The signalling pathway of phytochrome A (phyA) is complex. This thesis describes analysis of mutants with altered phyA-mediated responses for enhancement of understanding concerning phyA signalling. A novel Arabidopsis mutant ( gil1) has been isolated which defines a point of interaction between phytochrome signalling and gravity signalling. This mutant, in contrast to wild-type (wt), displays gravitropic orientation of hypocotyls under red (R) and far-red (FR) light. The phytochrome mediated agravitropism, observed in wt under R and FR, is mediated by phyA and phytochrome B (phyB). Analysis of the gil1 mutant phenotypes suggests that this mutant is impaired in both phyA and phyB mediation of agravitropism. The T-DNA insertion, which is most likely responsible for the phenotype associated with gil1, was located to chromosome V, between two genes predicted by sequence analysis. Reduced expression of one of these genes (K19M22.14) occurs in gil1. Database analysis of the sequence of the K19M22.14 gene suggests no homology to any recognised genes. The phyA signalling mutant fhy3 has diminished responses to FR but amplified responses to R. The phenotypes associated with these amplified responses to R are here characterised for a number of different alleles in three ecotypes of Arabidopsis. Results suggest that fhy3 has some enhanced responses to R, and that these are more apparent in some alleles/ecotypes. Analysis of the fhy3phyB double mutant indicates that phyB is required for the enhancement of R responses through FHY3. Isolation and preliminary characterisation of mutants (sofs) which suppress some phenotypes of fhy1 is presented. These mutants may define new components of the phyA signalling pathway.

Three plant genera with South American-Australasian disjunctive distributions were studied: Eucryphia, Griselinia and Coriaria . The aims of the project were: a) to assess the utility of different chloroplast and nuclear DNA sequences for phylogenetic reconstruction and b) by means of molecular clocks to establish whether or not this distribution is due to vicariance (continental drift) or more recent dispersal events. DNA was extracted, and regions of interest were amplified and sequenced. These were rpoA, trnL-F and trnU-K from the chloroplast genome, and rDNA 5.8S and intergenic spacers 1 and 2, Adh and two loci of the G3pdh gene from the nuclear genome. In each of the three genera, a single trans-Antarctic disjunction was indicated. Molecular phylogenies were produced using parsimony. Individual base pair variation was analysed in detail, and graphs were drawn to highlight variable regions. Sequences providing the most resolution were trnL-F, ITS and the two loci of the G3pdh. Robust molecular phylogenies were produced which are consistent with morphological, fossil and biogeographical evidence. Constancy of mutation rate across the different branches of the trees was checked using the Tajima test. Where constancy was established, the rate of evolution for the different gene regions was used to estimate the divergence times within each genera. Calibrations were performed using fossil data for Eucryphia and Coriaria average mutation rates derived from Eucryphia were applied to the Griselinia data set, owing to the absence of fossils. New Zealand became separated from Antarctica (and therefore South America) 95 - 80 million years ago, whereas average divergence times for Coriaria and Griselinia were found to be around 3 and 50 million years respectively. Similiarly, with respect to Eucryphia, Australia split from Antarctica 40 million years ago but the divergence time is 23.23 million years. The disjunction therefore must have arisen by dispersal which may have occurred either in the water by rafting or floating, or in the air in wind currents ( Eucryphia has winged seeds) or by means of birds (Coriaria and Griselinia have fleshy diaspores). A review of similar disjunctions in other plants and animals revealed that vicariance explanations were more likely to apply to groups at the taxonomic ranks of genus and above, whereas dispersal explanations were more likely to apply at the level of genus and below. The generic level is consequently of great interest.

