>Magister Scientiae - MSc / As the global human population grows, so does the demand for faster food production rates. Owing to this, agricultural practices have had to expand and move into semi-arid and arid regions, too, where frequent irrigation is essential. However, irrigated ground water contains many salt ions (mainly Na+ and Cl-) which contribute to soil salinization on croplands. Soil salinity negatively impacts crop growth and yield and thus, strategies for the alleviation of salt stress on crop plants have had to be developed. This study assessed the use of plant growth promoting bacteria (PGPB). The aim of this study was to isolate, identify and characterize bacterial endophytes isolated from the halophyte, Arctotheca calendula. Endophytes were identified using 16S rDNA and were screened for plant growth promoting properties including nitrogen fixation, phosphate and zinc solubilization, siderophore, ammonia and indole-3-acetic acid (IAA) when exposed to 0 mM, 300 mM and 600 mM NaCl. The endophytes had been identified as Erwinia persicina NBRC 102418T, Bacillus marisflavi JCM 11544T, Ochrobactrum rhizosphaerae PR17T, Microbacterium gubbeenense DSM 15944T and Bacillus zhangzhouensis DW5-4T and all of which had demonstrated some plant growth promoting characteristics. Thereafter, we aimed to demonstrate plant growth promotion of P. vulgaris cv. Star 2000 inoculated with PGPB under salinity stress. P. vulgaris cv. Star 2000 seeds were inoculated with the PGPB and exposed to 0 mM and 100 mM NaCl. Post-harvest, plants were assessed for their dry mass, cell death, superoxide concentration and nutrient content. It was discovered that salinity negatively impacted P. vulgaris cv. Star 2000’s dry mass, NaCl-induced cell death, and differentially influenced superoxide concentration, nutrient uptake and content of the leaf and root material in the inoculated and control treatments. However, the isolated PGPB had been able to mitigate the negative effects of soil salinity on P. vulgaris cv. Star 2000.

Synthetic polymers are widely used in basic day to day activities given the wide range of uses associated with their advantageous material properties. Polyethylene terephthalate (PET) is a widely used synthetic polymer with annual production exceeding 73.39 million tons. Out of all the PET material generated, only 30% PET is recycled because current mechanical and chemical recycling methods are not techno-economically viable. This leads to the accumulation of a large amounts of PET waste in the environment causing significant damage to terrestrial and aquatic ecosystems. An alternative to recycling is PET upcycling approaches strategize of converting PET waste into high-value products. This development enables a circular material economy for PET. There are several reports of PET upcycling strategies that describe hybrid-chemo biological approaches. However, efficient whole-cell microbial catalysts capable of selectively degrading PET into its original monomers of ethylene glycol (EG) and terephthalic acid (TPA), and simultaneously upcycling these monomers into high-value compounds is yet to be developed. The selection of an appropriate host strain for plastic upcycling is vital in developing industrially applicable whole-cell biocatalysts. Use of non-model organisms in industrial applications has gained attention over the recent years. The work presented here illustrates comprehensive genomic and phenomic investigations suggesting that the metabolic pathways of the newly identified, Erwinia aphidicola LJJL01, is a promising candidate for upcycling PET-degraded substrates. First, we performed a comprehensive phenomic characterization of E. aphidicola LJJL01 including SEM imaging, pH, optimal temperature, toxicity tolerance, antibiotic tolerance, and fatty acid profile. The metabolic capability of the strain was shown using a substrates utilization assay that includes 29 substrates which comprise C-6 sugars, C-5 sugars, sugar alcohols, acids, alcohols. Secondly, we developed an efficient system for plasmid-based expression and secretion of heterologous proteins. We established synthetic microbiology tools, including CRISPR/Cas9-based genomic editing, to engineer the E. aphidicola LJJL01 strain. Thirdly, we demonstrated successful heterologous expression of PET hydrolyzing enzymes such as PETase and MHETase from Ideonella sakaiensis together with their secretion signal peptides in E. aphidicola LJJL01. We assessed the strain's PET hydrolyzing activity using Bis(2-Hydroxyethyl) terephthalate (BHET), an intermediate molecule of PET as the model substrate. The strain yields 0.88 ±0.10 mol of TPA/mol of BHET in minimal salt medium within 48 hours and outperforms the commonly used platform organisms such as Pseudomonas putida KT2440. We also successfully expressed the thermostable leaf branch compost cutinase (LCC) in E. aphidicola LJJL01. For the first time we were able to demonstrate the synergistic activity of LCC and MHETase enzymes at 30 °C. Since the developed strains didn't show considerable PET degradation at ambient conditions, we developed a novel process to hydrolyze amorphous and commercial grade PET using cell-free supernatant of secreted LCC enzyme at 72°C (the glass transition temperature of PET). Finally, we further engineered the aromatic catabolism of the strain to demonstrate the potential of upcycling PET-degraded TPA into high-value platform chemicals such as cis, cis-muconate. Taken together, we demonstrated E. aphidicola LJJL01, a promising microbial chassis to develop whole-cell biocatalysts to upcycle PET and enable circular material economy.

