Le Phytophthora ramorum Werres est responsable de la mort de dizaines de milliers de chênes sur la côte ouest-californienne depuis 1995. On nomme cette maladie l’encre des chênes rouges ou la mort subite du chêne. Cet organisme appartient au même genre que le Phytophthora infestans, agent causal de la famine irlandaise de la pomme de terre du 19e siècle. Il fut découvert en 1993, infectant des rhododendrons et des viornes en Europe. Depuis, il a été démontré qu’il pouvait infecter plus d’une centaine d’espèces de plantes, non seulement sur la côte ouest américaine, mais également au Canada et dans plusieurs pays d’Europe. Des mesures de quarantaine ont été mises en place, essentiellement en pépinières où sa prolifération est la plus efficace, afin d’éviter sa propagation dans d’autres États américains ou d’autres pays. Il est donc nécessaire de développer des outils de détection, et d’identification. La détection moléculaire et le génotypage peuvent être des outils importants pour découvrir et mieux comprendre la biologie de ces populations et les mouvements de cet agent pathogène. La disponibilité des séquences complètes du génome du P. ramorum, depuis 2004, apporte une nouvelle ressource pour l’identification de gènes portant du polymorphisme et la conception d’outils pour les études de populations. Les objectifs de ce projet de recherche proposés sont : de développer des outils moléculaires pour identifier le P. ramorum et le différencier des autres Phytophthora; de découvrir des loci différenciant le polymorphisme intra-spécifique du P. ramorum; de réaliser des études de populations entre les populations européennes et nord-américaines connues avec les différents marqueurs développés. Par le biais d’analyses bioinformatiques et de séquençage d’ADN, la méthodologie employée consiste au développement d’outils de diagnostic tels que la PCR en temps réel utilisant des sondes et amorces spécifiques au P. ramorum sur trois loci et de les distinguer des autres espèces de Phytophthora connues. D’ailleurs, ces analyses ont permis d’identifier plusieurs polymorphismes de nucléotides simples (SNPs) (Single Nucleotide Polymorphisms), dans treize gènes totalisant 6.3 kb utilisant la notion de volatilité des codons. Dans une collection d’isolats provenant d’Europe et d’Amérique du nord, des profils de SNPs distincts et fortement corrélés avec l’origine géographique ont été identifiés. Les populations du P. ramorum en Californie et Oregon, présentent généralement trois profils uniques de SNPs et semblent plus être dérivés d’un ou quelques clones, quelques individus nouvellement trouvés présentant des insertions et délétions. En Europe plusieurs génotypes ont été retrouvés et les gènes sélectionnés semblent avoir des homologies avec des protéines de la paroi cellulaire et donc pourraient jouer un rôle dans l’adaptation. Cette thèse présente donc l’utilisation et la découverte de nouveaux gènes présentant du polymorphisme permettant de détecter et différencier le P. ramorum des autres espèces de Phytophthora mais également de connaître les origines et une identification des individus par leurs polymorphismes. / Phytophthora ramorum Werres is responsible of mortality of ten thousand of oak trees on the California coast since 1995. This disease is called sudden oak death, Ramorum blight, canker. This organism is on the same genus than Phytophthora infestans, the causal agent of Irish potato famine on the 19th century. P. ramorum was discovered in 1993 infecting Rhododendron and Viburnum in Europe. Since, it was demonstrated that it could infect more than one hundred plant species, not only on the American west coast but also in Canada and many European countries. Quarantine measures were placed in effect, principally in plant nurseries where the spread is more efficient to prevent propagation in other American States or other countries. That is necessary to develop detection and identification tools. The molecular detection and genotyping could be important tools to discover and understand le biology of the population and movement of this pathogen. The availability of complete sequences from the P. ramorum genome since 2004 permitted to use new resources for identification of gene sharing potential polymorphism and conception of tools for population studies. The objectives of this research project were: to develop molecular tools for identification of P. ramorum and differentiate it from other Phytophthora species; to discover loci differentiating intra-specific polymorphism of P. ramorum; and finally to realize population studies between European and North American population known with the different markers developed. With utilisation of bioinformatics and DNA sequencing, the method used was to develop diagnosis tool with real-time PCR using specific probes and primers for P. ramorum on three different loci and distinguish it from the other Phytophthora species known. Moreover, these analyses allowed identification of multiple single nucleotide polymorphisms (SNPs), in thirteen genes for a total of 6.3 kb based on codon volatility. In a collection of isolates from Europe and North America, distinct SNPs profiles and correlated with the geographic origin were identified. P. ramorum populations in California and Oregon present generally three unique SNPs profiles and seem to drift from one or few clones, new individual newly discovered with insertion-deletion mutation. In Europe, many genotypes were found and the selected genes had homologies with proteins implicated in cell wall. This could have an implication on adaptation and evolution. This thesis presents utilisation and discovery of new genes sharing polymorphisms allowing to detect and differentiate P. ramorum form other Phytophthora species and moreover to known the origin and identification of individuals by their polymorphisms.