This thesis describes the generation and screening of an A. thaliana M2 population for mutant lines affected in stamen development. The strategy utilised, was to mutagenise transgenic A. thaliana seed, homozygous for either the A6 or A9 promoter linked to the GUS gene, using -irradiation. The temporal expression patterns of the A9 and A6 promoters were evaluated for their use as genetic markers to delimit windows along the stamen differentiation pathway, into which subsequently isolated mutants could be placed. The TMS2 gene was also evaluated for its use as a visual reporter gene to aid in the isolation of mutant lines. The resulting M2 population was screened to identify mutants of the stamen differentiation pathway, by assaying for the absence or reduction of GUS activity in the floral buds. Four non-allelic male sterile mutants were identified and characterised, namely gne1, gne2, gne4 and gne7. Observations of anther histology show the abnormal differentiation of the tapetum and middle layer cells in gne1 and gne4 and the abnormal specification of these two tissue types in gne2. The fourth mutant line, gne7, shows asynchronous microspore development. Genetic map positions were ascertained for gne1, gne2 and gne7 using the A. thaliana W100F multimarker line and CAPS analysis. Additionally, CAPS analysis revealed that the PHYC gene was deleted in the gne7 mutant. This thesis also examines the sense and antisense expression of the AG gene under the control of the A6 and A9 promoter, as well as the analysis of the A9 promoter by 5' deletion analysis.

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RNA silencing pathways control the expression of genes and other DNA loci by the action of small RNA molecules and are found in many eukaryotes. In plants there are a number of RNA silencing pathways, of which RNA-directed DNA methylation (RdDM) is one. In this pathway the small RNA molecules direct DNA methylation, resulting in the down regulation of expression of the target locus. In terms of the mechanism of the pathway it is mostly well characterised but several gaps exist in our knowledge. These relate to its initiation, where it is not known how RdDM targets the correct locus; methylation, where it is unclear how the action of small RNAs triggers methylation; and chromatin modification, where it is unclear how methylated DNA is converted into higher order chromatin modification. These gaps in the pathway raised the possibility of the involvement of novel proteins and so this project aimed to identify and characterise mutants in these proteins. Screening of a library of putative RdDM mutants in Arabidopsis thaliana identified three alleles in MORC6, which encodes a GHKL ATPase containing protein associated with RdDM that is thought to form higher order chromatin in response to DNA methylation. Analysis of the three alleles revealed that morc6 mutants have no effect on siRNA production but at certain loci do have an effect on DNA methylation and so would suggest that MORC6 is also involved in the DNA methylation process in RdDM at specific loci. It was also shown that silencing by RdDM can still occur in morc6 mutants in a limited capacity and that this silencing is stochastic and cell autonomous in nature. These findings point to MORC6 also having further roles in RdDM other than higher order chromatin modification and so increase our understanding of the mechanism of RdDM.

