The time of bolting is an important factor in lettuce production because it affects the yield and quality of the harvested crop. Bolting is promoted by higher temperatures and is an increasing problem for growers with the current trend for warmer summers. Lettuce plants that are in the early stages of bolting are visibly indistinguishable from non-bolting plants, however there are changes in the biosynthesis of secondary metabolites which are produced to protect the young floral bud from insect attack. These compounds give the lettuce plant a bitter taste and render the crop unsaleable. The development of late bolting varieties, which would have a greater ‘holding ability’ in the field, would result in reduced crop losses and an extension to the growing season. In many plants, the timing of the transition from vegetative growth to flowering is controlled by environmental cues which serve to communicate growth conditions favourable for sexual reproduction and seed maturation. Studies in Arabidopsis have led to the identification of several different pathways that come together to regulate flowering time. Little research has been done on these response pathways in lettuce, however, research has shown that components of these pathways are conserved between Arabidopsis and other crop species. The aim of this project is to isolate genes regulating flowering time in lettuce in order that novel alleles of these genes can be used to manipulate bolting time. A lettuce BAC library has been screened and homologues of eight Arabidopsis flowering time genes, principally from the autonomous pathway, have been isolated. Functional orthologues of FLOWERING LOCUS T (FT) and the autonomous pathway gene, FLK have been characterised in lettuce, suggesting that there is conservation of the genes involved in flowering time in Arabidopsis and lettuce. Lettuce lines with a range of bolting times, including lines which bolt significantly later than wild-type have been identified from EMS mutagenised populations of cultivated lettuce and a diversity set of wild lettuce. Homozygous lines from a Lactuca sativa cv. Larissa EMS population with a reproducible late bolting phenotype when tested under commercial growing conditions have been identified. These lines have been made available to Rijk Zwaan® for inclusion in future breeding programs aimed at delaying bolting and improving the ‘holding’ ability’ of commercial lettuce crops. Genomic sequence of selected lettuce flowering time genes have been compared between the late bolting lines and wild-type looking for polymorphisms that may account for the late bolting phenotype. Polymorphisms within these genes were identified in some of the late bolting lines, however through analysing the polymorphism in segregating backcross populations they have been shown not to be causing the late bolting phenotype. Transcriptome sequencing has also been performed to identify polymorphisms in other, possibly novel, genes which may be causing the late bolting phenotype, as yet, no mutation segregating within the late bolting lines has been identified.

The rhizosphere has a rich fungal microbiome, including parasites, commensals and mutualists. An important group in the rhizosphere are assumed to be the arbuscular mycorrhizal fungi (AMF), which live in symbiosis with around 80% of plant species. AMF have been shown to increase plant yield, biomass, disease resistance, and shoot P. Plants exchange carbon in the form of sugars for nutrients assimilated by AMF. There is little known about AMF in association with Miscanthus giganteus, a productive bioenergy crop grown in the UK and abroad. Work was carried out to characterise the abundance, organisation, importance, function and stability over space and time of rhizosphere fungi and AMF in M. giganteus roots. Field samples from Lincolnshire were analysed using staining and molecular techniques, including small subunit rRNA gene terminal restriction fragment length polymorphism, clone libraries and amplicon pyrosequencing, and meta-transcriptomics. M. giganteus was also grown in a number of pot experiments, with various treatments including fungal inoculations and fungicide application. A number of fungal phyla were found in the roots, particularly Ascomycota, the composition of which shifted over time and exhibited diurnal patterns of activity. Fungi enhanced plant growth by a third, and were functionally active in the roots in the meta-transcriptome. AMF communities were found at much lower relative abundances in roots, and inoculation with AMF did not enhance M. giganteus growth. The work highlights the importance of the whole root mycobiome to plant growth and health, and the relatively small role Glomeromycota play in M. giganteus comparison with other fungi. The work also demonstrated the dynamic nature of fungal activity over hours, months, and years, and the complex interactions the fungal community has with environmental variables.

