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Final Version Lehrstuhl für Genetik der Technischen Universität München Genetic and transcriptome analysis of autopolyploid Arabidopsis thaliana (L.) Heynh. Zheng Yu Vollständiger Abdruck der von der Fakultät Wissenschaftszentrum Weihenstephan für Ernährung, Landnutzung und Umwelt der Technischen Universität München zur Erlangungdes akademischen Grades eines Doktors der Naturwissenschaften genehmigten Dissertation. Vorsitzender: Univ.- Prof. Dr. A. Gierl Prüfer der Dissertation: apl. Prof. Dr. R. A. Torres Ruiz Univ.- Prof. Dr. E. Grill Die Dissertation wurde am 13.10.2014 bei der Technischen Universität München eingereicht und durch die Fakultät Wissenschaftszentrum Weihenstephan für Ernährung, Landnutzung und Umwelt am 24.11.2014 angenommen. Table of contents Table of contents Zusammenfassung ........................................................................................ 1 Summary ........................................................................................................ 3 Acknowledgments ......................................................................................... 4 Abbreviation Index ......................................................................................... 5 1. Introduction ................................................................................................ 8 1.1 Polyploidisation in evolution and speciation ..................................................... 8 1.2 Mechanisms of polyploidy formation ................................................................ 9 1.3 Types of polyploids ........................................................................................ 10 1.4 Polyploidy can lead to immediate and extensive changes in gene expression 11 1.5 Aneuploids ..................................................................................................... 14 1.6 Aims of this work ............................................................................................ 15 2. Material and Methods .............................................................................. 16 2.1 Material .......................................................................................................... 16 2.1.1 Plant material .......................................................................................... 16 2.1.2 Bacteria ................................................................................................... 17 2.1.3 Kits and enzymes .................................................................................... 17 2.1.4 Solutions ................................................................................................. 17 2.1.5 Oligomers ................................................................................................ 24 2.2 Methods ......................................................................................................... 25 2.2.1 Plant Breeding ......................................................................................... 25 2.2.2 General Molecular Biological Methods .................................................... 26 2.2.3 Inducement of Arabidopsis plants into polyploid ...................................... 35 2.2.4 Chromosome staining.............................................................................. 35 2.2.5 Flow cytometry analysis .......................................................................... 36 2.2.6 Microarray ............................................................................................... 36 2.2.7 RT-PCR and qRT-PCR ........................................................................... 41 2.2.8 Amino acid extraction and GC MS measurement .................................... 42 3. Results ...................................................................................................... 44 3.1 Generation of Arabidopsis tetraploid lines ...................................................... 44 Table of contents 3.1.1 Induction via Colchicine treatment ........................................................... 44 3.1.2 Identification of polyploidy candidate lines ............................................... 45 3.1.3 Assessment of the polyploid candidate lines ........................................... 48 3.2 Gene expression analysis of tetraploid lines .................................................. 51 3.2.1 Microarray experiments with seedlings ................................................... 55 3.2.2 Microarray experiments with leaves ......................................................... 61 3.2.3 RT-PCR results ....................................................................................... 68 3.2.4 qRT-PCR results ..................................................................................... 69 3.2.5 Gene expression alterations in tetraploids of other A. thaliana ecotypes than Col-0 and Ler-0 ........................................................................................ 70 3.3 MRD1, a valuable marker for monitoring polyploidy in Arabidopsis thaliana Col-0 .................................................................................................................... 71 3.3.1 MRD1 up-regulated in Col-0 autopolyploid tissues .................................. 71 3.3.2 Methylation anaylsis of MRD1 genomic region in Col-0, Ler-0 diploid and tetraploid lines .................................................................................................. 75 3.3.3 Over-expression of MRD1 in Col-0 tetraploid is inherited in Col-0 tetraploid Ler-0 tetraploid hybrid ...................................................................................... 76 3.4 Gene expression analysis of triploid lines ...................................................... 78 3.4.1 Microarray analysis ................................................................................. 78 3.4.2 Expression of MRD1 in triploid lines ........................................................ 81 3.5 Physiologic effects of tetraploids (Amino acid analysis) ................................. 82 3.6 Seed weight measurement of Recombinant Inbred Lines (RILs) .................... 83 4. Discussion ................................................................................................ 89 4.1 Colchicine effects and induction of polyploidy ................................................ 89 4.2 Discussion about the overlaps of the transcriptome alteration lists................. 91 4.3 Alteration of transcriptome in A. thaliana autotetraploids depends on ecotype, i.e., genome composition. .................................................................................... 94 4.4 Transcriptome alterations in autotetraploid Arabidopsis are developmentally specific. ............................................................................................................... 95 4.5 The transcriptome alteration in triploids.......................................................... 97 Table of contents 4.6 The Arabidopsis thaliana transcriptome alteration response to tetraploidy has a genetic basis and displays epigenetic phenomena. ............................................. 98 4.7 Physiological effects of tetraploids ............................................................... 104 4.8 The usage of the induced tetraploid RILs ..................................................... 105 4.9 Implications for evolution and plant breeding ............................................... 107 5. References.............................................................................................. 109 6. Appendix Figures ................................................................................... 123 7. Appendix Tables .................................................................................... 133 8. Appendix Published Work..................................................................... 199 Zusammenfassung Zusammenfassung Polyploidie, der Besitz von mehr als den doppelten Chromosomensatz, ist ein wichtiger Faktor in der Evolution von Eukaryonten gewesen. In der Regel werden zwei Formen der Polyploidie besonders herausgestellt: Allopolyploidie und Autopolyploidie. Erstere entsteht im ersten Schritt aus der Hybridisierung zweier Spezies auf die eine Chromosomen-Verdoppelung folgt. Letztere entsteht aus der direkten Verdoppelung der Chromosomensätze innerhalb ein und derselben Spezies. Autopolyploidie ist in Pflanzen häufiger anzutreffen als noch vor kurzem angenommen, hat aber im Vergleich zur Allopolyploidie wenig Aufmerksamkeit erhalten. Synthetisch allopolyploidisierte Pflanzen weisen beträchtliche Transkriptom-Veränderungen auf, die zum Teil wahrscheinlich auf die Vereinigung ehemals divergenter regulatorischer Schaltwege zurückzuführen sind. Im Gegensatz dazu haben Autopolyploide relativ uniforme Genome was nur wenige Veränderungen der Genexpression vermuten ließ. In dieser Arbeit wurde mit Hilfe von Colchizin eine Serie von autotetraploiden Arabidopsis thaliana Pflanzen unterschiedlicher Ökotypen generiert. Zusätzlich wurden Triploide aus der Kreuzung dieser Tetraploiden und gewöhnlicher Diploiden erstellt. Die Tetraploiden wurden mit verschiedenen morphologischen und zytologischen Mitteln und zum Teil mittels LC-MS charakterisiert. Im Vergleich zu Diploiden zeigten autotetraploide Arabidopsis thaliana relativ häufig Transkriptom-Änderungen. Diese bzw. deren Frequenz war von der Herkunft der Genome abhängig. Die Expressionsänderungen betrafen Gengruppen, die schon in Allotetraploiden auffällig
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