Changes in cellular redox status are implicated in the regulation of developmental and defence-related responses. The absence of S-nitrosoglutathione reductase (GSNOR) function in Arabidopsis leads to an accumulation of cellular S-nitrosoglutathione (GSNO), a mobile reservoir of nitric oxide (NO) which impacts the cellular redox tone. Consequently, the GSNOR knockout mutant, atgsnor1-3 displays defects in growth, time to flowering and pathogen resistance. Although it is now well established that GSNO is a key redox signalling molecule, the molecular mechanisms that underpin GSNO function remains largely unknown. RAP1 (REDOX-ASSOCIATED PROTEIN 1) was identified based on its dynamic changes of expression in atgsnor1-3 and sid2 plants upon avirulent Pseudomonas syringae pv. tomato (Pst) DC3000 (avrB) challenge. Pathogen-induced RAP1 expression was shown to be independent of the plant hormones salicylic acid, jasmonic acid, abscisic acid and ethylene. Recombinant RAP1 protein was shown to exhibit E3 ligase activity in vitro. Application of the NO donors (GSNO and Cysteine-NO (CysNO)) reduced the E3 ligase activity of RAP1 significantly. Biotinswitch analysis showed that RAP1 was S-nitrosylated and site-directed mutagenesis of RAP1 suggested that the S-nitrosylated site is the cysteine residue C325. The rap1 line does not show obvious developmental phenotypes, however, overexpressing RAP1 enhanced lateral root branching in young seedlings. Overexpression of a truncated RAP1 (RAP1ΔRING) led to a loss of apical dominance. In addition, rap1/rap2 double mutants showed delayed flowering, suggesting RAP1 might be involved in the regulation of plant growth and development. RAP1 may also be involved in plant defence, as rap1, rap2 and rap1/rap2 mutants exhibited increased susceptibility to PstDC3000 and Arabidopsis powdery mildew. Interestingly, rap1 plants showed enhanced resistance to methyl viologen (MV), which is in line with the phenotype of atgsnor mutants. Also, expression of RAP1 was rapidly inducible by ultraviolet-B (UV-B) light. As RAP1 expression and RAP1 E3 ligase activity are redox-related, it is speculated that RAP1 may be involved in redoxmediated regulation of a broad range of physiological responses.

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The genus Sorbus is an example of a taxonomically complex group (TCG) with diversity derived from hybridisation, polyploidy and apomixis. The focus of this study was to elucidate the evolutionary relationships among nine Sorbus species including endemics of the Devon and north Somerset region of the south west UK, determine main routes of polyploid formation and investigate reproductive sustainability in order to make recommendations for Sorbus conservation. Molecular analysis showed that genetic structure patterns and genotypic diversity support the hypothesis that the study polyploids are a product of rare interspecific hybridisation, of single origins and are maintained through apomictic reproduction. PCoA, Neighbour Joining analysis and parental simulations reveal a reticulated relationship, with diversification the result of hybridisations between sexual diploid Sorbus torminalis and both tetraploid and triploid species. Hybridisation between S. torminalis and tetraploid Sorbus margaretae (subgenus Aria) have likely given rise to the study members of subgenus Tormaria through production of a triploid which has subsequently backcrossed to Sorbus torminalis to form further tetraploids. The discovery of a cryptic hybrid in subgenus Aria also suggests occasional hybridisation events among tetraploids are a possible route for further tetraploid formation These events illustrate key routes of polyploid formation, both illustrating the role of triploids in tetraploid formation via the triploid bridge and the key role in sexual diploids in diversification in Sorbus. Hand pollination experiments showed that self-incompatibility in the triploid species (Sorbus subcuneata) means reliance on congeneric pollen from sympatric tetraploid species for seed production. Reproductive sustainability in this species is severely compromised through spatial isolation from compatible congeners. Our findings are strong support for the development of conservation strategies that aim to safeguard current diversity through actions that increase reproductive sustainability and recruitment opportunities, and promote opportunities for on-going hybridisation for future diversification of Sorbus in this region.

