading was included for comparison.

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.

Thesis (Ph. D. Agriculture (Plant Protection)) -- University of Limpopo, 2013 / Global withdrawal of synthetic fumigant and non-fumigant nematicides due to their ecounfriendly impacts and high toxicity to non-target organisms, respectively, increased the research and development of alternatives for managing population densities of plantparasitic nematodes, particularly the root-knot (Meloidogyne species) nematodes. Although Meloidogyne species had been managed using genotypes that are resistant to plant-parasitic nematodes in various crops, various challenges negate the available or introgressed nematode resistance. In tomato (Solanum lycopersicum) production, nematode races and instability of nematode resistant genotypes under certain conditions necessitated the continued research and development of alternatives since most of the existing commercial tomato cultivars are highly susceptible to various biological races of Meloidogyne species. The aim of the study was to research and develop appropriate dosages of two phyto- nematicides which could be applied through drip irrigation system in open field tomato production systems, while the specific objectives were to: (1) determine whether a computer-based model could provide nonphytotoxic concentrations to tomato plants using fresh fruits of wild watermelon (Cucumis africanus) and wild cucumber (C. myriocarpus) under greenhouse conditions, (2) determine whether computer-based concentrations from the two plant species when using dried fruits would be less phytotoxic and more suppressive to nematodes, (3) investigate application time intervals for the two products, (4) determine responses of plant growth in tomato and nematode suppression in respect to the derived dosages, and and (5) validate dosages of fermented crude extracts from the two plant species with respect to plant growth of tomato and suppression of nematode numbers. xxxiii Greenhouse, microplot and field studies were set to test the hypotheses intended to achieve the stated objectives, with reliability of measured variables being ensured by using statistical levels of significance (P ≤ 0.05) and coefficients of determination (R2), while validity was ensured by conducting experiments at the same location over two seasons and/or by setting up factorial treatments. Firstly, fermented plant extracts of fresh fruits from C. africanus and C. myriocarpus consistently reduced population densities of Meloidogyne species by 80-92% and 50-90%, respectively. Tomato plants were highly sensitive to the two products as shown by the total degree of sensitivities (Σk) and biological index of 0 and 3, respectively. Also, the mean concentration stimulation range (MCSR) of 11% and 7% concentrations, respectively, attested to this phytotoxicity. Secondly, fermented crude extracts of dried fruits from C. africanus and C. myriocarpus also reduced population densities of Meloidogyne species by 78-97% and 87-97%, respectively. Tomato plants were highly tolerant to the two products in dried form as shown by the total degree of sensitivities (Σk) and biological index of 4 and 3, respectively. The MCSR values for C. africanus and C. myriocarpus dried fruits on tomato were 2.64% and 2.99%, respectively, which for the purpose of this study were individually adjusted to 3%, which translated to 36 L undiluted material/ha of 4 000 tomato plants. In subsequent studies, 3% concentration was used as the standard, along with double strength concentration, namely, 6% concentration. Thirdly, the MCSR values derived in Objective 4, namely 3% and 6% concentration for both Cucumis species using the CARD model were used in the optimisation of application time interval using the innovative concept of weeks (0, 1, 2, 3 and 4) in a 30-day month period. Application time interval for 3% and 6% concentrations of C. africanus fruits was xxxiv optimised at 2.40 and 2.61 weeks in a 30-day month period, respectively, which translated to 18 days [(2.4 weeks/4 weeks) × 30 days] and 20 days [(2.6 weeks/4 weeks) × 30 days], respectively. In contrast, for both concentrations from fermented crude extracts of C. myriocarpus fruits, application time interval was optimised at 16 days for 2.2 and 2.1 weeks, respectively. During optimisation of application frequencies, fermented crude extracts from C. africanus and C. myriocarpus reduced final population densities of M. incognita race 2 by 70-97% and 76-96%, respectively. Fourthly, optimum application intervals (time), allowed computation of dosage, which is a product of concentration and application frequency (dosage = concentration × application frequency). Fifthly, validation of the dosages under open field conditions suggested that 6% × 16-day dosage under crude extracts from C. myriocarpus fruit significantly (P ≤ 0.05) improved growth of tomato plants when compared with those of either 0% (untreated control) or 3% at 16 days. In contrast, dosages of C. africanus fruit at two application frequency had no effect on growth of tomato plants – suggesting that either of the dosages was suitable for use in tomato production since both reduced nematode numbers. During validation, the materials reduced nematode numbers by margins similar to those observed previously under other environments. In conclusion, crude extracts of the two Cucumis species have stimulatory concentrations which have potential similar reductive effects on population densities of Meloidogyne species and could serve as botanical nematicides. However, since plant responses to the two products differed in terms of their respective dosages and active ingredients, it implied that for further improvement of the two, the overriding focus should be on their interaction with the protected plants and nematode numbers. Ideally, future research xxxv should include environmental impact studies, especially on the influence of the products fruit quality of tomato, earthworms, fish and bees.