Powdery mildew, caused by the pathogen Blumeria graminis (DC) Speer (Syn. Erysiphe graminis DC) f. sp. tritici, is a major disease of wheat (Triticum aestivum L.). Race-specific resistance is easily identified in the field due to its qualitative phenotype and it is easy to incorporate because it is inherited as a single gene. Unfortunately, this type of resistance is easily overcome by the pathogen. Traits associated with quantitative trait loci (QTL) such as adult-plant resistance (APR), have become popular with plant breeders because of their durability over a wide geographic range and time. Due to the quantitative nature of these genes, they are difficult to study requiring multiple assessments of disease development under natural conditions in more than one location over a period of several weeks. Numerous QTL for APR to powdery mildew have been mapped in independent studies in different wheat backgrounds. The wheat cultivar Massey has been the subject of several studies due to its APR to powdery mildew that has remained effective for several decades. However, it has been difficult to identity simple sequence repeat (SSR) markers that are tightly linked to the QTL for APR in Massey. Such markers give breeders an advantage by allowing them to quickly identify and select for traits that would be difficult to distinguish in the field among breeding progeny from several backgrounds. Therefore, identification of tightly linked markers associated with APR to powdery mildew is necessary so that these traits can be selected for reliably in progeny. / Master of Science

L'utilisation de molécules stimulatrices de défense des plantes (SDP), également appelées inducteurs de résistance, constitute une alternative possible aux traitements fongicides conventionnels pour contrôler les maladies dues aux chanpignons phytopathogènes. Dans cette étude, nous avons mis en évidence que trois produits à caractère SDP (FSOV2, FSOV7 et FSOV10) protègent le blé (Triticum aestivum L.) contre la septoriose (Mycosphaerella graminicola, anamorphe Zymoseptoria tritici) lorsqu'ils sont utilisés de façon préventive, mais cette protection dépend fortement du cultivar considéré. Les cultivars Alixan, Premio et Altigo testés ici présentaient au départ des niveaux de résistance distincts à la septoriose. Les protections obtenues ne sont pas liées à un effet direct sur la germination des spores du champignon, mais à l'induction des mécanismes de défense chez le blé qui réduisent la nécrose foliaire et la sporulation du champignon. Ainsi, l'observation des différents stades du processus infectieux de M. graminicola en microscopie et le dosage des activités enzymatiques fongiques de dégradation des parois (CWDE) in planta révèlent que le niveau de protection induite varie avec le SDP appliqué et avec le cultivar traité. L'expression de neuf gènes impliqués dans différentes voies de défense, suivi par RTqPCR, et les activités enzymatiques peroxydase et phénylalanine ammonia lyase ont été mesurée au cours du temps, depuis le traitement par les SDP jusqu'à 5 jours après infection. Les résultats obtenus montrent, que les mécanismes de défense sont induits différemment en fonction du cultivar et en fonction du SDP appliqué. Ces résultats suggèrent que la réussite au champ des SDP est conditionnée de façon déterminante par le choix du couple SDP-cultivar. / The use of resistance inducers (RI) is a potential alternative to conventional fungicide treatments against plant fungal diseases. In the present study, we revealed that preventive applications of three RI conferred protection efficacies against M. graminicola, with protection levels varying with the wheat cultivar. Alixan, Premio and Altigo cultivars were previously known to exhibit distinct resistance levels to M. graminicola. The observed protections did not result from a direct effect on spore germination, but were related to the induction of wheat defense mechanisms. The induced resistances reduced foliar necrosis, as well as the sporulation level of the fungus. Microscopic observations of the infection process of M. graminicola and cell wall degrading enzymes (CWDE) activities measured in planta showed that the applied RI as well as the considered treated wheat cultivar influences the impact on the infection process and the protection efficacy. We investigated from the time of treatment until 5 days after inoculation plant peroxidase and phenylalanine ammonia lyase activities and the expression of nine genes involved in distinct defense pathways. Our results indicated that defense mechanisms are differently induced according both to the wheat cultivar and the RI. Therefore, the successful use of RI at the field level strongly depends on the RI-cultivar combination.

