Fusarium head blight (FHB) is a devastating fungal disease of wheat and other small grain cereals worldwide caused by a complex of toxigenic Fusarium spp. and non-toxigenic Microdochium spp. Infection leads to a reduction of grain yield, loss of grain quality and the production of harmful mycotoxins. Control methods for FHB include both cultural and chemical strategies, however the development of cultivars with improved FHB resistance is considered as the most sustainable method for controlling the impact of this disease. Resistance to FHB is a polygenic trait and can be improved by stacking multiple resistance genes together, however there are currently no highly FHB resistant genotypes with acceptable agronomic characteristics available, therefore passive disease resistance can potentially make significant contributions to improved FHB resistance. The aim of this study was to identify novel physiological traits in wheat conferring passive resistance to FHB using ground inoculated field experiments to enable disease escape mechanisms to be expressed, and spray inoculated glasshouse experiments to test if the identified traits were associated with genetic resistance. The most consistent traits relating to FHB were flag leaf length, plant height and awn length. Since these relationships were present in both field and glasshouse experiments, they are likely caused by a genetic linkage or pleiotropy, with genes conferring FHB resistance or susceptibility. Remaining leaf area was less consistently related to FHB, however, since canopy leaf area showed a positive relationship with the development of FHB in ground inoculated field experiments, there is a basis to support the role of reduced canopy leaf area as conferring passive resistance to FHB. In general, relationships were poor between visual FHB symptoms and both pathogen DNA and grain mycotoxin contamination. This was theorised to be due to the use of a mixed species inoculation which introduced antagonism between FHB species and which included more than one producer of several mycotoxins quantified. Therefore the use of visual FHB assessments under mixed species inoculation is concluded to be a poor indicator of both pathogen infection and mycotoxin contamination.

Groundnut, Arachis hypogaea (L.), can be attacked by a range of pathogens, including Aspergillus species, which can cause accumulation of the mycotoxin aflatoxin. Although some success in controlling this pathogen has been achieved with application of fungicides, their use is not always feasible in developing nations like Nigeria. The aim of this study was, therefore, to evaluate naturally-occurring plant oils and BCAs with a past history of efficacy as alternatives to fungicides for reduction of Aspergillus infection and aflatoxin accumulation in groundnut. Aspergillus strains and thirteen different plant essential oils were tested. The oils were derived from clove, camphor, vanilla, garlic, galangal, green oregano, lemon grass, neem, ginger, basil, tea tree, thyme and onion. The biocontrol agents used were fungi Trichoderma harzianum strain T-22, T. asperellum and T. viride from a commercial biocontrol product, TUSAL, and bacteria Pseudomonas chlororaphis ssp. aureofaciens and Bacillus amyloliquefaciens (strains MBI600, 62P, and 66P). The identities of a strain of A. niger, isolated from Nigerian groundnut samples, and of T. asperellum and T. viride were confirmed by PCR amplification of DNA and sequence comparison to reference isolates in the GenBank database. Some of the plant oils (clove, camphor and vanilla) and biocontrol agents (Trichoderma strains) tested proved effective in inhibiting the A. flavus and A. niger strains used in the research, in both in vitro and in planta experiments. Improved seedling emergence in pathogen-contaminated compost and reduced post-harvest pod infection were observed. Combinations of the most active BCAs and EOs also provided disease suppression. ELISA analysis of aflatoxin B1 in treated, A. flavus-inoculated groundnut pods showed a reduction in toxin concentrations, to a level below that recommended by the European Commission of 15 ppb. Of the control agents tested, the most effective were T. harzianum T-22 as a BCA and probably clove oil as a plant extract. Commercial products based on Trichoderma are used world-wide. EOs, have, to date, had little use in control of Aspergillus infection of groundnut. It was also demonstrated that detection of asymptomatic A. flavus pod infection could be achieved by the traditional method of surface sterilisation and plating out, and by use of a LAMP assay to detect pathogen DNA. The latter could provide a rapid, portable method for A. flavus detection in harvested groundnut pods and could have application in both developed and developing nations. Since low resource growers in nations like Nigeria need alternative, low-cost methods for protecting groundnut from Aspergillus infection, to produce a nutritionally-valuable, high protein foodstuff low in toxin contamination, such alternative methods of disease control may have a future role to play in global food security. It may prove possible to extract antifungal components from appropriate, locally-sourced plant material in a cost-effective manner. However, whether the level of disease control and suppression of aflatoxin accumulation reported here was adequate for possible commercial application is unclear. Further evaluation, including field experiments, is required.