This thesis describes the original and significant development of a hierarchical statistical framework in order to realign fine-scale spatial covariate data. An example of the utilisation of this framework is given within the context of biodiversity modelling. Biodiversity is of utmost importance to the correct functioning of ecosystems and the provision of services vital to humanity. Understanding of the impacts on biodiversity by environmental drivers and pressures can help appropriate responses to be taken, to mitigate, halt or reverse damage to habitats. Therefore, linking biodiversity measures with explanatory covariates in statistical models can help understand these relationships and the extent to which certain drivers and pressures are responsible for environmental change. When modelling biodiversity, the scale at which the variables are measured should be considered. Where data are measured at different scales, a situation of misalignment arises. Misaligned data may be subject to measurement error, which can influence the resultant model, if the data are not realigned. In order to realign covariate data, two transformation approaches can be implemented. The first method is to aggregate the response data to the level of the explanatory covariates. The second method is to downscale the covariate data to the response locations. This realignment process is more complex than aggregation of the response, since it requires the uncertainty estimation of the downscaled covariate predictions. The developed framework has possible further applications in fine-scale uncertainty estimation of model covariates, where the scale at which the covariates are given is coarser than that at which the response data are available. Chapter 1 provides an introduction to the main issues and challenges in the thesis: biodiversity, data measurement, modelling techniques, scale and data realignment. The three case studies used in the development of the hierarchical framework are also introduced. Data from Loch Leven on underwater plants are analysed in chapter 2. Carabid data from ten rural locations are considered in chapter 3. In the final case study in chapter 4, coverage abundance data from sites the Countryside Survey across Great Britain are modelled. In chapter 5 the data from chapter 4 are used as the impetus; a hierarchical framework for realigning covariate data is developed and a simulation is created in order to assess its performance relative to the non-realigned model. Chapter 6 provides a summary of the case studies as well as discussion of the main issues and proposals for additional development.

The oomycete Hyaloperonospora arabidopsidis (Hpa) is the causal agent of downy mildew of Arabidopsis thaliana; a system that can be used as a model for the study of plant-pathogen interactions. In order for successful colonisation, biotrophic pathogens such as Hpa suppress or evade plant defences through secretion of effector proteins into the plant to manipulate and disrupt the host immune system. Alignment of oomycete effector proteins has revealed a conserved amino acid sequence at the N-terminus with the consensus sequence RxLR (arginine, any, leucine, arginine), thus allowing the use of Bioinformatic approaches to identify putative effector proteins in the Hpa genome. Studying effector action and their targets in the host may help elucidate important components of the plant defence response, eventually leading to more durable crops. Expression of the Hpa effector HaRxL21 in planta has been shown to alter host susceptibility to Hpa, Botrytis cinerea and Pseudomonas syringae. Here the interaction targets of HaRxL21 are presented and interaction with the transcriptional co-repressor TOPLESS (TPL) has been validated in planta using BIFC and Co-IP. Using deletion and mutation analysis, the specificity of the interacting protein domains has been identified as between the CTLH domain of TPL and Leucine residues within the EAR motif of HaRxL21. Microarrays have revealed effects of HaRxL21 on host transcription, particularly up regulation of genes involved in ABA signalling and a decreased induction of SA responsive genes upon SA induction. Finally, work has been carried out to determine the biochemical function of HaRxL21, showing an increased stability of TPL in the presence of this effector.