Experiment s were conducted to see if Erwinia amylovora (Burrill) Winslow et al. overwinters inside living host tissue in Utah. Bacteria, collected from apple, pear, mountain ash, chokecherry and Pyracantha, were used in the experiment. Isolates taken from buds and inner bark plated on nutrient yeast dextrose agar, we re tested by serological and bacteriophage techniques. Those showing positive tests were then inoculated into Bartlett pear seedlings to test virulence. Both virulent and avirulent isolates were isolated from each species of plant in the experiment. Pathogenic bacteria were isolated from diseased tissue near cankers, as well as from apparently healthy inner bark as far as six inches below the cankers. Pathogenic bacteria were also isolated from healthy appearing buds in the vicinity of cankers. Nearly 15 percent of isolates from hosts other than apple and pear were pathogenic to Bartlett pear seedlings. A good deal of variation existed among the bacterial isolates. Antisera developed from four isolates of Erwinia amylovora proved to be a good means of identification for the pathogen.

No description available.

Erwinia soft rot is a widespread disease destructive to numerous important crop plants. Damage to plants is primarily due to celldegrading enzymes (CDEs) secreted by the bacteria. I am interested in potato (Solanum tuberosum) soft rot because it is of agricultural importance and it represents an ideal model system for understanding molecular events in plant-pathogen interactions. Much has been learned in vitro about the molecular genetics of CDEs in the past decade; however, little is known about their expression in plantae To study expression of genes for these enzymes during pathogenesis and plant responses to erwinias or their enzymes, I developed a membrane-separated system for simultaneous studies of potato and bacterial gene expression. This system facilitates the isolation of plant tissue-free bacterial cells and bacteria-free plant tissue for subsequent analysis of gene expression by RNA blot hybridization. Using this system, I demonstrated that in compatible interactions, rnRNAs for three Erwinia carotovora subsp. carotovora (Ecc) CDE genes were induced to high levels and were induced sequentially: exo-pectate lyase (PL), endo-PL, and then endopolygalacturonase (PG) with maximal mRNA accumulations at 6, 9, and 12 hr, respectively. Induction of these mRNAs was well correlated with tissue maceration. In the incompatible interaction, however, induction of all three Ecc genes was reduced several-fold compared to the compatible interaction. The kinetics of mRNA accumulation during pathogenesis were distinct from those of in vitro accumulation induced by polygalacturonic acid. My results confirm that in planta expression of these genes was induced by exo-PL reaction products as suggested by other researchers. In studies of plant genes correlated with plant responses to pathogens and environmental stresses [plant defenseresponse (PDR) genes], I also showed Ecc triggered active responses distinct from wound responses. I used gene probes for phenylalanine ammonia- lyase (PAL) and 3-hydroxy-3-methylglutaryl coenzyme A reductase (HMGR), key genes in the biosynthesis of phenylpropanoid- and terpenoidderived compounds believed to be important in plant defenses. Ecc inoculation caused much more rapid and greater increases in PAL mRNA and enzyme activity levels in potato tuber than wounding alone. Escherichia coli, a non-plant pathogen, carrying a plasmid which encodes Ecc endo-PL, also induced PAL mRNA accumulation. Ecc induced a specific HMGR isogene (HMGR1) not activated by wounding. My results support the existence of an HMGR mul-ci-gene family. Wounding resulted in a rapid and transient accumulation of HMGR2 mRNA followed by a slower accumulation of HMGR3 mRNA. These isogenes are distinct from the Ecc-induced HMGRI gene. / Ph. D.