A substantial increase in wheat yield is needed for global food security. This requires a comprehensive understanding of the physiological and genetic basis of yield determination. The present study aimed to dissect yield physiologically and genetically in a recombinant inbred line mapping population derived from bread wheat × spelt. A total of 201 traits were investigated in the field and glasshouse across three years, and these traits formed five themes: genetic variation in yield and yield components, and the usefulness of spelt as a genetic resource; tillering dynamics; biomass accumulation; flowering time and subsequent leaf senescence; and grain filling processes. Large genetic variation in all traits was found, and spelt showed many desirable traits and alleles independent of low threshability, so it can be used to broaden genetic diversity for yield improvement in bread wheat, while maintaining the free-threshing habit. Quantitative trait loci for tiller production and survival were identified, which were also affected by light environment under the canopy: low red:far red ratio (R:FR) led to early tillering cessation, few total shoots, high infertile shoot number and shoot abortion, probably resulting from an assimilate shortage due to early and enhanced stem growth induced by low R:FR. More fertile tillers normally contributed to plant yield and grain number, but reduced individual grain weight, partly because of smaller carpels and fewer stem water soluble carbohydrates at anthesis. In addition, preanthesis biomass accumulation increased yield and yield components. For grain weight, slightly early anthesis and delayed but fast leaf senescence were associated with larger grains. Carpel size at anthesis, grain dry matter and water accumulation, as well as grain morphological expansion, determined final grain weight, because of pleiotropy or tight gene linkages. These findings provide deeper insight into yield determination in wheat, and facilitate trait-based physiological and molecular breeding.

Despite the fact that urban regeneration has been practiced for more than 40 years, there is still a lack of rigorous research on what constitutes best practice in evaluating urban regeneration interventions. It can be argued that in the late 1970s and early 1980s, evaluations were mostly focused on assessing the feasibility of projects, while in the mid 1980s evaluations were mostly conducted to examine the outcomes of projects or programmes instead of their effectiveness. It was only after the late 1980s that programme evaluations were carried out to examine the effectiveness of a programme. However, in spite of this development, such assessments were still considered inadequate. In this research, for example, it was soon discovered that the evaluation of urban regeneration initiatives through a regional park programme was almost entirely performed in isolation without any attempt to compare them with other similar initiatives. The practice of a regional park programme in delivering urban regeneration initiatives is seen as an important programme in the UK given that it promotes a large area within a high urban population location. Additionally, a regional park provides the opportunities for recreational and leisure purposes especially for the locals and the region therefore plays a vital role as a visitor destination. Hence, in order to serve its purpose completely, the performance of this intervention is essential. The essence of this research therefore seeks to address the gaps and to inject a comparative dimension and find the appropriate tools to measure the performance of urban regeneration initiatives in contrast to the current standard evaluation procedures. The research has been designed with the aim of seeking practical and effective ways of applying the benchmarking method and realistic evaluation as a combined assessment tool in evaluating the performance of such initiatives. For this reason, the research focuses on the functioning of the urban regeneration schemes delivered through regional park programmes in the UK. In relation to this, a decision was taken to ‘benchmark’ the Mersey Waterfront Regional Park against the Lee Valley Regional Park and to examine both case studies by means of ‘realistic evaluation’. The rationale for choosing these particular regional parks was made based on the parks’ background. Both regional park programmes have placed emphasis on regeneration of their respective areas. The idea of this comparative exercise is therefore to explore the differences between the Mersey Waterfront and the Lee Valley in terms of programme implementation, project delivery, mechanisms for efficiency, outcomes of programme, the institutional arrangement, the key success factors and the key learning points. These areas of research were therefore justified for the purpose of measuring the performance of a regional park thus teasing out the practicality and potential of both evaluation methods. The end-result of this research discovered that there were various mechanisms affecting the performance of a regional park. Additionally, it was discovered that programme outcomes are influenced by programme settings and delivery mechanisms. The findings also reveal the key lessons to programme performance and the variations of work processes. Nevertheless, the most significant result is the practicality and benefits of using the benchmarking method and realistic evaluation as a combined assessment tool in examining urban regeneration initiatives delivered through regional parks.

