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Caracterização molecular e inoculação de Ralstonia solanacearum em Eucalyptus spp / Molecular characterization and inoculation of Ralstonia solanacearum in Eucalyptus sppFonseca, Natália Risso 18 July 2012 (has links)
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Previous issue date: 2012-07-18 / Conselho Nacional de Desenvolvimento Científico e Tecnológico / The Ralstonia wilt of eucalyptus, caused by Ralstonia solanacearum, is potentially one of the major disease of culture. Because of its high genetic and phenotypic
variability, currently R. solanacearum is considered a "species complex", subdivided into four taxonomic levels: species, filotipo, sequevar and clone. In order to understand the variability among isolates of R. solanacearum from eucalyptus and develop a protocol for inoculation and screening of resistant clones of eucalyptus to Ralstonia wilt this work was performed. The work was divided into two articles: (i) Molecular characterization of isolates of Ralstonia solanacearum in Eucalyptus spp.
and (ii) Method of inoculation and evaluation of resistant clones of Eucalyptus spp. to Ralstonia wilt caused by Ralstonia solanacearum. In Article 1, 19 isolates were
analyzed from different regions of eucalyptus in Brazil based on new classification (filotipo and sequevar) and its genetic variability. A product of 372 bp generated by
multiplex-PCR amplification using primers Nmult permitted the identification of all isolates analyzed as pertaining to filotipo II. Eighteen isolates were grouped in
subclade IIA and just one isolate in IIB. The phylogenetic tree generated from the endoglucanase (egl) gene sequences confirmed the classification of the isolates in filotipo II and separated them into sequevares. The strains AMC22, IBSBF2568 and IBSBF2576 were grouped into a single clade, as well as isolates UFV18 and UFV20, with 89% and 78% posterior probability, respectively, forming two new possible sequevares not defined yet. We also identified isolates belonging to sequevar 41 (100% probability) and 37 (88% probability). However, most of the isolates did not fit in any of previously described sequevar, or formed defined clades. The analysis of results of obtained fragments amplified by ERIC-PCR technique suggested a great genetic diversity among the isolates analyzed in this work. In addition, a high correlation between the geographical origin of isolates and the similarity showed by them was observed. In Article 2, three methods of inoculation and resistant of Eucalyptus spp. clones to Ralstonia wilt was evaluated: (i) soil infestation with R. solanacearum, (ii) dipping of sectioned roots in bacterial suspension, and (iii) injection of a bacterial suspension in the base of the stem. The injection method of a bacterial suspension at the stem base was the most efficient inoculation method of R. solanacearum on eucalyptus. Four, out of 21 clones tested for Ralstonia wilt resistance by this method, were classified as resistant by not showing symptoms of wilt and bacterial exudation up to 30 days after inoculation. / A murcha-de-Ralstonia do eucalipto, causada por Ralstonia solanacearum, constitui potencialmente, uma das principais doenças da cultura. Devido à sua ampla variabilidade, atualmente R. solanacearum é considerada um complexo de espécies , subdividida em quatro níveis taxonômicos: espécie, filotipo, sequevar e clone. Com o intuito de entender a variabilidade entre isolados de R. solanacearum provenientes de eucalipto e desenvolver um protocolo de inoculação e avaliação da resistência de clones de eucalipto à murcha-de-Ralstonia realizou-se este trabalho. Ele foi dividido em dois artigos: (i) Caracterização molecular de isolados de Ralstonia solanacearum de Eucalyptus spp. e (ii) Método de inoculação e avaliação
de resistência de clones de Eucalyptus spp. à murcha-de-Ralstonia causada por Ralstonia solanacearum. No artigo 1, foram analisados 19 isolados de R. solanacearum obtidos de eucalipto de diferentes regiões do Brasil quanto à nova
classificação (filotipo e sequevar) e quanto à variabilidade genética. Um produto de 372 pb gerado pela amplificação por PCR-multiplex, utilizando primers Nmult, permitiu identificar todos os isolados analisados no filotipo II. Dezoito isolados foram agrupados no subclado IIA e apenas um no IIB. A árvore filogenética gerada a partir das sequências do gene da endoglucanase (egl) confirmou a classificação dos isolados no filotipo II e os separou em sequevares. Os isolados AMC22, IBSBF2568 e IBSBF2576 agruparam-se em um único clado, assim como os isolados UFV18 e UFV20, com 89% e 78% de probabilidade posteriori, respectivamente, compondo dois novos possíveis sequevares, ainda não definidos. Foram identificados também isolados pertencentes ao sequevar 41 (100% de probabilidade) e 37 (88% de probabilidade). Entretanto, a maioria dos isolados não se enquadrou em nenhum sequevar descrito, nem formaram clados definidos. O resultado da análise de fragmentos amplificados pela técnica de ERIC-PCR indicou grande diversidade genética entre os isolados avaliados neste trabalho, havendo, em geral, uma alta correlação entre a origem geográfica dos isolados e a similaridade entre eles. No artigo 2, avaliaram-se três métodos de inoculação e a resistência de clones de Eucalyptus spp. à murcha-de-Ralstonia: (i) infestação do solo com R. solanacearum; (ii) imersão de raízes seccionadas em suspensão bacteriana; e (iii) injeção de suspensão bacteriana na base do caule. O método de inoculação de injeção de suspensão bacteriana na base do caule destacou-se como o mais eficiente para inoculações de R. solanacearum em eucalipto. De 21 clones avaliados quanto à resistência à murcha-de-Ralstonia por esse método, apenas quatro foram classificados como resistentes por não apresentarem sintomas de murcha e exsudação bacteriana até 30 dias após a inoculação.