Lhumectation des surfaces végétales, due principalement aux précipitations sous forme de pluie ou de rosée, joue un rôle déterminant lors de la phase de contamination des plantes par de nombreux agents phytopathogènes. La connaissance de la pluie et de la rosée constitue un élément fondamental pour létude et la compréhension du fonctionnement des modèles de simulation des épidémies et des systèmes d'avertissements agricoles. Lobjectif de cette recherche est de contribuer à lamélioration du système davertissement des principales maladies cryptogamiques affectant le blé dhiver au sud de Belgique et au G-D de Luxembourg. Notre démarche a consisté, dans un premier temps à évaluer les potentialités du radar météorologique de Wideumont. Nous avons décrit son fonctionnement général ainsi que son principe de mesure et nous avons détaillé les différentes sources derreur qui affectent les estimations de précipitations dérivées des observations radar. Les mesures radar sont moins précises que les mesures de précipitations par des pluviomètres. Néanmoins, le radar permet dobserver en temps réel les précipitations sur un large domaine avec une très bonne résolution spatiale et temporelle. La comparaison quantitative et qualitative des précipitations mesurées au sol avec celles estimées par le radar a été faite sur une période de trois ans (2003, 2004 et 2005). Les résultats de la validation des cumuls mensuels font apparaître que le radar a tendance à sous-estimer les précipitations. Lerreur calculée pour lensemble des stations varie entre -50% et +12%. La validation qualitative du radar a été réalisée sur des occurrences de cumuls horaires. Les indices calculés à partir des tables de contingence donnent des valeurs de POD (Probability Of Detection) entre 0.44 et 0.80 durant la période étudiée. Limpact des estimations radar sur les périodes dinfection de Septoria tritici simulées par PROCULTURE a été évalué durant trois saisons culturales (2003, 2004 et 2005) par comparaison entre les données de sortie du modèle (alimenté par des estimations radar de précipitations horaires) et les estimations visuelles du développement des symptômes de la maladie sur les trois dernières feuilles. Les outputs de PROCULTURE via les données radar ont montré un grand accord entre la simulation et lobservation. Le radar météorologique devrait dès lors être bénéfique pour des régions où le réseau des pluviomètres est inexistant (ou moins dense) et où lincidence de la septoriose est importante. Dans un deuxième temps, sur base dune recherche bibliographique, un modèle dhumectation a été choisi. Le modèle sélectionné, appelé SWEB, se base sur le bilan énergétique et le bilan hydrique. Il simule la durée dhumectation due à la pluie et à la rosée sur lensemble du couvert végétal à partir des données issues des stations agrométéorologiques. Le modèle a été ensuite testé et validé sur différentes variétés de blé dhiver. Les données de sortie du modèle ont été comparées statistiquement aux mesures des capteurs (préalablement calibrés) et aux données dobservation obtenues sur des parcelles expérimentales et au champ durant les saisons culturales 2006 et 2007. Sur base des résultats obtenus, le modèle SWEB semble sous-estimer la durée dhumectation et plus particulièrement pour les événements de la fin dhumectation (dryoff). Lerreur moyenne en général est inférieure à 90 minutes. Dans un troisième temps, afin dobtenir une relation entre les périodes dhumectation et le développement de la septoriose sur les trois dernières feuilles, les périodes dhumectation simulées par SWEB ont été comparées dune part aux périodes dinfection de Septoria tritici simulées par PROCULTURE et dautre part aux estimations visuelles. Le modèle de la durée dhumectation simule avec succès des périodes dhumectations, dues à la fois à la rosée et à la pluie, qui ont déclenché linfection de la septoriose observée sur des parcelles expérimentales. Une durée minimale dhumectation favorable à linfection des feuilles de blé par Septoria tritici a été déterminée. Il est donc désormais nécessaire délaborer un système opérationnel intégrant le radar météorologique, le modèle de la durée dhumectation et le modèle épidémiologique. Notre travail a permis dacquérir via lanalyse des données agrométéorologiques et des données phytopathologiques, les connaissances nécessaires à lélaboration dun tel système et de participer ainsi à lamélioration des modèles davertissements existants. En effet, nous avons analysé les avantages et les limites du système radar comme données dentrée aux modèles et son aptitude dans la spatialisation des données. Nous avons également testé le modèle dhumectation pour la détermination des périodes dinfection nécessaires au développement de la septoriose. Dans