No description available.

Thesis (M.E.S.)--The Evergreen State College, 2008. / Title from title screen viewed (4/7/2009). Includes bibliographical references (leaves 114-126).

No description available.

published_or_final_version / Ecology and Biodiversity / Doctoral / Doctor of Philosophy

Many oomycetes, such as the notorious potato late blight pathogen Phytophthora infestans, have devastating effects on crops. Recent findings have implied that eukaryotic plant pathogens deliver effector proteins inside host cells to facilitate colonization by modulating plant defences. Although the translocation mechanisms remain unknown, in oomycetes this process depends on a short conserved amino acid sequence located near the signal peptide of many secreted proteins. This sequence, termed the RxLR motif, is strikingly similar to the core RxLxE/D/Q host cell targeting-signal that is found in virulence proteins from the malaria parasite Plasmodium falciparum. Common infection strategies have been described for these divergent pathogens, albeit one is a plant pathogen while the other infects human cells. In this thesis, stable transformation of P. infestans, combined with a validated assay based on the intracellular recognition of the RxLR effector, A vr3a, was used to study the specificity of effector translocation in oomycetes and to demonstrate the functional similarity between translocation motifs from Plasmodium and two distantly related oomycetes. While accumulating evidence shows that RxLR effectors are delivered into the host cell, the subcellular targeting of these proteins is still unclear. Throughout this PhD project, the difficulty of visualizing translocated effectors during infection was tackled by seeking alternative approaches allowing the detection of fluorescently- tagged effectors once delivered into the plant cell. A further key research question addressed in this thesis was whether the mechanism of translocation required pathogen-encoded proteins or a pathogen- induced environment. Purified fluorescent protein fusions of A vr3a were used to demonstrate that this plant pathogen effector may hold the intrinsic ability to traverse the plasma membrane of animal cells.

Una de las opciones para el control de la enfermedad más devastadora del cultivo de papa (Solanum tuberosum), el tizón tardío, producido por Phytophthora infestans, es el desarrollo de variedades resistentes a este patógeno, mediante la transferencia directa de genes de resistencia R por ingeniería genética. En el siguiente trabajo de investigación, se usó el gen RB de Solanum bulbocastanum, que otorga un amplio espectro de resistencia a razas de P. infestans. Para dicho fin, se transformó genéticamente vía Agrobacterium tumefaciens la variedad susceptible de papa Desiree (Solanum tuberosum) con el vector binario pCIP68 que contiene el gen RB. Como resultado, se obtuvieron 19 plantas transformadas con el gen RB, confirmadas por la prueba de resistencia a kanamicina y por la prueba de reacción en cadena de la polimerasa (PCR). Las 19 plantas transgénicas fueron sometidas a infección en invernadero bajo condiciones de bioseguridad con el aislamiento POX067 de P. infestans perteneciente al linaje clonal EC-1 que es dominante en el Perú. Tres de las 19 plantas ([RB]54, [RB]56 y [RB]70) presentaron un alto nivel de resistencia al aislamiento POX067 de P. infestans.