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Psilídeos (Hemiptera: Psylloidea) associados a olerícolas e estudo das interações com suas plantas hospedeiras / Psyllids (Hemiptera: Psylloidea) associated with vegetable crops and study of interactions with their host plantsTaciana Melissa de Azevedo Kuhn 28 March 2018 (has links)
Os psilídeos (Hemiptera: Psylloidea) são insetos sugadores de floema que se destacam como vetores de bactérias associadas a doenças emergentes em várias culturas agrícolas, como \'Candidatus Liberibacter solanacearum\' (CaLsol), que afeta batata, cenoura e tomate na América do Norte e Central, Europa, África e Nova Zelandia. Estudos recentes mostram associações de CaLsol com diversas espécies de olerícolas e psilídeos vetores, sugerindo a existência de mais interações do que as atualmente conhecidas. No Brasil, ainda não há registros de CaLsol nem dos psilídeos já conhecidos como vetores. Embora Psylloidea seja um grupo diversificado, apenas 89 espécies encontram-se identificadas no Brasil, sendo a maioria delas em áreas de floresta, havendo poucas informações sobre psilídeos em olerícolas. Assim, os objetivos do presente trabalho foram: 1) Avaliar a diversidade de espécies de Psylloidea associadas a cultivos de olerícolas na região Centro-Sul do Brasil, buscando-se identificar a ocorrência de espécies vetoras ou potenciais vetoras de CaLsol; 2) Avaliar a preferência hospedeira, sobrevivência e desenvolvimento de duas espécies de psilídeos associados a olerícolas, Russeliana capsici Burckhardt e R. solanicola Tuthill, em diferentes espécies vegetais que poderiam atuar como hospedeiras de CaLsol ou dos vetores; 3) Caracterizar o comportamento alimentar de adultos e imaturos de R. solanicola em plantas com diferentes níveis de adequação para o seu desenvolvimento, usando a técnica Electrical Penetration Graph (EPG). No levantamento realizado com métodos diretos (rede entomológica, batida de planta e inspeção visual) e indiretos (bandeja amarela com água) em várias localidades de seis estados brasileiros, foram encontrados 2813 exemplares de psilídeos, pertencentes a 7 famílias e 20 gêneros, com maior frequência de R. solanicola (95,1%), R. capsici (91,6%) e Isogonoceraia divergipennis (85,4%) em Daucus carota, Capsicum annuum (pimenta) e Solanum tuberosum, respectivamente. Observaram-se imaturos de R. capsici em C. annuum, e de R. solanicola em D. carota e na planta espontânea Parthenium hysterophorus. Em ensaios de escolha, houve preferência para pouso e oviposição de R. solanicola em D. carota e P. hysterophorus, e de R. capsici em C. annuum, Nicandra physalodes e S. americanum. Observou-se desenvolvimento completo (ovo-adulto) de R. solanicola em D. carota, S. tuberosum, N. physalodes, P. hysterophorus, e Bidens pilosa, enquanto que R. capsici mostrou especificidade hospedeira, desenvolvendo-se apenas em C. annum (pimentão e pimenta). O estudo de EPG mostrou que ninfas e adultos de R. solanicola atingem o floema tanto em plantas hospedeiras (D. carota e P. hysterophorus) como em não hospedeiras (C. annuum e S. lycopersicum), mas com variações significativas em parâmetros de atividade estiletar que permitem diferenciar o comportamento alimentar nas diferentes espécies vegetais. Os estudos demonstram uma íntima associação de R. solanicola e R. capsici com cultivos de olerícolas e seu potencial como vetores de CaLsol, em caso de introdução deste patógeno no Brasil. / Psyllids (Hemiptera: Psylloidea) are phloem-feeding insects with increased importance as vectors of phloem-limited bacteria associated with emerging diseases in agricultural crops, e.g. \'Candidatus Liberibacter solanacearum\' (CaLsol), which causes severe losses in potatoes, carrots and tomatoes in North and Central America, Europe, Africa and New Zealand. Recent studies show associations of CaLsol with diverse species of vegetables and psyllid vectors, suggesting that more interactions than those currently known are likely. In Brazil, there are no records of CaLson and psyllid species already known as vectors. Although Psylloidea is a diversified group, only 73 species were identified in Brazil and most of them on forest trees, with scarce information about psyllids on vegetable crops. Therefore, the objectives of this work were: 1) To survey the diversity of psyllid species vectors associated with vegetable crops in the Central-South region of Brazil, aiming to identify vector or potential vector species of CaLsol; 2) To evaluate host plant preference, survival and egg-adult development of two psyllid species associated with vegetable crops, Russeliana capsici and R. solanicola, on various plant species that could serve as hosts of the pathogen or vectors; 3) To characterize the feeding behavior of adults and nymphs of R. solanicola on plants with variable levels of suitability as developing hosts, by using the Electrical Penetration Graph (EPG) technique. In the survey carried out with direct (sweep net, stem-tap, visual inspection) and indirect (yellow pan trap) methods in various localities of six Brazilian states, 2,813 psyllid speciments of 7 families and 20 genera were collected, with higher frequencies of R. solanicola (95,1%), R. capsici (91,6%) and Isogonoceraia divergipennis (85,4%) on Daucus carota, Capsicum annuum (pepper) and Solanum tuberosum, respectively. Immatures of R. capsici were observed on C. annuum, and those of R. solanicola were observed on D. carota and on the weed Parthenium hysterophorus. Choice tests in the laboratory revealed settling and oviposition preferences of R. solanicola on D. carota and P. hysterophorus, and of R. capsici on C. annuum, Nicandra physalodes and S. americanum. Complete egg-adult development was observed for R. solanicola on D. carota, S. tuberosum, Nicandra physalodes, P. hysterophorus and Bidens pilosa, whereas R. capsici showed host specificity by developing only on C. annum (green pepper and capsicum). The EPG study showed that R. solanicola nymphs and adults reach the phloem both on host (D. carota e P. hysterophorus) and non-host (C. annuum e S. lycopersicum) plants, but with significant differences on stylect activity parameters, allowing distinction of the feeding behavior among the different plant species. Overall, the studies indicate a close association of R. solanicola and R. capsici with vegetable crops, as well as their potential as vectors of CaLsol in case of introduction of this pathogen in Brazil.