une perspective dune meilleure opérationnalisation du système, lapproche envisagée pourrait facilement être intégrée dans le système existant pour la simulation dautres maladies comme les rouilles, loïdium et la fusariose à léchelle régionale. En définitive, ce travail aura prouvé une fois de plus lintérêt du "mariage" entre lagrométéorologie et la phytopathologie. [en] Summary - Weather-Radar Rainfall Measurement and Simulated Surface Wetness Duration for Septoria Leaf Blotch Risk Assessment. The persistence of free moisture on leaves, mainly as a result of precipitation in the form of rainfall or dew, plays a major role during the process of plant infection by most fungal pathogens. Acquiring rainfall and leaf moisture information is needed for accurate and reliable disease prediction and management. The objective of this research is to contribute to improve forecasting Septoria leaf blotch and other fungal pathogens on winter wheat in Belgium and Luxembourg./In the first part of this work, the potential of weather-radar rainfall estimates for plant disease forecasting is discussed. At first step, we focused on assessing the accuracy and limitations of radar-derived precipitation estimates, compared with rain-gauge data. In a second step, the Septoria leaf blotch prediction model PROCULTURE was used to assess the impact on the simulated infection rate of using, as input data, rainfall estimated by radar instead of rain gauge measurements. When comparing infection events simulated by PROCULTURE using radar-derived estimates and reference rain gauge measurements, the probability of detection (POD) of infection events was high (0.83 on average), and the false alarm ratio (FAR) of infection events was not negligible (0.24 on average). FAR decreased to 0 and POD increased (0.85 on average) for most stations, when the model outputs for both datasets were compared against visual observations of Septoria leaf blotch symptoms. Analysis of 148 infection events observed over three years at four locations showed no significant difference in the number of simulated infection events using either radar assessments or gauge measurements. This suggests that, for a given location, radar estimates are just as reliable for predicting infection events as rain gauges. As radar is able to estimate rainfall occurrence over a continuous space, unlike weather station networks that do observations at only a limited number of points, it has the great advantage of being able to predict the risk of infection at each point within an area of interest with an accuracy equivalent to rain gauge observations. This gives radar an important advantage that could significantly improve existing warning systems. In the second part, a physical model based on the energy balance, known as the Surface Wetness Energy Balance (SWEB), was applied for the simulation of Surface Wetness Duration (SWD) on winter wheat canopy. The model, developed in the United States on grapes canopies, was adapted for the winter wheat cultivars and was applied for use with agrometeorological data easily available from standard weather stations and weather-radar rainfall estimates. The SWEB model simulates surface wetness duration for both dew and rain events. The model was validated with data measured by sensors and with visual observations of SWD conducted in experimental plots during two cropping seasons in 2006 and 2007. The wetness was observed visually by assessing the presence or absence of surface water on leaves. Based on the results, the SWEB model appeared to underestimate surface wetness duration and especially for the dry-off events when compared statistically to visual observations. The error, on average, is generally less than 90 minutes. In order to establish a relationship between the surface wetness periods and Septoria leaf blotch development risk on the top three leaves, the SWEB model SWD outputs were compared with the number of hours of high probability of infection simulated by PROCULTURE as well as with visual plant diseases observations. A minimal surface wetness duration of favourable infection conditions for Septoria tritici was established. It is now required to develop an operational system that would integrate weather radar, surface wetness duration and foliar epidemic model. In this work, we have analyzed the advantages and limitations of the radar system as input to models and its ability for spatial interpolation of rainfall. We also tested the model for the determination of surface wetness periods required for Septoria Leaf Blotch Risk development. The proposed approach could be integrated in the existing system. Finally this approach shows once more the "happy marriage" between agrometeorology and plant disease management.