Our planet is growing rapidly in population and with that comes a demand for resources. To address issues in food security, scientists are looking to the underground parts of plants for novel mechanisms that will eventually lead to enhanced crop traits. Scientists are examining the underlying genetic frameworks to identify which genes play key roles in specific developmental processes. In this study we examined the model plant Arabidopsis thaliana as the roots are easily visualised, the genome has been sequenced, and there are many tools broadly available to work with. This thesis has used a multidisciplinary approach to uncover the signalling cascades revolving around the small signalling peptide RALF34, which is significantly involved in primary and lateral root growth. We have demonstrated, in the following chapters that RALF peptides are inherent to normative lateral root initiation, potentially regulated through shoot derived auxin. Furthermore, RALF4 and 34 peptides play a strong role in restricting primary root growth, and that together these peptides have an additive effect on cell elongation. Lastly, we identify several leucine-rich repeat receptor-like proteins, kinase proteins, and cell wall remodelling enzymes, which putatively play unique and diverse roles during primary and lateral root development. Taken together, this thesis provides novel and unique insights into new signalling pathways during root growth, which may in future aid in agronomic enterprises.

Programmed Cell Death (PCD) is an essential process utilised for the defence and development of all multicellular organisms. In plants however, relatively little is known about the genes involved with the regulation and execution of this process. In particular, even less is known about the molecular components which act high up in the PCD pathway. In this thesis, we carried out an investigation into the novel peptide-encoding gene KISS OF DEATH (KOD). In Arabidopsis, KOD was found to be involved with mediating the elimination of the suspensor, an organ which undergoes developmental PCD. Two mutant alleles of KOD showed reduced PCD in both the suspensor and during heat-shock induced PCD of root hairs. Over-expression of KOD in plant tissues was sufficient to cause death in leaves or whole seedlings and involved the activation of caspase-like proteolytic activity. KOD-induced PCD was found to require light in leaves and is also sensitive to the PCD suppressor genes AtBI-1 and P35. We suggest that KOD acts high up in the PCD cascade as its expression resulted in depolarisation of the mitochondrial membrane, which is an early step in plant PCD. KOD appears to be a plant-specific peptide that is sufficient to induce PCD in Arabidopsis in the absence of external triggers. Typical BLAST searches yielded no obvious homolog for KOD, therefore a bioinformatics screen of the Arabidopsis genome was carried out. This screen for small genes similar in size to KOD enabled us to detect 10 previously unidentified genes, one of which may represent a putative KOD homolog. In summary, KOD appears to be a novel pro-PCD component of the Arabidopsis cell death machinery and represents the first plant peptide to be involved with a form of developmental PCD.

Photoacclimation is a process by which photosynthetic capacity is regulated in response to environmental adjustments in terms of light regime. Photoacclimation is essential in determining the photosynthetic capacity to optimize light use and to avoid potentially damaging effects. Previous work in our laboratory has identified a gene, gpt2 (At1g61800) that is essential for plants to acclimate to an increase in growth irradiance. Furthermore, we observed that the accession Columbia-0 (Col-0) is unable to respond to increases in light. Therefore, a Quantitative Trait Locus (QTL) mapping analysis was performed in Landsberg erecta (Ler)/Columbia (Col) recombinant inbred line population to identify novel genes responsible for this variation to acclimation. In order to investigate the photoacclimation in Arabidopsis thaliana, photosynthetic capacity was measured in plants of the accession Wassileskija (WS) and in plants lacking expression of the gene At1g61800 (WS-gpt2) during acclimation from high to low light. Plants were grown for 6 weeks under high light (400 μmol.m-2.s-1) and half of them were transferred to low light (100 μmol.m-2.s-1) after six weeks. Gas exchange measurements were performed in order to measure the maximum capacity for photosynthesis. Acclimation to a decrease in light resulted in a decrease in the photosynthetic capacity in WS and WS-gpt2 plants. This shows that under lower or limiting light, photosynthesis was slowed down. Chlorophyll fluorescence analysis was carried out to measure changes in the quantum efficiency of PSII (ΦPSII) and non-photochemical quenching (NPQ) during acclimation. ΦPSII decreased in both WS and WS-gpt2 plants showing that under low light, PSII is more saturated. However, it was found that there was no significant changes in NPQ level for both WS and WS-gpt2. To estimate the total chlorophyll and chl a/b ratio, a chlorophyll composition analysis was performed. There was no significant changes in the total chlorophyll for both WS and WS-gpt2. However, the chlorophyll a/b ratio was seen to be decreased in low light plants representing an increase in light harvesting complexes relative to reaction centre core. Plants of WS and WS-gpt2 were also grown under natural variable light in an unheated greenhouse in Manchester, UK. This experiment was carried out to study the photosynthetic acclimation of plants under fluctuating light condition. A preliminary work on gene expression of gpt2 was conducted by doing reverse transcriptase PCR (RT-PCR). It shows that the gene expression of gpt2 decreased following transfer to low light plants in WS. Microarray analysis was also performed to investigate the role of GPT2 (if any) and to identify any potential gene that is important in high to low light acclimation.

