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Heat treatment is the most commonly practiced technology to add value to products derived from wood materials. Traditionally, heat treatment enhances the resistance of wood materials to weathering and decay fungi, but despite its wide use in sectors such as construction, wood preservation and food packaging, there has been little attempt to appl~ heat treatme'nt in other areas to manage food-borne and plant diseases. A preliminary study indicated that preheating increased the inhibitory. effect of pine wood shavings against the imp0l1ant foodborne pathogen of broilers, Salmonella Enteritidis (SE). Thus the first objective of this study was to optimise a heating regime to evaluate the effect of the enhanced inhibitory activity on SE in direct contact and also reducing ammonia emission of a constructed litter using heated wood. Heating to 120°C for 72 hours was the most effective treatment. In addition, heated pine wood had antimicrobial activity against other known microorganisms in poultry bedding including Staphylococcus aureus, Escherichia coli and Saccharomyces cerevisiae as well as SE. Hardwood shavings of ash, beech, red oak also showed antimicrobial activity against SE as did similarly treated softwood species such as pine and cypress. In vitro assays of dominant chemicals derived from fractionation of the extract demonstrated that bio-active fractions containing vanillin and dehydroabietic acid exhibited antimicrobial activity, but weak or no activity after purification. Overall, the in vitro assays suggested that a synergistic interaction occurred between vanillin and dehydroabietic acid decreasing the minimum inhibitor levels of vanillin. A second objective of the study was to investigate the potential of heat-treated woodchips of Japanese larch and rhododendron to control Phytophthora ramorum (PR) an invasive pathogen of larch in VK forests. Results demonstrated that heattreated pine, larch and rhododendron woodchips inhibited the recovery of zoospores of PR compared with air-dried woodchips. This inhibition was maintained even if the larch woodchips were diluted with soil. The in vitro assays revealed that their methanol crude extracts had an inhibitory effect on PR zoospores and also reduced germination of chlamydospores compared with extracts from air-dried wood. Chemical analysis of crude extracts of all three showed some of the induced compounds were present in all the extracts but differed in concentration. Coniferaldehyde was the most active compound against all three propagules. The dominant resin acids, DHAA and abietic acid (AB) decreased the minimum inhibitory level of the tested phenolic compounds against PR but had no effect when tested alone. Results of a field trial using heat-treated and air-dried woodchips were consistent with the bioassay results of crude extracts and indicated that heat treated materials have potential to reduce the survival of PR under natural conditions. Finally, based on xvi overall results of bioassays in both parts of this study a mechanism of action for the synergism between aromatic compounds such as vanillin and coniferaldehyde and resin acids dehydroabietic and abietic acid was hypothesized.

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La pourriture brune des fruits (BR), causée par les champignons du genre Monilinia, est une maladie courante qui peut provoquer jusqu’à 40% de pertes de récolte chez la pêche. Toutes les pêches cultivées sont plus ou moins sensibles à la moniliose. Aucune alternative aux traitements chimiques n’est disponible, ce qui rend nécessaire les applications de fongicides jusqu'au stade pré-récolte, qui sont préjudiciables pour l'environnement et peuvent laisser des résidus sur les fruits. Une revue de la littérature compile les connaissances disponibles sur le couple pêcher-monilioses.Le but de cette étude est d'étudier les facteurs de résistance du fruit à M. laxa à différents stades de croissance chez la pêche et de déterminer leur contrôle génétique.Nous avons focalisé d’abord sur quelques cultivars pour étudier l'évolution de la sensibilité des fruits à M. laxa au cours de leur développement en relation avec les caractéristiques structurales et biochimiques des fruits (conductance cuticulaire du fruit, micro-fissures de l’épiderme et composés de surface des fruits). Certains composés ont été détectés pour la première fois chez la pêche. Les résultats ont confirmé que lors de la phase I les fruits immatures sont sensibles à la moniliose. Au stade de durcissement du noyau, les fruits sont résistants, la conductance cuticulaire faible et les niveaux de composés de surface présentaient un pic de teneurs. A l’approche de la maturité, les fruits sont sensibles de nouveau. Au stade I, nous avons exploré le rôle des stomates et de la conductance du fruit immature en relation avec la sensibilité à M. laxa. Une centaine de génotypes d'une descendance interspécifique de pêchers appelée BC2 a été caractérisée par une infection au laboratoire, un suivi de pertes transpiratoires des fruits et une estimation de la densité de stomates (uniquement pour les nectarines). Des symptômes inattendus (une ‘tache claire’ qui ne progresse pas) ont été observés. La conductance cuticulaire était significativement liée à la probabilité d'infection, mais le nombre de stomates n’a montré aucun effet sur la probabilité d'infection. Des QTL contrôlant la résistance des fruits à la moniliose, à la conductance cuticulaire et au nombre de stomates ont été identifiés et des co-localisations observées.A maturité, le