The species of Acaena (Rosaceae) growing on the sub-Antarctic island of South Georgia have been examined from two different aspects - the world level and the insular level. A revision of the taxonomy and synonymy of the two sections of the genus containing A.tenera and A.magellanica has resulted in the reduction to synonymy of many species, and a complete synonymyn for Sect. Acrobyssinoideae Bitt. and for A.magellanica (Lam.) Vahl (which comprises most of Sect. Ancistrum Bitt.) is provided. Morphological descriptions are given for A.magellanica and A.tenera, and for plants from South Georgia which are judged to be the hybrid A.magellanica x tenera. An examination of aspects of generic morphology together with consideration of relevant biogeographical literature has resulted in the conclusion that the genus probably arose from tropical ancestral stock which may have been common to Poterium. Speciation within South America has resulted in a spectrum of types, from primitive woody species with racemic inflorescences and multispined fruits to more highly evolved species with less woody stems, few spined fruits and compact globular heads. Dispersion of the genus from South America has taken place at various times, resulting in different stages of generic evolution. The majority of the Australasian species are found in New Zealand and appear to have a common ancestor. The relationships of other disjunct species were traced and relatively recent long distance dispersal was found to be a satisfactory explanation for most of their distributions. The taxa on South Georgia were shown to be highly evolved. The inter-relationships between them are given in terms of breeding patterns and it is suggested that F1, hybrids are normally formed with A.tenera as the female, whilst F2 and any subsequent generations are probably due to backcrossing to A.magellanica as the male. A.magellanica appears to be generally outcrossing whilst the reverse is true of A.tenera. Examination of floral development showed no evidence of preformation of flowers in the previous season, initiation occurring simultaneously with snow melt at most sites. The rate of floral development appeared to be linked to site aspect. Seed germination studies showed a warm day/cold night regime to be the most effective. A.magellanica seedlings grew at a much higher rate than those of A.tenera, but seedling production on a per head basis was similar for both species. Under a given light regime there was a linear rate of leaf production for both taxa. Rates for seedling establishment in various soils at different sites were seen to correspond to a pattern predictable from the general ecological data for the species. Measurement of changes in standing crop of an A.magellanica community showed it to be highly productive, although the tnojof part of dry matter production was for vegetative rather than flowering tissue. Initial measurements of photosynthetic rates demonstrated marked differences between geographically isolated populations of A.magellanica. A significant rate of photosynthesis was found to occur at and below 0°C. in all the South Georgian taxa. These data were discussed in terms of adaptation of the taxa to South Georgia and the other sub-Antarctic islands, whilst the information gathered on these and other species was used to propose a hypothesis for the origin, evolution and distribution of the genus.

A collection of heritage variety accessions were characterised using Amplified Fragment length Polymorphisms (AFLPs) (200 accessions ) and multivariate analysis of morphological characters (366 accessions); key features of interest for the conservation of Plant Genetic Resources were the identification of diversity within and between accessions. Motivations and practices of heritage variety growers were explored using questionnaires. Heritage varieties are herein defined as traditional crop varieties that have a historical origin of over 40 years, are non-hybrid and non-GMO and are of cultural/heritage value to their users; they are part of the suite of plant genetic resources currently utilised by growers and of potential use to plant breeders in the future. A large range of morphological and genetic diversity was present between accessions in all crops; in addition, diversity was found within accessions, particularly in Vicia faba, Daucus carota and Cucumis sativum. Comparisons between data sets were made for diversity, relationships, comparisons with commercial standards and identifying potential duplicates. The synthesis of both data sets highlighted the three potential duplicates for further investigation by HSL (all in Pisum sativum). The findings highlight the importance of heritage varieties and the Heritage Seed Library, both culturally and in terms of conservation for present and future use.

Detailed descriptions of 3-D anatomically preserved specimens in paleobotany have been undertaken for over 100 years. Some of the most comprehensively characterised of these specimens are reproductive structures, especially cones and ovules. Throughout this time many of the ways of gaining information such specimens has remained static. In recent years new computer software and techniques have been developed that allow detailed 3- D computer reconstructions to be undertaken that allow holistic observations of the context of the whole organ. Detailed 3-D reconstructions have been undertaken of several genera of Palaeozoic and Mesozoic paleobotanical reproductive organs. These complex structures have undergone traditional preparation, such as serial sectioning, preparation specifically for reconstruction such as serial grinding and non-destructive scanning micro X-ray tomography. Reconstructions were then produced in bespoke software, Serial Paleontological Image Editing and Rendering System (SPIERS). The reconstructions produced provide a new understanding to the structure and functions of tissues within paleobotanical reproductive specimens. For the first time, specimens of extinct and extant genera have been compared using new reconstruction techniques in order to aid in the future understanding of their evolution and development, and to aid visualisation of complex structures for which illustrations in 2-D form are inadequate.