Scrub or woodland communities dominated by Acacia tortilis form one of the few tree-dominated natural ecosystems in the hyper-arid climate of Qatar, making it a very important tree species that provides an essential habitat both for native animals and domestic livestock. However, the conservation and sustainable management of this tree has so far been neglected and it is now severely impacted by overgrazing and wood fuel collection. This research investigates the main environmental, ecological and management factors affecting the growth and distribution of Acacia tortilis in Qatar, including the factors affecting its regeneration. It also aims to guide the implementation of conservation programmes and development of a strategy to forestall deforestation and prevent the extinction of Acacia tortilis in Qatar. Initially, field survey, remote sensing and GIS techniques, together with univariate and multivariate statistical modelling techniques, were used to explore environmental influences on distribution of A. tortilis in Qatar at a national scale. Different vegetation indices (VIs), normalized difference vegetation index (NDVI), soil adjusted vegetation index (SAVI), were derived for a time series of Landsat TM/ETM+ images for 1998 and 2010 and tested using ground-truth data to explore the temporal dynamics of Acacia-dominated ecosystems which indicated substantial reduction in vegetation greenness in 2010 than 1998. The initial approach had limited success due to difficulties of identifying Acacia tortilis communities accurately on satellite images due to the sparsity of tree cover and indicates the limitations of using remote sensing methods for tracing vegetation dynamics in Qatar and similar arid and hyper arid environments. The multinomial logistic regression model has a superior ability to predict Acacia distribution and is a suitable method in the prediction of the occurrence of different vegetation types. Phytogeographical investigations of the environmental and biotic factors that control the distribution of the Acacia tortilis at a local scale, in both areas protected and unprotected from human land use impacts, demonstrate that topographic factors and their control on soil and water conditions are fundamental determinants. The distinctive topography of Qatar has resulted in a heterogeneous soil landscape with extreme contrasts of chemical and physical soil conditions within and between depressions and more elevated positions in soil toposequences. Depressional land forms are more suitable for the Acacia tree growth than the surrounding higher ground because ENVIRONMENTAL DETERMINANTS OF ACACIA TORTILIS IN QATAR II depression soils have greater soil water content, soil depth, organic carbon and available phosphorus contents. Conversely, the absence of Acacia trees in summit areas is related to severe limitations for tree growth, including negligible soil water content and shallow soil depth caused by impeding bedrock or cemented horizons resulting in drought stress, as well as large contents of gypsum and/or CaCO3 in soils. The slope-controlled movement of eroded soil material, water and plant debris, and the localised leaching of soluble salts, are suggested to be important processes that lead to improved soil quality and better tree growth in depressions. The regeneration of Acacia tortilis through seedling establishment is perhaps surprisingly shown to be greater in the unprotected than in protected areas. This is attributed to the importance of ingestion by large mammals (mainly domestic herbivores) on the germination and recruitment of Acacia seedlings. The greater frequency of Acacia saplings in depressions within the unprotected areas is, however, also attributed to the presence of greater amounts of soil water, soil depth, available phosphorus, and organic carbon. Although the action of browsing may be regarded as positive, most anthropogenic impacts were shown to have negative effects on the condition and distribution of Acacia tortilis. The results proved that the impacts of cutting and browsing were severe in the unprotected sites, despite the evidence of more active regeneration. It is concluded that there is an urgent need to review the provision and management of protected habitats for Acacia tortilis in Qatar. It is suggested that cutting for domestic use should be restricted; that conservation efforts should be concentrated in depressions that favour tree growth; and that the livestock numbers should be limited to enable seedling establishment without excessive browsing.

The plant hormones ethylene, auxin and cytokinin have a pivotal role in plant growth, including differential cell elongation and division, tissue patterning, root development and apical hook formation. The POLARIS (PLS) gene in Arabidopsis thaliana is critical for correct signalling and crosstalk between these hormones and encodes a 36 amino acid PLS peptide which acts to negatively regulate the ethylene signalling pathway, subsequently mediating root growth and development. PLS is expressed in the tips of primary and lateral roots, and it has been previously shown to bind to the ethylene receptor ETR1 in yeast and onion cells. ETR1 has been previously characterised and was shown to be localised to the endoplasmic reticulum (ER) membrane, requiring a copper ion for correct ethylene binding function and transduction of the ethylene signal. In addition to previous work revealing the ethylene-mediated downregulation of the PLS gene, work in this thesis demonstrates that the expression and localisation of the PLS peptide are regulated by ethylene in the A. thaliana root. It is revealed that the PLS peptide localises to the ER in root cells, where it interacts with the A. thaliana ETR1 protein. Evidence is presented which highlights the importance of copper ions in the role of the PLS peptide. The PLS N-terminus is essential for correct peptide activity in A. thaliana seedlings and notably requires the presence of two cysteine residues that have the potential to coordinate a metal ion. Interestingly, the PLS/ETR1 interaction is evidently enhanced in the presence of copper ions. Moreover, the loss-of-function pls mutant exhibits altered responses to copper perturbations and there is strong evidence that the PLS peptide can coordinate copper ions in vitro. Therefore, it is proposed here that the PLS peptide regulates copper ion availability to the ETR1 receptor protein at the ER, mediating ethylene receptor function and downstream ethylene responses, and consequently acting to regulate root development and growth.