Submitted by Jorge Silva (jorgelmsilva@ufrrj.br) on 2018-08-22T19:15:30Z No. of bitstreams: 1 2013 - Evandro Silva Pereira Costa.pdf: 2748177 bytes, checksum: 3632d387d4cb90bea88d42726fae79ca (MD5) / Made available in DSpace on 2018-08-22T19:15:30Z (GMT). No. of bitstreams: 1 2013 - Evandro Silva Pereira Costa.pdf: 2748177 bytes, checksum: 3632d387d4cb90bea88d42726fae79ca (MD5) Previous issue date: 2013-12-18 / CAPES / The present work had the objective to characterize 59 accessions of tomato of the cherry group regarding its agronomic characteristics and resistance to the late blight and to select those more adapted to the organic agriculture. As standards were used: Carolina, Perinha ?gua Branca, Pending Yashi, Joanna and the hybrids Super Sweet, Sweet Million and Mascot F1. The experiments were conducted under field conditions in the Horticulture Sector of the Federal Rural University of Rio de Janeiro (UFRRJ) from June 2010 to November 2013 during which eight trials were carried out. In the different trials, productivity, number of total fruits, disease progression, morphological characteristics (coloration, shape, number of locules), physical (longitudinal and equatorial diameter), and physicochemical characteristics of fruits (total soluble solids - TSS , titratable total acidity - TTA, pH, TSS / TTA ratio). It was also evaluated the accumulation of dry mass of the stem, leaves and fruits, content and content of nitrogen (N), potassium (K) and phosphorus (P) in the respective organs. It was observed a great genetic variability between the accessions as to the physical and physical-chemical morphological attributes. Promising accesses were selected for use in breeding programs and with great productive potential and potential for cultivation in organic systems. Among these, we highlight the ENAS 1040, ENAS 1037, ENAS 1031 and ENAS 1026 accessions for cultivation in the spring / summer period and the accesses ENAS 1228, ENAS 1214, ENAS 1227 and ENAS 1220 by the highest total soluble solids (?Brix). The accessions ENAS 1121, EAS 1013, ENAS 1143 and ENAS 1029 were distinguished by the production of fruits with differentiated formats and the accesses ENAS 1007, ENAS 1008, ENAS 1037, ENAS 1033, ENAS 1017, ENAS 1036, ENAS 1062 and ENAS 1029 by coloring of the fruits. The accessions ENAS 1227 and 1026 stood out by the partial resistance to the late blight, equivalent to the standards 'Carolina' and 'Perinha ?gua Branca'. The accessions ENAS 1227, ENAS 1216, ENAS 1153 and ENAS 1060 were the ones that stood out the most regarding the resistance to the late blight and productivity. / O presente trabalho teve como objetivo caracterizar 59 acessos de tomateiro do grupo cereja quanto ?s suas caracter?sticas agron?micas e resist?ncia ? requeima e selecionar aqueles mais adaptados ? agricultura org?nica. Como padr?es foram utilizadas: Carolina, Perinha ?gua Branca, Pendente Yashi, Joanna e os h?bridos Super Sweet, Sweet Million e Mascot F1. Os experimentos foram conduzidos em condi??es de campo, no Setor de Horticultura da Universidade Federal Rural do Rio de Janeiro (UFRRJ) no per?odo de junho de 2010 a novembro de 2013 durante o qual realizaram-se oito ensaios. Nos diferentes ensaios, avaliaram-se produtividade, n?mero de frutos totais, progresso da requeima, caracter?sticas morfol?gicas (colora??o, formato, n?mero de l?culos), f?sicas (di?metro longitudinal e equatorial), e f?sico-qu?mica dos frutos (s?lidos sol?veis totais - SST, acidez total titulav?l - ATT, pH, rela??o SST/ATT). Avaliou-se, ainda, ac?mulo de massa seca do caule, folhas e frutos, teor e conte?do de nitrog?nio (N), pot?ssio (K) e f?sforo (P) nos respectivos ?rg?os. Observou-se grande variabilidade gen?tica entre os acessos quanto aos atributos morfol?gicos f?sicos e f?sico-qu?micos. Selecionaram-se acessos promissores para uso em programas de melhoramento e com grande potencial produtivo e com potencial para cultivo em sistemas org?nicos. Dentre estes, destacam-se os acessos ENAS 1040, ENAS 1037, ENAS 1031 e ENAS 1026 para cultivo no per?odo de primavera/ver?o e os acessos ENAS 1228, ENAS 1214, ENAS 1227 e ENAS 1220 pelos maiores teores de s?lidos sol?veis totais (?Brix). Os acessos ENAS 1121, EANAS 1013, ENAS 1143 e ENAS 1029 destacaram-se pela produ??o de frutos com formatos diferenciados e os acessos ENAS 1007, ENAS 1008, ENAS 1037, ENAS 1033, ENAS 1017, ENAS 1036, ENAS 1062 e ENAS 1029 pela colora??o dos frutos. Os acessos ENAS 1227 e 1026 destacaram-se pela resist?ncia parcial ? requeima, equivalente ? dos padr?es ?Carolina? e ?Perinha ?gua Branca?. Os acessos ENAS 1227, ENAS 1216, ENAS 1153 e ENAS 1060 foram os que mais se destacaram quanto a resist?ncia ? requeima e produtividade.

