Oil palm is a dynamic economic crop that provides good income and is a source of dietary energy for the global population by palm oil. However, oil palm has low resistance to basal stem rot (BSR) disease caused by Ganoderma boninense. It is hypothesised that the process of cell wall lignification could serve as the first line of defence in oil palm. Lignification delays the infection progress of G. boninense. This present study evaluated the underlying molecular and biochemical lignin biosynthesis events and the quantification and deposition patterns of lignin in oil palm upon G. boninense infection. In this study, an artificial in planta infection system was used to inoculate one month-old oil palm plantlets with G. boninense (GBLS strain) at three levels of treatments (control, T1; wounded, T2 and infected, T3). Post-infection analyses were conducted at 2 day intervals for a period of 8 days. The analyses included the disease severity index (DSI) and physical properties of the plantlets (height, weight, stem diameter, root length and leaf chlorophyll content), the degree of G. boninense colonisation on plantlets stem tissues, total phenolic content and total amount of G. boninense DNA in planta. The results showed a significant (P < 0.001) reduction in the leaf chlorophyll content (from 32.59 to 12.61 SPAD) and severe deterioration of the internal stem tissues. Escalation of DSI values (from 5.56 to 70.37%), total phenolic contents (from 1.78 to 3.07 mg g-1) and the quantity of G. boninense DNA (from 4.04 to 757.15 mg g-1) in the infected (T3) plantlets on 8 day post-inoculation (DPI) were observed. These differences (P > 0.05) were absent in control (T1) and wounded (T2) plantlets. Colorimetric enzyme assays and quantitative PCR amplifications (qPCR) were carried out to assess the enzyme activities and relative gene expressions of intermediate enzymes (phenylalanine ammonia lyase, PAL; cinnamate 4-hydroxylase, C4H; caffeic acid O-methyltransferase, COMT; cinnamyl alcohol dehydrogenase, CAD) for lignin biosynthesis in oil palm plantlets. Enzyme activities of PAL, C4H and COMT were generally induced in infected plantlets, except for CAD which was reduced in all plantlets throughout the experiment. Meanwhile, relative expression of EgPAL, EgCOMT and EgCAD were up-regulated in infected plantlets by 3 to 6 fold at 2 to 4 DPI as compared to the control plantlets, except for EgC4H which was initially down-regulated, but was induced later at 8 DPI with the highest change recorded of 13.22. A biphasic transient induction pattern of lignin biosynthesis genes was observed in oil palm plantlets upon infection by G. boninense. The lignothioglycolic acid (LTGA) assay, histochemical staining with toluidine blue-O (TBO), Maúle reagent and phloroglucinol-HCl and gas chromatography (GC) equipped with a flame ionisation detector (FID) were used to estimate and detect the total lignin content, lignin deposition patterns and the composition of lignin derivatives such as syringaldehyde and vanillin, respectively. Results showed the infected plantlets scored the highest level of total lignin content at 93.63 TGA g-1 derivatives at 8 DPI. Lignin was mainly deposited on the collenchyma and cuticle layers, as observed via staining with TBO and Maúle reagents, but red colouration from phloroglucinol-HCl, which stained for guaiacyl-lignin was absent in all specimens. Total amounts of syringaldehyde and vanillin increased in infected plantlets at 6 DPI, with higher increment of vanillin (353%) than syringaldehyde (59%) content. From this study, an early induction of lignification in oil palm was confirmed in response to the infection of G. boninense. This resulted in the accumulation and deposition of lignin compounds in the cell walls of oil palm. An increase in lignin content of oil palm was believed to have enhanced its tolerance towards G. boninense infection and delayed the progression of BSR disease, which could be a temporary solution to the BSR problem in oil palm. Further research for an effective cure or prevention is required.

