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The Responses of Arabidopsis Lyrata Ssp. Petraea to Environmental Stimuli

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The Responses of Arabidopsis Lyrata Ssp. Petraea to Environmental Stimuli The responses of Arabidopsis lyrata ssp. petraea to environmental stimuli Chloë Elizabeth Thompson Submitted in accordance with the requirements for the degree of Doctor of Philosophy The University of Leeds Faculty of Biological Sciences Institute of Integrative and Comparative Biology Centre for Plant Sciences September 2010 The candidate confirms that the work submitted is her own and that appropriate credit has been given where reference has been made to the work of others. This copy has been supplied on the understanding that it is copyright material and that no quotation from the thesis may be published without proper acknowledgement. © September 2010 The University of Leeds and Chloë Elizabeth Thompson. Acknowledgements Firstly I would like to thank my supervisor Professor Peter Urwin for his invaluable guidance and support throughout my Ph.D., and for introducing me to the world of molecular biology. Thank you also to my second supervisor Professor William Kunin for his ecological enthusiasm and advice. In addition, I would like to thank past and present members of the HJA/PEU lab and the WEK ecology group for their friendship and support. The following people deserve special thanks; Dr Philippine Vergeer for sharing her wealth of A. l. petraea knowledge; Jennie Hibbard for her invaluable technical support; Professor Howard Atkinson for his statistical words of wisdom; Siân Giddy for her IT wizardry; Dr Nathan Watson-Haigh for assistance with analysis of the microarray data; Professor Roger Butlin of the University of Sheffield for advice; Lance Penketh for assistance in the Plant Growth Suite; Martin Lappage for his friendship and horticultural support; Laura Davies for patiently answering many of my stupid questions and for her dedication to morning tea and biscuits; Nicky Atkinson for tea, cake, and being cheerful; Mark Goddard for his editorial skills and an unfailing commitment to the 14.56 tea break, and; my friends Lucy, Jane, and Steph of the James Farrell Concert Band for their weekly encouragement and word count targets. I am also very grateful to Dr Laura Jones for her assistance with printing and binding of the final thesis. Particular thanks must go to Dr Catherine Lilley for her continued support, encouragement, advice, and skills in panic prevention and alleviation. Finally I would like to thank Shaun Dowman for his support and faith in my abilities, and for always looking after me. This Ph.D. project was funded by the Biotechnology and Biological Sciences Research Council. ii Abstract Arabidopsis lyrata ssp. petraea has a fragmented distribution across Northern Eurasia, and its geographically isolated populations experience varying environmental conditions throughout the species’ range. A. l. petraea is consequently an appropriate test system to study the effects of abiotic stress on species’ distributions and for investigation of local adaptation. The main objective of this study was to investigate whether or not geographically isolated populations of A. l. petraea differ in their responses to environmental stimuli and thus demonstrate potential for local adaptation. Under controlled environmental conditions, populations from the British Isles and Norway demonstrated the highest average growth rates whilst the lowest rates were observed in Swedish populations. Populations also exhibited significantly altered growth rates under imposed hot and cold stress conditions than in their corresponding no-stress controls. The percentage of plants that flowered was significantly higher in Norwegian populations than for those from Sweden, Iceland, and the British Isles Molecular techniques were employed to investigate differential gene expression in populations of A. l. petraea from Norway, Sweden, Iceland, and the British Isles, both prior to and following exposure to cold temperature stress. Extent of up-regulation of expression following exposure to chilling differed for a number of genes including CCA1, NAC2, and SKIP16. Microarray analysis identified 207 genes that were differentially expressed between two focal populations, Leitrim (Ireland) and Helin (Norway), irrespective of temperature treatment (P <0.05, fold change >2). Approximately 6% of the A. l. petraea transcriptome was responsive to acclimation whilst expression of 75 genes, many annotated as unknown function, changed following exposure to freezing. The identified phenotypic variation is indicative of local adaptation, and populations from throughout the species’ range may thus harbour unique genetic variation. Further investigation of genes identified as important in plant responses to cold temperatures may facilitate crop improvement through GM technologies. iii Contents Acknowledgements ...................................................................................................................................................... ii Abstract ....................................................................................................................................................................... iii Contents ....................................................................................................................................................................... iv List of Figures ............................................................................................................................................................. ix List of Tables ............................................................................................................................................................... xi Abbreviations ............................................................................................................................................................. xii 1. General Introduction .........................................................................................................................................1 1.1 Species ranges .................................................................................................................................................1 1.2 The edge of the range ......................................................................................................................................2 1.2.1 Ecological factors .................................................................................................................................2 1.2.2 Evolutionary perspective ......................................................................................................................3 1.2.2.1 Lack of genetic variation in marginal populations ..........................................................................3 1.2.2.2 Gene flow counteracts local adaptation ...........................................................................................5 1.3 Evidence for local adaption in plants ..............................................................................................................6 1.4 The impact of climatic change on species ranges ...........................................................................................7 1.5 Responses of plants to abiotic stress ...............................................................................................................8 1.5.1 The responses of plants to cold stress ...................................................................................................9 1.6 The study species: Arabidopsis lyrata ssp. petraea ...................................................................................... 12 1.7 Project overview ........................................................................................................................................... 14 2. General Materials and Methods ..................................................................................................................... 18 2.1 Plant species and bacterial strains used ......................................................................................................... 18 2.1.1 Plant species ....................................................................................................................................... 18 2.1.2 E. coli strains ...................................................................................................................................... 18 2.1.3 Agrobacterium tumefaciens strains .................................................................................................... 18 2.2 Antibiotic stock solutions ............................................................................................................................. 18 2.3 General molecular biology methods used in DNA manipulation .................................................................. 20 2.3.1 Tissue Collection: A. l. petraea and A. thaliana ................................................................................. 20 2.3.3 Purification of DNA by phenol : chloroform extraction ..................................................................... 20 2.3.4 Extraction of Total RNA .................................................................................................................... 20 2.3.5 Estimation of nucleic acid concentration ............................................................................................ 21 2.3.6 Measurement of RNA quality ............................................................................................................ 21 2.3.7 Reverse transcription of RNA ...........................................................................................................
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