Venez nombreux pour soutenir Thomas, à la finale régionale du concours « Ma thèse en 180 secondes », qui aura lieu jeudi 28 avril, de 18h30 à 20h30, dans l’amphithéâtre Déléage (A027) du campus Lettres et Sciences Humaines de Nancy (23 boulevard Albert 1er). Entrée libre et gratuite !
Retrouvez l’interview de Thomas ici et plus d’infos ici.
Pr. Martin Lascoux, Professor at the Department of Ecology and Genetics, Uppsala University (Sweden) will be at INRA-Nancy on Dec 15th for the PhD dissertation of Antoine Persoons. He will give a seminar in the conference room of INRA Nancy at 10:00 am on the following topic:
“Clinal variation and the genetic basis of adaptive traits in trees”
Here is an abstract of his seminar:
Identifying the loci underlying the variation in quantitative traits and detecting the selection acting on them remains, to this day, one of the main challenges in biology. Genome wide association studies (GWAS) have become the main approach to identify the genetic factors controlling complex traits. Limitations of GWAS have, however, started to become evident and different strategies have been offered to alleviate those. In particular, GWAS have limited power unless very large datasets are used. They therefore remain prohibitively expensive, and often not so informative, for non-model organisms with limited or nascent genome resources such as forest trees. So, at least in the short term, a more targeted strategy, combining common gardens, population genetics, physiological and expression studies of candidate genes remains a very fruitful alternative. We will illustrate this with recent studies of clinal variation in phenological traits in forest trees, with special focus on boreal conifers, oaks and poplars. Some general features emerge from these different studies: first, they confirm the presence of strong latitudinal clines in phenological traits such as growth cessation. Second, most of the studies highlight the importance of genes belonging to the photoperiodic pathway and the circadian clock in the control of growth cessation. For instance, in both Norway and Siberian spruces, FTL2, a homolog of the main integrators for flowering time in A. thaliana, exhibits evidence of local adaptation and significant latitudinal variation in expression. Finally, the study of parallel clines in phenological traits, offers a first glimpse at the importance of parallel or convergent evolution in forest trees. They thereby provide us with a bit of information on the genetic architecture of important adaptive traits.
Please join us for this seminar.
Thanks a lot Marc for organizing this great “Mushroom Day” !
About 105 different species have been identified… not so bad for such a dry year !
English version: see below
Titre du sujet de thèse :
Architecture génétique de traits d’histoire de vie liés au pouvoir pathogène de l’agent de la rouille du peuplier.
Ecole doctorale : RP2E (Ressources, Procédés, Produits, Environnement)
Financement (acquis) : INRA Département EFPA (Ecologie des Forêts, Prairies et milieux Aquatiques) & Région Lorraine
Résumé de la thèse
L’objectif de la thèse est d’étudier l’architecture génétique de traits d’histoire de vie liés au pouvoir pathogène de l’agent de la rouille du peuplier, Melampsora larici-populina. Nous faisons l’hypothèse que l’agressivité du champignon risque d’augmenter suite au déploiement au champ de nouveaux cultivars de peuplier portant des résistances quantitatives. L’objectif général de cette thèse est de mieux comprendre le potentiel d’évolution de l’agressivité des agents pathogènes, afin d’alimenter la réflexion sur les stratégies de sélection de résistances durables, en particulier chez le peuplier.
Contexte et enjeux
Le peuplier constitue une production importante en Europe pour le bois d’industrie et sa contribution à des filières énergétiques est en nette progression. La rouille du peuplier, causée par le champignon pathogène Melampsora larici-populina constitue la principale contrainte phytosanitaire de la populiculture en Europe et dans le monde. La sélection de variétés de peupliers résistants à la rouille était basée pendant des décennies sur la sélection d’hybrides F1 interspécifiques, portant majoritairement des résistances qualitatives monogéniques et dominantes, basées sur la relation gène-pour-gène. Cependant, les déploiements successifs au champ de cultivars de peuplier à résistances qualitatives se sont soldés par les contournements systématiques de ces résistances par l’agent pathogène, témoignant de leur caractère non durable à moyen et long terme (Xhaard et al., 2011). La connaissance du déterminisme génétique des facteurs de virulence qui causent les contournements de résistance serait souhaitable, tant sur le plan fondamental (interactions entre loci d’avirulence et loci de résistance) que sur le plan appliqué (stratégies de gestion spatio-temporelle des résistances qualitatives).
