Nodules and lateral roots are both key organs for the uptake of nutrients by plants. During nodulation, leguminous plants form root nodules, housing symbiotic Rhizobial bacteria able to fix atmospheric nitrogen, allowing the plant to utilise it. Lateral roots are formed by all plants and allow the root system to be extended laterally, increasing the region of soil from which nutrients may be taken up. Formation of lateral roots and nodules share developmental features such as single cell-type origins of the primordia, and hormonal and nutrient regulatory mechanisms, so it is hypothesised that the evolution of nodulation co-opted elements of pre-existing genetic mechanisms of lateral root formation. To test this hypothesis, Arabidopsis thaliana (non-legume) genes similar to known Medicago truncatula (legume) nodulation genes were screened for phenotypic effects. Mutants of Arabidopsis NODGS and a GRAS-domain SCR-like transcription factor were found to confer lateral root phenotypes, suggesting evidence for the co-option hypothesis. The mutants were examined further using cell-type specific transcriptomics through Fluorescence-Activated Cell Sorting (FACS) to identify genomic components underlying the possible co-option. For the purposes of future research, the translation of FACS transcriptomics to Medicago was evaluated, validating microarray probe design for the most recent genome annotation but also highlighting challenges faced in analysing more complex plant roots. The GRAS-domain SCR-like transcription factor mutant was found to modulate lateral root development through pathways involving the phytohormone gibberellic acid (GA). Treatment with GA rescued some components of the GRASdomain SCR-like transcription factor phenotype, indicating a potential role for the gene in activating GA biosynthesis. A second mutant, of NODGS, was also found to affect lateral root development with some dependence on nitrate level. Existing knowledge suggested a role in root morphogenesis and flagellin-triggered signalling, and this work implies a level of cell-type specificity in gene function.

Studies on the molecular organisation and properties of the first three enzymes of pyrimidine biosynthesis, carbamoyl phosphate synthetase (CPTase), aspartate transcarbamoylase (ATCase) and dihydroorotase (DHOase), in various organisms have been reviewed. The molecular organisation of these three enzymes has been investigated in wheat using gel filtration chromatography. CPSase activity could not be detected in gel filtered extracts and in crude extracts from wheat seedlings was shown to be highly labile. ATCase and DHOase activity was detected and the molecular weights of these enzymes were estimated to be 1.03 x 105 ( 1.4 x 10^4) and 8.6 x 10^4 (6 x 103), respectively. At no time during these investigations were high molecular weight species (consistent with the presence of a multifunctional complex containing these enzymes) detected. During the course of these investigations, a protease was detected which was shown to co-migrate with ATCase and DHOase activities. This protease was shown to be insensitive to the serine protease inhibitor PMSF, but was partially inactivated by iodoacetamide, consistent with the protease being a member of the cysteinyl protease family. Inclusion of iodoacetamide during chromatography also failed to reveal high molecular weight species of these enzymes. Antisera were raised against purified wheat ATCase and were characterised by their ability to inactivate the enzyme. These antisera were then used to probe western blots of crude extracts from wheat seedlings and screen a wheat cDNA expression library to ATCase sequences. Western blotting failed to show any immunoreactive species in extracts prepared under conditions which suppressed protease activity (SDS, -mercaptoethanol), although a low molecular weight (approximately 3.7 x 10^4) ATCase could be detected in samples obtained after gel filtration chromatography. Antisera also showed very little cross-reactivity with the ATCase from E.coli a result consistent with studies on the enzyme from B. subtilis.

Plants as sessile organisms have adapted highly sophisticated cellular processes to cope with environmental stress conditions, which include the initiation of complex transcriptional regulatory circuits. The heat shock transcription factors (HSFs) have been shown to be central regulators of plant responses to abiotic and biotic stress conditions. However, the extremely high multiplicity in plant HSF families compared to those of other kingdoms and their unique expression patterns and structures suggest that some of them might have evolved to become major regulators of other non-stress related processes. Arabidopsis thaliana HSFA1b (AtHSFA1b) has been shown to be a major regulator of various forms of plant responses to abiotic and biotic stresses. However, it has also been suggested that overexpression of AtHSFA1b results in a subtle developmental effect in Arabidopsis thaliana and Brassica napus in the form of increased seed yield and harvest index. Through genome-wide mapping of the AtHSFA1b binding profile in the Arabidopsis thaliana genome, monitoring changes in the AtHSFA1b-regulated-transcriptome, and functional analysis of AtHSFA1b in Saccharomyces cerevisiae under non-stress and heat stress conditions, this study provides evidence of the association of AtHSFA1b with plant general developmental processes. Furthermore, the outcome of this research shows that AtHSFA1b controls a transcriptional regulatory network operating in a hierarchical manner. However, in an agreement with a previously suggested model, the results from this study demonstrate that the involvement of AtHSFA1b in the regulation of heat stress response in Arabidopsis thaliana is possibly limited to the immediate and very early phases of heat stress response which also results in a collapse in its transcriptional network which seems to be accompanied by a general shutdown in plant growth and development.