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Avaliação do potencial produtivo de dois cultivares de tomate visando diminuir a incidência de murcha bacteriana, no Iranduba-Amazonas / Evaluation of the productive potential of two tomato cultivars aiming to reduce the incidence of the bacterial wilt in Iranduba-AmazonasSilva, Maria do Socorro Monteiro da 06 April 2011 (has links)
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Previous issue date: 2011-04-06 / Fundação de Amparo à Pesquisa do Estado do Amazonas / The tomato, it belongs to the Solanaceae family, is one of the most consumed vegetables in Amazonas State, and the most marketed fruits come from the southern and southeast states, where weather conditions are more pleasant. Bacterial wilt, caused by the bacterium Ralstonia solanacearum, was established as one of the most important diseases for the tomato crop. Due to soil and climatic requirements, the tomato production is practiced with more intensity in the coldest and the driest regions in Brazil (Southeast, South and Midwest). In the humid tropical regions, the climatic conditions, permanently hot and humid, favors the survival of this bacterium that is the main reason that discourages the production of this crop in this region due to low productivity. With the purpose of indicating the technological innovations that enable the production of this vegetable in large scale, this study aims to evaluate the potential production and trade of two tomato cultivars and management techniques to decrease the incidence of bacterial wilt in protected cultivation systems, in the region of Iranduba - Amazon. The tomato cultivars used were C-38 and Santa Barbara, both developed by Embrapa Eastern Amazon, Belém/PA with a history of tolerance bacterial wilt, they were planted succeeding maize, in two treatments and in other, in successive crops. The data evidences the importance of combining techniques with resistant plant material from crops, because in the management systems that the tomato was planted in succession to maize, mortality was lesser than conventional management system and the productivity (approximately 22,65 t ha-¹) was higher than the average of the Amazonas State (approximately 14,60 t ha-¹). Comparated to the Santa Barbara cultivars, the C-38 cultivar showed higher productivity and characteristics of shape, weight and number of fruit with greater acceptance by the interal market / O tomate, pertencente à família das solanáceas, representa uma das hortaliças mais consumidas no Estado do Amazonas, sendo que a maioria dos frutos comercializados é proveniente dos estados do sul, sudeste e centro-oeste, onde as condições climáticas são mais amenas. A Murcha Bacteriana, causada pela bactéria Ralstonia solanacearum, constitui-se como uma das doenças mais importante para a cultura. Devido às exigências edafoclimáticas do tomateiro, sua produção é praticada com mais intensidade nas regiões mais frias e secas do Brasil. Já nas regiões do trópico úmido, as condições de clima, permanentemente quente e úmido, favorecendo a sobrevivência desta bactéria é o principal motivo que desestimula a produção da cultura nesta região devido a baixa produtividade. Com a finalidade de indicação de inovações tecnológicas que possibilitem a produção desta hortaliça em grande escala, este trabalho objetiva avaliar o potencial produtivo e comercial de duas cultivares de tomate e técnicas de manejo visando diminuir a incidência de murcha bacteriana, em sistema de cultivo protegido, na região de Iranduba AM. Os cultivares utilizados, C-38 e Santa Bárbara, ambos desenvolvidos pela Embrapa Amazônia Oriental, Belém/PA com histórico de tolerância à murcha bacteriana, foram plantados sucedendo o milho, em dois tratamentos e em outro, em cultivos sucessivos. Os dados obtidos evidenciaram a importância da combinação de material vegetal resistente com técnicas de cultivos, pois nos sistemas de manejo em que o tomate foi plantado em sucessão ao milho, apresentou mortalidade inferior ao sistema de manejo convencional, sendo que a produtividade obtida, na média do experimento, de 22,65 t ha-1foisuperior à média do estado do Amazonas(14,60 t ha-1). Comparativamente ao cultivar Santa Bárbara, o cultivar C-38 apresentou maior produtividade e características de formato e número de frutos com maior aceitação pelo mercado interno
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Caractérisation de protéines PPR impliquées dans le stress biotique chez A. thaliana. / Characterization of PPR Proteins Involved in Biotic Stress in A. thaliana.Malbert, Bastien 10 December 2018 (has links)
A la différence des mammifères, les plantes ne possèdent pas de cellules spécialisées dans la défense face aux pathogènes. Chaque cellule végétale peut déclencher une réponse immunitaire. Pour interagir avec succès avec la plante, les pathogènes doivent alors supprimer ou contourner les défenses de l’hôte. Afin d’y parvenir, les bactéries pathogènes disposent des effecteurs, des protéines qui peuvent être injectées dans la cellule végétale. De nombreux effecteurs sont connus pour cibler les organites lors de l’infection, confirmant l’importance du chloroplaste et de la mitochondrie dans les mécanismes de défense des cellules végétales. Dans ces conditions, il demeure vital pour la plante de garder la main sur l’expression des gènes des organites afin d’assurer une réponse proportionnée au risque encouru sans pénaliser la croissance de façon disproportionnée. A la différence de l’expression des gènes nucléaires, la régulation de l’expression des gènes des organites se fait principalement lors d’étapes très complexes de maturation post-transcriptionnelle. Parmi les protéines impliquées dans ces étapes de maturation, on trouve les protéines pentatricopeptide repeat (PPR). Les protéines PPR sont impliquées dans de nombreuses étapes de maturation des ARN des organites, comme l’édition C vers U ou l’épissage. Elles sont également présentes chez d’autres eucaryotes, mais n’ont jamais été étudiées chez les bactéries. L’hypothèse testée dans le cadre de la thèse est que ces protéines PPR, qu’elles soient d’origine exogène ou endogène, sont impliquées dans des modifications de l’expression des gènes des organites en condition de stress biotique. Afin de tester notre hypothèse, nous nous sommes intéressés à PGN (Pentatricopeptide repeat protein for Germination on NaCl) chez la plante modèle A. thaliana. Caractérisée par Laluk et al. (2011), le mutant KO montre une sensibilité accrue au nécrotrophe Botrytis cinerea, et l’expression du gène codant pour cette protéine est induite après infection. Nous avons mis en évidence des défauts d’édition dans la séquence non codante en amont de nad6 et dans cox2, deux gènes mitochondriaux. Leur édition ne varie cependant pas en condition d’infection par Botrytis cinerea. Dans la même optique, à la suite d’un crible bio-informatique, nous nous sommes intéressés à deux protéines PPR bactériennes que nous avons trouvées chez les phytopathogènes Erwinia amylovora et Ralstonia solanacearum. Probablement obtenues par les bactéries par transfert horizontal de gènes, il s’agit de la première caractérisation de PPR bactériennes à notre connaissance. Ces protéines possèdent des caractéristiques d’effecteurs, c’est—dire des protéines injectées par la bactérie dans la plante durant l’infection. Si nous n’avons pas vu de modification du transcriptome des organites de la plante provoqué par la surexpression de ces protéines PPR exogènes, nous avons cependant