{"id":5622,"date":"2015-11-20T16:58:41","date_gmt":"2015-11-20T16:58:41","guid":{"rendered":"https:\/\/mycor.iam.inrae.fr\/IAM\/?p=5622"},"modified":"2015-12-16T08:29:20","modified_gmt":"2015-12-16T08:29:20","slug":"phd-defense-persoons-a","status":"publish","type":"post","link":"https:\/\/mycor.iam.inrae.fr\/IAM\/?p=5622","title":{"rendered":"PhD Defense: Antoine Persoons"},"content":{"rendered":"

\"these_Antoine_Persoons\"<\/a><\/p>\n

Les contournements de r\u00e9sistance par Melampsora larici-populina<\/em>, l’agent de la rouille du peuplier\u00a0: impact d\u00e9mographique et d\u00e9terminisme g\u00e9n\u00e9tique<\/strong><\/p>\n

Jury de th\u00e8se<\/span> :
\nMartin LASCOUX Professeur, Universit\u00e9 d’Uppsala, Rapporteur
\nChristophe LEMAIRE, Maitre de Conf\u00e9rence, Universit\u00e9 d’Angers, Rapporteur
\n\u00c9ric GELHAYE, Professeur, Universit\u00e9 de Lorraine, Examinateur
\nPierre GLADIEUX, Charg\u00e9 de recherche, INRA Montpellier, Examinateur
\nS\u00e9bastien DUPLESSIS, Directeur de recherche, INRA Nancy, Directeur de th\u00e8se
\nSt\u00e9phane DE MITA, Charg\u00e9 de recherche, INRA Nancy, Co-Directeur
\nMembre invit\u00e9\u00a0: Fabien HALKETT, Charg\u00e9 de recherche, INRA Nancy, Co-Directeur<\/p>\n

