Molecular Genetic Causes of Columnar Growth in Apple (Malus x domestica) Dissertation zur Erlangung des Grades Doktor der Naturwissenschaften (Dr. rer. nat.) am Fachbereich Biologie der Johannes Gutenberg-Universität Mainz vorgelegt von Romina Petersen geboren am 20.04.1986 in Wiesbaden Mainz, 2014 Dekan: 1. Berichterstatter: 2. Berichterstatter: Tag der mündlichen Prüfung: There is nothing like looking if you want to find something […] You certainly usually find something, if you look, but it is not always quite the something you were after. JRR Tolkien, The Hobbit Cumulative Statement Cumulative Statement This thesis is based on the following seven research articles, which are presented as attachments and are referred to in the introduction, results summary and discussion by their respective numbers: Paper 1: Petersen R., Krost C. (2013) Review: Tracing a key player in the regulation of plant architecture – The columnar growth habit of apple trees (Malus x domestica). Planta 238(1): 1-22 Paper 2: Otto D., Petersen R., Krost C., Schmidt E.R., Brandl R., Brauksiepe B., Braun P. (in press) Molecular Characterization of the Co Gene Region in Malus x domestica. Acta Hort Paper 3: Otto D.*, Petersen R.*, Brauksiepe B., Braun P., Schmidt E.R. (2014) The columnar mutation (“Co gene”) of apple (Malus x domestica) is associated with an integration of a Gypsy-like retrotransposon. Mol Breeding 33: 863-880 *: joint first authorship Paper 4: Krost C., Petersen R., Schmidt E.R. (2012) The transcriptomes of columnar and standard type apple trees (Malus x domestica) – a comparative study. Gene 498(2): 223-230 Paper 5: Krost C., Petersen R., Braun P., Schmidt E.R. (in press) Deep sequencing of the shoot apical meristem transcriptome of columnar apple trees (Malus x domestica). Acta Hort Paper 6: Krost C., Petersen R., Lokan S., Brauksiepe B., Braun P., Schmidt, E.R. (2013) Evaluation of the hormonal state of columnar apple trees (Malus x domestica) based on high-throughput gene expression studies. Plant Mol Biol 81(3): 211-220 Paper 7: Petersen R., Djozgic H., Rieger B., Rapp S., Schmidt E.R. (under review) Columnar apple primary roots share some features of the columnar-specific gene expression profile of aerial plant parts as evidenced by comparative RNA-Seq analysis. VII Table of Contents Table of Contents Cumulative Statement ................................................................................................................................ VII Table of Contents ............................................................................................................................................IX Figures and Tables ..................................................................................................................................... XIII List of Abbreviations ................................................................................................................................... XV Abstract ................................................................................................................................................................. 1 Zusammenfassung .......................................................................................................................................... 2 General Introduction ..................................................................................................................................... 3 The Domesticated Apple, Malus x domestica ..................................................................................... 3 Apple Genomics .............................................................................................................................................. 5 Transposable Elements ............................................................................................................................... 7 Apple Transcriptomics ............................................................................................................................. 11 Columnar Growth and Plant Growth Regulation .......................................................................... 13 Aims ................................................................................................................................................................. 15 Results Summary .......................................................................................................................................... 17 There Is No Mutation in a Protein Coding “Columnar Gene” ................................................... 17 The Co Mutation Is a Gypsy-44 LTR Retrotransposon Insertion ............................................. 19 Tissue-specific Differential Gene Regulation in the Gypsy-44 Region .................................. 20 The Overall Gene Expression Pattern of Columnar Trees ......................................................... 24 General Discussion ...................................................................................................................................... 27 The Molecular Basis of Columnar Growth ....................................................................................... 27 Choice of Plant Material and RNA-Seq Analysis Methods ......................................................... 35 References ........................................................................................................................................................ 39 Attachments ..................................................................................................................................................... 49 Paper 1: Tracing a key player in the regulation of plant architecture – The columnar growth habit of apple trees (Malus x domestica) .................................................. 51 Abstract .......................................................................................................................................................... 51 Keywords ....................................................................................................................................................... 51 Abbreviations ............................................................................................................................................... 52 Introduction .................................................................................................................................................. 52 History and Development of the Columnar Growth Habit ........................................................ 60 Phenotype Characteristics of Columnar Type Apple Trees ...................................................... 61 Mapping and Analyzing the Columnar Gene Region .................................................................... 64 Analysis of Quantitative Trait Loci in the Columnar Gene Region ......................................... 67 Phytohormone Levels in Columnar Apple Trees ........................................................................... 68 Transcriptome Analyses of Columnar Type Apple Trees .......................................................... 71 Conclusion ..................................................................................................................................................... 73 Acknowledgements ................................................................................................................................... 74 References ..................................................................................................................................................... 74 Paper 2: Molecular Characterization of the Co gene region in Malus x domestica .............. 85 Keywords ....................................................................................................................................................... 85 Abstract .......................................................................................................................................................... 85 Introduction .................................................................................................................................................. 86 Material and Methods ............................................................................................................................... 86 Results and Discussion ............................................................................................................................. 88 IX Table of Contents Conclusion ...................................................................................................................................................... 92 Acknowledgements .................................................................................................................................... 93 Literature Cited ............................................................................................................................................ 93 Paper 3: The columnar mutation (“Co gene”) of apple (Malus x domestica) is associated with an integration of a Gypsy-like retrotransposon .................................................. 95 Abstract ........................................................................................................................................................... 95 Keywords .......................................................................................................................................................