It is important to understand the underlying plant defense mechanisms in order to establish best strategies to reduce losses due to diseases in cereals. The current available information is mostly on model organisms and their plant-pathogen interactions. However, this study is focused on the identification of genes involved in the resistance mechanism of one of the most devastating diseases of wheat, yellow rust. The strategy undertaken was to use differential display method (DD) together with microarray technology, on yellow rust differential lines of wheat (Avocet-Yr1 and Avocet-Yr10) infected with the virulent and avirulent Puccinia striiformis f. sp. tritici races (Pst: PST17, PST45, 169E136 and 232E137) together with appropriate control infections. DD primer combinations of ninety allowed the detection of fourteen differentially expressed genes which were also confirmed by real-time QRT-PCR analysis. All of but one were found to be novel sequences in wheat genome. Among those, two very important genes were identified as full ORF including 5&rsquo / and 3&rsquo / end untranslated regions (UTR) / namely cyclophilin like protein (putative antifungal activity) and ubiquitin conjugating enzyme (E2). The sequence homology analysis of the cloned gene fragments reveled that the genes detected have roles in ubiquitinylation, programmed cell death (apoptosis), putative antifungal activities, disease resistance, pathogen related responses, including a few with no known function. In addition to DD analysis, using wheat Affymetrix &ldquo / GeneChip&rdquo / , we identified 93 differentially expressed ESTs of wheat in response to avirulent pathogen attack. We also investigated the differential expression profiles of wheat leaves during the virulent infections and determined 75 differentially regulated ESTs. 1Selected ESTs were further analyzed using QRT-PCR analysis and 15 were confirmed to be differentially regulated. For the further characterization of the identified genes, such as determination of their putative roles in disease response, functional studies have to be performed. For this purpose, BSMV (Barley Stripe Mosaic Virus) mediated virus induced gene silencing (VIGS) method is optimized in this thesis for wheat. We have successfully managed to silence the endogenous PDS gene (Phytoene desaturase) of wheat which can be used as a positive control for the monitoring of silencing of the genes we have identified. Our results show that BSMV mediated VIGS can be used efficiently and effectively to silence wheat genes that we identified through differential display and microarray analysis and can be used to study the functions of those genes

Les maladies d'origine tellurique sont difficilement contrôlables par la lutte chimique ou variétale et se caractérisent par des processus et des échelles spatio-temporelles différents de ceux des maladies aériennes. En particulier, les modes de dispersion des agents pathogènes du sol permettent l'apparition et le maintien d'une forte structure spatiale de ces maladies, qui se développent souvent sous forme de foyers. Cette agrégation influence à la fois la dynamique temporelle des épidémies et la relation dégâts-dommages, ce qui en fait un élément important du raisonnement des méthodes de lutte. L'objectif de cette thèse est de comprendre et de modéliser le développement spatio-temporel des épidémies d'origine tellurique afin d'en déduire des stratégies de gestion susceptibles de limiter les risques associés, en particulier en agissant sur la structure spatiale de ces maladies. Pour ce faire, deux modèles ont été développés. Le premier, spatialement explicite et assez détaillé biologiquement, a été paramétré en conditions contrôlées dans le cas du piétin-échaudage du blé. Le test de ce modèle à l'aide de données issues du champ montre une bonne précision malgré un biais positif et indique des pistes pour améliorer la valeur prédictive du modèle. Le second modèle, plus simple et plus générique, utilise la théorie de la hiérarchie pour simuler le développement d'épidémies à plusieurs échelles spatiales simultanément. Il permet de tester des hypothèses concernant le fonctionnement des épidémies et les liens entre incidences à différentes échelles, et en particulier l'effet de la structure spatiale du peuplement hôte et de l'inoculum primaire sur la dynamique et l'agrégation de la maladie. Dans le cas du piétin-échaudage, pour lequel nous avons montré l'importance de la structure spatiale de l'inoculum primaire, ces simulations conduisent à préconiser des semis différents en fonction du rang dans la succession culturale.

Take-all is the name given to the disease caused by a soilborne fungus Gaeumannomyces graminis (Sacc.) von Arx and Olivier var. tritici Walker (Ggt), an ascomycete of the family Magnaportheaceae (Cook, 2003). This fungus is an aggressive soil-borne pathogen causing root rot of wheat (primary host), barley and rye crops (secondary host). The flowering, seedling, and vegetative growth stages can be affected by the infection of the whole plant, leaves, roots, and stems. Infections of roots result in losses in crop yield and quality primarily due to a lowering in nutrient uptake. Take-all is most common in regions where wheat is cultivated without adequate crop rotation. Crop rotation allows time between the planting dates of susceptible crops, which causes a decrease in the inoculum potential of soilborne plant pathogens to levels below an economic threshold by resident antagonistic soil microbial communities. Soilborne disease suppressiveness is an inherent characteristic of the physical, chemical, and/or biological structure of a particular soil which might be induced by agricultural practices and activities such as the cultivation of crops, or the addition of organisms or nutritional amendments, causing a change in the microfloral environment. Disturbances of soil ecosystems that impact on the normal functioning of microbial communities are potentially detrimental to soil formation, energy transfers, nutrient cycling, and long-term stability. In this regard, an overview of soil properties and processes indicated that the use of microbiological and biochemical soil properties, such as microbial biomass, the analysis of microbial functional diversity and microbial structural diversity by the quantification of community level physiological profiles and signature lipid biomarkers are useful as indicators of soil ecological stress or restoration properties because they are more responsive to small changes than physical and chemical characteristics. In this study, the relationship between physico-chemical characteristics, and different biological indicators of soil quality of agricultural soils