The late blight pathogen, Phytophthora infestans, is the most destructive pathogen of its solanaceous hosts potato and tomato. It is a threat to global food security and it is therefore important to understand the cellular and molecular dynamics underlying colonisation of its host plants. This greater understanding will inform strategies to improve host plant resistance. In addition to studying the cell biology of the interaction, it is important to understand the temporal changes in gene expression and regulation during host-pathogen interactions at the earliest infection time points. Previously published transcriptomic studies of P. infestans used two days post infection (dpi) as the earliest sampling time point. Expression of a marker gene (Hmp1) for biotrophy and a selection of effector coding genes has been reported as early as 12 hours post inoculation (hpi), suggesting that infection was initiated before then. Transcriptomic studies of P. infestans have focussed mostly on leaf tissue, and there is still a lack of research on the transcriptome of P. infestans grown in alternative plant tissues such as tubers, or in host cell-free apoplastic fluid. This thesis explores transcriptomic studies of the early, biotrophic stages of potato infection by Phytophthora infestans, which is critical for understanding which genes are involved at what stages of infection development. By using the latest sensitive microarray technology to study the P. infestans transcriptome in an infection time course that remained biotrophic for its duration, a list of 1,707 transcripts of P. infestans were discovered to be differentially expressed. This list included 114 transcripts for RxLR effectors, out of which 26 were detected from 12 hours post infection, including: Avr2, Avr3a, Avrblb1 (ipi01), Avrblb2, and the recently characterised RD2. Also of interest was that transcripts encoding a PAMP (CBEL) detected at 12 hours, were suppressed in the pathogen by 24 hours. Transcripts encoding 55 RxLR effectors were co-expressed (with >95 % correlation coefficient) with the biotrophy marker gene Hmp1, suggesting that these effectors are important throughout the biotrophic stages of infection. QRT-PCR and cell biology data supported the expression of the biotrophy marker gene Hmp1 as early as 12 hours after infection and this was further supported by the co-expression of avirulence genes such as Avr2 and Avr3a. A set of 17 transcripts, including six cytoplasmic effectors (RxLR effectors), as well as a transcript encoding an apoplastic effector (glucanase inhibitor), was found to be infection-specific, supporting the hypothesis that these genes might have roles in establishing biotrophy. By examining pathogen behaviour in tuber tissue, clear cell biology evidence of functional haustoria was found. Gene expression analysis of a selection of leaf infection-related genes suggested that effectors are used to promote infection also in host tuber tissue. However, some cytoplasmic RXLR effector proteins such as PITG_05146 and PITG_15128, which were up-regulated during biotrophic infection of leaf tissue, were not detected during tuber infection, indicating potential differences in pathogenic requirements. A microarray experiment was conducted on in vitro stages of zoospores, and mycelium grown in apoplastic fluid of N. benthamiana, nutrient rich pea broth, and sterile water. This revealed 13,819 transcripts that were differentially expressed between any two conditions. This list included transcripts encoding 322 RxLR effectors, of which avirulence effectors such as Avr2, Avr3a, and RD2 were highly up-regulated during hyphal growth in apoplastic fluid compared to other in vitro stages. This provides evidence that the apoplast contains chemical signals that induce expression of infection-related genes in P. infestans. Curiously, the leaf infection-specific genes identified in Chapter 3 were not expressed when P. infestans was grown in apoplastic fluid, revealing that additional stimuli are required for induction of all necessary pathogen genes during infection. Future research, building upon the findings from this project, should be focused on the following areas: 1) Explore whether haustoria are produced only in order to deliver effectors or if there are other purposes as well, such as nutrient uptake; 2) The continued exploration of differences between genes co-expressed with Hmp1 during leaf infection, tuber infection, and in apoplastic fluid to further dissect the transcriptional regulation of these genes; 3) Identify whether Hmp1-co-expressed genes of unknown function may play a role in haustorium formation; 4) Investigate, using molecular transformation and cell biology, whether secreted proteins co-expressed with Hmp1 are secreted from haustoria; 5) Investigate the role(s) of infection-specific genes in establishing disease. 6) Transcriptomic studies of P. infestans biotrophic infection of tuber tissue to determine the differences in pathogenic adaptation in this tissue type, compared to leaf infection.

