{"id":5260,"date":"2015-07-02T14:11:30","date_gmt":"2015-07-02T14:11:30","guid":{"rendered":"https:\/\/mycor.iam.inrae.fr\/IAM\/?p=5260"},"modified":"2015-09-08T14:01:12","modified_gmt":"2015-09-08T14:01:12","slug":"phd-position-3","status":"publish","type":"post","link":"https:\/\/mycor.iam.inrae.fr\/IAM\/?p=5260","title":{"rendered":"PhD position"},"content":{"rendered":"

English version: see below<\/strong><\/em><\/p>\n

Titre du sujet de th\u00e8se\u00a0:<\/strong><\/p>\n

Architecture g\u00e9n\u00e9tique de traits d\u2019histoire de vie li\u00e9s au pouvoir pathog\u00e8ne de l\u2019agent de la rouille du peuplier.<\/p>\n

Encadrants :<\/strong><\/h4>\n

Pascal FREY (DR2, HDR), directeur de la th\u00e8se<\/h4>\n

Fabien HALKETT (CR1), co-encadrant<\/h4>\n

St\u00e9phane DE MITA (CR2), co-encadrant<\/h4>\n

Laboratoire d\u2019accueil :<\/strong><\/h4>\n

UMR Interactions Arbres \u2013 Microorganismes<\/h4>\n

INRA\/Universit\u00e9 de Lorraine<\/h4>\n

Centre INRA Nancy-Lorraine<\/h4>\n

54280 Champenoux<\/h4>\n

https:\/\/mycor.iam.inrae.fr\/IAM\/<\/a><\/h4>\n

Universit\u00e9 d\u2019inscription de l\u2019\u00e9tudiant en th\u00e8se<\/strong>\u00a0: Universit\u00e9 de Lorraine<\/h4>\n

Ecole doctorale\u00a0: <\/strong>RP2E (Ressources, Proc\u00e9d\u00e9s, Produits, Environnement)<\/p>\n

Financement (acquis)\u00a0: <\/strong>INRA D\u00e9partement EFPA (Ecologie des For\u00eats, Prairies et milieux Aquatiques) & R\u00e9gion Lorraine<\/p>\n

R\u00e9sum\u00e9 de la th\u00e8se<\/strong><\/p>\n

L\u2019objectif de la th\u00e8se est d\u2019\u00e9tudier l\u2019architecture g\u00e9n\u00e9tique de traits d\u2019histoire de vie li\u00e9s au pouvoir pathog\u00e8ne de l\u2019agent de la rouille du peuplier, Melampsora larici-populina<\/em>. Nous faisons l\u2019hypoth\u00e8se que l\u2019agressivit\u00e9 du champignon risque d\u2019augmenter suite au d\u00e9ploiement au champ de nouveaux cultivars de peuplier portant des r\u00e9sistances quantitatives. L\u2019objectif g\u00e9n\u00e9ral de cette th\u00e8se est de mieux comprendre le potentiel d\u2019\u00e9volution de l\u2019agressivit\u00e9 des agents pathog\u00e8nes, afin d\u2019alimenter la r\u00e9flexion sur les strat\u00e9gies de s\u00e9lection de r\u00e9sistances durables, en particulier chez le peuplier.<\/p>\n

Contexte et enjeux<\/strong><\/p>\n

Le peuplier constitue une production importante en Europe pour le bois d\u2019industrie et sa contribution \u00e0 des fili\u00e8res \u00e9nerg\u00e9tiques est en nette progression. La rouille du peuplier, caus\u00e9e par le champignon pathog\u00e8ne Melampsora larici-populina<\/em> constitue la principale contrainte phytosanitaire de la populiculture en Europe et dans le monde. La s\u00e9lection de vari\u00e9t\u00e9s de peupliers r\u00e9sistants \u00e0 la rouille \u00e9tait bas\u00e9e pendant des d\u00e9cennies sur la s\u00e9lection d\u2019hybrides F1 intersp\u00e9cifiques, portant majoritairement des r\u00e9sistances qualitatives monog\u00e9niques et dominantes, bas\u00e9es sur la relation g\u00e8ne-pour-g\u00e8ne. Cependant, les d\u00e9ploiements successifs au champ de cultivars de peuplier \u00e0 r\u00e9sistances qualitatives se sont sold\u00e9s par les contournements syst\u00e9matiques de ces r\u00e9sistances par l\u2019agent pathog\u00e8ne, t\u00e9moignant de leur caract\u00e8re non durable \u00e0 moyen et long terme (Xhaard et al.,<\/em> 2011). La connaissance du d\u00e9terminisme g\u00e9n\u00e9tique des facteurs de virulence qui causent les contournements de r\u00e9sistance serait souhaitable, tant sur le plan fondamental (interactions entre loci d\u2019avirulence et loci de r\u00e9sistance) que sur le plan appliqu\u00e9 (strat\u00e9gies de gestion spatio-temporelle des r\u00e9sistances qualitatives).<\/p>\n