mis en évidence une baisse significative du taux d’incidence de la maladie provoquée par E. amylovora en l’absence d’un gène fonctionnel codant pour sa PPR chez la plante hôte Malus domestica « Golden delicious ». Pour la PPR d’E. amylovora comme celle de R. solanacearum, nous avons également trouvés plusieurs interactants en double hybride levure chez A. thaliana, représentant de nombreuses cibles putatives à étudier. Afin de réaliser ces expérimentations et d’obtenir ces résultats, nous avons eu besoins d’outils particuliers. Nous avons donc développé un pipeline spécifique d’analyse de données de séquençage d’ARN ainsi qu’une méthode améliorée de prédiction des zones de fixation des protéines PPR, ouvrant la voie à une caractérisation simplifiée de nombreuses protéines. / Compared to mammals, plants do not have highly specialized cells involved in defense against pathogens. Each plant cell is able to start an immune response. To interact successfully with plants, pathogens have to block or bypass host defenses. To do so, phytopathogenic bacteria can use effectors, which are basically bacterial proteins injected in the plant cell during infection. Several effectors are known to target organelles during infection, supporting the idea that chloroplasts and mitochondria are key players in plant cell defense. As a reason, it remains necessary for the plant to keep organellar gene expression under control in order to ensure a response in proportion to the risk, without penalizing growth. Unlike nuclear gene expression, organellar gene expression regulation goes through highly complex post-transcriptional maturation steps. Among proteins involved in these events, PPR proteins (for pentatricopeptide repeat) are known to be very important. PPR proteins are involved in several RNA maturation steps in organelles, like C to U editing or splicing. They are studied in several eukaryotes, but not in bacteria. During my PhD studies, the hypothesis is exogenous or endogenous PPR proteins are involved in organellar gene expression modifications during biotic stress. To test our hypothesis, we work on PGN (Pentatricopeptide repeat protein for Germination on NaCl) in plant model A. thaliana. Characterized by Laluk et al. (2011), the KO mutant displays an enhanced sensitivity to the necrotrophic pathogen Botrytis cinerea, and PGN gene expression is induced after infection. We find two editing defects for the KO mutant, in nad6 5’ non coding sequence and in cox2 coding sequence. However, editing at these two sites does not vary in wild type plants during Botrytis cinerea infection.Using a bioinformatic screen, we find several bacterial PPR proteins. Two of them are encoded by bacterial plant pathogens: Erwinia amylovora and Ralstonia solanacearum. To our knowledge, these proteins, putatively obtained through horizontal gene transfer, are the first bacterial PPR proteins to be characterized. They also share similarities with bacterial effectors. If overexpression of these bacterial PPR proteins in A. thaliana does not unveil organellar transcriptome modifications, we show a decrease of the incidence rate of the disease caused by E. amylovora in the host plant Malus domestica “Golden delicious” without a functional gene coding for the PPR protein. For both Erwinia and Ralstonia PPR, we find several interactants in A. thaliana using Yeast Two Hybrid, each of them representing a potential target that could be studied. In order to perform these experiments and obtain these results, we needed very specific tools. During the PhD studies, we develop an RNAseq analysis pipeline and an enhanced method to predict PPR binding sites, opening the way to an easier characterization of several PPR proteins.
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Biologie des populations du complexe d'espèces Ralstonia solanacearum appliquée à l'épidémiologie de la bactériose vasculaire de la pomme de terre à Madagascar / Population biology of the species complex Ralstonia solanacearum to unravel major traits in potato bacterial wilt epidemiology in the highlands of MadagascarRavelomanantsoa, Santatra Herilalaina 26 September 2016 (has links)
Nous avons exploré la diversité génétique du complexe d'espèces Ralstonia solanacearum (ceRs) pour caractériser et comprendre les graves épidémies de flétrissement bactérien qui sévissent à Madagascar. Une large collection de souches (n=1224; 75 sites) est constituée. Les souches sont assignées aux phylotypes I, III, et la grande majorité associée à l'épidémie appartiennent au groupe IIB-1 (‘Brown rot’ des anglo-saxons) signalé pour la première fois à Madagascar. L'approche MLVA (RS2-MLVA9) a révélé leur apparenté aux souches IIB-1 distribuées mondialement, suggérant ainsi une introduction malheureuse à Madagascar. Trois populations clonales se propagent par des tubercules infectées. Le génotypage des souches du phylotype III, avec le schéma hautement résolutif RS3-MLVA16 que nous avons développé, a révélé une forte diversité génétique structurée géographiquement en onze populations clonales bien différenciées. Cette structure reflète un caractère endémique des populations suggérant l'absence de transmission par tubercules. Les souches malgaches sont différentes de celles d'Afrique continentale. Les souches IIB-1 et III présentent deux modèles épidémiologiques différents. Les variétés de pomme de terre cultivées à Madagascar n'ont montré aucune résistance génétique vis-à-vis du panel de souches malgaches. Cependant, dans nos conditions expérimentales les accessions 720118 et 800934 sont résistantes aux souches I-31 non détectées pour l'instant à Madagascar, mais prévalentes dans l'océan Indien. Nous disposons ainsi d'un outil robuste pouvant être appliqué à l'étude du phylotype III, d'une vue globale de la structure des populations et d'épidémiologie du ceRs. / This thesis is exploring genetic diversity, population structure and molecular epidemiology of the Ralstonia solanacearum species complex (Rssc) causing potato bacterial wilt outbreaks in Madagascar. We characterized a large collection of strains (n=1224; 75 sites) collected from potato production areas. Surprisingly, the large outbreaks were associated with IIB-1 strains (Brown rot) while a few were associated with phylotypes I and III. This is the first report of phylotype IIB-1 in Madagascar. The IIB-1 strains were genotyped based on MLVA (RS2-MLVA9). And Malagasy phylotype IIB-1 clustered with worldwide distributed strains. Fine scale genetic investigation suggested three clonal populations that were introduced and spread through latently infected tuber-seeds. Phylotype III strains were genotyped with the highly discriminatory RS3-MLVA16 scheme we developed. Genetic population analyses revealed a high genetic diversity within phylotype III strains that geographically structured into 11 clonal populations. This support the endemic character of the phylotype III population in Madagascar and suggests no transmission with potato tubers. Malagasy strains were distinct from continental African strains. A clear-cut epidemiological profile is shown between IIB-1 and III strains. Genetically, no bacterial wilt resistance properties were shown for the most popular Malagasy potato cultivars, except two cultivars: 720118 and 800934 that showed strong resistance to phylotype I-31 strain that are predominantly distributed in the Indian Ocean. This study offered tool to genotype phylotype III strains and gives an insights into population structure and epidemiology of the Rssc.