This was a project joint between the University of Dundee and The James Hutton Institute where both parties were interested in further understanding the interactions between plant host proteins and pathogen effector proteins. An objective of this thesis was to determine the host target of the Phytophthora infestans effector PiAVR2 and the means by which this avirulence protein is recognised by the potato resistance protein, R2. Prior to this PhD, forward genetic studies identified three RXLR effector encoding genes within the AVR2 locus. By use of transient co-expression with the resistance gene R2 it was determined which of these genes was PiAVR2. A virulent form of PiAVR2, named PiAVR2-like, was found within isolates of P. infestans. Isolates which only express PiAVR2-like are virulent on potato cultivars expressing R2. Isolates which express both forms, or only the PiAVR2 form, are avirulent on cultivars expressing R2. This suggests that expressing only PiAVR2-like is key to the virulence of the pathogen on R2 expressing cultivars. There are 10 known orthologues of R2 which all recognise PiAVR2. However none can recognise PiAVR2-like. The characterisation of the means by which P. infestans overcomes R2 resistance has provided a strategy, based on identifying R genes that recognise PiAVR2-like, to provide durable late blight disease resistance. It was also discovered that both PiAVR2 and PiAVR2-like physically interact with the same host target proteins, BSL1, BSL2a and BSL2b. The BSLs are part of a family of Kelch repeat containing Ser/Thr phosphatases which function as activators of the brassinosteroid signal transduction pathway. It was shown that silencing of the BSL1 and BSL2a genes within plants results in the attenuation of PiAVR2 recognition by R2. In the case of BSL1 it was further shown that an interaction between R2 and BSL1 only occurs in the presence of PiAVR2. This implies that R2 recognises PiAVR2 by an indirect mechanism, utilising either the Guard or Decoy Hypotheses, and that BSL1 is essential for this recognition. This is the first reported demonstration of indirect recognition of an intracellular eukaryotic plant pathogen effector protein.