Depuis une vingtaine d\u2019ann\u00e9es, la recherche de r\u00e9sistances plus durables a conduit les am\u00e9liorateurs \u00e0 s\u2019orienter vers la s\u00e9lection de r\u00e9sistances quantitatives, \u00e0 d\u00e9terminisme g\u00e9n\u00e9tique plus complexe. Cependant, la r\u00e9sistance quantitative peut \u00e9galement s\u2019\u00e9roder du fait de l\u2019augmentation de l\u2019agressivit\u00e9 des agents pathog\u00e8nes, d\u00e9finie comme la composante quantitative du pouvoir pathog\u00e8ne (Pariaud et al.<\/em>, 2009). Par cons\u00e9quent, il est primordial d\u2019\u00e9tudier l\u2019\u00e9volution potentielle des traits d\u2019agressivit\u00e9 et leurs \u00e9ventuels compromis \u00e9volutifs (Lannou, 2012).<\/p>\n

De plus, la s\u00e9lection de traits favorables peut conduire \u00e0 des trade-offs<\/em>, c\u2019est-\u00e0-dire des compromis entre traits d\u2019histoire de vie (Laine & Barr\u00e8s, 2013). Les trade-offs<\/em> entre traits peuvent refl\u00e9ter des strat\u00e9gies d\u2019adaptation de l\u2019agent pathog\u00e8ne \u00e0 l\u2019h\u00f4te (comp\u00e9tition et\/ou dispersion) suivant les traits sur lesquels les individus investissent prioritairement (Pariaud et al.,<\/em> 2009) et peuvent donc jouer un r\u00f4le primordial au cours des processus \u00e9pid\u00e9miques. L\u2019\u00e9tude de ces trade-offs<\/em> entre traits quantitatifs peut ainsi permettre de mieux comprendre les param\u00e8tres qui conditionnent une \u00e9pid\u00e9mie.<\/p>\n

Hypoth\u00e8ses de travail et objectifs de la th\u00e8se<\/strong><\/p>\n

L\u2019hypoth\u00e8se principale est que l\u2019agressivit\u00e9 de M. larici-populina<\/em> pourrait augmenter suite au d\u00e9ploiement de nouveaux cultivars de peuplier portant des r\u00e9sistances quantitatives. Par cons\u00e9quent, une connaissance de l\u2019architecture de ces traits et de leurs trade-offs<\/em> \u00e9ventuels devrait permettre d\u2019orienter les strat\u00e9gies de s\u00e9lection pour des r\u00e9sistances durables (McDonald & Linde, 2002).<\/p>\n

L\u2019objectif central de la th\u00e8se propos\u00e9e est d\u2019\u00e9tudier l\u2019architecture g\u00e9n\u00e9tique des traits d\u2019histoire de vie qualitatifs (facteurs de virulence) et quantitatifs (composantes d\u2019agressivit\u00e9) chez l\u2019agent de la rouille du peuplier. Pour cela, les techniques de NGS (Next Generation Sequencing<\/em>) seront utilis\u00e9es.<\/p>\n

Les objectifs d\u00e9taill\u00e9s de ce projet de th\u00e8se seront\u00a0:<\/p>\n

    \n
  1. de cartographier les facteurs de virulence et les QTL d\u2019agressivit\u00e9 par une approche de re-s\u00e9quen\u00e7age de descendances (autof\u00e9condations et allof\u00e9condations) obtenues par croisements contr\u00f4l\u00e9s de M. larici-populina <\/em>(Pernaci et al.,<\/em> 2014\u00a0; Pernaci 2015).<\/li>\n
  2. de cartographier ces m\u00eames traits qualitatifs et quantitatifs par une approche de GWAS<\/em> (Genome-Wide Association Study\u00a0<\/em>; Hamblin et al.,<\/em> 2011) sur des populations naturelles de M. larici-populina.<\/em><\/li>\n
  3. d\u2019\u00e9tudier les compromis \u00e9volutifs (trade-offs<\/em>) entre ces traits, qui peuvent conditionner l\u2019adaptation de M. larici-populina<\/em> aux r\u00e9sistances du peuplier.<\/li>\n<\/ol>\n