The management of weed species Alopecurus myosuroides (black-grass) in arable agriculture is largely achieved through use of herbicides. However, resistant populations are increasingly commonplace and new modes of action are proving elusive. Growers use integrated weed management (IWM) strategies to manage the weed seedbank, such as rotational ploughing to bury seed and delayed drilling to reduce weed numbers within a crop. Competitive cultivars may contribute to IWM, but testing cultivars is a long, expensive process. The aims of this studentship were to identify the traits that confer enhanced crop competitive ability and determine if these can be used to predict competitive ability of new cultivars. This was investigated on outdoor sand-beds and in field trials. Commercial wheat cultivars were grown alongside A. myosuroides. Various wheat traits were measured throughout growth. The seed return of A. myosuroides was quantified at maturity, and yield was harvested in the field. Pearson’s correlations and multivariate analysis were used to identify traits related to competition, and Linear Mixed Models (LMM) were used to identify predictive traits. Two models of crop-weed interactions were parameterised for the cultivars. Potential interactions between cultivar choice and other IWM strategies (delayed sowing and increased sowing rate) was assessed experimentally and through simulation models. Cultivar differences in suppressive ability were most evident between the extreme ends. Various traits were related to a cultivar’s ability to suppress A. myosuroides seed return, such as early height and tillering parameters, though no traits were consistent across all experiments. Few traits could be related to tolerance to yield loss. Suppressive ability can be ascertained early in the growing season, but the relationship with individual traits can change direction, possibly depending on the availability of belowground resources. Generally, earlier maturity and a conserved tillering strategy appears to be more suppressive. Cultivar choice is largely compatible with delayed sowing and increased sowing date. The effect of environmental variability on relationships between traits and competitive ability requires further investigation before they can be employed as predictors, particularly in the context of belowground competition.

Paclitaxel (Taxol) was first isolated from the bark of the pacific yew tree as an important anticancer compound. Its efficacy and unique mode of action has seen demand increase, but full chemical synthesis is not economically viable and this has led to a search for alternative production sources. Current supply is met by semi- synthesis from its natural precursor, 10-deacetylbaccatin III (found in yew tree needles) or from yew cell suspension cultures. However, engineering of the key biosynthetic genes into heterologous hosts could provide an alternative for paclitaxel production. This study aimed to utilise the geranylgeranyl diphosphate precursor pool present in fruit of the yellow flesh (r) tomato mutant for the production of novel taxanes. A synthetic polycistronic construct was designed and created to contain the first four Taxol biosynthetic pathway genes, which were codon-optimised for recombinant protein expression in tomato plants. The first genes in the Taxol biosynthesis pathway, namely taxadiene synthase (TXS), taxadien-5α-hydroxylase (T5OH), taxadien-5α-acetyltransferase (T5AT), and taxoid 10β-hydroxylase (T10BOH) were successfully introduced into tomato plants using an optimised Agrobacterium-mediated transformation protocol. Plants expressing the TXS and T5OH transgenes were analysed; however, GS-MS analysis failed to detect the expected compounds taxadiene and taxadiene-5α-ol. Plants harbouring TXS, T5OH, and T5AT were successfully generated, and plants containing T10BOH were also generated; however, the production of downstream taxanes or novel taxanes was not investigated owing to time constraints. The localisation of T5OH, T5AT, and T10BOH was investigated by tagging putative leader sequences to green fluorescent protein (GFP). Confocal microscopy was used to detect GFP in Arabidopsis thaliana root cells. All three Taxol biosynthetic proteins were found to be localised to the endoplasmic reticulum membrane.

