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THÈSE POUR OBTENIR LE GRADE DE DOCTEUR DE L'université DE MONTPELLIER Structure Et Dynamique De La Diversité Génétique D

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THÈSE POUR OBTENIR LE GRADE DE DOCTEUR DE L'université DE MONTPELLIER Structure Et Dynamique De La Diversité Génétique D THÈSE POUR OBTENIR LE GRADE DE DOCTEUR DE L’UNIVERSITÉ DE M ONTPELLIER En Ecologie et Biodiversité École doctorale GAIA Unité de recherche AGAP En partenariat international avec l’Université Libanaise, LIBAN Titre de la thèse Structure et dynamique de la diversité génétique de l’amandier cultivé au Liban : facteurs biologiques et anthropiques Présentée par Bariaa HAMADEH Le 28 Septembre 2018 Rapport de gestion Sous la direction de Hélène JOLY et Lamis CHALAK 2015 Devant le jury composé de [Statut Bruno FADY, directeur de recherche, INRA Examinateur, Président du jury jury] Thierry ROBERT, maître de conférences, Université Paris-Sud XI Rapporteur [Statut Daniel PRAT, professeur, Université de Lyon Rapporteur jury] Romain SIMENEL, chargé de recherche, IRD Examinateur [Statut Hélène JOLY, chercheur, CIRAD Directrice de thèse jury] Lamis CHALAK, professeur, Université Libanaise Directrice de thèse [Statut Pascale MAIZI, maître de conférences, SupAgro Co-encadrante de thèse, Membre invité jury] [Statut jury] [Statut jury] [Statut jury] INTRODUCTION GENERALE----------------------------------------------------------------------4 I. Contexte et enjeu--------------------------------------------------------------------------------5 II. Effet de l’homme sur la dynamique de la diversité des plantes cultivées ------------7 II.1 la domestication---------------------------------------------------------------------------------------7 II.2 Interaction entre homme et forces évolutives---------------------------------------------------10 II.2.1 Sélection--------------------------------------------------------------------------------------------10 II.2.2 Migration/diffusion-------------------------------------------------------------------------------12 II.2.3 Dérive-----------------------------------------------------------------------------------------------13 II.3 Facteurs culturels et diversité des plantes cultivées--------------------------------------------14 III. Problématique de la thèse--------------------------------------------------------------------15 III.1 Modèle d’étude: cadre bio géographique de la thèse ------------------------------------------15 III.1.1 L’amandier ----------------------------------------------------------------------------------------15 III.1.2 Le Liban-------------------------------------------------------------------------------------------19 III.2 Questions de recherche et démarche-------------------------------------------------------------21 III.3 Plan de la thèse-------------------------------------------------------------------------------------22 CHAPITRE 1--------------------------------------------------------------------------------------------28 Impact of ancient and modern human-mediated gene flow on the genetic structure of cultivated almonds in the Menditerranean Basin ------------------------------------------------29 CHAPITRE 2--------------------------------------------------------------------------------------------66 Taxonomie locale et caractérisation de la diversité de l’amandier cultivé au Liban ------67 CHAPITRE 3------------------------------------------------------------------------------------------100 Evolution of almond genetic diversity and farmer practices in Lebanon: Impacts of the diffusion of a graft-propagated cultivar in a traditional system based on seed- propagation---------------------------------------------------------------------------------------------101 DISCUSSION GENERALE ET PERSPECTIVES--------------------------------------------142 Dynamique de la diversité génétique et diffusion des amandiers cultivés au Liban, influence des savoirs et des pratiques: regards croisés génétique – anthropologie------143 1) Dynamique d’introduction, diversité nommée et diversité variétale --------------144 2) Dynamique de la diversité génétique, diffusion et pratiques de propagation----147 3) Quelques implications pour la conservation--------------------------------------------151 i) Conservation ex situ---------------------------------------------------------------152 ii) Conservation in situ---------------------------------------------------------------152 iii) Conservation des ressources génétiques spontanées--------------------------153 iv) Utilisation durable-----------------------------------------------------------------153 ANNEXES----------------------------------------------------------------------------------------------------155 Remerciements Mes premiers remerciements s’adressent tout d’abord à mes encadrantes, Lamis Chalak et Hélène Joly, pour leur disponibilité, et leurs conseils, tout au long de cette thèse. Merci