    Publications r\u00e9centes des responsables de la th\u00e8se, en rapport avec le projet propos\u00e9\u00a0:<\/strong><\/p>\n

    Pernaci, M., De Mita, S<\/strong>., Andrieux, A., P\u00e9trowski, J., Halkett, F<\/strong>., Duplessis, S., and Frey, P<\/strong>. (2014). Genome-wide patterns of segregation and linkage disequilibrium: the construction of a linkage genetic map of the poplar rust fungus Melampsora larici-populina<\/em>. Frontiers in Plant Science<\/em> 5,<\/strong> 454<\/a>.<\/p>\n

    Persoons, A., Morin, E., Delaruelle, C., Payen, T., Halkett, F., Frey, P., De Mita, S<\/strong>., and Duplessis, S. (2014). Patterns of genomic variation in the poplar rust fungus Melampsora larici-populina<\/em> identify pathogenesis-related factors. Frontiers in Plant Science<\/em> 5,<\/strong> 450<\/a>.<\/p>\n

    Barr\u00e8s, B., Dutech, C., Andrieux, A., Halkett, F<\/strong>., and Frey, P<\/strong>. (2012). Exploring the role of asexual multiplication in poplar rust epidemics: impact on diversity and genetic structure. Molecular Ecology<\/em> 21,<\/strong> 4996-5008<\/a>.<\/p>\n

    Xhaard, C., Barr\u00e8s, B., Andrieux, A., Bousset, L., Halkett, F<\/strong>., and Frey, P.<\/strong> (2012). Disentangling the genetic origins of a plant pathogen during disease spread using an original molecular epidemiology approach. Molecular Ecology<\/em> 21,<\/strong> 2383-2398<\/a>.<\/p>\n

    Xhaard, C., Fabre, B., Andrieux, A., Gladieux, P., Barr\u00e8s, B., Frey, P<\/strong>., and Halkett, F.<\/strong> (2011). The genetic structure of the plant pathogenic fungus Melampsora larici-populina<\/em> on its wild host is extensively impacted by host domestication. Molecular Ecology<\/em> 20,<\/strong> 2739-2755<\/a>.<\/p>\n

    Autres r\u00e9f\u00e9rences bibliographiques<\/strong><\/p>\n

    Hamblin, M.T., Buckler, E.S., and Jannink, J.L. (2011). Population genetics of genomics-based crop improvement methods. Trends Genet<\/em> 27,<\/strong> 98-106.<\/p>\n

    Laine, A.L., and Barr\u00e8s, B. (2013). Epidemiological and evolutionary consequences of life-history trade-offs in pathogens. Plant Pathology<\/em> 62,<\/strong> 96-105.<\/p>\n

    Lannou, C. (2012). Variation and selection of quantitative traits in plant pathogens. Annual Review of Phytopathology<\/em> 50,<\/strong> 319-338.<\/p>\n

    McDonald, B.A., and Linde, C. (2002). Pathogen population genetics, evolutionary potential, and durable resistance. Annual Review of Phytopathology<\/em> 40,<\/strong> 349-379.<\/p>\n

    Pariaud, B., Ravign\u00e9, V., Halkett, F., Goyeau, H., Carlier, J., and Lannou, C. (2009). Aggressiveness and its role in the adaptation of plant pathogens. Plant Pathology<\/em> 58,<\/strong> 409-424.<\/p>\n

    Pernaci, M. (2015). Etude des traits d\u2019histoire de vie de Melampsora larici-populina<\/em>, agent de la rouille du peuplier : de leur d\u00e9terminisme g\u00e9n\u00e9tique \u00e0 leurs cons\u00e9quences \u00e9volutives. Th\u00e8se de Doctorat, Universit\u00e9 de Lorraine, 200 p.<\/p>\n

    Candidature :<\/strong><\/p>\n

    Envoyer un CV, une lettre de motivation et les coordonn\u00e9es de 2 personnes de r\u00e9f\u00e9rence \u00e0 Pascal Frey (pascal.frey@nancy.inra.fr<\/a>) avant le 1er octobre 2015.<\/p>\n