Modern bread wheat (Triticum aestivum) initially derived from wild progenitors which underwent hybridisation and domestication events. It is hypothesised that modern plant breeding has reduced the genetic variation among modern cultivars (Sparkes, 2010). Ancient wheat species form a conduit between wild ancient wheat and cultivated Triticum species, and may harbour the genetic variation required to supplement the modern bread wheat gene pool. The current work investigated a range of morphological and physiological aspects of several ancient species including several representatives of spelt, emmer and einkorn. These were compared to modern bread wheat in two field and three glasshouse experiments with the aim to investigate their resource use efficiency, where radiation use and water use formed the crux. The main components of the current work relate to 1) canopy interception characteristics 2) leaf photosynthetic capabilities and 3) water use. Spelt genotypes demonstrated increased WUE and green area longevity compared with modern bread wheat. Emmer displayed increased WUE, assessed on three scales using instantaneous transpiration efficiency (ITE), biomass to water uptake ratios, and carbon isotope discrimination (Δ13C). In addition, the mechanisms whereby emmer, einkorn and spelt maintained ITE appeared to differ. Emmer was observed to increase photosynthetic rates, whereas spelt maintained low transpiration as a result of low stomatal conductance. Einkorn however, maintained ITE through an intermediate of both of these mechanisms. This was further supported by species differences for maximum photosynthetic rates (Asat) which, for emmer and einkorn, were comparable with modern bread wheat. Investigation of WUE through Δ13C and biomass production to water uptake ratios ranked species similarly, showing emmer and spelt to have superior WUE during grain filling. Additionally, spelt was observed to produce biomass comparable to modern bread wheat, thought to be due to enhanced RUE (observed in one field trial) or increased green area longevity rather than increased assimilation capability. In field experiments, biomass production and light interception was relatively high for einkorn species, however this was believed to derive from excessive tiller production due to poor emergence. Overall, ancient species did partition a larger proportion of assimilates toward tillers. Modern bread wheat produced fewer tillers, but directed more biomass towards the ear, and therefore had greater harvest indices (HI) compared to all ancient species. Despite this broad analysis, further investigation of the mechanisms responsible for these traits is required. This research therefore indicates that there is sufficient variation for traits, which could be used to improve radiation and water use efficiency, and therefore warrants further exploration. With further investigation, resource capture and utilisation efficiency, and the morphological traits that confer these advantages in these genotypes, genetic markers could be identified with the aim to introduce valuable traits for the production of novel modern bread wheat varieties. The differences observed between these ancient wheat species and modern bread wheat provide an opportunity through which modern wheat gene pools may be improved to stabilise yields, particularly in sub-optimal environmental conditions, thus increasing biomass production per unit resource, thereby enhancing the productivity and the efficiency of crop systems.

