Slipper orchids (subfamily Cypripedioideae) comprise five genera; Paphiopedilum, Cypripedium, Phragmipedium, Selenipedium, and Mexipedium. Phylogenetic relationships of the genus Paphiopedilum, were studied using nuclear ribosomal ITS and plastid sequence data. The results confirm that Paphiopedilum is monophyletic and support the division of the genus into three subgenera Parvisepalum, Brachypetalum and Paphiopedilum. Four sections of subgenus Paphiop edilum (Pardalopetalum, Cochlopetalum, Paphiopedilum and Barbata) are recovered with strong support for monophyly, concurring with a recent infrageneric treatment. Section Coryopedilum is also recovered with low bootstrap but high posterior probability values. Relationships in Barbata remain unresolved, with short branch lengths and narrow geographical distributions suggesting it may have undergone rapid radiation. Genome sizes were measured for seven taxa in Paphiopedilum and chromosome and genome size data mapped onto the phylogenetic framework, showing no clear trend in increase in chromosome number in the genus. The diploid chromosome number of 2n = 26 in subgenera Parvisepalum and Brachypetalum suggests it is the ancestral condition, with higher chromosome numbers in Cochlopetalum and Barbata pointing to centric fission possibly having occurred independently in these sections. Although species in Barbata have larger genome sizes than other sections, any trend of genome size evolution remains unclear in the genus. Eight primer pairs for plastid microsatellites were designed from consensus sequences generated from different genera, most of them shown to be applicable across the subfamily. High levels of variation in allele size were observed at interspecific levels but at intraspecific level, low levels were observed in Cypripedium calceolus. The application of plastid microsatellites for population genetic analyses in C. calceolus was limited because few of them are polymorphic and low numbers of alleles were detected. Results were generally congruent with a previous study. Within the limits of this data, the plastid haplotype distribution of C. calceolus in western and northern Europe could indicate possible recolonisation routes from three main refugia, following glaciations. Size variation has also been detected in other species in some markers but sampling was sparse.

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The published work submitted for consideration for the degree of Ph.D. (by Research Publication) consists of two parts of the Flora of Bhutan, describing the monocotyledons (some 942 species) with the exception of Orchidaceae. Together with these are ten precursor papers relating to these parts of the Flora: the papers include descriptions of new species, nomenclatural discussion (including typifications) and phytogeographic information. The critical review gives the historical background for the whole Flora project, together with the methods used in my own contribution and some of my more interesting findings. An enumeration of new taxa described, and new combinations made, is given in an appendix.

The overall aim of this thesis was, to evaluate the potential of molecular markers, specifically SNPs and microsatellites, within DUS (Distinct, Uniform and Stable) testing of Lolium species. In the current DUS testing system new candidate cultivars are compared to all existing cultivars in common knowledge which is very labour intensive and expensive. As candidates pass, they become part of the reference collection. The reference collection is reaching an unmanageable size; therefore alternative testing methods are being sought. Initially morphological data for 23 cultivars comprising of Lolium perenne, L. mutiflorum, L. hybridum and Festulolium was analysed to define the relationships between them. The species grouped together, with the hybrids linking with the Italian ryegrasses. The exception to this rule was the hybrid Foyle, which linked more closely with the perennial ryegrasses. Another exception was the perennial ryegrass Bealey that linked more closely with the Italians. These groupings were then used to evaluate how successful the molecular markers were at replicating the same relationships. Initially, cytoplasmic diversity was analysed using Single Nucleotide Polymorphisms (SNPs). SNPs were ascertained from individuals within the sample set of cultivars. Screening for these SNPs highlighted species separation, but individual cultivars could not be identified. Again, Bealey linked with the Italian ryegrass cultivars. Patterns of cytoplasmic diversity were then analysed using microsatellites. Again, the split between L. perenne and L. multiflorum was marked, with Bealey as an exception. Further investigation into the cytoplasmic diversity was carried out, specifically the 'potential for identifying Essentially Derived Varieties (EDVs). Use of markers in this way relies on a low mutation rate over the loci, which was not the case in this study. The findings of the study are discussed with respect to the utility of cytoplasmic markers as a complement to the DUS testing system, and future directions suggested.

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Second generation biofuels are seen as a sustainable solution to the problem of dwindling fossil fuels stocks. However, the process of converting lignocellulosic biomass to sugars for fermentation is expensive due the recalcitrance of these materials to enzymatic digestion. The identification of quantitative trait loci (QTL) in the model grass species Brachypodium distachyon was undertaken in order to improve our understanding of genes that affect straw digestibility. Initially, the study focused on the analysis of natural accessions to determine if there was variation, in terms of digestibility and cell wall composition, within the species and to identify lines suitable for producing recombinant inbred lines (RILs). This information was successfully used to initiate the production of a RIL population that can be used in future research. I made use of a pre-existing RIL population produced previously from a bi-parental cross between Bd21 and Bd3.1 to study pathogen resistance. This RIL population was screened for straw digestibility using a semi-automated robotic platform. This data together with the genotype data was used to identify QTL linked to digestibility. A single QTL was detected on chromosome 5 together with a further QTL on chromosome 3 that acted in epistasis. A candidate gene for each of the QTLs was identified by reviewing those located within the QTL regions. The chromosome 5 candidate gene encodes a glycosyl hydrolase family 43 family protein likely involved in xylan biosynthesis and the chromosome 3 candidate gene is a cellulose synthase-like subfamily A protein that has a possible glucomannan 4-beta-mannosyltransferase function. Functionality was analysed by studying the cell wall composition of selected RILs and corresponding Arabidopsis thaliana T-DNA lines to determine any differences in the secondary cell wall structure. The results indicated that the differences in digestibility are associated with subtle differences in cell wall composition.