    Comp\u00e9tences recherch\u00e9es<\/strong><\/p>\n

    Le(la) candidat(e) devra avoir de bonnes comp\u00e9tences en g\u00e9n\u00e9tique (g\u00e9n\u00e9tique quantitative, g\u00e9n\u00e9tique des populations, g\u00e9nomique) et en bioinformatique. Il(elle) devra avoir des connaissances de base en \u00e9cologie et un int\u00e9r\u00eat pour la biologie \u00e9volutive et la pathologie v\u00e9g\u00e9tale. Un go\u00fbt prononc\u00e9 pour le travail en \u00e9quipe est indispensable.<\/p>\n

     <\/p>\n

    ————————————————————————————————-<\/p>\n

    Title of the thesis<\/strong><\/p>\n

    Genetic architecture of pathogenicity-associated life history traits in the poplar rust fungus.<\/p>\n

    Advisors:<\/strong><\/h4>\n

    Pascal FREY (Senior scientist), main supervisor<\/h4>\n

    Fabien Halkett (Junior scientist), co-supervisor<\/h4>\n

    St\u00e9phane DE MITA (Junior scientist), co-supervisor<\/h4>\n

    <\/h4>\n

    Host laboratory<\/strong><\/h4>\n

    Department of Tree – Microbe Interactions<\/h4>\n

    INRA \/ University of Lorraine<\/h4>\n

    INRA Nancy-Lorraine Research Centre<\/h4>\n

    54280 Champenoux<\/h4>\n

    https:\/\/mycor.iam.inrae.fr\/IAM\/<\/a><\/h4>\n

    \u00a0<\/strong>Funding (acquired):<\/strong> INRA EFPA Scientific division (Ecology of Forests, Grasslands and Aquatic environments) & Region Lorraine. Duration 3 years. Monthly net salary about \u20ac1400.<\/p>\n

    \u00a0<\/strong>Thesis summary<\/strong><\/p>\n

    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<\/em>. 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.<\/p>\n

    Context and challenges<\/strong><\/p>\n

    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<\/em>, 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\u2019s 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).<\/p>\n

    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 & Barr\u00e8s, 2013).<\/p>\n

    Working hypotheses and objectives of the thesis<\/strong><\/p>\n

    The main hypothesis is that the aggressiveness of M. larici-populina<\/em> 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).<\/p>\n

    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.<\/p>\n

    The detailed objectives of this PhD project will be:<\/p>\n

      \n
    1. To map avirulence loci and aggressiveness QTLs through whole-genome re-sequencing of selfed and\/or outcrossed progenies obtained from controlled crosses of M. larici-populina<\/em> (Pernaci et al, 2014; Pernaci 2015).<\/li>\n
    2. To map the same kind of qualitative and quantitative traits through an approach of Genome-Wide Association Study (GWAS; Hamblin and al., 2011) in natural populations of M. larici-populina<\/em>.<\/li>\n
    3. To assess the potential trade-offs between those traits, which can condition the adaptation of the pathogen to the resistance of the host.<\/li>\n<\/ol>\n

      \u00a0<\/strong>Recent publications of the thesis advisors in relation to the proposed project<\/strong><\/p>\n

      Pernaci, M., De Mita, S<\/strong>., Andrieux, A., P\u00e9trowski, J., Halkett, F<\/strong>., Duplessis, S., and Frey, P<\/strong>. (2014). Genome-wide patterns of segregation and linkage disequilibrium: the construction of a linkage genetic map of the poplar rust fungus Melampsora larici-populina<\/em>. Frontiers in Plant Science<\/em> 5,<\/strong> 454<\/a>.<\/p>\n

      Persoons, A., Morin, E., Delaruelle, C., Payen, T., Halkett, F., Frey, P., De Mita, S<\/strong>., and Duplessis, S. (2014). Patterns of genomic variation in the poplar rust fungus Melampsora larici-populina<\/em> identify pathogenesis-related factors. Frontiers in Plant Science<\/em> 5,<\/strong> 450<\/a>.<\/p>\n

      Barr\u00e8s, B., Dutech, C., Andrieux, A., Halkett, F<\/strong>., and Frey, P<\/strong>. (2012). Exploring the role of asexual multiplication in poplar rust epidemics: impact on diversity and genetic structure. Molecular Ecology<\/em> 21,<\/strong> 4996-5008<\/a>.<\/p>\n