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Épidémiologie moléculaire du complexe d’espèces Ralstonia solanacearum, agent du flétrissement bactérien, dans les îles du Sud-Ouest de l’océan Indien / Molecular epidemiology of the Ralstonia solanacearum species complex causal agent of bacterial wilt, in the Southwest Indian Ocean islandsAfonso Mendes-Yahiaoui, Noura 20 June 2018 (has links)
Dans les îles du sud-ouest de l'océan Indien (SOOI) (Comores, Maurice, Mayotte, Réunion, Rodrigues et Seychelles), le flétrissement bactérien causé par le complexe d'espèces Ralstonia solanacearum (ceRs) est une phytobactériose considérée comme l'une des plus nuisibles pour les productions vivrières ou d'exportation. Les travaux de thèse présentés dans ce manuscrit avaient pour principal objectif l'exploration du niveau et de la distribution de la diversité génétique du ce Rs et de la structure génétique de ses populations dans le SOOI. Nous avons mené de vastes campagnes d'échantillonnage qui ont permis de constituer une large collection de 1704 isolats, principalement à partir de Solanacées (tomate, pomme de terre, piment, aubergine, poivron) et de géranium rosat. L'assignation phylogénétique des isolats a montré une très forte prévalence du phylotype I (88 %), qui est distribué dans chaque île du SOOI, tandis que les phylotypes II (9 %) et III (3 %) ne sont trouvés qu'à La Réunion. Deux souches de phylotype IV ont par ailleurs été signalées à l'île Maurice, représentant le premier rapport de ce groupe phylogénétique dans le SOOI. Une approche phylogénétique et de génotypage (MLSA/MLST) basée sur l'analyse de séquences de 6 gènes de ménage et 1 gène associé à la virulence (egl) a permis de révéler les relations génétiques entre 145 souches représentatives (diversité géographique + hôte d'isolement) du SOOI et 90 souches mondiales de référence. Le développement et l'application d'un schéma MLVA basé sur 17 séquences répétées en tandem (VNTR) sur près de 1300 souches a permis de révéler que les populations de phylotype I sont organisées en complexes clonaux dans le SOOI et que le niveau de diversité génétique est très contrasté selon les îles, Maurice présentant la plus forte diversité génétique. Un résultat majeur de cette thèse est la mise en évidence du déploiement d’une lignée génétique (sequevar I-31 ; STI-13 ; MT-035), surreprésentée dans les îles du SOOI, qui pourrait avoir été introduite via du matériel végétal contaminé depuis l'Afrique de Sud ou l’Afrique de l'Ouest. Nos études préliminaires montrent que l'haplotype majoritaire MT-035 (i) est le probable haplotype fondateur du complexe clonal le plus prévalent dans le SOOI, (ii) présente un pouvoir pathogène élevé (large gamme d'hôtes comprenant des plantes cultivées et des adventices, et forte agressivité sur Solanacées) et (iii) possède une forte aptitude à la compétition dans l'environnement via la production de bactériocines. Ces travaux permettront in fine de renforcer l'épidémiosurveillance et orienter les stratégies de lutte vis-à-vis de cet agent phytopathogène, notamment via le déploiement de cultivars résistants. / In the southwest Indian Ocean (SWIO) islands (Comoros, Mauritius, Mayotte, Réunion, Rodrigues and Seychelles), bacterial wilt caused by the Ralstonia solanacearum species complex (Rssc) is considered one of the most harmful plant disease for food crops or export. The main objective of this work presented in this manuscript was to explore the level and the distribution of the genetic diversity of Rssc and the genetic structure of its populations in SWIO. We conducted extensive sampling campaigns that resulted in a large collection of 1704 isolates, mainly from Solanaceae (tomato, potato, chilli, eggplant, pepper) and geranium rosat. The phylogenetic assignment of the isolates showed a very high prevalence of phylotype I (88 %), which is distributed in each island of the SWIO, while phylotypes II (9 %) and III (3 %) are found only in Réunion. Two phylotype IV strains have also been reported in Mauritius, representing the first report of this phylogenetic group in SWIO. A phylogenetic and genotyping approach (MLSA/MLST) based on sequence analysis of 6 housekeeping genes and 1 gene associated with virulence (egl) revealed the genetic relationships between 145 representative SWIO strains (geographic diversity + host) and 90 global reference strains. The development and application of MLVA scheme based on 17 variable number of tandem repeat sequences (VNTR) on nearly 1300 strains revealed that phylotype I populations are organized into clonal complexes in SWIO and that the level of genetic diversity is highly contrasted according to the islands, with Mauritius having the highest genetic diversity. This work highlights the deployment of a genetic lineage (Sequevar I-31, STI-13, MT-035), overrepresented in SWIO islands, which could have been introduced via contaminated plant material from South Africa or West Africa. Our preliminary studies show that the main haplotype MT-035 (i) is the probable founding haplotype of the most prevalent clonal complex in SWIO, (ii) has high pathogenicity (wide range of hosts including cultivated plants and weeds, and high aggressiveness on Solanaceae) and (iii) has a strong ability to compete in the environment via the production of bacteriocins. This work will ultimately strengthen epidemiosurveillance and guide control strategies of this plant pathogen, including the deployment of resistant cultivars.