Depuis une vingtaine d’années, la recherche de résistances plus durables a conduit les améliorateurs à s’orienter vers la sélection de résistances quantitatives, à déterminisme génétique plus complexe. Cependant, la résistance quantitative peut également s’éroder du fait de l’augmentation de l’agressivité des agents pathogènes, définie comme la composante quantitative du pouvoir pathogène (Pariaud et al., 2009). Par conséquent, il est primordial d’étudier l’évolution potentielle des traits d’agressivité et leurs éventuels compromis évolutifs (Lannou, 2012).
De plus, la sélection de traits favorables peut conduire à des trade-offs, c’est-à-dire des compromis entre traits d’histoire de vie (Laine & Barrès, 2013). Les trade-offs entre traits peuvent refléter des stratégies d’adaptation de l’agent pathogène à l’hôte (compétition et/ou dispersion) suivant les traits sur lesquels les individus investissent prioritairement (Pariaud et al., 2009) et peuvent donc jouer un rôle primordial au cours des processus épidémiques. L’étude de ces trade-offs entre traits quantitatifs peut ainsi permettre de mieux comprendre les paramètres qui conditionnent une épidémie.
Hypothèses de travail et objectifs de la thèse
L’hypothèse principale est que l’agressivité de M. larici-populina pourrait augmenter suite au déploiement de nouveaux cultivars de peuplier portant des résistances quantitatives. Par conséquent, une connaissance de l’architecture de ces traits et de leurs trade-offs éventuels devrait permettre d’orienter les stratégies de sélection pour des résistances durables (McDonald & Linde, 2002).
L’objectif central de la thèse proposée est d’étudier l’architecture génétique des traits d’histoire de vie qualitatifs (facteurs de virulence) et quantitatifs (composantes d’agressivité) chez l’agent de la rouille du peuplier. Pour cela, les techniques de NGS (Next Generation Sequencing) seront utilisées.
Les objectifs détaillés de ce projet de thèse seront :
Publications récentes des responsables de la thèse, en rapport avec le projet proposé :
Pernaci, M., De Mita, S., Andrieux, A., Pétrowski, J., Halkett, F., Duplessis, S., and Frey, P. (2014). Genome-wide patterns of segregation and linkage disequilibrium: the construction of a linkage genetic map of the poplar rust fungus Melampsora larici-populina. Frontiers in Plant Science 5, 454.
Persoons, A., Morin, E., Delaruelle, C., Payen, T., Halkett, F., Frey, P., De Mita, S., and Duplessis, S. (2014). Patterns of genomic variation in the poplar rust fungus Melampsora larici-populina identify pathogenesis-related factors. Frontiers in Plant Science 5, 450.
Barrès, B., Dutech, C., Andrieux, A., Halkett, F., and Frey, P. (2012). Exploring the role of asexual multiplication in poplar rust epidemics: impact on diversity and genetic structure. Molecular Ecology 21, 4996-5008.
Xhaard, C., Barrès, B., Andrieux, A., Bousset, L., Halkett, F., and Frey, P. (2012). Disentangling the genetic origins of a plant pathogen during disease spread using an original molecular epidemiology approach. Molecular Ecology 21, 2383-2398.
Xhaard, C., Fabre, B., Andrieux, A., Gladieux, P., Barrès, B., Frey, P., and Halkett, F. (2011). The genetic structure of the plant pathogenic fungus Melampsora larici-populina on its wild host is extensively impacted by host domestication. Molecular Ecology 20, 2739-2755.
Autres références bibliographiques
Hamblin, M.T., Buckler, E.S., and Jannink, J.L. (2011). Population genetics of genomics-based crop improvement methods. Trends Genet 27, 98-106.
Laine, A.L., and Barrès, B. (2013). Epidemiological and evolutionary consequences of life-history trade-offs in pathogens. Plant Pathology 62, 96-105.
Lannou, C. (2012). Variation and selection of quantitative traits in plant pathogens. Annual Review of Phytopathology 50, 319-338.
McDonald, B.A., and Linde, C. (2002). Pathogen population genetics, evolutionary potential, and durable resistance. Annual Review of Phytopathology 40, 349-379.
Pariaud, B., Ravigné, V., Halkett, F., Goyeau, H., Carlier, J., and Lannou, C. (2009). Aggressiveness and its role in the adaptation of plant pathogens. Plant Pathology 58, 409-424.
Pernaci, M. (2015). Etude des traits d’histoire de vie de Melampsora larici-populina, agent de la rouille du peuplier : de leur déterminisme génétique à leurs conséquences évolutives. Thèse de Doctorat, Université de Lorraine, 200 p.
Candidature :
Envoyer un CV, une lettre de motivation et les coordonnées de 2 personnes de référence à Pascal Frey (pascal.frey@nancy.inra.fr) avant le 1er octobre 2015.