contrôle génétique de la résistance à la moniliose et des composés biochimiques de l'épiderme des fruits a été étudié. Pendant trois ans, les fruits de la BC2 ont été infectés avec une suspension de spores de champignon selon deux modalités. La BC2 a affiché une forte variabilité de résistance à la moniliose. Malgré une faible stabilité entre les années, des génotypes à haut niveau de résistance ont été identifiés. De plus en 2015, nous avons exploré la variation des composés de l'épiderme des fruits au sein de la BC2. Les composés phénoliques, les terpènes et dérivés ont été quantifiés par HPLC. La relation entre la résistance à la moniliose et la présence et / ou les niveaux de certains composés de l'épiderme et le contrôle génétique de ces composés ont été étudiés.La moniliose des fruits de pêche est un problème complexe qui est encore loin d'être résolu. Des progrès ont été accomplis dans la connaissance des caractéristiques structurales et biochimiques impliquées dans la résistance et des régions du génome qui pourraient conférer une certaine tolérance à la maladie ont été détectées. Des travaux supplémentaires sont nécessaires pour développer des marqueurs moléculaires pour la sélection assistée par marqueurs. Les résultats obtenus suggèrent que des solutions pour l'avenir résident dans l’association de cultivars tolérants _ moins sensibles aux micro-fissures et à haute teneur en composés épidermiques potentiellement inhibiteurs du développement du champignon _ avec des pratiques culturales réduisant les risques de fissuration des fruits et d'apparition de conditions climatiques favorables à la propagation de la moniliose. / Brown rot (BR) in peach fruit caused by the fungus Monilinia spp. is a common disease that can provoke as much as 30 to 40% losses of crop. Currently, all cultivated peaches are more or less sensitive to BR. No other alternative than chemical treatment is available, hence fungicide applications are required until pre-harvest. Such applications are damaging the environment and may let residues in fruits. A review of literature was accomplished to compile the knowledge scattered in the literature from many years. The aim of this study is to investigate the factors of resistance of the fruit to M. laxa at different stages of fruit growth and their genetic control by studying contrasted genotypes and an interspecific peach progeny. The first focus was made on few cultivars to study the evolution of sensibility of fruits to M. laxa during their development in relation with structural and biochemical characteristics of the fruit, e.g. cuticular conductance, micro-cracks and fruit surface compounds. Some compounds were detected for the first time on peach fruit. The results confirmed that during the stage I immature fruits are susceptible to BR. Fruit cuticular conductance was high probably due to high density of stomata and thin cuticule in formation. In contrary, at pit hardening stage fruits were resistant, cuticular conductance was low and the levels of surface compounds exhibit a peak. When maturity approaches, fruit become susceptible again. With rapid development of the fruit during this stage, the surface compounds were diluted and micro-cracks often appear which resulted in high cuticular conductance. At stage I we explored the different physical characteristics of the immature fruit in relation with susceptibility to M. laxa. A hundred of individuals of an interspecific peach progeny called BC2 were characterized through laboratory infection, monitoring of fruit transpiratory losses and estimating stomata density (only for nectarines). Unexpected symptoms (not progressing ‘clear spot’) were observed. The cuticular conductance was significantly linked to the likelihood of infection, but the stomata number had no effect on the likelihood of infection. QTL controlling fruit resistance to BR, cuticular conductance and stomata number have been identified and some co-locations observed. At maturity stage we investigated the genetic control of BR resistance together with biochemical compounds of fruit epidermis. For three years, mature fruits from the BC2 progeny were infected with two modalities of infection: spray until runoff in the orchard to measure infection probability and drop in the laboratory conditions in order to observe the characters of beginning, progression and speed of infection. The BC2 progeny displayed high variability for BR resistance. Despite low stability between years, genotypes with high level of resistance were identified. In addition in 2015, we explored the variation in epidermis compounds of fruit within the BC2 progeny. Phenolic compounds, terpenoids and derivatives were quantified by HPLC. The relationship between BR resistance and presence and/or levels of certain epidermis compounds and the genetic control of these compounds were investigated. BR of peach fruit is a complex problem which is still far from resolved. Progress has been made in the knowledge of structural and biochemical characteristics involved in BR resistance and regions of the genome that could confer certain disease tolerance have been detected. Further work is needed to develop molecular markers for marker assisted selection. The results obtained suggest that solutions for the future lie in associations of tolerant cultivars _ less susceptible to micro-cracks and with high content of epidermis compounds potential inhibitor of the fungus development _ with cultural practices reducing both risks of fruit cracking and occurrence of micro-climatic conditions favorable to BR spread and sporulation.