Crop wild relatives are important for agriculture due to the genetic richness they possess. They have been used in plant breeding to develop high yielding varieties; varieties with improved resistance to biotic and abiotic stresses, and enhanced nutritional content. Securing their conservation in the long-term is critical to enable the continuous development of crops’ varieties able to respond to future challenges. The work presented in this thesis is a contribution to the effort of understanding the ex situ conservation gaps of crop wild relatives, their expected response to climate change and their needs for conservation. Methods used in this thesis include species distribution modelling, gap analyses, a case study assessing the preliminary IUCN Red List categories, species distribution projections onto future climate change scenarios, and an estimation of the global value of crop wild relatives based on their likelihood of being used in plant breeding, and the contributions of their associated crops to human diets and agricultural production systems. The methods used here can be applied to more crop genepools for global conservation planning, and can also be adapted for analysis at the regional and national level. The results presented here are being used to improve the conservation of the wild relatives of 29 crops.

DNA topology is dependent on axis proteins during eukaryotic cellular processes. Chromosome axis organization is complex during meiosis, when DNA repair needs to be coordinated with homology searching and synapsis. Although roles for the axis component Topoisomerase II (TOPII) and the post-translational modification (PTM) of ASY1 homologues during meiosis have previously been reported, few studies have been performed in plants. The aim of this thesis is to investigate the effects of these proteins on meiotic DNA topology and axis morphology, and their implications for homologous recombination (HR) in Arabidopsis thaliana. Using a combination of cytogenetic and molecular techniques, we show the role of PTM of ASY1 differs from that of its budding yeast orthologue. Phosphorylation of a plant specific set of residues in ASY1 affected chiasmata distribution. Analysis of the first TOPII mutants described in plants also revealed a link with HR. Chromosome replication, condensation and segregation phenotypes were consistent with previous studies of TOPII in other organisms. For the first time, we report that TOPII and chromosome movement collaborate in interlock resolution during meiosis, confirming predictions from decades ago. Overall, these investigations have revealed new roles for the axis in plant meiosis, which could have potential for crop breeding.

Plant performance under reduced water availability has traditionally been assessed as drought resistance and more recently as water use efficiency (WUE). An extensive body of work has been established over the past 15 years where the natural variation of water use efficiency has been studied in the model species Arabidopsis thaliana (Arabidopsis). At the same time, a substantial degree of criticism has arisen with respect to the use of drought resistance and WUE as measures of plant performance, due to the lack of relatedness of these parameters to reproductive performance, i.e. yield. The work in this thesis is centered on understanding the physiological and genetic basis of water use and water productivity as alternative measures of plant performance under the context of reduced water availability. The first part of this study describes an extensive assessment of the natural variation of water use and water productivity in Arabidopsis in relation to numerous key physiological, phenological, and developmental parameters. Furthermore, this work concisely relates plasticity of key traits to historical climatic variation. A fundamental aspect of this work was the clarification that it is possible to estimate long term water use to a high degree of accuracy based on short term water use, i.e. soil drying rate, and flowering time. Flowering time was demonstrated to be the predominant driver of vegetative performance and water use, however it appeared to be genetically uncoupled from reproductive performance. This is in contrast to previous work that suggests WUE, measured as the ratio of C12 to C13 isotopes (δ13C), is positively associated with flowering time. Additionally, it was demonstrated that multiple commonly employed proxies of reproductive performance including total biomass, WUE, and flowering time, were not sufficient at predicting seed yield in Arabidopsis across multiple environments. The second part of this study involved the genetic dissection of water use and productivity related traits in Arabidopsis through a quantitative trait loci (QTL) mapping study and a genome wide association study (GWAS). QTL mapping using a recombinant inbred line (RIL) population developed from the ecotypes Col-0 and C24 revealed two key flowering time genes, FLOWERING LOCUS C (FLC) and FRIGIDA (FRI), as key regulators of water use. It was demonstrated that a combination of non-functional alleles of both FLC and FRI reduced long term water use via a shorted life cycle, which is again in contrast to previous work relating to the genetic dissection of WUE in Arabidopsis. Crucially, it was observed that reduced water use mediated in this fashion did not detrimentally impact upon reproductive performance. GWAS was employed subsequent to the QTL mapping in order to identify candidate genes underlying the variation for productivity as a unique trait and also as a factor of water use, i.e. water productivity. GWAS identified multiple promising candidate genes that potentially underlie the heritable genetic variation for flowering time, water use, and water productivity.