Compétences recherchées
Le(la) candidat(e) devra avoir de bonnes compétences en génétique (génétique quantitative, génétique des populations, génomique) et en bioinformatique. Il(elle) devra avoir des connaissances de base en écologie et un intérêt pour la biologie évolutive et la pathologie végétale. Un goût prononcé pour le travail en équipe est indispensable.
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Title of the thesis
Genetic architecture of pathogenicity-associated life history traits in the poplar rust fungus.
Funding (acquired): INRA EFPA Scientific division (Ecology of Forests, Grasslands and Aquatic environments) & Region Lorraine. Duration 3 years. Monthly net salary about €1400.
Thesis summary
The aim of the thesis is to study the genetic architecture of life history traits related to pathogenicity in the poplar rust fungus, Melampsora larici-populina. We assume that the aggressiveness of the fungus may increase following the deployment in the field of new poplar cultivars with quantitative resistance. The general objective of this thesis is to better understand the potential evolution of aggressiveness in pathogens, to fuel the debate on sustainable resistance breeding strategies, especially in poplar.
Context and challenges
Poplar is an important product for the wood industry worldwide and its contribution to energy systems has increased recently. Poplar rust, caused by the pathogenic fungus Melampsora larici-populina, is the main phytosanitary constraint for commercial poplar cultivation in Europe and worldwide. In the last 50 years many rust-resistant cultivars were bred and released, but each of the qualitative resistance genes (i.e. major resistance genes) released have been overcome by pathogen evolution within a short period (Xhaard et al., 2011). Qualitative resistance is particularly subject to breakdown by pathogen evolution for perennial hosts, such as poplar trees, because of the wide inequality between the pathogen’s rapid generation time and the time needed to deploy new host varieties. Knowledge of the genetic determinism of the virulence factors leading to resistance breakdown would be beneficial both from an academic perspective (e.g. to decipher interactions between avirulence loci and resistance loci) and from an applied perspective (e.g., for determining strategies of spatiotemporal management of qualitative resistance).
The failure of qualitative resistances to control poplar rust has prompted breeders to search for quantitative resistance, which is supposed to be more durable. However quantitative resistance can also be challenged by the evolution of aggressiveness, which is the quantitative component of pathogenicity, determined by several disease-associated traits (Pariaud et al., 2009). Thus it is of primary importance to assess the potential evolution of aggressiveness traits in the pathogen and the potential trade-offs between these traits (Lannou, 2012; Laine & Barrès, 2013).
Working hypotheses and objectives of the thesis
The main hypothesis is that the aggressiveness of M. larici-populina could increase following the deployment of new poplar cultivars with quantitative resistance. Therefore, knowledge of the architecture of aggressiveness traits and their potential trade-offs would be useful in order to guide breeding strategies towards durable resistance (McDonald & Linde, 2002).
The central aim of the proposed thesis is to study the genetic architecture of qualitative (virulence factors) and quantitative (aggressiveness components) traits in the poplar rust fungus. To this aim, whole-genome re-sequencing techniques will be used.
The detailed objectives of this PhD project will be:
Recent publications of the thesis advisors in relation to the proposed project
Pernaci, M., De Mita, S., Andrieux, A., Pétrowski, J., Halkett, F., Duplessis, S., and Frey, P. (2014). Genome-wide patterns of segregation and linkage disequilibrium: the construction of a linkage genetic map of the poplar rust fungus Melampsora larici-populina. Frontiers in Plant Science 5, 454.
Persoons, A., Morin, E., Delaruelle, C., Payen, T., Halkett, F., Frey, P., De Mita, S., and Duplessis, S. (2014). Patterns of genomic variation in the poplar rust fungus Melampsora larici-populina identify pathogenesis-related factors. Frontiers in Plant Science 5, 450.
Barrès, B., Dutech, C., Andrieux, A., Halkett, F., and Frey, P. (2012). Exploring the role of asexual multiplication in poplar rust epidemics: impact on diversity and genetic structure. Molecular Ecology 21, 4996-5008.
Xhaard, C., Barrès, B., Andrieux, A., Bousset, L., Halkett, F., and Frey, P. (2012). Disentangling the genetic origins of a plant pathogen during disease spread using an original molecular epidemiology approach. Molecular Ecology 21, 2383-2398.
Xhaard, C., Fabre, B., Andrieux, A., Gladieux, P., Barrès, B., Frey, P., and Halkett, F. (2011). The genetic structure of the plant pathogenic fungus Melampsora larici-populina on its wild host is extensively impacted by host domestication. Molecular Ecology 20, 2739-2755.