This thesis set out to investigate the processes that determine the richness and composition of plant communities on derelict land in the West Midlands. Experimental work included vegetation surveys, soil seed bank investigation, field mapping and seed rain trapping methods. Interpretation of the data involved a range of approaches including vegetation classification and ordination, comparative analysis of plant functional attributes and the development of regression models incorporating landscape and habitat variables. Derelict habitats were identified as holding a diverse array of communities at the early stages of succession which are poorly represented by current vegetation classifications, functional diversity is however much lower in pioneer communities. The majority of these species employing the expected strategies of early succession notably high reproductive capacity and seeds which are small, highly dispersive and form persistent seed banks. Dense seed banks were typically formed on sites and were dominated by a small set of consistently occurring species. Changes in seed bank density and composition were consistent with time represented both by the chronosequence of sites and increasing soil depth. Little evidence was found to suggest that diversity or species composition is linked to site connectivity related to either patch density or the presence of linear features. These findings have considerable implications for application of principles of metapopulation and island biogeography principles to urban conservation. In particular the trend for planners to designate urban wildlife corridors is questioned as being probably of no benefit to native diversity and indeed these features are identified as being instead potentially significant pathways for invasive alien species. The most important factors influencing the composition of sites were seen to be those linked closely with past and present human activity. Particularly significant are the nature of dereliction substrates and haphazard disturbances such as fire and tipping which influence vegetation succession temporally and spatially.

Comparison of seven isolates of rust from leek (Allium porrum), three from chives (Allium schoenoprasum), one from A. scorodoprasum and one from A. babingtonii on the basis of telial and uredinial morphology showed there to be three morphologically distinct species. Application of these criteria to herbarium material confirmed these findings and showed the rust on leeks in the U.K. to be the same species found on European leeks, garlic and certain wild Allium spp. from the Mediterranean. It is suggested that the following names be adopted, viz. Puccinia allii (DC.) Rud. for the rust on leeks, Puccinia mixta Fuck. for the rust on chives and Uromyces ambiguus (DC) Lev. for the rust on A. babingtonii. Infection studies on isolates of each rust supported the morphological evidence, and showed the three species to have different, extensive but overlapping host ranges within the genus Allium. In the ampeloprasum complex, A. kurrat accessions were highly susceptible to leek rust whereas some accessions of A. ampeloprasum and A. babingtonii had high levels of quantitative resistance. There was no evidence of 'hypersensitive-type' resistance in the complex. Tests within one leek cultivar (Musselburgh) showed older plants to be more resistant than seedlings in at least two quantitative components. However leaf tissue appeared to become more susceptible to infection with age, except in the leaf tips, which did not change in susceptibility over time. Inoculation of 16 leek cultivars with leek rust isolates from different geographical areas, and subsequent analysis during the disease cycle of several components of resistance (viz; latent period, pustule density and pustule length) showed that some cultivars performed consistently better against all isolates. However, in most cases there was a considerable and complex cultivar-isolate-component interaction. There was no evidence of physiologic specialisation in the isolates, but low levels of specialisation could have been hidden by the high level of variation in the experiments. Comparison of field cultivars of garlic with equivalent virus-free material using an isolate of leek rust gave inconclusive results, and further study of the rust-garlic-virus interaction is recommended. Major trends in the infection/resistance studies included a high level of environmentally-dependent variation and a lack of 'hypersensitive-type' resistance, even in host species quite distantly related to the normal host.

Mechanical properties of the plant cell wall are important in many industrial applications including biofuels, food quality and biotechnology. The plant cell wall consists of a network of cellulose microfibrils cross-linked with hemi-cellulose and interpenetrated by pectin. It is known that changes in the composition and architecture of the cell wall lead to detectable differences in the mechanical properties, but the relationship is not yet fully understood. In this work, three cell wall mutations of Arabidopsis thaliana, ida, mur1 and qua-2 (Snakeskin/sks), were compared to the Columbia (col0) wild type. Shoot and root growth were characterised to evaluate the effects of the mutations on plant growth. The ida mutation behaved like col0, with mur1 and sks showing increasingly severe effects of mutation on growth. Cells were also grown in suspension culture and an investigation of the wall components of both plant tissue and suspension cultured cells was conducted. An increase in pectin caused by the culturing process, and differences in cellulose content due to the mutations were found. The mean force required to break the suspension cultured cells (the rupture force) and deformation at rupture were obtained by compression testing. Force-deformation data from cell compressions were mathematically modelled up to deformations below the elastic limit of the cell walls, allowing the derivation of a low strain elastic modulus (E). Significant reductions in E for mur1 compared to col0 and ida and between sks compared to ida were observed. Similarities were drawn between the effects of genotype changes at both plant and single cell levels in that mur1 and sks were significantly different to ida and col0 for shoot, root and cell wall material properties.