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Regulation of Desiccation Tolerance in Xerophyta Seedlings and Leaves

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Regulation of Desiccation Tolerance in Xerophyta Seedlings and Leaves Regulation of desiccation tolerance in Xerophyta seedlings and leaves. RAFE LYALL Thesis presented for the degree DOCTOR OF PHILOSOPHY In theUniversity Department of Molecular of Cape and Cell Town Biology University of Cape Town February 2016 i The copyright of this thesis vests in the author. No quotation from it or information derived from it is to be published without full acknowledgement of the source. The thesis is to be used for private study or non- commercial research purposes only. Published by the University of Cape Town (UCT) in terms of the non-exclusive license granted to UCT by the author. University of Cape Town Acknowledgements I would like to thank my Supervisors, Prof. Nicola Illing and Dr. Rob A. Ingle, for their substantial support and guidance throughout the work involved in this thesis. Thanks must also be given to Faezah Davids, whose help and advice was an invaluable asset throughout my studies. I would like to thank all current and past members of Lab 425 (the EvoDevo Lab) for advice, troubleshooting and assistance on the work presented here, and for making the process fun. Special thanks to Stephen Schlebusch, for general assistance in the realm of Bioinformatics, and to Evan Milborrow, who tirelessly performed the total RNA extractions required for sequencing. I am grateful to Nicola Mulder, Suresh Maslamoney, Ayton Meintjes and Gerrit Botha, from the UCT Computational Biology Division, for access to their hardware for the assemblies and the guidance provided. Finally, I would like to thank my family, who supported me and put up with me throughout this process. ii Table of Contents Chapter 1: Vegetative Desiccation Tolerance in Plants 1.1 Introduction ...................................................................................................................................... 1 1.1.1 Plant adaptations to water stress .................................................................................................. 1 1.1.2 Phylogeny of VDT in plants ............................................................................................................ 3 1.1.3 Seeds: a toolbox of desiccation tolerance spare parts? ................................................................ 5 1.2 The molecular basis of desiccation tolerance ................................................................................... 6 1.2.1 Stresses invoked during desiccation .............................................................................................. 6 1.2.2 Protective molecules invoked during desiccation ......................................................................... 9 1.2.2.1 Sugars .......................................................................................................................................... 9 1.2.2.2 LEA proteins .............................................................................................................................. 11 1.2.2.3 Antioxidants .............................................................................................................................. 14 1.2.2.4 Heat shock proteins (HSP)......................................................................................................... 15 1.2.2.5 Oleosins ..................................................................................................................................... 16 1.3 Seed development and embryo DT ................................................................................................ 17 1.3.1 Gene networks involved in seed maturation ............................................................................... 19 1.3.1.1 The AFL network ....................................................................................................................... 20 1.3.1.2 LEC1 and the NF-Y complex ...................................................................................................... 22 1.3.1.3 The bZIP family: ABI5 and the ABF genes ................................................................................. 23 1.3.1.4 ABA signal transduction ............................................................................................................ 25 1.3.1.5 Long-lived mRNAs ..................................................................................................................... 28 1.3.2 Gene networks involved in seed germination ............................................................................. 30 1.3.3 The point of no return.................................................................................................................. 32 1.3.4 Epigenetic networks involved in seed DT .................................................................................... 36 1.3.3.1 Epigenetic gene regulation: an overview .................................................................................. 37 1.3.3.2 PRC2 and PRC1: regulators of developmental gene repression ............................................... 39 1.3.3.3 Epigenetic control of the embryonic to vegetative transition .................................................. 42 1.4 Gene networks involved in VDT and drought tolerance in adult tissues ........................................ 45 1.4.1 Desiccation tolerance mechanisms in lower plants ..................................................................... 45 1.4.2 Drought tolerance mechanisms in DS plants ............................................................................... 50 1.4.3 Desiccation tolerance mechanisms in resurrection plants .......................................................... 56 1.5 Aims of the current study ............................................................................................................... 58 iii Chapter 2: Post-germinative seedling DT and the “point of no return” in Xerophyta 2.1 Introduction .................................................................................................................................... 62 2.2 Materials and Methods ................................................................................................................... 65 2.2.1 Plant material ............................................................................................................................... 65 2.2.2 Germination and growth conditions ............................................................................................ 65 2.2.3 Photography and seedling measurements .................................................................................. 66 2.2.4 Response of X. viscosa seeds to various dormancy-breaking treatments ................................... 66 2.2.5 The effect of developmental stage on seedling survival after rapid dehydration ....................... 67 2.2.6 The impact of PEG and sucrose treatment on seedling revival after dehydration ...................... 67 2.2.7 The effect of a reduced dehydration rate on seedling survival ................................................... 68 2.2.8 Statistical analysis ........................................................................................................................ 68 2.3 Results ............................................................................................................................................. 70 2.3.1 Germination and growth of X. viscosa, X. humilis seedlings ....................................................... 70 2.3.2 The effect of developmental stage on seedling survival after rapid dehydration ....................... 72 2.3.3 The impact of PEG or sucrose pre-treatment on seedling survival after dehydration ................ 75 2.3.4 The effect of PEG priming and reduced dehydration rate on seedling survival .......................... 79 2.4 Discussion ........................................................................................................................................ 83 2.4.1 Xerophyta seedlings show a transient decline in DT, which can be rescued by PEG or sucrose . 84 2.4.2 Xerophyta seedling survival is influenced by desiccation rate .................................................... 88 2.5 Supplementary Data ....................................................................................................................... 91 Chapter 3: De novo transcriptome assembly and analysis of desiccating leaves of X. humilis 3.1 Introduction .................................................................................................................................... 93 3.1.1 RNA Sequencing ........................................................................................................................... 94 3.1.2 De novo transcriptome assembly ................................................................................................ 97 3.2 Materials and methods ................................................................................................................. 104 3.2.1 Plant material ............................................................................................................................. 104 3.2.2 Leaf collection and RWC calculation .......................................................................................... 104 3.2.3 Experimental design, RNA extraction and quality assessment .................................................. 105 3.2.4 RNA Sequencing ......................................................................................................................... 107
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