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Exploration Génétique De La Polyploïdie Du Genre Juniperus (Cupressaceae) Perla Farhat

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Exploration Génétique De La Polyploïdie Du Genre Juniperus (Cupressaceae) Perla Farhat Exploration génétique de la polyploïdie du genre Juniperus (Cupressaceae) Perla Farhat To cite this version: Perla Farhat. Exploration génétique de la polyploïdie du genre Juniperus (Cupressaceae). Génétique des plantes. Université Paris Saclay (COmUE); Université Saint-Joseph (Beyrouth), 2019. Français. NNT : 2019SACLS125. tel-03311356 HAL Id: tel-03311356 https://tel.archives-ouvertes.fr/tel-03311356 Submitted on 31 Jul 2021 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. Exploration génétique de la polyploïdie du genre Juniperus (Cupressaceae) 2019SACLS125 : Thèse de doctorat de l’Université Saint-Joseph et NNT de l'Université Paris-Saclay préparée à l’Université Paris-Sud École doctorale n°567 Sciences du végétal : du gène à l'écosystème (SdV) Spécialité de doctorat : Biologie Thèse présentée et soutenue à Beyrouth, le 31 mai 2019, par Perla FARHAT Composition du Jury : Richard MAROUN Professeur, Université Saint-Joseph Président Joan VALLÈS Professeur, Universitat de Barcelona Rapporteur Thierry GAUQUELIN Professeur, Université Aix Marseille Rapporteur Bouchra DOUAIHY Maitre de conférence, Université Libanaise Examinatrice Michel DRON Professeur, Université Paris-Saclay Examinateur Thierry ROBERT Maitre de conférence, Université Paris-Sud Directeur de thèse Magda BOU DAGHER KHARRAT Professeur, Université Saint-Joseph Co-Directrice de thèse Sophie NADOT Professeur, Université Paris-Sud Invitée À mon ange, mon oncle Tony de qui j'ai hérité l’amour des plantes, À ma famille, Et à tous ces genévriers que j'adore… 1 Remerciements Ce n'est pas par hasard que cette section est placée en premier dans un rapport de thèse! Même avant la table des matières!! En effet, sans l’aide de toutes les personnes citées ci-dessous, je n’aurais pas pu commencer et terminer ma thèse! Je tiens donc à les remercier sincèrement de m'avoir accompagnée et aidée à mener à bout cette thèse. Je tiens tout d’abord à remercier le Conseil National de la Recherche Scientifique au Liban (CNRS-L), le Conseil de la recherche de l’Université Saint-Joseph et l’Université Paris-Sud pour le financement de ce projet de thèse. Je suis très reconnaissante à la Faculté des sciences de l’USJ, à son doyen le Professeur Richard Maroun, à l’école doctorale "Sciences, d'Ingénierie et de Technologie (EDSIT)" et au laboratoire "Biodiversité et Génomique Fonctionnelle". Mes grands remerciements vont également à l'Université Paris-Sud, Université Paris Saclay, l'école doctorale "Sciences du Végétal: du gène à l'écosystème (SDV)" et au laboratoire "Ecologie, Systématique et Evolution". Merci beaucoup de m'avoir donnée la possibilité de faire cette thèse au sein de vos établissements et avec vos équipes de choc. Mes plus grands remerciements vont à Dr Sonja Siljak-Yakovlev, celle qui m’a sauvée quand le monde s’est écroulé sou mes pieds : au moment où le co-directeur de thèse précédent était contraint à abandonner le travail pour des raisons personnelles. Vous avez cru en ce projet et en moi (sans même connaître mes capacités) et vous avez redonné vie à ce projet dans le laboratoire de votre affiliation ESE. En plus, vous avez été d’un grand soutien pendant mon séjour en France avec vos yeux passionnés par la science, avides à découvrir et pleins d’espoir. Assurez-vous que je n’oublierai jamais vos petits conseils et suggestions, je les garderai toujours en mémoire. De plus, je suis reconnaissante au co-directeur de cette thèse, Dr Thierry Robert, qui a accepté le défi et m’a pris sous son aile ! Il a cru en ce projet dès la première seconde. Je suis vraiment chanceuse de vous avoir comme directeur de thèse. Vous m'avez fait confiance et donné une grande liberté pour choisir et concevoir les expériences et apprendre l’autonomie. Vous m'avez beaucoup soutenue au cours de cette thèse. Que puis-je dire pour vous, Prof. Magda Bou Dagher Kharrat, tous les remerciements du monde ne suffiront peut-être pas. Je n'oublierai pas que vous avez rédigé la proposition de ma thèse à l'hôpital pour ne pas rater la date limite pour postuler à la bourse et pour me donner l'occasion de travailler sur 2 ce beau sujet. Je n'oublierai jamais toutes nos visites de terrain pleines d’action, d’infractions et des fous rires. Merci d'être la directrice de thèse et la grande sœur en même temps. Je voudrais également remercier vivement Prof. Robert P. Adams, le père des genévriers, qui a été d’un grand soutien lors de ma thèse et qui m'a confié du matériel inestimable de sa précieuse collection de genévriers. "Un pour tous et tous pour un", voilà comment nous vivons dans notre famille et c'est cet amour qui m'a encouragée tout au long de ma thèse. Le plus grand merci va à mes parents : Yasmina et Farhat, à mes sœurs, frères, nièces, neveux, belles