El fuego bacteriano de las rosáceos es una enfermedad de fácil diseminación dificil control que afecta a los frutales de pepita, principalmente peral y manzano, y a plantas ornamentales. El agente etiológico de esta enfermedad es Erwinia amylovora, una enterobacteria considerada como organismo de cuarenta en la Unión Europea.Esta bacteria ha sido identificada en la mayoría de los paises del centro y norte de Europa, y en los últimos veinte años también se ha extendido por los países del Mediterráneo. en España, se han detectado diversos focos desde 1995, en distintos hospedadores procedentes de varias Comunidades Autonómas, habiéndose aplicado programas intensivos de erradicación en casi todas ellas. En esta investigación se ha llevado a cabo una caracterización fenotípica y genotípica de una amplia colección de aislados españoles de E. Amylovora de diversos orígenes geográficos, hospedadores y años de aislamiento. La evaluación de los datos obtenidos, tras la realización de análisis fisiológicos, bioquímicos y moleculares de las cepas españolas, ha mostrado su escasa diversidad fenotípica y genotípica. No obstante, los resultados de la cracterización molecular mediante electroforesis en campo pulsante y otras técnicas, apoyan dos hipotesis sobre el origen y la diseminación del fuego bacteriano en nuestro país; en primer lugar, la introducción de material vegetal infectado procedente de otros países de Europa como posible responsable de varios de los focos de infección de esta enfermedad en España, y en segundo lugar, la existencia de, al menos, tres fuentes de inóculo distintas. Por otro lado, la primera descripción de una cepa de E. amylovora que carece del plásmido PEA29 de forma natural, representa una novedad con implicaciones importantes para el diagnóstico molecular de la enfermedad, asi como para la hipótesis acerca del papel de este plásmido en la virulencia del patógeno del fuego bacteriano. / Donat Luis, MV. (2004). Caracterización fenotípica y genotípica de aislados españoles de Erwinia amylovora [Tesis doctoral]. Universitat Politècnica de València. https://doi.org/10.4995/Thesis/10251/1859

Erwinia amylovora, a quarantine organism of the European Union (EU), is the causal agent of fire blight. This disease causes substantial economic losses in all countries where it is present and its control turns out difficult, due to the absence of effective chemical and biological treatments and the ability of persistence and dissemination of E. amylovora. Cupric treatments constitute the base of the integrated management of fire blight in the European Union countries, because the antibiotics, although have been proved useful against this disease, are forbidden in the EU for plant treatments. This thesis, mostly performed in a P2 security lab, is aimed to dilucidate molecular mechanisms implicated in the response of E. amylovora to copper sulfate as a stress factor, considering that copper is a well known toxic element for bacterial cells over a certain threshold concentration. The global objective was first addressed with the study of a selection of genes that have been related in other bacterial models with copper stress or with stress in general. The quantification of the rpoS gene expression in presence of copper showed that, at least in long-term survival, this gene may be involved in the E. amylovora response to copper stress. Second, a transcriptomic study was performed by microarray after subdue the bacteria to a copper shock treatment. The analysis of the microarray results showed that 44 genes were differentially expressed in presence of this metal. Each one of these genes was studied by gene ontology and, after comparing them with databases published in NCBI, they were classified in functional categories. The gene expression of twenty-five out of fourty-four differentially expressed genes was validated by real-time PCR. In the validation, copA gene was expressed more than 19-fold in presence than in absence of copper and, because of that, it was selected together with other seven genes (soxS, yjcE, ygcF, yhhQ, galF, arcB, EAM_3469), which also showed an increased expression, to generate mutants of E. amylovora. The responses of mutants to copper, and the fact that the wild phenotype was restored in the complemented mutants, has shown the role of copA, soxS, yjcE, ygcF, arcB and yhhQ genes in the E. amylovora in vitro survival against copper stress. Besides, the