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Apple scab, the most serious disease of apple is caused by fungal pathogen Venturia inaequalis. Knowledge about the apple response to apple scab attack on the cellular and tissue level is insufficient. For studies of Malus-Venturia interaction on the cellular and tissue level, the establishment of methods for cell structures visualization in apple leaves is necessary. In this work, the experimental plant material grown in vitro and ex vitro was successfully established and the method of apple infection by conidia of V. inaequalis was optimized. Various methods of cell components visualization such as vital staining, in situ immunolocalization, transformation, environmental scanning electron microscopy and confocal microscopy, were tested. Cell structures, such as the cytoskeleton, the cell wall and the cuticle were visualized in apple leaves. Preliminary experiments following specific the changes of cell wall structures induced by V. inaequalis attack were performed. Further, changes of cuticle structure, the first barrier for penetration of pathogen to plant tissues during infection, were observed during the leaf ontogenesis. Powered by TCPDF (www.tcpdf.org)

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.

Apple scab is the most important disease of apples in most of the world. The disease, caused by Venturia inaequalis, is controlled by numerous fungicide applications, regardless of the presence of inoculum in the orchard. Better timing of fungicide applications could be achieved if the airborne ascospore concentration (AAC) was considered in decision making. AAC can be measured in real time using spore traps. In this project, the relationship between AAC and lesions development was studied under controlled and natural conditions for five cultivars: Empire, McIntosh, Jonagold, Royal Gala, and Spartan. Potted trees were exposed to different airborne ascospore inoculum and the corresponding AAC were measured using spore traps. The spatial distribution of ascospores was studied in a commercial apple orchard plot. The potential ascospore dose (PAD) and the AAC were measured in 40 quadrats in the spring of 1999. (Abstract shortened by UMI.)

Diss. (sammanfattning) Uppsala : Sveriges lantbruksuniv., 2003. / Härtill 5 uppsatser.

Philosophiae Doctor - PhD / In this dissertation three computational approaches are presented that enable optimization of reference-free transcriptome reconstruction. The first addresses the selection of bona fide reconstructed transcribed fragments (transfrags) from de novo transcriptome assemblies and annotation with a multiple domain co-occurrence framework. We showed that selected transfrags are functionally relevant and represented over 94% of the information derived from annotation by transference. The second approach relates to quality score based RNA-seq sub-sampling and the description of a novel sequence similarity-derived metric for quality assessment of de novo transcriptome assemblies. A detail systematic analysis of the side effects induced by quality score based trimming and or filtering on artefact removal and transcriptome quality is describe. Aggressive trimming produced incomplete reconstructed and missing transfrags. This approach was applied in generating an optimal transcriptome assembly for a South African isolate of V. inaequalis. The third approach deals with the computational partitioning of transfrags assembled from RNA-Seq of mixed host and pathogen reads. We used this strategy to correct a publicly available transcriptome assembly for V. inaequalis (Indian isolate). We binned 50% of the latter to Apple transfrags and identified putative immunity transcript models. Comparative transcriptomic analysis between fungi transfrags from the Indian and South African isolates reveal effectors or transcripts that may be expressed in planta upon morphogenic differentiation. These studies have successfully identified V. inaequalis specific transfrags that can facilitate gene discovery. The unique access to an in-house draft genome assembly allowed us to provide preliminary description of genes that are implicated in pathogenesis. Gene prediction with bona fide transfrags produced 11,692 protein-coding genes. We identified two hydrophobin-like genes and six accessory genes of the melanin biosynthetic pathway that are implicated in the invasive action of the appressorium. The cazyome reveals an impressive repertoire of carbohydrate degrading enzymes and carbohydrate-binding modules amongst which are six polysaccharide lyases, and the largest number of carbohydrate esterases (twenty-eight) known in any fungus sequenced to date

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