Potentiel évolutif du pouvoir pathogène de Venturia inaequalis en lien avec la domestication du pommier et l'utilisation de résistances quantitatives en amélioration variétale

Human activities are one of the great evolutionary forces on plant pathogen populations. Controlling their impact is currently a great challenge for sustainable agriculture. The aim of this thesis was to evaluate the impact of apple domestication and of use of quantitative resistances in breeding programs, on the pathogenicity of the causal agent of apple scab, Venturia inaequalis. We compared pathogenicity of V. inaequalis isolates from wild and domesticated apples using cross-inoculations. Then, we compared their pathogenicity on domesticated apple pyramiding several quantitative resistance factors (QTL) to evaluate the potential role of wild apple as a source for highly aggressive isolates. Finally we evaluated selective pressures exerted by resistant QTL on a mixed inoculum using quantitative pyrosequencing. We demonstrated that apple domestication was associated with a important change in pathogenicity. Although isolates from wild apple were able to infect domesticated apple pyramiding several QTL, they were not more aggressive than isolates from domesticated apple, suggesting that they did not represent a supplementary threat for apple orchards. Finally, we clearly differentiated the impact of QTL according to their spectrum of action; the broad spectrum QTL did not exert differential selective pressures, which suggests that they have a higher durability.Maîtriser l'impact des modifications liées à l'activité humaine sur les populations de pathogènes des cultures est un des grands enjeux actuels pour la mise en place d'une agriculture durable. L'objectif de cette thèse était d'évaluer l'impact de la domestication du pommier et de l'utilisation de résistances quantitatives dans les variétés en cours de sélection, sur le pouvoir pathogène du champignon Venturia inaequalis, responsable de la tavelure. Par des inoculations croisées sur pommiers sauvages et domestiques, nous avons comparé le pouvoir pathogène de souches isolées de milieux naturels et cultivés. Puis nous avons comparé le pouvoir pathogène de ces souches sur des génotypes de pommier domestique cumulant plusieurs facteurs de résistances quantitatives (QTL) afin d'évaluer si les pommiers sauvages pouvaient héberger des souches plus agressives que les pommiers domestiques. Enfin, nous avons évalué les pressions de sélection exercées par ces QTL de résistance sur un mélange de souches par pyroséquençage quantitatif. Nos résultats montrent que la domestication du pommier se serait accompagnée d'une modification importante du pouvoir pathogène de V. inaequalis. Les souches issues de pommiers sauvages sont capables d'infecter des génotypes cumulant un grand nombre de facteurs de résistance mais elles ne sont pas plus agressives que les souches issues de pommiers domestiques ; elles ne représenteraient donc pas une menace supplémentaire pour les vergers. Enfin nous différencions nettement l'impact de QTL à spectre d'action étroit et large ; ces derniers, n'exerçant pas de pression de sélection différentielle entre souches co-inoculées, seraient plus durables

Stable Isotope Probing-RNA Strategy to Study Plant/Fungus Interactions

International audienceThe use of stable-isotope probing (SIP) allows tracing specific labeled substrates into fungi leading to a better understanding of their role in biogeochemical cycles and their relationship with their environment. Stable isotope probing combined with ribosomal RNA molecule, conserved in the three kingdoms of life, and messenger RNA analysis permits the linkage of diversity and function. Here, we describe two methods designed to investigate the interactions between plants and their associated mycorrhizal compartment by tracing carbon flux from the host plant to its symbionts

Stable Isotope Probing-RNA Strategy to Study Plant/Fungus Interactions

The use of stable-isotope probing (SIP) allows tracing specific labeled substrates into fungi leading to a better understanding of their role in biogeochemical cycles and their relationship with their environment. Stable isotope probing combined with ribosomal RNA molecule, conserved in the three kingdoms of life, and messenger RNA analysis permits the linkage of diversity and function. Here, we describe two methods designed to investigate the interactions between plants and their associated mycorrhizal compartment by tracing carbon flux from the host plant to its symbionts

Stable-Isotope Probing RNA to Study Plant/Fungus Interactions

International audienceThe use of stable-isotope probing (SIP) allows tracing specific labeled substrates into fungi leading to a better understanding of their role in biogeochemical cycles and their relationship with their environment. Stable-isotope probing combined with ribosomal RNA molecule, conserved in the three kingdoms of life, and messenger RNA analysis permits the linkage of diversity and function. Here, we describe two methods designed to investigate the interactions between plant and its associated mycorrhizal compartment by tracing carbon flux from the host plant to its symbionts

Data_AUDPC

This file contains: the AUDPC (Area under the disease progress curve) calculated on the sporulation percentage of the most infected leaf of each replicate. Percentage of leaf showing sporulation was scored visually at 14, 21 and 28 days after inoculation. Cross pathogenicity tests were done in a quarantine controlled climate chamber. Forty isolates from five populations were inoculated onto three Malus species ('Tested_species') with two to four accessions ('Tested_accession') per Malus species. Population names indicate the geographic origin (Asia or EU:Europe), the environment of origin (Wild or Agro: Agro-ecosystem) and the host of origin of the isolates (Malus sieversii, M. x domestica or M. sylevstris). Inoculations were done in 10 experiments

The importance of the microbiome of the plant holobiont

International audiencePlants can no longer be considered as standalone entities and a more holistic perception is needed. Indeed, plants harbor a wide diversity of microorganisms both inside and outside their tissues, in the endosphere and ectosphere, respectively. These microorganisms, which mostlybelong to Bacteria and Fungi, are involved in major functions such as plant nutrition and plant resistance to biotic and abiotic stresses. Hence, the microbiota impact plant growth and survival, two key components of fitness. Plant fitness is therefore a consequence of the plant per se and its microbiota, which collectively form a holobiont. Complementary to the reductionist perception of evolutionary pressures acting on plant or symbiotic compartments, the plant holobiont concept requires a novel perception of evolution. The interlinkages between the plant holobiontcomponents are explored here in the light of current ecological and evolutionary theories. Microbiome complexity and the rules of microbiotic community assemblage are not yet fully understood. It is suggested that the plant can modulate its microbiota to dynamically adjust to itsenvironment. To better understand the level of plant dependence on the microbiotic components, the core microbiota need to be determined at different hierarchical scales of ecology while pan-microbiome analyses would improve characterization of the functions displayed

Is the diversity of the active plant root microbiome spatially structured?

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Is the diversity of the active plant root microbiome spatially structured?

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Data from: Evolution of pathogenicity traits in the apple scab fungal pathogen in response to the domestication of its host

Understanding how pathogens emerge is essential to bring disease-causing agents under durable human control. Here, we used cross-pathogenicity tests to investigate changes in life history traits of the fungal pathogen Venturia inaequalis associated with host-tracking during the domestication of apple and subsequent host range expansion on the wild European crabapple (Malus sylvestris). Pathogenicity of 40 isolates collected in wild and domesticated ecosystems were assessed on the domesticated apple, its central Asian main progenitor (M. sieversii) and M. sylvestris. Isolates from wild habitats in the centre of origin of the crop were not pathogenic on the domesticated apple and less aggressive than other isolates on their host of origin. Isolates from the agro-ecosystem in central Asia infected a higher proportion of plants with higher aggressiveness, on both the domesticated host and its progenitor. Isolates from the European crabapple were still able to cause disease on other species but were less aggressive and less frequently virulent on these hosts than their endemic populations. Our results suggest that the domestication of apple was associated with the acquisition of virulences in the pathogen following host-tracking. The spread of the disease in the agro-ecosystem would also have been accompanied by an increase in overall pathogenicity