implication of copA gene has also been proved in planta, in copper treated shoots from pear trees. Finally, all the results obtained along this thesis have allowed to elaborate a putative model of the different genetic mechanisms that seem are involved in the interaction between E. amylovora and copper. The most important mechanism seems to be to face up reactive oxygen species (ROS) by the activation of the soxS and yjcE genes. The activity of these genes is supported by CopA protein, which pumps copper from inside the cell out to the periplasmic space. The activation of arcB gene, which allows the change from aerobic metabolism to anaerobic metabolism, would also help E. amylovora to reduce ROS. Taking together, the results of this thesis have allowed an approximation to the genetic basis of E. amylovora response to copper stress and they constitute a start point to move forward in the knowledge of the molecular mechanisms underlying that response. / Erwinia amylovora, organismo de cuarentena en la Unión Europea (UE), es el agente causal del fuego bacteriano. Esta enfermedad produce grandes pérdidas económicas en todos los países en los que está presente y su control resulta muy difícil, debido a la carencia de tratamientos químicos y biológicos eficaces y a la persistencia y facilidad de diseminación de E. amylovora. Los tratamientos con compuestos cúpricos constituyen la base de la gestión integrada del fuego bacteriano en los países de la UE, puesto que el uso de antibióticos, aunque se ha demostrado útil contra esta enfermedad, está prohibido en la UE para el tratamiento de bacteriosis en plantas. Esta tesis, realizada en su mayoría en un laboratorio de seguridad biológica P2, pretende dilucidar mecanismos moleculares implicados en la respuesta de E. amylovora al sulfato de cobre como factor de estrés, ya que este metal es un elemento tóxico para las células bacterianas por encima de una determinada concentración umbral. El objetivo global se abordó, en primer lugar, con el estudio de una selección de genes que se han relacionado en otros modelos bacterianos con el estrés que produce el cobre o con el estrés en general. La cuantificación de la expresión del gen rpoS en presencia de cobre mostró que este gen puede estar implicado en la supervivencia a largo plazo de E. amylovora para combatir el estrés que produce este metal. En una segunda aproximación, se realizó un estudio transcriptómico mediante microarray tras someter a la bacteria a un breve tratamiento de cobre. El análisis de los resultados del microarray reveló que 44 genes se expresaban de forma diferencial en presencia del metal. Cada uno de ellos se estudió mediante gene ontology y por comparación con las bases de datos publicadas en el NCBI, y así se clasificaron en categorías funcionales. Las categorías de estrés y transporte fueron las más abundantes, tanto respecto a los genes que aumentaron su expresión tras la aplicación de cobre como a los que la disminuyeron. De los 44 genes que se expresaron de forma diferencial, se validó la expresión de 25 de ellos por PCR en tiempo real. En dicha validación, el gen copA se expresó 19 veces más en presencia que en ausencia de cobre, por lo que fue seleccionado, junto con siete genes más (soxS, yjcE, ygcF, yhhQ, galF, arcB, EAM_3469), en los que el incremento en la expresión fue menos pronunciado, para generar mutantes de E. amylovora. La respuesta de los mutantes a la presencia de cobre, y la restauración de fenotipos al complementar las mutaciones generadas, han revelado el papel de los genes copA, soxS, yjcE, ygcF, arcB y yhhQ en la supervivencia in vitro de E. amylovora frente al estrés por cobre. Además, la implicación del gen copA se ha demostrado también in planta en brotes de peral tratados con cobre. Finalmente, todos los resultados obtenidos han permitido elaborar un posible modelo de los diferentes mecanismos genéticos que parecen estar implicados en la interacción de E. amylovora con el cobre. El mecanismo más importante parece ser combatir las especies reactivas del oxígeno (ERO), mediante la activación de la expresión de los genes soxS e yjcE. La actividad de estos genes está apoyada, además, por la proteína CopA, que bombea cobre desde el interior celular al espacio periplásmico. La activación del gen arcB, que permite el cambio de un metabolismo aerobio a uno anaerobio, también ayudaría a la reducción de las ERO. En definitiva, los resultados