Other references
Hamblin, M.T., Buckler, E.S., and Jannink, J.L. (2011). Population genetics of genomics-based crop improvement methods. Trends Genet 27, 98-106.
Laine, A.L., and Barrès, B. (2013). Epidemiological and evolutionary consequences of life-history trade-offs in pathogens. Plant Pathology 62, 96-105.
Lannou, C. (2012). Variation and selection of quantitative traits in plant pathogens. Annual Review of Phytopathology 50, 319-338.
McDonald, B.A., and Linde, C. (2002). Pathogen population genetics, evolutionary potential, and durable resistance. Annual Review of Phytopathology 40, 349-379.
Pariaud, B., Ravigné, V., Halkett, F., Goyeau, H., Carlier, J., and Lannou, C. (2009). Aggressiveness and its role in the adaptation of plant pathogens. Plant Pathology 58, 409-424.
Pernaci, M. (2015). Etude des traits d’histoire de vie de Melampsora larici-populina, agent de la rouille du peuplier : de leur déterminisme génétique à leurs conséquences évolutives. Thèse de Doctorat, Université de Lorraine, 200 p.
Application
Send CV, cover letter and contact details of two referees to Pascal Frey (pascal.frey@nancy.inra.fr) before 1 October 2015.
Required skills
The candidate should have good skills in genetics (quantitative genetics, population genetics, genomics) and bioinformatics. He/she should have basic knowledge in ecology and an interest in evolutionary biology and plant pathology. A taste for teamwork is essential. Knowledge of French will be an asset but is not mandatory.
Hommage aux victimes de l’attentat contre Charlie Hebdo. Toutes nos pensées vont aux familles et proches.
The GFPF seminar (Groupe Francophone de Pathologie Forestière) was held recently for three days in Hendaye from 14-16 October 2014
Jointly organized by the Département de la Santé des Forêts (DSF-MAAF) and the UMR IAM and partially funded by grants from Labex ARBRE, the seminar gathered 38 participants, mostly from DSF, INRA Bordeaux and INRA Nancy-Lorraine, including 10 scientists or technicians from the UMR IAM. Fourteen presentations were given, including six by IAM team members, about recent results on the epidemiology of the major pathosystems currently being studied: Poplar rust, Alder Phytophthora and Ash Dieback.
The seminar’s major focus was on the introduction of emerging diseases, such as Ash dieback, ink diseases (on oaks and chestnuts) due to Phytophthora cinnamomi and Pitch Canker, a new disease on Pines caused by Gibberella circinata. This fungus is common in North America where it causes canker and necrosis on twigs, branches, trunks and roots of many pine species. It was introduced in Europe in the 1990s and is now well established in northern Spain. Aside from a few cases that appeared in the early 2000s, the disease has not yet spread to France. The GFPF meeting also included field tours of forests in Spain to visit infected areas to better understand the disease symptoms and the host range. Discussions also addressed the risk of Pitch Canker spreading to France, particularly to southwestern France where the climate would favor establishment of this disease and where the presence of susceptible species is particularly dense.
Claude Husson, GFPF coordinator
Photo : Visit of a pine forest in Spain with presence of Pitch canker caused by Gibberella circinata
A more detailed report (in French) is available on the DSF website.
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Le séminaire bisannuel du GFPF (Groupe Francophone de Pathologie Forestière) s’est déroulé à Hendaye du 13 au 16 octobre 2014
Organisé conjointement par le Département de la Santé des Forêts (DSF-MAAF) et l’UMR IAM avec un cofinancement du Labex ARBRE, ce séminaire a rassemblé trente-huit participants, provenant essentiellement du DSF, de l’INRA Bordeaux et de l’INRA Nancy-Lorraine, dont 10 agents (permanents ou non) de l’UMR IAM. Les sessions en salle (1 journée) ont permis à l’UMR IAM de diffuser leurs derniers résultats sur l’épidémiologie des principaux pathosystèmes abordés dans l’Unité (6 présentations orales) : la rouille du Peuplier, le Phytophthora de l’Aulne et la chalarose du Frêne.