The first theme covers sweetpotato in the marketing chain from farm to consumer. In East Africa, research explored ways of improving the handling and transport of sweetpotato, shelf life and storage of fresh roots on the farms to increase incomes and food security. Transport and handling were investigated using a novel ‘electronic sweet potato’ where it was found that it was the large number of minor vibrational type impacts that cause the most root damage. Reducing the sack weight and using fibreboard boxes reduced damage. A shelf-life investigation into the types of injury occurring through poor handling suggested that skinning injury, followed by broken roots caused the greatest shelf-life losses. The second theme explores sensory evaluation and consumer preference of sweetpotato and other food commodities. Research explored the variability of sensory parameters and acceptability of sweet potato cultivars with location and season in Tanzania and developed a model for predicting the acceptability of new cultivars derived from breeding programmes. The approach was extended to the acceptance of biofortified sweetpotato containing ß-carotene differences in acceptance between locations and ethnic groups for rice and cassava products, variations in roasting conditions and shelf-life of peanut butter, and relationships between acceptability, market price and affordability of rice. Over 1,800 consumers were interviewed. This research suggests consumers in rural and urban Africa tend to be open to new products and this is contrary to views often held. Consumer acceptance was found to be ‘multi-modal’ with distinct variations within populations. Consumers in these different segments also had distinct socio-economic populations. Acceptability differed for rice and cassava products with respect to location, gender and age but not within ethnic group.

Studies were undertaken to investigate the potential for using sorghum bran from a traditional wet-milling process as a raw material for the fermentative production of value-added products, namely ethanol and itaconic acid. This was deemed of importance because renewable ethanol sources are required to replace environmentally unfriendly fossil-based fuels, while renewable itaconic acid could replace fossil-based industrial monomers if an economically viable source can be found. Emphasis was placed on optimising both yields (g/l) and substrate conversion, as a function of the theoretical maximum possible, for both compounds. The compositions of sorghum white bran (WB) and red bran (RB) were first elucidated to determine their suitability for downstream fermentation uses. Results revealed that the brans appeared to contain adequate components for biomass growth, with approximate carbohydrate, protein, lipid and ash contents of 69 %, 16 %, 3 %, 2 % and 70 %, 17 %, 4 %, 1 % found in WB and RB, respectively. Second, methods to obtain glucose-rich hydrolysates (for later use in fermentations) from the sorghum bran were investigated. It was found that amylolytic enzymes could produce enzyme hydrolysates (WBEH and RBEH) with glucose contents ranging from 48 g/l to 61 g/l. Alternatively, the brans could be digested to simple sugars using 3 % H2SO4 which converted up to 70.5 % of the bran into glucose, with dilute acid hydrolysates (WBDAH and RBDAH) having glucose contents ranging from 48 g/l - 57 g/l. Levels of the common fermentation inhibitors hydroxymethylfurfural, furaldehyde and vanillin were relatively low in all sorghum bran hydrolysates. Spot plate tests and phenotypic microarrays revealed that several yeast species metabolised and thrived on the hydrolysates. Ethanol mini-fermentations were successful with Kluyveromyces marxianus attaining the highest 88.9 % of theoretical maximum ethanol on RBEH, with other yeast strains also producing high yields. Production of itaconic acid by fermentation with 46 isolates of Aspergillus terreus was then attempted. Screening experiments on a defined glucose medium revealed that IA production levels were not normally distributed in nature. The highest producers were employed in 25 ml fermentation using the sorghum hydrolysates as a feedstock but the yields were found to be low compared to use of the defined glucose medium, with the highest yield (by isolate 49-22) being 5.5 g/l which corresponds to just 32.4 % conversion efficiency. Several approaches were therefore investigated to attempt to improve IA yields from A. terreus fermentations. Firstly, several hydrolysate purification techniques were attempted. The use of activated charcoal improved RBDAH yields very slightly, although most treatments resulted in lower IA yield. Secondly, ultraviolet mutagenesis was attempted using two high IA producing isolates, 49-22 and 49-5. Several promising mutants were obtained including one showing a 3.5-fold increase over the parent. However, these high yields could not be replicated in subsequent