han permitido una aproximación al sustrato genético de la respuesta de E. amylovora al estrés por cobre, y constituyen un punto de partida para avanzar en el conocimiento de los mecanismos moleculares implicados en dicha respuesta. / E. amylovora, organisme de quarantena a la Unió Europea (UE), és l'agent causal del foc bacterià. Aquesta malaltia produeix grans pèrdues econòmiques a tots els països on està present, i el seu control resulta molt difícil, a causa de l' absència de productes químics i biològics eficaços i també per la capacitat de persistència i disseminació d'E. amylovora. Els tractaments amb composts cúprics constitueixen la base de la gestió integrada del foc bacterià als països europeus, ja que l'ús d'antibiòtics, tot i que s'ha demostrat eficaç per a combatre aquesta malaltía, està prohibit a la UE per al tractament de bacteriosi en plantes. Aquesta tesi, realitzada majoritàriament a un laboratori de seguretat biològica P2, pretén dilucidar mecanismes moleculars implicats en la resposta d'E. amylovora davant del coure com a factor d'estrés, ja que el coure és un element tòxic per la cèl.lula per damunt d'una determinada concentració umbral. L'objectiu global es va abordar, en primer lloc, amb l'estudi d'una selecció de gens relacionats en altres models bacterians amb l'estrés que produeix el coure, o amb l'estrés en general. La quantificació de l'expressió del gen rpoS en presència de coure va mostrar que aquest gen pot estar implicat en la supervivència a llarg termini d'E. amylovora per a combatre l'estrés que produeix aquest metall. En una segona aproximació, es va realitzar un estudi transcriptòmic mitjançant microarrays després de sotmetre els bacteris a un breu tractament de coure. L'anàlisi dels resultats dels microarrays va revelar que 44 gens s'expressen de forma diferencial en presència del metall. Cadascun d'ells es va estudiar mitjançant gene ontology i, per comparació amb les bases de dades publicades al NCBI, es van classificar en categories funcionals. Les categories d'estrés i transport van ser les més enriquides, tant en els gens que augmentaren la seua expressió després de l'aplicació de coure com en aquells que la van reduir. Dels 44 gens que s'expressaren de forma diferencial, es va validar l'expressió de 25 d'ells per PCR a temps real. En la validació, el gen copA es va expressar 19 vegades més en presència que en absència de coure, per aquesta raó va ser seleccionat junt amb set gens més (soxS, yjcE, ygcF, yhhQ, galF, arcB, EAM_3469), en els que l'increment de l'expressió va ser menys pronunciada, per a generar mutants d'E. amylovora. La resposta dels mutants a la presència de coure, i la restauració dels fenotips originals al complementar les mutacions generades, han revelat el paper dels gens copA, soxS, yjcE, ygcF, arcB i yhhQ en la supervivència in vitro d'E. amylovora davant a l'estrés per coure. A més a més, la implicació del gen copA s'ha demostrat també in planta, en brots de perera tractats amb coure. Finalment, tots els resultats obtinguts han permès elaborar un possible model dels diferents mecanismes genètics que semblen estar implicats en la interacció d'E. amylovora amb el coure. El mecanisme més important sembla ser combatre les especies reactives de l'oxigen (ERO), mitjançant l'activació de l'expressió dels gens soxS i yjcE. L'activitat d'aquestos gens és recolzada també per l'acció de la proteïna copA, que bombeja coure des de l'interior cel.lular a l'espai periplàsmic. L'activació del gen arcB, que permet el canvi d'un metabolisme aerobi a un metabolisme anaerobi, també ajudaria a reduir la producción de les ERO. En conclusió, els resultats han suposat una aproximació al substrat genètic de la resposta d'E. amylovora a l'estrés per coure, i constitueixen un punt de partida per avançar en el coneixement dels mecanismes moleculars implicats en aquesta resposta. / Águila Clares, B. (2017). Elucidating the molecular basis of copper stress in Erwinia amylovora [Tesis doctoral]. Universitat Politècnica de València. https://doi.org/10.4995/Thesis/10251/81658