conducive, suppressive, and neutral with respect to take-all disease of wheat as caused by the soilborne fungus Gaeumannomyces graminis var. tritici (Ggt), were investigated using various techniques. The effect of crop rotation on the functional and structural diversity of soils conducive to take-all disease was also investigated. Through the integration of quantitative and qualitative biological data as well as the physico-chemical characteristics of the various soils, the functional and structural diversity of microbial IV communities in the soils during different stadia of take-all disease of wheat were characterised. All results were evaluated statistically and the predominant physical and chemical characteristics that influenced the microbiological and biochemical properties of the agricultural soils during different stadia of take-all disease of wheat were identified using multivariate analyses. Although no significant difference @ > 0.05) could be observed between the various soils using conventional microbiological enumeration techniques, the incidence of Gliocladium spp. in suppressive soils was increased. Significant differences @ < 0.05) were observed between agricultural soils during different stadia of take-all disease of wheat. Although no clear distinction could be made between soils suppressive and neutral to take-all disease of wheat, soils suppressive and conducive to take-all disease of wheat differed substantially in their community level physiological profiles (CLPPs). Soils suppressive / neutral to take-all disease were characterised by enhanced utilisation of carboxylic acids, amino acids, and carbohydrates, while conducive soils were characterised by enhanced utilisation of carbohydrates. Shifts in the functional diversity of the associated microbial communities were possibly caused by the presence of Ggt and associated antagonistic fungal and bacterial populations in the various soils. It was evident that the relationships amongst the functionality of the microbial communities within the various soils had undergone changes through the different stages of development of take-all disease of wheat, thus implying different substrate utilisation capabilities of present soil microbial communities. Diversity indices were calculated as Shannon's diversity index (H') and substrate equitability (J) and were overall within the higher diversity range of 3.6 and 0.8, respectively, indicating the achievement of very high substrate diversity values in the various soils. A substantial percentage of the carbon sources were utilised, which contributed to the very high Shannon-Weaver substrate utilisation indices. Obtained substrate evenness (equitability) (J) indices indicated an existing high functional diversity. The functional diversity as observed during crop rotation, differed significantly (p < 0.05) from each other, implying different substrate utilisation capabilities of present soil microbial communities, which could possibly be ascribed to the excretion of root exudates by sunflowers and soybeans. Using the Sorenson's index, a clear distinction could be made between the degrees of substrate utilisation between microbial populations in soils conducive, suppressive, and neutral to take-all disease of wheat, as well as during crop rotation. Furthermore, the various soils could also be differentiated on the basis of the microbial community structure as determined by phospholipid fatty acid (PLFA) analysis. Soil suppressive to take-all disease of wheat differed significantly (p < 0.05) from soils conducive, and neutral to take-all disease of wheat, implying a shift in relationships amongst the structural diversity of microbial communities within the various soils. A positive association was observed between the microbial phospholipid fatty acid profiles, and dominant environmental variables of soils conducive, suppressive, and neutral to take-all disease of wheat. Soils conducive and neutral to take-all disease of wheat were characterised by high concentrations of manganese, as well as elevated concentrations of monounsaturated fatty acids, terminally branched saturated fatty acids, and polyunsaturated fatty acids which were indicative of Gram-negative bacteria, Gram-positive bacteria and micro eukaryotes (primarily fungi), respectively. These soils were also characterised by low concentrations of phosphorous, potassium, percentage organic carbon, and percentage organic nitrogen, as well as low soil pH. Soil suppressive to take-all disease of wheat was characterised by the elevated levels of estimated of biomass and elevated concentrations of normal saturated fatty acids, which is ubiquitous to micro-organisms. The concentration of normal saturated fatty acids in suppressive soils is indicative of a low structural diversity. This soil was also characterised by high concentrations of phosphorous, potassium, percentage organic carbon, and percentage organic nitrogen, as well as elevated soil pH. The relationship between PLFAs and agricultural soils was investigated using principal component analysis (PCA), redundancy analysis (RDA) and discriminant analysis (DA). Soil suppressive to take-all disease of wheat differed significantly (p < 0.05) from soils conducive, and neutral to take-all disease of wheat, implying a shift in relationships amongst the structural diversity of microbial communities within the various soils. A positive association was observed between the microbial phospholipid fatty acid profiles, and dominant environmental variables of soils conducive, suppressive, and neutral to take-all disease of wheat. Hierarchical cluster analysis of the major phospholipid fatty acid groups indicated that the structural diversity differed significantly between soils conducive, suppressive, and neutral to take-all disease of wheat caused by Gaeumannomyces graminis var. tritici. The results indicate that the microbial community functionality as well as the microbial community structure was significantly influenced by the presence of take-all disease of wheat caused by Gaeumannomyces graminis var. tritici, and that the characterisation of microbial functional and structural diversity by analysis of community level physiological profiles and phospholipid fatty acid analysis, respectively, could be successfully used as an assessment criteria for the evaluation of agricultural soils conducive, suppressive, and neutral to take-all disease of wheat, as well as in crop rotation systems. This methodology might be of significant value in assisting in the management and evaluation of agricultural soils subject to the prevalence of other soilborne diseases. / Thesis (M.Sc. (Microbiology))--North-West University, Potchefstroom Campus, 2004.

