The history of cytological and genetical studies within the genus Pelargonium, especially P. x Hortorum Bailey, is reviewed, and the practical techniques for handling anal pelargoniums are described. Following the introduction, Part I describes the Mendelian inheritance of alternative traits for characters red spotted pink petals, White-eyed pink flowers, golden leaf, flower doubleness and nectary spur, male sterility, leaf zonation patterns, and flower colours; at least 16 genes are involved. An examination of the extranuclear character plastid inheritance in Part II led to the new hypothesis, that the switch between alternative patterns of plastid segregation after G x W plastid crosses was determined by the presence of both dominant alleles versus absence of either dominant allele of two nuclear genes. Finally, in Part III, many of the genes described in Part I and II are tested in various combination for their independent assortment. The complete linkage of the genes for flower doubleness and nectary spur could not be distinguished from the pleiotropic effect of one gene. There was no evidence for even partial linkage of any other genes.

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Heat shock transcription factors (HSFs) play an important role in providing plants with tolerance or resistance to various environmental stresses. It was proposed that the Clade A1 HSF group may encode the "master regulator(s)" of both the abiotic and biotic stress response, and they were also implicated in growth and development. The number of HSF genes within the Cia de A1 group is highly variable between species, with Arabidopsis having four members compared to Oryza having one equivalent homo log. Previous studies suggested that the Arabidopsis Clade A1 group may have redundant roles in both the stress response and development. The main aim of this study was to determining the functional significance of having multiple Clade A1 HSF homo logs as key transcriptional activators in both the abiotic and biotic stress response. This was done using a physiological approach under non-stressed and stressed conditions and a comparative gene expression approach, with loss of function and over-expressing HSF mutants. Members of the Clade A1 HSFs influenced basal thermotolerance, basal resistance, and plant growth and development. Comparing the gene expression results with those of physiological experiments, it appears that although the Clade A1 HSFs may have specific regulatory roles, there is still a significant level of redundancy and complementation. Three key proteins involved in both stress and development were common to all Clade A1 HSFs, HSP90.1, ROF2 and HSP70. All Clade A1 HSFs appear to be involved in ABA stress signalling, with HSFAlb being the most divergent in gene expression and having a key role in immunity and oxidative stress signalling, and HSFAla and HSFAle involved in growth, abiotic and biotic stress signalling. These results suggest that the Clade A1 HSFs function together as key master regulator to both abiotic and biotic stresses in addition to playing an important role in plant growth and development.

Floral organ detachment takes place at a specifically programmed stage during development. However, sepals of the mutant hawaiian skirt (hws-l) fail to shed and are retained until silique desiccation. The mutant is a consequence of a 28bp deletion in the ORF of the F-box gene At3g61590, which is part of one of the three core subunits of the SCF complex of plant ubiquitin E3 ligases (Gonzalez-Carranza et al., 2007). To dissect the role of HWS in regulating plant development, hws-l seeds were mutagenized with EMS and a series of F2 populations were obtained. The 35.1, a suppressor line was identified and studied in detail. The mapping of the 35.1 showed that the mutated gene is located in the APETALAl (At1g69120) gene locus and sequencing analysis showed an amino acid change from Ser to Phe in the conserved MADS box domain. To confirm this observation, a 35.1/hws-l plant was crossed with an ap1 T-DNA insertion line (NASC ID: N651561) and the phenotype of ap1 is observed in the progenies. qPCR was performed to detect expression of genes involved in the hypothesised regulatory network and indicated that HWS may play a role in repressing APl expression. This regulatory network is likely to control sepal boundary formation with a CUCl and CUC2 related regulatory network.

This study is the first to define the S. violaceoruber species group and shows that a number of named species including S. coelicolor, S. lividans and S. griseoruber, amongst others, to be the same species, forming a tight clade in a multigene analysis. Comparisons were made to strains of S. grisells to determine the overall similarity in the context of studying horizontal gene transfer of the streptomycin biosynthetic gene cluster. All type strains grouping with S. violaceorllber-are considered to be synonyms of this species. Phylogenetic analysis was done using the house-keeping genes 16S rRNA, gyrB, recA and tlpB. Genes for adaptive functions were also used and these included those for chiF (chitinase) and strA (streptomycin resistance), which provide an adaptive function to the organisms. Soil isolates identified as S. platensis, S. limoslls and S. violaceorllber were found to contain either partial or the entire streptomycin gene clusters. In isolates closely related to S. grisells the location of the streptomycin cluster was the same as that in the type strain S. grisells DSM 40236. Analysis of CR20 (8. platensis), 651 (S. limoslls) and ASB37 (S. violaceoruber) indicated that the streptomycin cluster was in a different position compared to S. griseus DSM 40236. The exact location of the streptomycin cluster on the chromosomes of these strains has yet to be elucidated. Algorithms used to determine gene histories were applied to the gene sequences of the house-keeping genes and cMF and strA and analysis confirmed· gene transfer ofstrA from a putative S. griseus source to soil isolates identified as being phylogenetically distinct from S. grisells. strA gene sequences demonstrated this gene to have a significantly different gene history from the house-keeping genes and that it was evolving at a much faster rate. This study also placed chiF with the house-keeping genes and confirmed previous findings that chiF is an ancient gene transfer event into the Streptomyces genome and which has ameliorated over time. The statistical analysis of the phylogenetic trees was able to identify a core set of genes that can be used for phylogeny and that have not been subjected to transfer events. S. coelicolor A3(2)(W) and ASB37 were found to be closely related to S. coelicolor M145, however these strains differed in their phenotypic properties. Comparative genomic hybridisation between S. coelicolor A3(2)(W) and ASB37 against S. coelicolor M145 have revealed extensive genetic differences which correlated with the observed phenotypes.