Environmental use of genetically-engineered microorganisms (GEMs) has raised concerns over potential ecological impact. Development of microcosm systems useful in preliminary testing for risk assessment will provide useful information for predicting potential structural, functional, and genetic effects of GEM release. This study was executed to develop techniques that may be useful in risk assessment and microbial ecology, to ascertain which parameters are useful in determining risk and to predict risk from releasing an engineered strain of Erwinia carotovora. A terrestrial microcosm system for use in GEM risk assessment studies was developed for use in assessing alterations of microbial structure and function that may be caused by introducing the engineered strain of E. carotovora. This strain is being developed for use as a biological control agent for plant soft rot. Parameters that were monitored included survival and intraspecific competition of E. carotovora, structural effects upon both total bacterial populations and numbers of selected bacterial genera, effects upon activities of dehydrogenase and alkaline phosphatase, effects upon soil nutrients, and potential for gene transfer into or out of the engineered strain. No significant difference was found in survival of the engineered strain as compared to its wildtype parent. Both strains survived for over two months in microcosms. The effects of both strains upon populations of total bacteria and selected bacterial genera were determined; while some effects upon community structure were observed, they were not significant. The engineered strain was not found to be a superior competitor compared to its parent; three different doses of engineered and wildtype strains were used. ln addition, neither strain affected activities of dehydrogenase or alkaline phosphatase in soil. Likewise, no effects were observed upon the nutrients monitored. However, transfer of the kanamycin resistance gene that had been inserted into the engineered E. carotovora strain may have occurred. Five species of indigenous bacteria displayed kanamycin resistance 15 days after being exposed to the engineered Erwinia. DNA from these strains was isolated, purified, and hybridization experiments executed to determine if any homology existed between these DNAs and the kanamycin resistance gene that had been inserted into E. carotovora. Using biotin-Iabeled probes and Iow-stringency washing conditions, homology was observed. However, before gene transfer can be proven, additional studies, including amplification and sequencing, may be required. Although a simple microcosm design was employed, it yielded sufficient information to conclude that release of the engineered Erwinia carotovora will not affect any of the microbial measures of integrity that were studied in a manner different from that of the wildtype. Effects upon plant material and other higher taxa will be the focus of future studies. / Ph. D.

Le feu bactérien et le psylle causent d’importantes pertes économiques dans les zones de production du poirier dans le monde entier. Le développement de nouvelles variétés de poirier résistantes à ces bio-agresseurs constitue un enjeu majeur dans le cadre d’un programme de lutte intégrée. L’objectif de ce projet de thèse est l'étude du déterminisme génétique de la résistance vis-à-vis de ces deux bio-agresseurs. La thèse a été réalisée dans le cadre d’une collaboration internationale entre Fondazione Edmund Mach (Italie), Institut de Recherches en Horticulture et Semences (France) et Plant & Food Research (Nouvelle-Zélande). Une descendance interspécifique de poirier T003 x ‘Moonglow’ a été développée avec pour objectif de cumuler les résistances au feu bactérien et au psylle provenant de variétés asiatiques et européennes de Pyrus. Deux cartes génétiques ont été élaborées pour T003 et ‘Moonglow’ sur la base de marqueurs SNP (Single Nucleotide Polymorphism) et SSR (microsatellite), et la cartographie de QTLs (Quantitative Trait Loci) a permis de démontrer le déterminisme polygénique de la résistance à ces bio-agresseurs. Une sélection assistée par marqueurs (MAS) peut donc être engagée pour ces deux caractères. Des incompatibilités génétiques ont aussi été observées dans une partie de la descendance, ce qui a permis de cartographier pour la première fois chez le poirier les zones du génome liées au phénomène de « nécrose hybride ». Le développement de marqueurs liés aux gènes létaux devrait permettre aux sélectionneurs d’éviter les combinaisons incompatibles en croisement qui peuvent impacter certains caractères agronomiques co-ségrégant avec ces gènes létaux. / The goal of this PhD project was to study the genetic architecture of pear resistance to two of its most significant diseases and pests, fire blight