pour votre soutien et de m’avoir épaulé à différentes périodes de la thèse. Je suis extrêmement sensible à vos qualités humaines d'écoute et de compréhension. Hélène, je te remercie encore, entre les lignes. Je remercie aussi ma co-encadrante Pascale Maizi pour ses maints conseils pour les aspects anthropologiques. Je souhaite exprimer ma gratitude à Geo Coppens pour les discussions enrichissantes et sa contribution. Je vous remercie pour votre accueil chaleureux à chaque fois que j'ai sollicité votre aide. Je tiens à remercier les membres du jury d’avoir accepté d’évaluer mon travail : Thierry Robert, Daniel Prat, Hélène Rizk, Bruno Fady et Romain Simenel. Je remercie également Bouchaib Kadari, Jean-Frédéric Terral et Xavier Perrier, pour les discussions constructives et d’avoir guidé mes réflexions lors de mes comités de suivi de thèse. Eric Garine pour les discussions et la bibliographie autour de la nomenclature et taxinomie vernaculaire. Je tiens à remercier, Michel Afram, Directeur de l’IRAL, qui m’a soutenu et m’a permis de bénéficier des facilités de l’IRAL ainsi que d’un support financier et logistique jusqu’au juin 2016. Je tiens aussi à remercier Philippe Jarne et Yildiz Aumeeruddy-Thomas qui m’ont accueillie au CEFE et Claire Billot qui m’a accueillie dans l’équipe DDSE de l’UMR AGAP pour la poursuite de mon travail. Je tiens à remercie Fawaz el Omar (Doyen de l’EDST, Université Libanaise) et Marc Bouvy (directeur de l’ED GAIA, Université de Montpellier) ainsi que Zeinab Ibrahim (EDST, UL) et Véronique Dubois (service Handiversité, UM), d’avoir facilité ma reprise de thèse. Merci surtout aux agriculteurs et pépiniériste libanais qui ont participé à cette étude et qui ont partagé une partie de leurs connaissances ! Je remercie tous ceux qui m’ont soutenu à différentes périodes de la thèse. Au CEFE, Richard Joffre, Finn Kjellberg, Edmon Dounias, Sophie Caillon, Thierry Winkel, et bien d’autres personnes ! Laure mer ci de m’avo ir guidé au laboratoire. Au CIRAD, l’équipe DDSE et surtout Luc Baudouin, Aziz Saidou et Mathieu Thomas de m’avoir aidé à la compréhension de certains logiciels. Guylaine, merci surtout pour ton coup de main de dernière minute. Merci à mes amis Sali, Oula, Suzy, Clélia, Lucie, Aziz, Menad et bien d’autres, pour ce que vous êtes. Jack, merci pour les papillons ! Mohammad merci pour m’avoir accompagné sur le terrain sur l’amandier en 2014! Danièle, Jean-François, Elsa ma très belle famille, merci pour vos encouragements et votre soutien affectif. Je remercie aussi Joelle pour le temps libéré. Maman et Papa, le merci ne suffit pas car cette thèse est le fruit de votre soutien constant. Mounah, Athar et Mohammad, grand merci pour votre soutien affectif. Finalement, Jules et Léon Yahia, je vous remercie d’avoir rempli mon quotidien de bonheur. Je vous remercie vous deux pour votre soutien et d’avoir été à mes côtés dans cette traversée… Préambule Cette thèse s’inscrit sous la thématique générale de l’évaluation de la diversité génétique des arbres fruitiers dans le cadre de la Stratégie Nationale du Liban pour la Conservation et la Gestion des Ressources Phytogénétiques pour l’Alimentation et l’Agriculture . De plus, cette thèse est une contribution à l’observatoire Libano -Français de l’environnement O -life. Les travaux de la thèse ont démarré dans le cadre du projet FruitMed 901-007 soutenu par la fondation Agropolis et du projet Franco-Li banais CEDRE réf. 09 E F6/L 24 mis en œuvre en France par le ministère de l'Europe et des Affaires étrangères (MEAE) et le Ministère de l'Enseignement supérieur, de la Recherche et de l’Innovation (MESRI), et au Liban, par le Ministère de l’Éducation et de l’Enseignement Supérieur. Ma thèse a été initialement lancée pendant que j’occupais le poste de chercheur à l’Institut National de Recherches Agronomiques du Liban (IRAL), et où j’ai bénéficié d'un salaire régulier et de facilités diverses (Novembre 2012 - Juin 2016). Pendant la thè se j’ai aussi bénéficié d’un soutien pour les jeunes chercheurs du programme BioDivMex (Septembre 2018). Il s’agit d’une thèse en cotutelle entre l’Université Libanaise et l’Université de Montpellier. Le travail s’est déroulée en alternance entre Montpellier et le Liban dans différents laboratoires d’accueil : de novembre 2012 jusqu’à décembre 2014 dans l’UMR CEFE (Centre d’Ecologie Fonctionnelle et Evolutive), équipe Interactions Bio-Culturelles, puis de février 2015 à sa soutenance dans l’UMR AGAP (Amélioration Génétique et Adaptation des Plantes), équipe Dynamique de la Diversité, Sociétés et Environnement. La collecte du matériel végétal s’est déroulée au Liban dans le cadre de mes fonctions à l’IRAL, en collaboration avec l’Université libanaise . Le marquage moléculaire a été réalisé au laboratoire de biologie moléculaire de l'UMR CEFE et dans celui de la plateforme technique du Labex CeMed de l’Université de Montpellier. L'analyse des données, tant
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