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Óleo essencial de mostarda e controle experimental da murcha bacteriana do tomateiro (Ralstonia solanacearum): efetividade e toxidez ao patógeno / Essential oil of mustard an d bacterial wilt on experimental control in tomato (Ralstonia solanacearum): effectiveness and toxicity to the pathogenPontes, Nadson de Carvalho 13 February 2009 (has links)
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Previous issue date: 2009-02-13 / Fundação de Amparo a Pesquisa do Estado de Minas Gerais / The occurrence of bacterial wilt is one of the main restrictions to the tomato production in tropical areas, mainly due to the lack of effective methods of control. The research had the objective to evaluate the efficiency of the essential oil of mustard in the treatment of the soil for the suppression of the population of Ralstonia solanacearum. Initially, different selective mediums were evaluated for the detection and quantification of the bacterial population in the soil. Among the appraised mediums, only two mediums showed appropriate sensibility for the detection of the bacteria, and the South Africa Selective Medium - Elphinstone (SMSA-E) showed the highest recovery tax of the bacteria in the soil, the lowest repression index to the R. solanacearum and highest suppression index of background microorganisms. In the evaluation of the EOM gaseous effect against R. solanacearum, this was capable to inhibit it in vitro development completely. The bacterial colonies that were exposited to the EOM gaseous increased the linkage of cellular metabolites. Anaerobic and gram-positive bacterias were less sensitivity to the product than R. solanacearum. The recovery of the bacteria was not observed with the selective medium SMSA-E, after substratum fumigation for seven days with EOM in concentrations over 100µL of ITCA/L of soil. The tomato plants cultivated in the substratum submitted to this same treatment had not present symptoms of bacterial wilt after 45 days of the transplant. / A ocorrência de murcha bacteriana é um dos principais fatores limitantes ao cultivo de tomate em regiões tropicais, principalmente devido à falta de métodos efetivos de controle. O presente trabalho teve como objetivo avaliar a eficiência do óleo essencial de mostarda no tratamento do solo para a supressão da população de Ralstonia solanacearum. Inicialmente, avaliaram-se diferentes meios seletivos para a detecção e monitoramento da população da bactéria no solo. Dos meios avaliados, apenas dois apresentaram sensibilidade adequada para a detecção da bactéria, sendo que, o meio South Africa Selective Medium Elphinstone (SMSA-E) possibilitou a maior taxa de recuperação da bactéria no solo, com baixo índice de repressão ao patógeno alvo e alto índice de supressão à microrganismos contaminantes. Quanto ao efeito dos vapores do EOM sobre R. solanacearum, estes foram capazes de inibir completamente o seu desenvolvimento in vitro. A exposição das colônias bacterianas aos vapores do EOM ocasionou aumento do extravasamento de metabólitos celulares. Bactérias anaeróbicas facultativas e/ou gram-positivas foram menos sensíveis ao produto que R. solanacearum. Após fumigação por sete dias do substrato com EOM em concentrações a partir de 100µL de ITCA/L de solo, não se observou a recuperação da bactéria com o meio seletivo SMSA-E. As plantas de tomate cultivadas no substrato submetido a este mesmo tratamento não apresentaram sintomas de murcha bacteriana após 45 dias do transplante.
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Formação de biofilme, atividade antibiofilme de extratos vegetais e avaliação de métodos de extração de proteínas em fitobactériasMALAFAIA, Carolina Barbosa 25 January 2016 (has links)
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Previous issue date: 2016-01-25 / CAPES / A formação de biofilme é uma característica importante para as bactérias, por ser uma formação natural e altamente influenciada pelo ambiente circundante, confere aos microrganismos alta tolerância às adversidades e torna-se importante na virulência para patógenos. Sendo assim, apresentamos nesta tese uma investigação da adesão bacteriana e desenvolvimento de biofilme das fitobactérias Ralstonia solanacearum (Rsol) e Acidovorax citrulli (Acc), agronomicamente importantes, sobre superfícies hidrofóbicas, foi investigado também o emprego de extratos vegetais de plantas oriundas da Caatinga, na inibição da adesão bacteriana e sua capacidade bactericida contra R. solanacearum, e foi determinado o método mais eficiente na preparação amostras proteicas para R. solanacearum, A. citrulli e Pectobacterium carotovorum subsp. carotovorum (Pcc) para aplicação em estudos futuros de investigação molecular da formação de biofilmes fitopatogênicos. A formação de biofilme por diferentes isolados bacterianos após 24h de incubação em diferentes meios de cultura foi quantificado pelo método de cristal violeta e suas estruturas observadas por microscopia eletrônica de varredura e microscopia confocal. Foram avaliados também 22 extratos aquosos de 16 plantas coletadas na Caatinga quanto a capacidade de inibição da formação de biofilme de Rsol. Quanto à eficiência na obtenção de proteínas, foram testados os métodos de Trizol, Fenol, Centrifugação e Lise e avaliados através de eletroforese uni e bidimensional. Quanto a formação de biofilme os resultados obtidos indicam que, nas condições testadas, isolados de Rsol se mostrou diferente entre os isolados tanto quantitativa quando morfologicamente onde os isolados B5-5 CGH26 CGH8 e SCN 21 foram moderados ou fortes produtores de biofilme. Já os isolados de Acc não foram bons produtores de biofilme, apresentando apenas os isolados Acc1.43 e Acc 1.73 como fortes formadores de biofilme com quantidade e morfologia semelhantes. No screening de atividade antibiofilme, dentre os extratos testados apenas ramos de Harpochilus neesianus e folhas de Myroxylon peruiferum apresentaram atividade antibiofilme superior a 83% e 50%, respectivamente, e Jacaranda rugosa apresentou atividade antimicrobiana contra todos os isolados de Rsol testados. Quanto à extração de proteínas de alta qualidade o método de Lise foi o mais eficiente para Rsol e Pcc, apresentando respectivamente 369 ± 4 e 212 ± 3 diferentes spots de proteínas, contudo para Acc o método de centrifugação foi o mais indicado com 224 ± 8 spots. De acordo com os resultados deste estudo conclui-se que a formação de biofilme pode ser quantitativa e estruturalmente distinta entre isolados da mesma espécie. O screening das propriedades antimicrobianas das plantas fornece base de dados para o desenvolvimento de novos agentes antibacterianos naturais contra fitopatógenos seguros para o meio ambiente e para o desenvolvimento de estudos moleculares da formação de biofilme faz-se necessária uma prévia determinação de métodos para obtenção das macromoléculas a serem analisadas, sendo assim a seleção de métodos de extração é um ponto crucial para obtenção de amostras de qualidade para analises confiáveis. / Biofilm formation is an important feature for bacteria due to its naturally occurring and highly influence by the surrounding environment, giving to the microorganisms high tolerance to adversity and becoming essential in virulence for pathogens. Thus, we present in this thesis an investigation about bacterial adhesion and biofilm development of the phytobacteria Ralstonia solanacearum (Rsol) and Acidovorax citrulli (Acc), agronomically important, on hydrophobic surfaces; it was also investigated the use of plant extracts from the Caatinga region through the inhibition of the bacterial adhesion and its bactericidal activity against R. solanacearum. The most efficient method to prepare protein samples for R. solanacearum, A. citrulli and Pectobacterium carotovorum subsp. carotovorum (Pcc) was determined to be applied in future studies of molecular investigation of the formation of pathogenic biofilms. The biofilm formation by different bacterial strains after 24 h incubation in distinct culture media was quantified by the crystal violet method and its structures were observed by scanning electron microscopy and confocal microscopy. There were also evaluated 22 aqueous extracts from 16 plants collected in the Caatinga as its potential of inhibition of Rsol biofilm formation. In what concerns the efficiency in obtaining proteins, Trizol, Phenol, centrifugation, and Lyse were the methods evaluated by one- and two-dimensional electrophoresis. The results for biofilm formation demonstrate that, under the tested conditions, Rsol strains were different, both quantitatively and morphologically, and the strains namely B5-5, CGH26, CGH8, and SCN 21 were moderate or strong biofilm producers. Regarding the results for Acc strains, it is possible to note that they were not good biofilm producers, unless the strains Acc1.43 and Acc1.73 that were considered strong biofilm producers with similar quantity and morphology patterns. In relation to the screening of antibiofilm activity, only branches of Harpochilus neesianus and leaves of Myroxylon peruiferum presented antibiofilm activity with values higher than 83% and 50%, respectively, and Jacaranda rugosa showed activity antimicrobial against all the tested Rsol strains. The extraction of high quality proteins was performed most efficiently by the Lysis method for Rsol and Pcc, respectively with 369 ± 4 and 212 ± 3 different spots of proteins, however the centrifuge method was better for Acc with 224 ± 8 spots. According to the results of this study it is possible to conclude that biofilm formation can be quantitatively and structurally distinct from strains of the same species. The screening of the antimicrobial properties of the plants provides data as a basis for the development of new natural antibacterial agents against safe phytopathogens for the environment; in addition, for the development of molecular studies about the biofilm formation it is necessary a preliminary determination of the methods suitable for obtaining the macromolecules to be analyzed, so the selection of extraction methods is a crucial point for obtaining quality samples for reliable analysis.