      Xhaard, C., Barr\u00e8s, B., Andrieux, A., Bousset, L., Halkett, F<\/strong>., and Frey, P.<\/strong> (2012). Disentangling the genetic origins of a plant pathogen during disease spread using an original molecular epidemiology approach. Molecular Ecology<\/em> 21,<\/strong> 2383-2398<\/a>.<\/p>\n

      Xhaard, C., Fabre, B., Andrieux, A., Gladieux, P., Barr\u00e8s, B., Frey, P<\/strong>., and Halkett, F.<\/strong> (2011). The genetic structure of the plant pathogenic fungus Melampsora larici-populina<\/em> on its wild host is extensively impacted by host domestication. Molecular Ecology<\/em> 20,<\/strong> 2739-2755<\/a>.<\/p>\n

      \u00a0<\/strong>Other references<\/strong><\/p>\n

      Hamblin, M.T., Buckler, E.S., and Jannink, J.L. (2011). Population genetics of genomics-based crop improvement methods. Trends Genet<\/em> 27,<\/strong> 98-106.<\/p>\n

      Laine, A.L., and Barr\u00e8s, B. (2013). Epidemiological and evolutionary consequences of life-history trade-offs in pathogens. Plant Pathology<\/em> 62,<\/strong> 96-105.<\/p>\n

      Lannou, C. (2012). Variation and selection of quantitative traits in plant pathogens. Annual Review of Phytopathology<\/em> 50,<\/strong> 319-338.<\/p>\n

      McDonald, B.A., and Linde, C. (2002). Pathogen population genetics, evolutionary potential, and durable resistance. Annual Review of Phytopathology<\/em> 40,<\/strong> 349-379.<\/p>\n

      Pariaud, B., Ravign\u00e9, V., Halkett, F., Goyeau, H., Carlier, J., and Lannou, C. (2009). Aggressiveness and its role in the adaptation of plant pathogens. Plant Pathology<\/em> 58,<\/strong> 409-424.<\/p>\n

      Pernaci, M. (2015). Etude des traits d\u2019histoire de vie de Melampsora larici-populina<\/em>, agent de la rouille du peuplier : de leur d\u00e9terminisme g\u00e9n\u00e9tique \u00e0 leurs cons\u00e9quences \u00e9volutives. Th\u00e8se de Doctorat, Universit\u00e9 de Lorraine, 200 p.<\/p>\n

      \u00a0<\/strong>Application<\/strong><\/p>\n

      Send CV, cover letter and contact details of two referees to Pascal Frey (pascal.frey@nancy.inra.fr<\/a>) before 1 October 2015.<\/p>\n

      \u00a0<\/strong>Required skills<\/strong><\/p>\n

      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.<\/p>\n

       <\/p>\n

       <\/p>\n","protected":false},"excerpt":{"rendered":"

      English version: see below Titre du sujet de th\u00e8se\u00a0: Architecture g\u00e9n\u00e9tique de traits d\u2019histoire de vie li\u00e9s au pouvoir pathog\u00e8ne de l\u2019agent de la rouille du peuplier. Encadrants : Pascal FREY (DR2, HDR), directeur de la th\u00e8se Fabien HALKETT (CR1), … Continue reading →<\/span><\/a><\/p>\n","protected":false},"author":1,"featured_media":0,"comment_status":"closed","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[5],"tags":[],"class_list":["post-5260","post","type-post","status-publish","format-standard","hentry","category-job"],"_links":{"self":[{"href":"https:\/\/mycor.iam.inrae.fr\/IAM\/index.php?rest_route=\/wp\/v2\/posts\/5260","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/mycor.iam.inrae.fr\/IAM\/index.php?rest_route=\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/mycor.iam.inrae.fr\/IAM\/index.php?rest_route=\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/mycor.iam.inrae.fr\/IAM\/index.php?rest_route=\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/mycor.iam.inrae.fr\/IAM\/index.php?rest_route=%2Fwp%2Fv2%2Fcomments&post=5260"}],"version-history":[{"count":0,"href":"https:\/\/mycor.iam.inrae.fr\/IAM\/index.php?rest_route=\/wp\/v2\/posts\/5260\/revisions"}],"wp:attachment":[{"href":"https:\/\/mycor.iam.inrae.fr\/IAM\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=5260"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/mycor.iam.inrae.fr\/IAM\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=5260"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/mycor.iam.inrae.fr\/IAM\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=5260"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}