Take-all is the name given to the disease caused by a soilborne fungus Gaeumannomyces graminis (Sacc.) von Arx and Olivier var. tritici Walker (Ggt), an ascomycete of the family Magnaportheaceae (Cook, 2003). This fungus is an aggressive soil-borne pathogen causing root rot of wheat (primary host), barley and rye crops (secondary host). The flowering, seedling, and vegetative growth stages can be affected by the infection of the whole plant, leaves, roots, and stems. Infections of roots result in losses in crop yield and quality primarily due to a lowering in nutrient uptake. Take-all is most common in regions where wheat is cultivated without adequate crop rotation. Crop rotation allows time between the planting dates of susceptible crops, which causes a decrease in the inoculum potential of soilborne plant pathogens to levels below an economic threshold by resident antagonistic soil microbial communities. Soilborne disease suppressiveness is an inherent characteristic of the physical, chemical, and/or biological structure of a particular soil which might be induced by agricultural practices and activities such as the cultivation of crops, or the addition of organisms or nutritional amendments, causing a change in the microfloral environment. Disturbances of soil ecosystems that impact on the normal functioning of microbial communities are potentially detrimental to soil formation, energy transfers, nutrient cycling, and long-term stability. In this regard, an overview of soil properties and processes indicated that the use of microbiological and biochemical soil properties, such as microbial biomass, the analysis of microbial functional diversity and microbial structural diversity by the quantification of community level physiological profiles and signature lipid biomarkers are useful as indicators of soil ecological stress or restoration properties because they are more responsive to small changes than physical and chemical characteristics. In this study, the relationship between physico-chemical characteristics, and different biological indicators of soil quality of agricultural soils conducive, suppressive, and neutral with respect to take-all disease of wheat as caused by the soilborne fungus Gaeumannomyces graminis var. tritici (Ggt), were investigated using various techniques. The effect of crop rotation on the functional and structural diversity of soils conducive to take-all disease was also investigated. Through the integration of quantitative and qualitative biological data as well as the physico-chemical characteristics of the various soils, the functional and structural diversity of microbial IV communities in the soils during different stadia of take-all disease of wheat were characterised. All results were evaluated statistically and the predominant physical and chemical characteristics that influenced the microbiological and biochemical properties of the agricultural soils during different stadia of take-all disease of wheat were identified using multivariate analyses. Although no significant difference @ > 0.05) could be observed between the various soils using conventional microbiological enumeration techniques, the incidence of Gliocladium spp. in suppressive soils was increased. Significant differences @ < 0.05) were observed between agricultural soils during different stadia of take-all disease of wheat. Although no clear distinction could be made between soils suppressive and neutral to take-all disease of wheat, soils suppressive and conducive to take-all disease of wheat differed substantially in their community level physiological profiles (CLPPs). Soils suppressive / neutral to take-all disease were characterised by enhanced utilisation of carboxylic acids, amino acids, and carbohydrates, while conducive soils were characterised by enhanced utilisation of carbohydrates. Shifts in the functional diversity of the associated microbial communities were possibly caused by the presence of Ggt and associated antagonistic fungal and bacterial populations in the various soils. It was evident that the relationships amongst the functionality of the microbial communities within the various soils had undergone changes through the different stages of development of take-all disease of wheat, thus implying different substrate utilisation capabilities of present soil microbial communities. Diversity indices were calculated as Shannon's diversity index (H') and substrate equitability (J) and were overall within the higher diversity range of 3.6 and 0.8, respectively, indicating the achievement of very high substrate diversity values in the various soils. A substantial percentage of the carbon sources were utilised, which contributed to the