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Ingénierie agroécologique et santé des cultures : Conception innovante de systèmes de cultures recourant aux plantes mycorhizotrophes pour la bioprotection de la tomate contre le flétrissement bactérien / Agroecological engineering and crop health : innovative design of cropping systems mixing mycorrhizal plants to biocontrol tomoat bacterial wiltOffroy-Chave, Marie 06 February 2015 (has links)
L’ingénierie agroécologique vise à produire des savoirs actionnables, pour concevoir des systèmes de cultures économiquement et écologiquement performants, par la valorisation de régulations naturelles. Notre problématique est centrée sur la santé des cultures, et plus particulièrement sur la bactérie phytopathogène Ralstonia solanacearum, agent du flétrissement bactérien alors qu’une souche extrêmement agressive menace la production de tomates en plein champ en Martinique. La nécessité d’explorer et de développer des alternatives aux méthodes conventionnelles de protection des plantes (variétés résistantes, pesticides), actuellement inefficaces, invite à la mise en œuvre d’une démarche de conception innovante. Nos travaux montrent que la mobilisation d’une barrière rhizosphérique est une stratégie de régulation biologique alternative. Différents processus y contribuent, telle que la mycorhization, symbiose entre racines et champignons mycorhiziens à arbuscules, présents dans la plupart des sols. Nous montrons que la mobilisation de réseaux de mycorhizes indigènes à partir d’un sol agricole permet une mycorhization précoce de la tomate. De plus, l’association de plantes aux propriétés mycorhizotrophes et assainissantes en conditions contrôlées montre des effets bioprotecteurs partiels et ouvre de nouvelles perspectives de combinaisons entre processus. Ces combinaisons sont mobilisables par des leviers d’actions multi-scalaires. Nous avons produit une grille d’analyse générique de ces leviers d’action pour la conception, par des trajectoires d’innovation multidirectionnelles, de « systèmes de culture bioprotégés ». Dans le contexte agricole martiniquais, une démarche d’apprentissage permet en effet l’émergence d’une dynamique de co-conception de systèmes de cultures recourant aux plantes mycorhizotrophes. Nos travaux proposent des outils pour une exploration collective de nouvelles stratégies de gestion durable de la santé des cultures. / Agroecological engineering aims to produce actionable knowledge to design economically and environmentally efficient cropping systems, based on the exploitation of natural regulation mechanisms. Our issue is centered on crop health, especially on the plant pathogenic bacterium Ralstonia solanacearum (bacterial wilt agent), of which an extremely aggressive strain threatens field tomato production in Martinique. The need to explore and develop alternatives to conventional methods of plant protection (resistant varieties, pesticides), ineffective in our case, calls for the implementation of an innovative design approach. Our work shows that the protection of the roots via the formation of a self-sustaining rhizospheric barrier may be an alternative biological control strategy. Different processes contribute, such as mycorrhizal symbiosis between roots and arbuscular mycorrhizal fungi, which are present in most soils. We show that the mobilization of indigenous mycorrhizal networks from an agricultural soil allows early mycorrhization of tomatoes. In addition, the association of plants with mycorrhizal and sanitizing properties in controlled conditions showed partial bioprotective effects and opens up new prospects for combinations between processes. These combinations may be exploited in various ways. We produced a generic analysis grid of key levers to design "healthy cropping systems " through multi-directional innovation trajectories. In Martinique's agricultural context, a learning process allows the emergence of a dynamic co-design of cropping systems using mycorrhizal plants. Our work thus provides tools for collective exploration of new sustainable management strategies for crop health.