experiments. Thirdly, attempts were made to induce the sexual cycle of A. terreus in order to generate genetically diverse offspring that might include progeny with improved IA production. A molecular diagnostic was used to determine mating type and several isolates of opposite MAT were crossed in all possible combinations on three media under various temperature and gaseous exchange conditions. Hyphal masses containing cleistothecia, asci and ascospores were produced from two weeks onwards, which varied in number according to conditions and crossing partners. Most isolates were of low fertility, but 49-40, 49-43 and 49-44 were identified as “super-maters”. Sorghum flour agar (SFA) produced approximately seven times more structures than other agar media assayed, the effect of temperature varied according to media, whilst allowing gas exchange resulted in more hyphal masses than sealing the plates. Although asci containing 4-8 ascospores were identified, difficulties were encountered in obtaining viable ascospore offspring. Only one putative recombinant offspring was obtained, as evidenced by molecular verification using RAPD-PCR and MAT markers. This isolate exhibited low IA yields in fermentations. Finally, fermentation optimisations were performed using the response surface methodology approach. A half-factorial screening experiment was used to select three fermentation factors then a central composite design (CCD) performed to obtain the optimum conditions. Optimum conditions for IA fermentation using RBDAH as a feedstock were found to be 30 oC, pH 4.0 and an A. terreus inoculum of 1.0 x106 spores/ml, resulting in 13.5 g/l IA and 28.3 % of theoretical maximum possible conversion, representing a 2.45-fold increase over non-optimised values obtained in initial time-point experiments. Higher pH and inoculum sizes, with lower temperatures favoured IA formation. Scale up to fermentation volumes of 200 ml and 500 ml was performed and these also generated even higher yields of 13.9 g/l and 16.3 g/l IA, corresponding to 49.6 % and 46.1 % of theoretical maximum respectively. Overall, it was concluded that hydrolysates obtained from the wet-milling of sorghum bran can be used in the fermentative production of value-added chemicals with promising yields and efficiency, which warrants further research attention.

Bud rot disease has been considered as a devastating disease of oil palm in Latin America. Severe outbreaks of this disease have been reported in Colombia, Brazil, Ecuador, Panama and Suriname. The causal agent of bud rot disease in Colombia has been identified as Phytophthora palmivora. This pathogen is known to be responsible for several tropical diseases such as black pod and stem canker disease of cocoa, especially during the rainy season. Phytophthora palmivora has also been reported to attack durian, rubber, pepper and jackfruit causing diseases in various parts of the plant such as fruit, leaves and stems. However, no outbreaks of the disease have been reported in oil palm in Malaysia or other Southeast Asian countries. Several aspects of research need to be conducted to understand why this pathogen causes problems in oil palm in South America but not in Southeast Asia. This study aimed to analyze variation between the Colombian P. palmivora isolates that cause bud rot disease in comparison with Malaysian isolates and other isolates gathered from different hosts and regions. Our hypothesis was that P. palmivora isolates from the different regions and/or hosts have different molecular characteristics and have dissimilar levels of pathogenicity. Sequence alignments of several genetic markers, the internal transcribed spacer (ITS) of the ribosomal RNA (rRNA) gene cluster, beta-tubulin (β-tubulin), translation elongation factor 1 alpha (EF-1α), cytochrome c oxidase subunit I (CoxI) and subunit II (CoxII) genes failed to distinguish between Colombian oil palm isolates and P. palmivora from different hosts and regions. It was concluded that these markers are more suitable for inter-specific studies between species but not for intra-specific evaluation within species of P. palmivora. However, a new marker named as P. palmivora hypothetical avirulence effector protein (PpHPAVR) along with analyses of amplified fragment length polymorphisms (AFLPs), separated the Malaysian and Colombian isolates into distinct clades. This indicates that there is genomic variation within P. palmivora isolates. The zoospores of P. palmivora from various hosts and demographic origin were shown to have the ability to cause infection to oil palm seedlings, durian and rubber. However, not enough evidence has been collected to confirm that pathogenicity correlates with the distinct clades observed with AFLPs and PpHPAVR. Phytophthora palmivora species-specific diagnostic using PCR and loop-mediated isothermal amplification (LAMP) have been developed based on the PpHPAVR region.