L'intensification de l'agriculture a amélioré de façon considérable la production alimentaire ces dernières cinquante années mais elle s'est accompagnée d'un impact croissant sur l'environnement. En particulier, la modernisation de l'agriculture a impliqué une simplification de la structure des paysages agricoles rendant nos agro-ecosystèmes plus sensibles au risque épidémique. L'utilisation de la diversité génétique des cultures est une solution prometteuse pour réduire le risque d'occurrence et de propagation des maladies des cultures. Elle nécessite cependant une gestion collective des espaces agricoles. En conséquences, l'échelle d'étude ne doit plus se focaliser sur la parcelle mais sur le paysage. Dans cette thèse, nous nous interessons aux processus se déroulant à l'échelle du paysage et au rôle de la diversité des plantes cultivées pour le contrôle des épidémies. Nous avons identifié trois questions: comment les populations pathogènes se propagent-elles dans un paysage d'hôtes hétérogène ? Comment les différents génotypes composant la population pathogène entrent-ils en compétition au sein d'une population hôte diversifiée ? et, à plus long terme, comment les populations pathogènes évoluent-elles en réponse à la structure des populations hôtes ? Chacune de ces questions a été approfondie grâce à l'analyse de données obtenues en condition de production mais aussi par des approches théoriques. Nous avons montré que la composition et la structure spatiale des populations hôtes influence fortement la population pathogène. Cependant, les recommandations que peut fournir ce travail pour gérer la diversité génétique dépendent de l'objectif visé. / Agriculture intensification has improved food production impressively in the past 50 years but this came with an increasing impact on the environment. In particular, modern agriculture has led to the simplification of the environmental structure over vast areas. As a consequence, agro-ecosystems are particularly susceptible to epidemics. The increase of crop genetic diversity is a promising way for reducing the risk of occurrence and development of diseases in crops but the technical and organisational conditions required to manage the genetic resources at this scale have not been established yet. This will require shifting the scale of crop protection investigations from the field to the agricultural landscape. In this PhD thesis we focus on landscape-scale processes and on the potential role of functional diversity in cultivated landscapes to better control plant diseases. We identified three questions: how does a pathogen population spread over a heterogeneous host landscape? How do pathogen genotypes compete in a diversified host population? And, in a longer term, how do pathogen populations evolve in response to host landscape structure? Each of these questions is investigated through the analysis of real data and the development of theoretical approaches. We demonstrate that the composition and the spatial structure of the host landscape greatly influence the pathogen population dynamics and evolution. The recommendations that this work could provide in order to practically manage the genetic resources will depend on the desired aim and will request further collaborative work withthe professional operators.