very high Shannon-Weaver substrate utilisation indices. Obtained substrate evenness (equitability) (J) indices indicated an existing high functional diversity. The functional diversity as observed during crop rotation, differed significantly (p < 0.05) from each other, implying different substrate utilisation capabilities of present soil microbial communities, which could possibly be ascribed to the excretion of root exudates by sunflowers and soybeans. Using the Sorenson's index, a clear distinction could be made between the degrees of substrate utilisation between microbial populations in soils conducive, suppressive, and neutral to take-all disease of wheat, as well as during crop rotation. Furthermore, the various soils could also be differentiated on the basis of the microbial community structure as determined by phospholipid fatty acid (PLFA) analysis. Soil suppressive to take-all disease of wheat differed significantly (p < 0.05) from soils conducive, and neutral to take-all disease of wheat, implying a shift in relationships amongst the structural diversity of microbial communities within the various soils. A positive association was observed between the microbial phospholipid fatty acid profiles, and dominant environmental variables of soils conducive, suppressive, and neutral to take-all disease of wheat. Soils conducive and neutral to take-all disease of wheat were characterised by high concentrations of manganese, as well as elevated concentrations of monounsaturated fatty acids, terminally branched saturated fatty acids, and polyunsaturated fatty acids which were indicative of Gram-negative bacteria, Gram-positive bacteria and micro eukaryotes (primarily fungi), respectively. These soils were also characterised by low concentrations of phosphorous, potassium, percentage organic carbon, and percentage organic nitrogen, as well as low soil pH. Soil suppressive to take-all disease of wheat was characterised by the elevated levels of estimated of biomass and elevated concentrations of normal saturated fatty acids, which is ubiquitous to micro-organisms. The concentration of normal saturated fatty acids in suppressive soils is indicative of a low structural diversity. This soil was also characterised by high concentrations of phosphorous, potassium, percentage organic carbon, and percentage organic nitrogen, as well as elevated soil pH. The relationship between PLFAs and agricultural soils was investigated using principal component analysis (PCA), redundancy analysis (RDA) and discriminant analysis (DA). Soil suppressive to take-all disease of wheat differed significantly (p < 0.05) from soils conducive, and neutral to take-all disease of wheat, implying a shift in relationships amongst the structural diversity of microbial communities within the various soils. A positive association was observed between the microbial phospholipid fatty acid profiles, and dominant environmental variables of soils conducive, suppressive, and neutral to take-all disease of wheat. Hierarchical cluster analysis of the major phospholipid fatty acid groups indicated that the structural diversity differed significantly between soils conducive, suppressive, and neutral to take-all disease of wheat caused by Gaeumannomyces graminis var. tritici. The results indicate that the microbial community functionality as well as the microbial community structure was significantly influenced by the presence of take-all disease of wheat caused by Gaeumannomyces graminis var. tritici, and that the characterisation of microbial functional and structural diversity by analysis of community level physiological profiles and phospholipid fatty acid analysis, respectively, could be successfully used as an assessment criteria for the evaluation of agricultural soils conducive, suppressive, and neutral to take-all disease of wheat, as well as in crop rotation systems. This methodology might be of significant value in assisting in the management and evaluation of agricultural soils subject to the prevalence of other soilborne diseases. / Thesis (M.Sc. (Microbiology))--North-West University, Potchefstroom Campus, 2004.

Thesis (Ph. D.)--University of Wisconsin--Madison, 1919. / Title from added collective thesis title page. Part 1 reprinted from Phytopathology, vol. 4, no. 4 (Aug. 1914), p. [323]-326, plate XXI ; Part 2 reprinted from Phytopathology, vol. IX, no. 2 (Feb. 1919), p. [93]-103, plate IX ; Part 3: Bulletin / United States Department of Agriculture, no. 818 (5 Jan. 1920) (see OCLC #16627505), 14 p., V p. of plates ; Part 4: Bulletin / United States Department of Agriculture, no. 842 (7 Sept. 1920) (see OCLC #16627722), 40 p., VI p. of plates. Includes bibliographical references.

