Influence of micropropagation through somatic embryogenesis on somaclonal variation in coffee (Coffea arabica) : assessment of variations at the phenotypical, cytological, genetic and epigenetic level Roberto Bobadilla Landey To cite this version: Roberto Bobadilla Landey. Influence of micropropagation through somatic embryogenesis onso- maclonal variation in coffee (Coffea arabica) : assessment of variations at the phenotypical, cytologi- cal, genetic and epigenetic level. Vegetal Biology. Université Montpellier II - Sciences et Techniques du Languedoc, 2013. English. NNT : 2013MON20087. tel-01016417 HAL Id: tel-01016417 https://tel.archives-ouvertes.fr/tel-01016417 Submitted on 27 Nov 2014 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. UNIVERSITÉ MONTPELLIER II SCIENCES ET TECHNIQUES DU LANGUEDOC THÈSE Présentée pour l’obtention du titre de Docteur en Sciences de l’Université Montpellier II Formation Doctorale : Biologie Intégrative des Plantes École Doctorale : SIBAGHE – Systèmes Intégrés en Biologie, Agronomie, Géosciences, Hydro sciences et Environnement par Roberto Bobadilla LANDEY Influence of micropropagation through somatic embryogenesis on somaclonal variation in coffee ( Coffea arabica ): assessment of variations at the phenotypical, cytological, genetic and epigenetic level Soutenue publiquement devant le jury composé de, Rapporteur Marie-Anne Lelu-Walter, Directrice de Recherche, INRA Orléans Rapporteur Stéphane Maury, Professeur, Université Orléans Examinateur Michel Nicole, Directeur de Recherche, IRD Montpellier Examinateur Alberto Cenci, Chercheur, Bioversity International Montpellier Directeur de thèse Hervé Etienne, Chercheur, CIRAD Montpellier 1 A mis padres y hermanos … …Por qué siempre están conmigo y siempre han creído en mí. Agradezco a Mi familia, que siempre me ha apoyado y está pendiente de mí. Hervé Etienne, por aceptar trabajar conmigo y por todos sus consejos, suerte con tus nuevos proyectos. June Simspon por creer en mí y recomendarme a este proyecto. Michel Nicole, chef gracias por todo. Benoît Bertrand, Alberto Cenci, Philippe Lashermes, Romain Guyot, Juan Carlos Herrera, Frédéric Georget y demás personas de mi equipo, verdaderos especialistas que contribuyeron en mi tesis, gracias por todos sus consejos para mejorar nuestros artículos y por sus enseñanzas. Sylvain Santoni, boss gracias por todo, la siguiente vez secuenciación a fondo. Eveline Dechamp, Isabelle Jourdan, Muriel Latreille, Morgane Ardisson, Audrey Webber, Katia Gil Vega por su asistencia técnica, sin ustedes no hubiera hecho ni una PCR. A todos mis amigos y compañeros, gracias a ustedes nunca me sentí lejos de casa. 2 ABBREVIATIONS 2, 4-D 2, 4-dichlorophenoxyacetic acid 6-BA 6-benzylaminopurine 6-g-g-Dimethylallylaminopurine (2iP) ABA acid absisic AFLP Amplified Fragments Length Polymorphisms AS agroforestry systems BAC Bacterial Artificial Chromosome CGA chlorogenic acids DAPI 4’,6 -diamidino-2-phenylindole, EG Embryo germination medium ESP embryogenic suspensions FISH Fluorescence FCM flow cytometry GA Gibberellins GISH genomic in situ hybridization HFSE High frequency somatic embryogenesis IAA indole-3-acetic acid IBA indole-3-butyric acid LFSE Low frequency somatic embryogenesis LTR Long Terminal Repeat MSAP Methylation sensitive Amplified Polymorphisms NAA naphthaleneacetic acid NGS Next Generation Sequencing PCR Polymerase Chain Reaction PEMs Proembryogenic masses PTC Plant tissue culture RFLP Restriction fragment length polymorphism RT-PCR Reverse transcriptase polymerase chain reaction SDS Sodium Dodecyl Sulfate SE Somatic Embryogenesis SNP single nucleotide polymorphism SSAP Sequence Specific Amplified Polymorphisms SCE secondary embryogenesis SV Somaclonal variaiton TE Transposable element TDZ Thidiazuron 3 SUMMARY LIST OF FIGURES LITERATURE REVIEW .................................................................................................. 10 LIST OF TABLES LITERATURE REVIEW .................................................................................................... 11 CHAPTER I .............................................................................................................................................. 14 LITERATURE REVIEW ............................................................................................................................. 14 PART I .................................................................................................................................................... 15 Generalities about coffee .................................................................................................................. 15 Coffee consumption, cultivation and economical trade ............................................................... 15 Coffee taxonomy ........................................................................................................................... 16 Speciation and genome features of C. arabica ............................................................................. 18 Characteristics of coffee cultivated species .................................................................................. 20 Cytological aspects of genus Coffea .............................................................................................. 22 PART II ................................................................................................................................................... 23 Coffee breeding ................................................................................................................................. 23 Development of F1 hybrid varieties .................................................................................................. 23 Description of the hybrid vigour in Coffea arabica ........................................................................... 24 Performance of selected hybrids ...................................................................................................... 25 F1 hybrids and coffee beverage quality ............................................................................................ 26 PART III .................................................................................................................................................. 27 Plant tissue culture and micropropagation ....................................................................................... 27 Methods of sexual and asexual of propagation in plants and tissue culture ................................ 27 Totipotency and the developmental pathways of plant regeneration ............................................. 28 Plant growth regulators (PGRs) and their implication in the developmental pathways of organogenesis and somatic embryogenesis ..................................................................................... 29 De novo organogenesis and its applications ..................................................................................... 30 Somatic embryogenesis .................................................................................................................... 32 Direct and indirect somatic embryogenesis ...................................................................................... 33 4 Somatic embryogenesis vs. zygotic embryogenesis .......................................................................... 34 Applications of somatic embryogenesis ............................................................................................ 35 Somatic embryogenesis in bioreactors ......................................................................................... 36 Coffee propagation and micropropagation ...................................................................................... 37 Sexual and traditional vegetative techniques for coffee propagation .......................................... 37 Somatic embryogenesis ................................................................................................................ 37 Scaling up of coffee micropropagation ......................................................................................... 40 PART IV .................................................................................................................................................. 42 Somaclonal variation ......................................................................................................................... 42 Definition and extent of the problem ........................................................................................... 42 Qualitative and quantitative trait affectation by somaclonal variation ............................................ 42 Somaclonal variation rates ................................................................................................................ 44 Genetic mechanisms associated to SV .............................................................................................. 44 Cytological mechanisms associated with SV ....................................................................................