sœurs et beaux-frères. Je suis si chanceuse d’avoir une si belle famille. Je vous remercie fortement. À tous mes amis, surtout les plus proches : Alodie Snirc, Amani Ojeil, Katia Saadé, Rana Jardak, Rhéa Kahale, Stephanie Le Prieur et Yuincho Lo. Je n’aurais pas pu y arriver sans votre soutien, votre aide et votre amour. J'ai de la chance de vous avoir dans ma vie. Vous n’êtes pas seulement ma deuxième famille; mais des membres de ma famille. À toutes les personnes qui m’ont prêté main forte dans les manipes, merci beaucoup. Dr. Oriane Hidalgo pour son aide dans la reconstruction ancestrale de la taille du génome, Professeur Ilia Leich et le laboratoire Jordwell au Royal Botanical Gardens, Kew pour les facilités données pendant les mesures de la taille du génome. Dr Najat Takvorian pour son aide précieuse dans les expériences de transformation bactérienne. Carole Saliba, Liliane Bou Khdoud, Rana Jardak, Rhéa Kahale pour le coup de main dans les extractions d’ADN. Anthony Roukoz, Gaelle Daou, Manea Mln et Lucy Tbt pour avoir participé dans les mesures des milliers de pollen de genévriers. Dr Mickael Bourge et Nicolas Valentin pour la mesure de la taille du génome. Je tiens à remercier l’association Jouzour Loubnan et plus particulièrement Anthony Roukoz de m’avoir ouvert les portes du Laboratoire de Conservation et de Germination des Graines pour y effectuer des tests et des expérimentations sur les semences de genévrier. Merci beaucoup à tous les fournisseurs d'échantillons et plus particulièrement le Conservatoire Botanique des Alpes (France) représenté par Luc Garreau, le passionné des thurifères qui nous a guidés durant notre excursion dans les Alpes à la recherche de J. thurifera et J. sabina. 3 Liste des abbreviations % Pourcentage °C Degré centésimal µg Microgramme µl Microlitre 2C DNA Quantité totale d’ADN par génome 2n Nombre de chromosome dans une cellule diploide ADN Acide Désoxyribonucléique AFLP Amplified fragment length polymorphism BAYLU Baylor University Herbarium BCN University of Barcelona Herbarium BLB Bering Land Bridge C value Quantité totale d’ADN par génome haploïde CBNA National Alpine Botanical Conservatory CCDB Chromosome Counts Database cm centimètre CMF Cytométrie en flux CTAB cetyltrimethyl ammonium bromide CV Pourcentage de variation Cx Monoploid genome size df Degrees of freedom dNTPs Deoxyribonucleotide triphosphates EDTA Ethylenediaminetetraacetic acid EE Représente le génome d'une espèce diploide FAM 6-fluorescein amidite (6-FAM) FCM Flow cytometry GNB Gif nuclear-isolation buffer GS Genome size h heure INRA Institut national de la recherche agronomique ITS Internal Transcribed Spacer 4 JS J. sabina JT J. thurifera K Genetic clusters L. Linnee LB buffer Lithium borate buffer m Mètre M Molaire Mbp Megabase pairs MCMC Markov chain Monte Carlo mg Milligramme min minutes mM Millimolaire MOPS 4-morpholine propane sulphonate Mw Megawatt Mya Million years ago n Nombre de chromosome dans une cellule haploïd NALB North Atlantic Land Bridge nDNA ADN nucléaire ng Nanogramme Nj Neighbor Joining nrDNA ADN ribosomal nucléaire ONF Office National des Forêts pb Paire de base PBF Polyploïdie de basse Fréquence PCR Polymerase chain reaction pg Picogramme pH Potential hydrogen PH Putative hybrid PHF Polyploïdie de haute Fréquence PI Propidium iodide PLP Proportion de fragments polymorphes pmol Picomole 5 PP Représente le génome d'une espèce diploide PPEE 2 séries de chromosomes non homologues P et E PPI Polyploïdie pas d’information PPPP 2 séries de chromosomes homologues P PVP Polyvinil pirolidoine Q Genome admixture proportions RBGK Royal Botanic Gardens Kew rpm Révolutions par minute s seconde s.s sensus stricto sect. section SNP Single Nucleotide polymorphism SSR Simple Sequence Repeats TE Tris-EDTA TG Taille du génome Tm Melting temperature Tris Tris (Hydroxymethyl) aminomethane UICN Union internationale pour la conservation de la nature v. Version WGD Whole genome duplication x Niveau de ploïdie 6 Liste des figures Figure 1. Plan de la thèse. ...................................................................................................................................... 12 Figure 2. Illustration simplifiée de l'autopolyploïdie et de l'allopolyploïdie. PP représente le génome de l’espèce 1. EE représente le génome de l’espèce 2. PPPP est le génome de la progéniture suite à l’autopolyploïdie et PPEE est le génome de la progéniture suite à l’allopolyploïdie. ........................................................................... 14 Figure 3. Exemples des voies de formation des tétraploïdes via l’allopolyploïdie et l'autopolyploïdie en une étape (les rectangles représentes les taxons et les cercles représentes les gamètes). ....................................................... 16 Figure 4. Exemples des voies de formation des tétraploïdes par autopolyploïdie via un pont triploïde (les rectangles représentes les taxons et les cercles représentes les gamètes).
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