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

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.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.ANGERS-BU Lettres et Sciences (490072106) / SudocSudocFranceF

Organisation génomique globale des facteurs de résistance à la tavelure (Venturia inaequalis), à l'oïdium (Podosphaera leucotricha) et au feu bactérien (Erwinia amylovora) chez le pommier (Malus x domestica)

L'objectif de cette thèse était d'étudier l'organisation génomique des facteurs de résistance du pommier. Nous avons effectué la cartographie génétique d'une descendance de pommier, puis étudié le déterminisme génétique de la résistance partielle à la tavelure, l'oïdium et le feu bactérien dans trois descendances de pommier par analyse QTL. Nous avons enfin cartographié des gènes candidats de résistance et de défense. Les facteurs de résistance cartographiés au cours de ce travail et au cours d'autres travaux menés par d'autres équipes ont été réunis sur une même carte génétique. Nous avons observé une tendance forte au regroupement de facteurs de résistance différents et des colocalisations entre QTL, gènes majeurs et gènes candidats qui nous permettent de formuler quelques hypothèses sur la fonction des QTL et gènes majeurs du pommier. Ces résultats nous permettent d'envisager des stratégies de création de variétés de pommier à résistances multiples et durables.The purpose of this thesis was to determine the genomic organization of resistance factors in apple. We first constructed a genetic linkage map of an apple progeny. Then we studied the genetic determinism underlying partial resistance to scab, powdery mildew and fire blight in three progenies through a QTL analysis. At last, candidate genes presumably involved in resistance or defense against pathogens were mapped. The disease resistance factors identified during this study, and additional resistance factors (QTL and major genes) identified during previous studies were located on the same synthetic genetic linkage map. Most resistance factors were organized in clusters. Several co-localizations between QTL, candidate genes, and major genes occured, which led us to formulate some hypotheses about the putative functions of the genes and QTL mapped. From these results, strategies to create apple varieties carrying multiple resistances may be defined.ANGERS-BU Lettres et Sciences (490072106) / SudocSudocFranceF

Genetic correlations between accumulated plant biomass and WUE (A), and mean plant transpiration and WUE (B) for an apple core collection.

<p>The correlations between traits were evaluated using the bootstrap resampling method. Regression lines were presented for significant correlations. Each point represents the genetic value for one genotype.</p

Broad-sense heritability (A) and genetic coefficient of variation (CV) (B) for the genetic values of morphological and physiological traits for an apple core collection.

<p>For each trait, the number of the model selected according to the Bayesian Information Criterion (BIC) minimization is presented at the top of heritability bars. Refer to <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0145540#pone.0145540.t001" target="_blank">Table 1</a> for traits abbreviation and to <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0145540#pone.0145540.s001" target="_blank">S1 Table</a> for model details.</p

Genetic variation of morpho-physiological traits in an apple core collection

<p>Dataset used for the preparation of the manuscript “Genetic variation of morphological traits and transpiration in an apple core collection under well-watered conditions: towards the identification of morphotypes with high water use efficiency”</p> <p>The dataset presented includes information for morphological and physiological traits for 183 genotypes of an INRA apple core collection. This collection was grown under well-watered condition in the Phenoarch phenotyping platform in Montpellier (France). Trees were evaluated during the first year of growth after grafting them on M9 rootstock. A first file includes individual information for four plants for each genotype. A second file includes the Best Linear Unbiased Predictors (BLUP’s) of genetic values for each morpho-physiological trait and genotype. Mixed effect models taking into account the spatial heterogeneity within the phenotyping platform were used to estimate BLUPs values.</p

Relationships between plant transpiration (A), plant leaf area at the end of the experiment (B) and leaf transpiration (C) with the Y-axis representing residuals of the relationship between accumulated plant biomass and WUE in Fig 3A.

<p>Regression lines were presented for significant correlations. Each point represents the genetic value for one genotype.</p

Relationships between measured and estimated whole-plant leaf area (A) and plant biomass (B) at the end of the experiment.

<p>Measured plant biomass was obtained after weighing all the plants of the collection. Measured plant leaf area was obtained after measuring the leaf area for all the leaves for two replicates for each genotype. Estimated values were determined using non-destructive phenotyping technologies based on plant imaging. Each point represents one plant. Dashed lines indicate the 1:1 slope and the straight lines represent the regression line between measured and estimated values.</p