Understanding the complex metabolic networks present in organisms, through the use of high throughput liquid chromatography coupled mass spectrometry, will give insight into the physiological changes responding to stress. However the lack of a proper work flow and robust methodology hinders verifiable biological interpretation of mass profiling data. In this study a novel workflow has been developed. A novel Kernel based feature alignment algorithm, which outperformed Agilent’s Mass profiler and showed roughly a 20% increase in alignment accuracy, is presented for the alignment of mass profiling data. Prior to statistical analysis post processing of data is carried out in two stages, noise filtering is applied to consensus features which were aligned at a 50% or higher rate. Followed by missing value imputation a method was developed that outperforms both at model recovery and false positive detection. The use of parametric methods for statistical analysis is inefficient and produces a large number of false positives. In order to tackle this three non-parametric methods were considered. The histogram method for statistical analysis was found to yield the lowest false positive rate. Data is presented which was analysed using these methods to reveal metabolomic changes during plant pathogenesis. A high resolution time series dataset was produced to explore the infection of Arabidopsis thaliana by the (hemi) biotroph Pseudomonas syringe pv tomato DC3000 and its disarmed mutant DC3000hrpA, which is incapable of causing infection. Approximately 2000 features were found to be significant through the time series. It was also found that by 4h the plants basal defence mechanism caused the significant ‘up-regulation’ of roughly 400 features, of which 240 were found to be at a 4-fold change. The identification of these features role in pathogenesis is supported by the fact that of those features found to discriminate between treatments a number of pathways were identified which have previously been documented to be active due to pathogenesis

L'enjeu de la thèse est de proposer une stratégie de gestion durable de la résistance génétique à la rouille brune du blé, basée sur des sources de résistance quantitative. Nous proposons d'identifier des résistances se traduisant par une diminution des performances du pathogène sur les différentes phases du cycle infectieux. Ainsi, l'exercice de contraintes diversifiées sur le pathogène devraient ralentir son adaptation et augmenter la durabilité de la résistance. La confrontation d'un ensemble de génotypes de blé à trois isolats de rouille brune a permis de mesurer le niveau de résistance pour cinq composantes en serre (efficacité d'infection, période de latence, taille de lésion, sporulation par lésion, sporulation par unité de surface sporulante), et à différentes étapes de l'épidémie au champ. Nous avons mis en évidence une grande diversité des composantes affectées, et une variabilité importante pour toutes les composantes. Le développement d'un modèle statistique a permis d'établir que l'ensemble des composantes intervient dans la détermination du niveau de résistance à l'échelle épidémique, mais l'efficacité d'infection et la latence sont les composantes qui jouent le rôle le plus important pour déterminer le niveau de résistance au champ. L'impact d'une composante sur le niveau global de résistance change selon les étapes de l'épidémie. Les trois isolats utilisés ont exprimé un profil d'agressivité contrasté vis-à-vis des différentes composantes. La cartographie des QTLs associés aux différentes composantes de résistance a permis d'établir que la diversité phénotypique observée est liée à une diversité génotypique. / The issue of this thesis is to propose a durable management of genetic resistance to wheat leaf rust, based on quantitative resistance. We propose to identify resistance factors reducing pathogen development across the different stages of the infectious cycle. Diversifying constraints exerted by host resistance on the pathogen development should slow down the pathogen adaptation, and increase resistance durability. A set of wheat genotypes was confronted to three leaf rust isolates, and resistance level was measured for five components in the greenhouse (infection efficiency, latent period, lesion size, spore production per lesion, spore production per unit of sporulating tissue), as well as at different stages of field epidemics. Across the germplasm investigated, the resistance components involved were diversified, and their resistance level varied. Developing a statistical model, we established that all the components are involved in the resistance level observed in field epidemics, the most important components being infection efficiency and latent period. The incidence of a component on the field resistance level varied across epidemic stages. The three pathogen isolates used displayed contrasted aggressiveness profiles, according to the different resistance components. QTL mapping of resistance associated to the different components showed that phenotypic diversity corresponded to genotypic diversity.

Le mildiou de la vigne est causé par l’oomycète Plasmopara viticola, qui s’attaque aux parties aériennes non-lignifiées affectant la production viticole. Une alternative à l’utilisation de pesticides est l’utilisation de variétés de vigne à la résistance durable, et un programme pour leur création par croisement entre espèces résistantes et la vigne cultivée, Vitis vinifera, est en cours. Ce programme nécessite l’identification de nouveaux gènes de résistance, ce que le projet vise à faire par (1) le criblage de vignes résistantes avec des effecteurs conservés chez P. viticola, (2) l’étude fonctionnelle d’effecteurs candidats. Le criblage de plantes résistantes n’a conduit à l’identification d’aucun nouveau facteur de résistance majeur. L’étude fonctionnelle d’effecteurs a permis la mise en évidence d’une nouvelle famille d’effecteurs chez P. viticola et a conduit à l’identification de deux effecteurs Pv33, nucléaire, et Pv47, associé au réticulum endoplasmique, qui induisent des défenses végétales. / Grapevine downy mildew is caused by the oomycete Plasmopara viticola, which attacks the aerial non-lignified tissues affecting wine production. An alternative to the use of pesticides is the use of vine varieties with sustainable resistances. A programme aiming to create such varieties by crossing resistant species with the cultivated grapevine, Vitis vinifera, is ongoing. Within this program requiring the indentification of new resistance genes, which the project aims to do by (1) screening resistant vines with effectors stored in P. viticola, (2) performing a functional study of candidate effectors. The screening of resistant plants did not lead to the identification of any new major resistance factors. The functional study of effectors revealed a new family of effectors in P. viticola and led to the identification of two effectors Pv33, nuclear, and Pv47, associated with the endoplasmic reticulum, which induce plant defences.