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Dynamique évolutive de Ralstonia solanacearum en réponse aux pressions de sélection de l'aubergine résistante : approche populationnelle, de génétique évolutive et fonctionnelle de la durabilité de la résistance / Evolutionnary dynamics of Ralstonia solanacearum in response to selective pressure : population, functional and evolutionnary genetic aproches of plant resistance durabilityGuinard, Jérémy 14 December 2015 (has links)
Ralstonia solanacearum, une béta-proteobactérie d'origine tellurique, est l'une des phytobactérioses les plus nuisibles au niveau mondial. Cette bactérie est capable d'infecter plus de 250 espèces différentes dont certaines présentent un intérêt économique majeur (tomate, pomme de terre, tabac). R. solanacearum est divisée en 4 phylotypes distincts présentant des origines géographiques différentes : I (asiatique), IIA et IIB (américain), III (africain), IV (indonésien). Parmi ces phylotypes, le phylotype I est en expansion démographique, hautement recombinogène, réparti mondialement et possède une large gamme d'hôtes. Il possède donc un fort potentiel évolutif (sensu McDonald et Linde, 2002). Afin de contrôler cette bactérie, la lutte génétique reste la méthode la plus prometteuse : elle consiste à déployer des cultivars possédant différents sources de résistance (i.e., des gènes de résistance). La variété d'aubergine AG91-25 (E6) possède un gène majeur de résistance (ERs1) lui permettant de contrôler certaines souches de R. solanacearum de phylotype I. Cependant, la gestion de cette résistance requiert d'étudier au préalable sa durabilité afin d'en éviter le contournement. Cette durabilité peut être estimée en étudiant le potentiel évolutif d'un agent pathogène face à cette source de résistance, ainsi qu'en décryptant les mécanismes moléculaires de l'interaction entre l'hôte (gène R) et le pathogène (effecteur de types trois). Afin d'étudier la dynamique évolutive de R. solanacearum sous une pression de sélection exercée par la variété résistante E6, nous avons mis en place un essai d'évolution expérimentale au champ. Cet essai est composé de trois couples de microparcelles d'aubergines résistantes E6 et d'aubergines sensibles E8, implantées deux fois par an, pendant trois ans (soit 5 cycles). Un schéma MLVA (« Multi-Locus VNTR Analysis ») composé de 8 loci minisatellites a été développé afin de caractériser les souches extraites de ces cycles de cultures. Ces VNTR sont spécifiques aux souches de R. solanacearum de phylotype I, hautement polymorphes et discriminants à toutes les échelles : mondiale, régionale et locale. Nos résultats démontrent une absence de contournement de la résistance d'E6 par les populations parcellaires de R. solanacearum, confirmant le caractère durable de cette résistance. Cette variété aurait fortement réduit les populations bactériennes du sol, ne leur permettant plus d'infecter l'hôte résistant. Parallèlement, 100% des plants d'E8 sont morts à partir du cycle 2. La maladie au sein des microparcelles semble progresser selon une dynamique de « plante-à-plante ». Une baisse de la diversité génétique a aussi été observée au cours des cycles de culture répétés d'E8, associée à l'augmentation en fréquence de deux haplotypes. Cependant, aucune structuration génétique claire n'a été observée à l'échelle de la parcelle entière ou de la microparcelle. En revanche, les données d'isolement par la distance semblent indiquer qu'une structure spatiale semble être en cours d'établissement. L'ensemble de nos résultats suggère une structure épidémique clonale de nos populations parcellaires. Nous nous sommes aussi intéressés à l'implication de 10 ET3 dans l'interaction R. solanacearum vs aubergine résistante (E6). La distribution des 10 ET3 candidats est variable au sein d'une collection de souches phylogénétiquement diverses (91 souches) : ripAJ et ripE1 sont les ET3 les plus partagés alors que ripP1 et ripP2 sont les moins fréquemment. Certains ET3 présentent peu (ripAJ) voire pas (ripE1 et ripP2) de polymorphisme de taille, alors que d'autres (ripAU) sont extrêmement polymorphes. Cependant la composition en effecteurs d'une souche ne semble pas être corrélée à un phénotype sur aubergine E6. Nous avons identifié le gène d'effecteur ripAX2 comme ayant une fonction d'avirulence sur aubergine résistante E6. Sa reconnaissance par E6 semble s'opérer au niveau de la zone hypocotylaire. / Ralstonia Solanacearum is a soilborn beta-proteobacterium responsible of bacterial wilt on Solanaceaous crops. This bacterium is considered as one of the most harmful plant disease worldwide. This bacterium possesses the ability to infect more than 250 different species, including crops with major economic importance (tomato, potato, tobacco, eucalyptus…). R. solanacearum is divided into four phylotypes originated from different areas: I (Asian), IIA and IIB (American), III (African), IV (Indonesian). Among these phylotype, phylotype I is currently in demographic expansion, is highly recombinogenic and has a wide hosts range. Thus, altogether, these characteristics demonstrated that this phylotype has a high evolutionary potential (sensu McDonald and Linde, 2002). In order to control this bacterium, genetic plant resistance seems to be the most promising method. This method consists in using cultivars with different source of resistance such as resistance genes and/or resistant QTLs. The AG91-25 (E6), an eggplant cultivar possessing a major resistance gene (ERs1), is capable to control some of phylotype I strains of R. solanacearum. However, in order to optimize the management of this resistance and to avoid its fast breakdown, we need to deeply investigate the durability of this resistant gene. Durability can be estimated by studying the evolutionary potential of our pathogen faced to E6 source of resistance and by understanding the molecular mechanisms underlying the interaction between the host (R gene) and its pathogene (Type III Effector – T3E). In order to study R. solanacearum evolutionary dynamics under selective pressure from E6 resistant cultivar, we set up an experimental evolution trial in the field. This trial consisted of three couples of resistant (E6) and susceptible eggplants (E8) microplots, implanted twice a year during three years, hence consisting of 5 cycles. A Multi-Locus VNTR Analysis (MLVA) scheme, consisting of 8 minisatellite loci, was developed in order to characterize the strains extracted from these crop cycles. These VNTRs were specific to R. solanacearum phylotype I strains, they were highly polymorphic and discriminatory at different scale: globally, regionally and locally.Our results showed no breakdown of E6 resistance by R. solanacearum populations, which confirms that this resistance is durable. It seemed that this cultivar reduced the soil bacterial population, preventing bacterial population to infest the resistant host. At the same time, 100% of the E8 plants have died, starting at cycle 2. Bacterial wilt seemed to spread with a “plant-to-plant” dynamics within each microplot. Genetic diversity reduction was also observed during the successive cycle of susceptible eggplant, associated with the increase of frequency of two main haplotypes. However, we failed to identify a clear genetic structuration, neither at the plot scale nor at the microplot scale. Nevertheless, isolation-by-distance data seemed to show that a spatial structure is currently establishing. Altogether, our results suggested that our plot populations appeared to have a clonal epidemic structure.We also looked into 10 T3Es' involvement in the interaction between R. solanacearum and the resistant eggplant (E6). Their distribution was completely different within a collection of phylogenetically diverse strains (91 strains): ripAJ and ripE1 are the most shared T3Es whereas ripP1 and ripP2 were the less common T3E whithin our collection of strains. Some T3Es showed few (ripAJ) or no length polymorphism at all (ripE1 and ripP2) whereas some other (ripAU) are extremely polymorphic. Nevertheless, the T3E effector repertoire did not seemed to be correlated to a specific phenotype on E6 eggplant. Its recognition by E6 seemed to occur in the hypocotyle region rather than in the mesophyll, highlighting a possible organ-specificity of the interaction between ERs1 and ripAX2.
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