R\u00e9sum\u00e9<\/span>: Melampsora larici-populina<\/em> est un champignon pathog\u00e8ne responsable de la rouille foliaire sur les peupliers, causant de graves dommages dans les plantations du monde entier. Presque toutes les r\u00e9sistances des peupliers d\u00e9ploy\u00e9es en France ont \u00e9t\u00e9 contourn\u00e9es et l’\u00e9v\u00e9nement majeur est survenu en 1994 avec le contournement de la r\u00e9sistance R7 largement d\u00e9ploy\u00e9e en populiculture. Dans le but d’identifier des g\u00e8nes candidats li\u00e9s \u00e0 la pathog\u00e9nicit\u00e9, j’ai men\u00e9 une \u00e9tude de g\u00e9nomique comparative bas\u00e9e sur le s\u00e9quen\u00e7age de 15 isolats. Cette analyse a mis \u00e0 jour des patrons de polymorphisme corr\u00e9l\u00e9s \u00e0 la distribution des virulences au sein des isolats tout en r\u00e9v\u00e9lant la n\u00e9cessit\u00e9 d’une \u00e9tude populationnelle. Pour se faire, une \u00e9tude de g\u00e9n\u00e9tique des population bas\u00e9e sur le g\u00e9notypage de 600 isolats de M. larici-populina<\/em> \u00e9chantillonn\u00e9s de 1992 \u00e0 2012 a \u00e9t\u00e9 conduite. Cette analyse m’a permis de d\u00e9crire l’histoire d\u00e9mographique des populations de M. larici-populina<\/em> et de documenter l’impact majeur du contournement de la R7 sur la structure des populations. Enfin, j’ai men\u00e9 une analyse de g\u00e9nomique des populations afin d’obtenir un scenario d\u00e9mographique d\u00e9crivant les liens historiques entre les populations et d’identifier les r\u00e9gions sous s\u00e9lection. Cette analyse est bas\u00e9e sur le s\u00e9quen\u00e7age en Illumina de 86 isolats r\u00e9partis en quatre populations cl\u00e9s mises en \u00e9vidence par l’analyse de la structure g\u00e9n\u00e9tique des populations. Plus de 1 000 000 positions polymorphes ont \u00e9t\u00e9 identifi\u00e9es. Un scenario fiable a \u00e9t\u00e9 identifi\u00e9 par ABC \u00e0 partir duquel les enveloppes de confiance des indices de g\u00e9n\u00e9tique des populations ont \u00e9t\u00e9 mesur\u00e9es. L’analyse du g\u00e9nome scan qui a \u00e9t\u00e9 r\u00e9alis\u00e9e sur les 86 g\u00e9nomes en utilisant ces m\u00eames indices a r\u00e9v\u00e9l\u00e9e 20 r\u00e9gions g\u00e9nomiques contenant 14 g\u00e8nes candidats potentiellement impliqu\u00e9es dans le contournement de la R7.
\nMots cl\u00e9s: champignon phytopathog\u00e8ne, co\u00e9volution, g\u00e9n\u00e9tique des populations, scan g\u00e9nomiqueAbstract<\/span>: Melampsora larici-populina<\/em> is a pathogenic fungus responsible of poplar leaf rust, causing severe damages in plantations worldwide. Almost all poplar resistances deployed so far in France have been overcome and a major event that occurred in 1994 with the breakdown of resistance R7 mostly used in poplar cultivation. In order to identify candidate genes linked to pathogenicity, I conducted a comparative genomics study based on the sequencing of 15 isolates. This analysis revealed polymorphism patterns correlated to the distribution of virulences among isolates while the necessity of a population genetics study. I then analyzed the genetic structure of a comprehensive collection of 600 isolates of M. larici-populina<\/em> sampled from 1992 to 2012. This analysis demonstrated the major impact of the R7 breakdown on populations. Finally, I conducted a population genomics analysis to obtain a demographic scenario describing the historical links between populations and to identify genomic regions under selection. This analysis is based on the Illumina sequencing of 86 isolates in four key populations identified by the population genetic analysis. Over 1,000,000 polymorphic positions were identified. The best demographic scenario was assessed using Approximate Bayesian Computation algorithms based on coalescent simulations. Using this demographic scenario, I computed the confidence interval of several population genetic indices. This genome scan analysis was performed on the 86 genomes using this same indices and revealed 20 genomic regions containing 14 avirulence 7 candidate genes.<\/div>\n

Key words: phytopathogenetic fungus, coevolution, population genetics, genome scan<\/p>\n","protected":false},"excerpt":{"rendered":"

Les contournements de r\u00e9sistance par Melampsora larici-populina, l’agent de la rouille du peuplier\u00a0: impact d\u00e9mographique et d\u00e9terminisme g\u00e9n\u00e9tique Jury de th\u00e8se : Martin LASCOUX Professeur, Universit\u00e9 d’Uppsala, Rapporteur Christophe LEMAIRE, Maitre de Conf\u00e9rence, Universit\u00e9 d’Angers, Rapporteur \u00c9ric GELHAYE, Professeur, Universit\u00e9 … Continue reading →<\/span><\/a><\/p>\n","protected":false},"author":2,"featured_media":0,"comment_status":"closed","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[4],"tags":[],"class_list":["post-5622","post","type-post","status-publish","format-standard","hentry","category-seminarmeeting"],"_links":{"self":[{"href":"https:\/\/mycor.iam.inrae.fr\/IAM\/index.php?rest_route=\/wp\/v2\/posts\/5622","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\/2"}],"replies":[{"embeddable":true,"href":"https:\/\/mycor.iam.inrae.fr\/IAM\/index.php?rest_route=%2Fwp%2Fv2%2Fcomments&post=5622"}],"version-history":[{"count":0,"href":"https:\/\/mycor.iam.inrae.fr\/IAM\/index.php?rest_route=\/wp\/v2\/posts\/5622\/revisions"}],"wp:attachment":[{"href":"https:\/\/mycor.iam.inrae.fr\/IAM\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=5622"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/mycor.iam.inrae.fr\/IAM\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=5622"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/mycor.iam.inrae.fr\/IAM\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=5622"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}