Doctor of Philosophy / Department of Agronomy / Gina Brown-Guedira / Allan K. Fritz / Aegilops tauschii, the D-genome donor of modern wheat, has served as an important source of genetic variation in wheat breeding. The objective of this research was to characterize and utilize multiple Ae. tauschii-derived pest resistance genes contained in the germplasm KS96WGRC40. Two Ae. tauschii-derived genes, H23 and Cmc4, provide resistance to the Hessian fly (HF) and wheat curl mite (WCM), respectively. A linkage analysis of a testcross population estimated 32.67% recombination between H23 and Cmc4 on chromosome 6DS in wheat indicating that the two genes are not tightly linked as previous mapping reports show. Haplotype data of recombinant lines and physical mapping of linked microsatellite markers located Cmc4 distal to H23. Haplotype data indicated that both KS89WGRC04 and KS96WGRC40 have the distal portion of 6DS derived from Ae. tauschii. Microsatellite primer pairs BARC183 and GDM036 were more useful than the previously published linked markers in identifying lines carrying Cmc4 and H23, respectively. Through phenotypic selection and advancement within the testcross population, three TC1F2:4 lines were identified as homozygous resistant for H23 and Cmc4 and have the complete terminal segment of 6DS from Ae. tauschii. Two lines are more desirable than the original germplasm releases and can serve as a source of resistance to both HF and WCM in an elite background. A linkage analysis of a segregating recombinant inbred line population identified an Ae. tauschii-derived gene of major effect conferring resistance to Septoria leaf blotch (STB) and another Ae. tauschii-derived gene of major effect conferring resistance to soil-borne wheat mosaic virus (SBWMV) in the germplasm KS96WGRC40. The STB resistance gene in KS96WGRC40 is located in the distal 40% of the short arm of chromosome 7D flanked by microsatellite markers Xgwm044 and Xbarc126. Two previously reported STB genes, Stb4 and Stb5, have been mapped to 7DS in the same region as the STB resistance gene in KS96WGRC40. The uniqueness of the STB resistance genes on 7DS is questionable. The SBWMV resistance gene in KS96WGRC40 is located on chromosome 5DL linked to microsatellite marker Xcfd010. The SBWMV resistance gene within KS96WGRC40 was derived from TA2397 via KS95WGRC33.

Pyrenophora tritici-repentis (Ptr) is the necrotrophic fungus responsible for tan spot of wheat (Triticum aestivum). Ptr causes disease on susceptible wheat cultivars through the production and secretion of host-selective toxins (HSTs). HSTs are compounds that are only known to be produced by fungi and considered to be primary determinants of pathogenicity. Infiltration of these toxins into sensitive wheat elicits the same symptoms as the pathogen, which simplifies investigations of host- pathogen interactions due to exclusion of the pathogen. These characteristics make HSTs ideal molecules to dissect molecular plant-microbe interactions. Known HSTs of Ptr include Ptr ToxA (ToxA), Ptr ToxB (ToxB) and Ptr ToxC (ToxC). ToxA is the most characterized toxin of Ptr, as well as the first proteinaceous HST identified. The proposed mode-of-action for ToxA includes internalization into sensitive wheat mesophyll cells, localization to the chloroplast, photosystem perturbations and elicitation of high amounts of reactive oxygen species (ROS), all of which lead to necrosis. However, it is still unknown how ToxA is transported to the chloroplast. To identify additional interacting components involved in ToxA symptom development, genes were silenced in tobacco plants (Nicotiana benthamiana) using the tobacco rattle virus (TRV) virus-induced gene-silencing (VIGS) system. Four genes were identified that potentially could play a role in ToxA-induced cell death: a 40S ribosomal subunit, peroxisomal glycolate oxidase (GOX), a thiamine biosynthetic enzyme (Thi1), and the R-gene mediator, Sgt1. Ptr exhibits a complex race structure determined by the HST(s) produced and the symptom(s) elicited on sensitive wheat cultivars. Currently, there are eight characterized races and other HSTs and races have been proposed. Isolate SO3 was discovered in southern Oregon and elicits ToxA-like symptoms on a wheat differential set, yet lacks the ToxA gene. The transcriptome of SO3 was sequenced, assembled, and aligned to a ToxA-producing isolate, Pt-1C-BFP, which will aid in the identification of the protein(s) that may be responsible for these ToxA-like symptoms. SO3 contains a set of 497 sequences that were not found in the ToxA-producing isolate Pt-1C-BFP (BFP). These sequences should be further investigated to identify those that encode small secreted proteins (SSPs) and could potentially serve as HSTs and pathogenicity factors of SO3. / Graduation date: 2013