Plants exhibit significant developmental plasticity due to their sessile nature. A complex network of signals controls this development. The aim of the research described in this thesis was to use a genetic screen to isolate a mutant of Arabidopsis thaliana that exhibited an enhanced seedling de-etiolation phenotype in more than one monochromatic light condition thus isolating a repressor of photomorphogenesis that operated downstream of multiple photoreceptor families.

Methods for the extraction of uncompleted host RNA from turnip yellow mosaic virus infected Chinese cabbage plants and for the electrophoretic fractionation of ribosomes, ribosomal sub-units, polyribosomes and virus particles are described and characterised. The changes that occurred in ribosomal RNA fractions and in polyribosome status of sequentially ageing leaves of uninfected and TYMV-infected Chinese cabbage plants were examined using these techniques. The peak accumulation of chloroplast and cytoplasmic ribosomal RNA occurred at different times in the young leaves but following leaf maturity both fractions declined at a similar rate. The high levels of polyribosomes observed in the youngest leaves fell during leaf expansion to a level that was largely maintained after full leaf expansion was achieved. The effects of the virus on these patterns of change were attributable to its effect on chloroplast metabolism and periods of multiplication. The senescence of excised leaf discs was also studied and differences in the patterns of change of ribosomal RNA were found between different incubation treatments. Retardation of senescence of the leaf discs by lightor kinetin principally affected levels of cytoplastic ribosomal RNA. A different pattern of senescence in excised leaf discs and attached leaves was observed with an accelerated rate of loss of chloroplast ribosomalel RNA in the former. Kinetin was seen to elicit a different pattern of response in TYMV-infected discs compared to uninfected discs.

Plants produce a wide range of complex secondary metabolites that have many applications, for example as pharmaceutical agents. Gene discovery and the elucidation of these unique biosynthetic pathways is challenging since many of the enzymatic transformations are unprecedented. In Catharanthus roseus, the sole producer of the valuable anti-cancer compounds vinblastine and vincristine, the biosynthetic pathway for these alkaloids is highly complex and crucial steps are still unknown. Recently, the tight transcriptional co-regulation of the early part of this pathway enabled discovery of some of the central enzymatic steps by analysing the gene co-expression patterns and testing potential candidates using virus induced gene silencing. Additionally, it has become apparent that some plant secondary metabolite pathways exhibit physical clustering of pathway related genes in the genome. This thesis highlights how both strategies of gene discovery can be applied for the targeted discovery of genes for missing steps in biosynthesis of non-model plants. Co-expression analysis to identify candidates and subsequent testing of these candidates using virus induced gene silencing has led to the discovery and subsequent characterisation of the enzyme tabersonine 3-oxygenase (T3O), a key oxidation step in vindoline biosynthesis. This thesis furthermore reports the first C. roseus whole genome sequence. Additionally a BAC library was obtained and selected BACs sequenced. Analysis of the combined sequencing data established that gene clustering does indeed occur for alkaloid biosynthesis in C. roseus and yielded a new set of candidates for so far unknown pathway enzymes. Selected candidates have been tested by silencing or expression and results are discussed. The sequence information provides a valuable resource for the wider community, available as a searchable, publically available database (http://medicinalplantgenomics.msu.edu/). The work presented in this thesis highlights how next generation sequence data can be exploited to elucidate complex secondary metabolic pathways.

Understanding plant responses to environmental stresses is a key strategy to meet the challenges of food security, adequate nutrition and sustainable agriculture. Environmental stresses limit plant growth and crop yields. In this thesis, the roles of Late Embryogenesis Abundant 5 (LEA5) and Ethylene Responsive Factor 109 (ERF109) in plant growth and stress tolerance were investigated. These two genes are involved in the regulation of plant redox processes. LEA5 was previously shown to provide tolerance to oxidative stress. Furthermore, previous studies using transgenic A. thaliana found that the over-expression of LEA5 resulted in plants with a greater biomass. However, the precise functions of LEA5 in these processes are unknown. In this thesis, genetic and protein interaction approaches were used to investigate the role of LEA5. Protein interaction studies, which used tandem affinity purification (TAP) of protein complexes combined with mass-spectrometry revealed several LEA5 interacting partners, including genes associated with stress tolerance. Transgenic crops provide a promising avenue to reduce yield losses, improve growth. Homozygous transgenic barley plants expressing LEA5 were found to have an altered shoot phenotype compared to WT barley plants. ERF109 is part of a regulatory network that has a major role in the adjustment of A. thaliana leaves to reach homeostasis after high-light stress. Understanding the roles of transcriptional regulatory networks and their effects on downstream target genes will aid in the development of stress tolerant crops. Phenotype analysis of erf109 mutants presented here suggest that ERF109 has a role in the control of shoot growth in the absence of stress. Moreover, protein interactions of ERF109 were elucidated using TAP, a number of which might explain the phenotypic characteristics of the erf109 mutants. Taken together, this information could be used in breeding programmes to improve the predictability and sustainability of crop yields by enhancing stress tolerance.