and psylla, which cause severe yield losses in all the main pear production regions worldwide. The development of new pear varieties with resistance against these two biotic stresses is of major interest for Integrated Pest Management. This project was designed in a joint collaboration among Fondazione Edmund Mach (Italy), Institut de Recherches en Horticulture et Semences (France) and Plant & Food Research (New-Zealand). The interspecific pear F1 progeny T003 x ‘Moonglow’ was developed with the purpose of cumulating resistances to fire blight and psylla deriving from Asian and European pear cultivars. Single nucleotide polymorphism (SNP) and simple sequence repeat (SSR)-based genetic maps were built for T003 and ‘Moonglow’. Quantitative Trait Loci (QTLs) were detected for the resistances, demonstrating their polygenic nature. Marker-assisted selection (MAS) can now be applied for these two traits. Furthermore, the segregating population exhibited genetic incompatibilities, and the genomic regions associated with hybrid necrosis were mapped for the first time in pear. Development of molecular markers linked to the lethal genes should allow breeders to avoid crosses leading to incompatible combinations that could affect the expression of important agronomic traits co-segregating with these genes.

Depuis la domestication du pommier, l’homme a progressivement sélectionné des variétés plus performantes, notamment pour la qualité du fruit, la productivité ou la résistance aux pathogènes. Les bases génétiques de ces caractères ont été explorées par cartographie en descendances F1 ne permettant d’explorer qu’une infime partie de la diversité génétique disponible.L’objectif de la thèse portait sur l’analyse des bases génétiques de caractères de qualité du fruit et de résistance du pommier à la tavelure et au feu bactérien dans des collections représentant une diversité plus large. Le génotypage de core collections de variétés anciennes s’est fait à l’aide de deux puces 8k et 480kSNPs ou grâce à du ré-séquençage de gènes. Des traces de différenciation génétique entre pommes à cidre et à couteau ont été identifiées et partiellement reliées à la voie des polyphénols. Après analyse de l’étendue du déséquilibre de liaison à large et fine échelle, une approche de génétique d’association a permis l’identification de régions génomiques associées à la variation de plusieurs caractères de qualité du fruit, dont le haut du groupe de liaison 16 rassemblant l’acidité (locus Ma), la fermeté, la jutosité et l’amertume (gène LAR). Pour la résistance au feu bactérien, une région contenant un homologue du gèneNPR1 (activateur de défenses) a été identifiée.Cette thèse a ainsi permis de préciser la localisation potentielle de QTLs identifiés préalablement par cartographie génétique et d’identifier de nouvelles ressources utiles dans de futurs programmes de sélection assistée par marqueurs. / Since apple domestication, humans have progressively selected improved varieties, especially for traits linked with fruit quality, productivity or resistance to pathogens. The genetic bases underlying these traits have been explored thanks to genetic mapping in F1 segregating populations that only allows the study of a small part of the available genetic diversity. The aim of this work was to analyze the genetic bases of fruit quality and disease resistance against apple scab and fire blight, in collections of old apple varieties representing a much larger diversity. Genotyping of core collections was performed either with arrays of 8k and 480k SNPs or by resequencing of chosen genes. Signs of genetic differentiation were identified between cider and dessert apples and were partially linked to the polyphenols pathway. After studying linkage disequilibrium, both on a large and a small scale, an association genetics approach allowed the identification of genomic regions associated with the variation of several fruit quality traits. Especially, the top of linkage group 16 was found to be linked with acidity (locus Ma), firmness, juiciness and bitterness (LAR gene). Concerning the resistance of apple to fire blight, a region containing a homolog of the NPR1 gene (defense activator) was identified. This thesis allowed the refining of the putative localization of previously identified QTLs and the identification of new genetic resources that could be useful in future selection programs using marker assisted selection.