Les Truffes sont des champignons ascomycètes ectomycorhiziens appartenant à la famille des Tuberaceae et plus précisément au genre Tuber. On dénombre à ce jour plus d’une trentaine d’espèces de Tuber en Europe. Lors de ce travail de thèse, nous nous sommes plus précisément focalisés sur le modèle Tuber aestivum-uncinatum. Cette truffe communément appelée « Truffe de Bourgogne » présente un intérêt à la fois gastronomique et culturel.La première partie de ce travail de thèse a porté sur la clarification du statut taxonomique de la truffe de Bourgogne (Tuber uncinatum). Pour cela, nous avons utilisé une approche multi-marqueurs combinant des marqueurs génétiques couramment utilisés à l’échelle interspécifique. Nos analyses ont montré que les deux taxons Tuber aestivum (la truffe d’été) et Tuber uncinatum sont conspécifiques. Durant la deuxième partie, nous nous sommes intéressés à la diversité génétique de Tuber aestivum. Pour cela, nous avons tout d’abord développé des marqueurs microsatellites spécifiques par une approche de « direct shotgun pyrosequencing ». Cette méthode a permis le développement de 15 marqueurs microsatellites polymorphes. Nous les avons ensuite utilisés pour génotyper des individus provenant de différentes localisations en Europe. Nous avons pu identifier quatre sous populations différenciées qui ne correspondent pas, pour la majorité, à une répartition géographique. Cependant, un des clusters se différencie des autres à la fois par sa situation géographique (sud de la France) et ses caractéristiques génétiques (présence d’allèles rares). Ces résultats préliminaires pourraient indiquer l’existence d’un écotype particulier attaché à une écologie méridionale, Tuber aestivum sensu stricto.Nous nous sommes ensuite intéressés, dans la troisième partie de ce travail de thèse à la diversité aromatique de Tuber aestivum à l’échelle locale. Les résultats obtenus permettent de mettre en évidence l’existence d’une différenciation modérée entre les individus issus d’une truffière naturelle et les individus issus d’une truffière plantée. D’une saison de récolte à l’autre, une stabilité génotypique a été observée. Au niveau aromatique, seuls les composés C8 semblent être liés aux génotypes.Dans la dernière partie, nous nous sommes intéressés à l’analyse de données de récolte sur plus de trente ans au sein d’une truffière plantée de noisetiers inoculés initialement par Tuber melanosporum. Grâce à des analyses statistiques simples, nous avons pu noter les fluctuations tant en quantité qu’en poids des truffes récoltées suivant les saisons et les arbres truffiers. Il apparait que le remplacement de Tuber melanosporum par Tuber aestivum s’est fait de manière très rapide (trois ans). La disparition de Tuber melanosporum peut probablement être expliquée par la fermeture de la canopée des noisetiers, Tuber melanosporum n’appréciant pas un ombrage excessif / Truffles are ectomycorrhizal Ascomycota fungi belonging to the Tuberaceae family and more specifically to the Tuber genus. More than thirty Tuber species are currently described in Europe. In this thesis, we specifically focused on the Tuber aestivum-uncinatum model. This truffle is commonly called "Burgundy Truffle" and has a gastronomic and cultural interest.The first part of this thesis focused on the taxonomic status of the Burgundy truffle (Tuber uncinatum). For this, we used a multi-marker approach combining several genetic markers commonly used at the interspecific scale. Our analyses showed that the two taxa, Tuber aestivum (summer truffle) and Tuber uncinatum are conspecific.In the second part, we addressed the genetic diversity of Tuber aestivum. To do this, we firstly developed specific microsatellite markers by "direct shotgun pyrosequencing". This method has allowed the development of 15 polymorphic microsatellite markers. Then, we used those markers to genotype individuals from different European locations. We have identified four differentiated subpopulations that not correspond, for the majority, to a geographical distribution. However, one cluster differs from the others by its location (south of France) and its genetic characteristics (presence of rare alleles). These preliminary results may indicate the existence of a particular ecotype attached to a southern ecology: Tuber aestivum sensu stricto.We were then interested, in the third part of this thesis, to the aromatic diversity of Tuber aestivum at a local scale. Our results highlight the existence of a moderate differentiation between individuals from a natural truffle orchard and individuals from planted orchard. From one season to another, genotypic stability was observed. Only C8 volatile organic compounds seem to be related to the genotypes.In the last part, we analyzed harvesting data, over more than thirty years, from an hazelnut truffle orchard initially inoculated by Tuber melanosporum. Through simple statistical analyzes, we noted changes in both quantity and weight of truffles harvested according to the seasons and hazelnut trees. It appears that Tuber aestivum rapidly replaced Tuber melanosporum (in three years). The disappearance of Tuber melanosporum can probably be explained by the canopy closure; Tuber melanosporum not appreciating excessive shading.

Truffles are economically important fungi that are naturally present in the territory of the Czech Republic. Their geographical distribution is traditionally documented by the field incidence of fruitbodies. Advanced detection methods, however, enabled us to detect the presence of Tuber spp. at localities without a need for finding the underground fruitbodies. In this work, a molecular genetic detection method based on the polymerase chain reaction with specific primers was used. It enables us to determine the occurrence of members of the genus Tuber including Tuber aestivum in the studied samples. Members of the genus Tuber were detected in 67 cases out of a total of 190 samples. Highly probably, Tuber borchii, Tuber foetidum, Tuber rufum, Tuber dryophilum, Tuber umbilicatum, Tuber huidongense, Tuber oligospermum and Tuber aestivum have been detected. Since the sequence similarity with the closest species is relatively low in some cases, some of the obtained sequences might belong to hitherto unknown truffle species. Environmental factors analyzed explain only a small portion of the variability, acted weakly and cannot be taken as decisive for the presence or the absence of a species in a sample. The occurrence of truffles in the slopes of the study area was noted and it seems to be still more...

Tuber aestivum is an ectomycorrhizal ascomycete with underground fruit bodies. It is an economically important species, but has been regarded as endangered in Sweden. My inventory has increased the number of reported localities from 3 to 31. It has long been debated whether T. aestivum and T. uncinatum are conspecific or not, so a clarification would help conservation biology and cultivation. My study included 117 fruit bodies of both taxa from 8 countries. The phylogenetic (ITS) and microscopic analyses showed that the two taxa were synonyms and that the spore reticulum height, used to separate the taxa, is not diagnostic. T. aestivum was clearly different from T. mesentericum, which I reported new to Sweden. The Gotland T. aestivum population was genetically distinct (RAPD) from other European specimens. The genetic variation suggested sexual reproduction. The habitat of 18 T. aestivum sites on Gotland were analysed and compared with data from France. No striking functional differences in soil chemistry were found, so a possible T. aestivum ecotype on Gotland would rather be an adaptation to the colder and drier climate. Selecting local T. aestivum inoculum for truffle orchards in Northern Europe could be important for successful truffle production. In 1999, 10 experimental truffle orchards with a total of 240 oak and hazel seedlings were established on Gotland, and as a result of this project 3000 commercial oak seedlings were planted in 2000-2001. In 2004, T. aestivum mycorrhiza was still present in all of the 22 orchards studied on Gotland, some in soils different from natural habitats. In addition, the project has also generated a truffle cultivation association, a truffle company, truffle dog breeding and export of T. aestivum to France.