Investigations were carried out into the allelopathic potential of the invasive alien annual Himalayan Balsam (Impatiens glandulifera Royle) using a series of bioassays, including ones developed or adapted for this study. They were evaluated for their suitability to detect three of the four main modes of allelochemical release, namely leaching, exudation and decomposition. Assays which involved the measurement of lettuce radicles and hypocotyls gave reliable results and allowed a range of different Impatiens material, both living and dead, to be assessed and ranked according to the allelopathic effects demonstrated. Attempts were made to isolate resource competition from allelopathy using separately grown but connected donor and receiver plants and a density dependent design where single I. glandulifera plants were grown in pots with variable numbers of receiver plants. Results proved inconclusive. Initial experiments showed that the allelopathic potential of I. glandulifera varied according to the organ from which the material was derived. Pods, leaves and stems produced the greatest inhibition of lettuce seedlings. Effects on germination were not significant at most of the concentrations tested. Live roots of I. glandulifera plants produced pronounced orange staining of the agar into which they were placed and showed clear evidence of distance dependent inhibition of lettuce radicles. Effects were limited to growth rather than germination of the test plants. Germinating I. glandulifera seeds caused a significant inhibition of lettuce radicle elongation when the two species were grown together in an agar medium. The inhibitory effects increased significantly with increasing exposure time. Increasing I. glandulifera seedling number also produced significant reductions in lettuce radicle length. Dormant seeds, by contrast, stimulated growth. Dead seeds did not produce significant changes to the growth of the test plants. When rhizosphere soil was gathered from pot grown I. glandulifera plants, the results were mixed. Initial samples inhibited growth, whereas those collected from dying plants over a period of weeks stimulated growth. Further experimentation is required before the indications of allelopathic interactions demonstrated here can be applied to the behaviour of wild populations of I. glandulifera.

As plants are sessile organisms, processes controlling plant growth and development must react to fluctuations in the external environment to aid plant survival. However, as the climate of the Earth changes and becomes more extreme, plants become less able to develop to their optimal capacity and this can have an adverse effect on crop yield and biofuel feedstock production. Thus, it is becoming increasingly important to understand the molecular mechanisms used by plants to respond to external stimuli. One important system that plants utilise in their response to environmental fluctuations is the circadian clock. The circadian clock is a time-measuring device that buffers the timing of plant growth and development against fluctuations in the local environment, such as temperature, light quality and light intensity. Importantly, the circadian clock is also able to measure day-length (photoperiod). Thus, plant development and growth is co-ordinated with photoperiod that is closely linked to seasonal changes. A key example of this is the time taken for a plant to flower. Flowering of Arabidopsis thaliana occurs specifically in long-days (LDs) of spring/summer months. Thus, the circadian clock is a key regulator promoting flowering in LD conditions. In conjunction with experimental studies, mathematical modelling has proven to be a successful method of elucidating the mechanisms that underlie complex biological systems. One example of this 'systems biology' approach is in uncovering the components that make up the Arabidopsis circadian clock mechanism. Previous research in our group has also led to the development of a model describing photoperiodic flowering that is tentatively linked to the circadian clock mechanism. In this thesis I shall develop on these models to highlight five key results: 1. using rhythmic PHYTOCHROME INTERACTING FACTOR 4 (PIF4) and PIF5 mRNA as an example, I shall show that multiple circadian regulators are required to describe rhythmic transcription of target genes across multiple photoperiods; 2. the stabilisation of CONSTANS (CO) protein by the blue light-signalling component FLAVIN-BINDING, KELCH REPEAT, F-BOX 1 (FKF1) is required to for flowering in LDs and has a relatively larger impact on photoperiodic flowering than FKF1-dependent degradation of CYCLING DOF FACTOR 1 (CDF1), an inhibitor of flowering; 3. multiple components of the circadian clock play specific post-translational roles in photoperiodic flowering to promote the acceleration of flowering specifically in LDs; 4. temperature regulation of photoperiodic flowering can be explained through an interaction between CO and PIF proteins, limiting the effects of temperature to a specific time-window in a 24-hour day; 5. red light- and temperature-control of the circadian clock can be explained by altering the post-translational regulation of circadian clock components.