Cette année, le séminaire était principalement axé sur les maladies émergentes d’origine exotique, comme la chalarose, l’encre du chêne et du châtaignier due à Phytophthora cinnamomi et surtout le Pitch Canker, une maladie sur Pin causée par Gibberella circinata. Ce champignon commun en Amérique du Nord et qui provoque des dégâts sur rameaux, branches, troncs et racines sur de nombreuses espèces de Pin et sur Douglas a été introduit en Europe à la fin des années 1990. Il est aujourd’hui bien implanté en Espagne et notamment dans le pays basque espagnol. En France, malgré quelques rares mentions au début des années 2000, la maladie ne s’est jusqu’à présent pas développée. Des visites de terrain en Espagne ont permis aux participants de se familiariser avec les symptômes de la maladie et de débattre sur le risque Pitch Canker en France, notamment dans le sud-ouest où le climat semble favorable et où la densité de plantations d’espèces sensibles est très élevée.
Claude Husson, animateur du GFPF
Un compte-rendu plus détaillé est disponible sur le site du DSF.
Photo : Visite d’une pinède en Espagne avec présence de Pitch canker causé par Gibberella circinata
| Name | Michael Grillo |  |
| Team | Ecology of forest pathogenic fungi team | |
| In interaction with | Stéphane De Mita | |
| Subject | Analysis of population genomic diversity in Mediterranean populations of the legume Medicago truncatula in response to symbiotic local adaptation. | |
| Type of visit | Scientific stay, coming from University of Illinois at Urbana-Champaign | |
| Period | April, 7th to 16th, 2014 |
A postdoctoral position on forest epidemiology modeling is available at the Agroclim (INRA, Avignon) and Tree/Microorganism Interactions laboratories (INRA, Nancy) in France.
The Agroclim and Tree/Microorganism Interactions (IAM) laboratories are seeking a highly-qualified post-doctoral researcher to work on a joint project assessing the impacts of climate change on the establishment and development of crop and forest pathosystems in France. Climate change largely questions food security, but its impact on fungal diseases has been under explored, resulting in poor anticipation by management strategies designed to limit epidemics. The most significant work on climate change’s impact on diseases in France is related to forests, with INRA already having developed research models resulting in a fine description of plant x pathogen x climate interactions, as well as operational approaches largely used in forest health to identify and quantify the risks associated to future bioclimatic niches. The main objective of this post-doctoral appointment will be to improve these existing models and use them on a country-wide scale in order to identify areas favorable to the development of selected diseases, both for present and for future climates. This will be done for two forest foliar pathogens (Dothistroma Needle Blight disease on laricio pine and Diplodia pinea on pine) and two soft and durum wheat aerial fungi (stem and leaf rusts).
The successful candidate should hold a PhD with a background in epidemiology or agronomy/forestry, and also have experience in modeling. Excellent written and spoken skills in French or English are a must. The project is part of the larger framework of the newly started research network CLIF (Climate change and fungal diseases) within the INRA meta-programme, Adaptation of Agriculture and Forests to Climate Change. The successful candidate would join a group of approximately 30 scientists, including two international leaders in the field.
The appointment is for two years, with a provisional start date of July 2014. The candidate’s time would be split between the two labs, with 15 months spent at the Agroclim unit in Avignon (http://www6.paca.inra.fr/agroclim) and 9 months at the Tree/Microorganism Interactions unit in Nancy (https://mycor.iam.inrae.fr/IAM/)
Candidates must send their CV and a cover letter to Marie Launay (Agroclim, Avignon) mlaunay@avignon.inra.fr and Benoit Marcais (IAM, Nancy) benoit.marcais@nancy.inra.fr.
Candidates will be encouraged to apply for an AgreenSkills fellowship that will bring the gross monthly salary up to €3500. The next call for submission is 5 May 2014, 24:00 CET. To find out more about the programme and whether you are able to apply for a fellowship, visit www.agreenskills.eu
One of the AgreenSkills eligibility requirements is not having spent more than 12 months in France within the last 3 years immediately prior to the expected date of recruitment.
Today, Marc Buée successfully defended his HDR, entitled “Structures and roles of forest fungal communities”. Congratulations Marc for this brilliant defense!
Marc Buée a brillamment défendu son HDR aujourd’hui, intitulée “Structures et rôles des communautés fongiques forestières”, devant le jury composé de :
Mme. Monique GARDES, Professeur Université Toulouse 3 (Rapporteur)
M. Robin DUPONNOIS, Directeur de Recherches IRD, Montpellier (Rapporteur)
M. Lionel RANJARD, Directeur de Recherches INRA, Dijon (Rapporteur)
Mme Corinne LEYVAL, Directrice de Recherches CNRS, Nancy (Examinatrice)
M. Laurent SAINT-ANDRE, Chercheur Sénior CIRAD, Nancy (Examinateur)
M. Eric GELHAYE, Professeur Université de Lorraine, Nancy (Examinateur)
Bravo Marc pour cette soutenance brillante !