Oil palm is an important crop to the economy of Malaysia and Indonesia. There have been considerable efforts to improve crop quality of crop to meet the growing demands for edible oil in the world. However, the threat of pests and diseases in Malaysian oil palm has increasingly challenged the production of crude palm oil, sometimes to the point of driving plantations to closure and conversion of estate land for commercial development. The most devastating disease in oil palm is basal stem rot (BSR), caused by the root-rot pathogen Ganoderma boninense. The disease has been observed in both young and mature oil palm and in both inland and coastal plantations. Epidemiology of BSR was explained through infection by spores and by mycelium from previously infected oil palm and coconut stands, and the presence of G. boninense in the basal stem and soil surrounding infected palms. The life cycle of G. boninense could extend to years as the fungus can remain as resting structures in palm tissues and as recalcitrant spores spread by wind and rain splash in estates. Shade house trials have been successful in producing artificially infected Ganoderma-oil palm BSR symptoms. However, the current method uses oil palm seedlings of three to 12 months and involves inoculation with G. boninense that has pre-colonised a rubber wood block for one month. This method requires a minimum of six months to observe BSR-like symptoms, a time consuming effort. The aim of this work was to develop an efficient artificial infection assay that uses clonal oil palm plantlets as hosts for BSR disease through the inoculation of G. boninense isolate GBLS. The experiment was set up with treatments of T1: non-treatment control, T2: wounded plant control and T3: wounded and GBLS-infected plants. During the incubation period of 42 days, T3 plants consistently showed significant stunting (5.18% and 13.41% shorter than T1 and T2, respectively) and loss of weight (57.58% and 61.00% lighter than T1 and T2, respectively). The T3 plants also had significantly thinner leaves (38.70% and 37.71% narrower than T1 and T2, respectively) and lower chlorophyll contents (42.95% and 64.88% lower SPAD readings than T1 and T2, respectively). Disease severity on the T3 plants was 100% by 6 weeks, indicating death of oil palms. The quantity of GBLS DNA present in T3 samples was highest at Day 14, corresponding to the active growth phase of the pathogen, while on Day 42, the quantity of DNA increased to 13.58% of Day 14 readings, indicating continuous growth in vivo. The method developed was time-sensitive and reliable for screening oil palm for response during the plant-pathogen interaction. The work examined the hypothesis that G. boninense utilizes lignin degrading enzymes (LDEs) such as laccase, lignin peroxidase (LiP) and manganese-dependent peroxidase (MnP) to breakdown oil palm lignin, causing primary cell, tissue and stem rot. Therefore, the role of laccase was investigated during the interaction in otherwise symptomless oil palm tissues. A small gene fragment (208 bp) of laccase was isolated from total DNA of G. boninense GBLS and sequencing showed it to contain 89% homology to basidiomycete laccase. GBLS reduced the total lignin content of oil palm in T3 plants (48.86% and 53.18% lower than T1 and T2, respectively). However, neither laccase nor MnP enzymes were produced in significantly higher amounts in T3 as compared to T1 and T2, indicating the need to differentiate the presence of plant and fungal laccases. Transcript abundance for GBLS laccase gene using qPCR indicated that laccase was induced during the interaction, with maximum laccase detected on Day 28. However, this did not place laccase as a virulence factor although the presence of higher amounts of laccase towards the end of the experiment corresponds to loss of lignin and plant death. Therefore, laccase and other LDEs need further investigations to be confirmed as virulence factors. This work reports a novel infection assay for G. boninense interaction with oil palm and was the first study to have investigated the role of G. boninense laccases in the devastating BSR disease.

Nitrogen availability is central to global food security. Understanding how plants respond to nitrogen could help develop crops with improved nitrogen use. This study aims to investigate how lateral root (LR) and nodule development are balanced in response to low (0.1 mM) and high (5 mM) NH4NO3 concentrations in the model legume Medicago truncatula var. Jemalong A17 using phenotypic and gene regulatory network analysis. High concentrations of NH4NO3 have an inhibitory effect on nodulation. The phenotypic measurements of root architecture of A17 in response to NH4NO3 and rhizobia showed that at high NH4NO3 rhizobia affected LR development. Total root size was less (P < 0.05) in rhizobia inoculated samples compared to the absence of rhizobia. This was due to a shorter primary root and less number of LRs. Whole genome profiling of early (2 and 6 hour) root responses to high NH4NO3 and rhizobia identified 4793 genes that were differentially expressed (significance cutoff of P<0.05). The early (2 and 6 h) responses to high NH4NO3 were mainly independent of the rhizobia effect and N-induction especially at 2 h time point was the predominant response. Some of the components of the autoregulation of nodulation (AON) pathway are also involved in LR development. The sunn-1 mutant is impaired in correct AON signals that lead to hypernodulation with short LRs at low N. Whole genome expression analysis of A17 and sunn-1 root samples identified 7186 significantly (P<0.05) expressed genes showing rhizobia and/or SUNN-regulated responses. These genes could be components of the AON pathway with putative role in balancing the number of nodules with LR development. Using motif analysis tools we identified motifs with putative promoters that were mainly Nodule specific cysteine rich peptides (NCRs). We suggest that these NCRs may be involved in regulating LR and nodule development depending on the plant N status.

Wheat is the third most widely consumed crop after rice and maize globally. The Green Revolution increased the Indian wheat production tremendously since the 1960s using semi-dwarf wheat varieties and subsequent trait-based breeding under non-hostile soils. In addition to grain yield, wheat is an important source of dietary zinc (Zn) and other mineral elements in many countries. Dietary Zn deficiency is widespread, especially in developing countries, and there are wide scale efforts to breed wheat with increased grain Zn concentrations in South Asia. It is not clear if further grain yield and quality traits such as grain Zn concentration improvements can be sustained due to 1) narrow genetic diversity in modern wheat, and 2) limited land availability e.g., many soils are marginal due to salinity, alkalinity, acidity and mineral nutrient imbalances. The first aim of this thesis was to quantify grain yield and yield components, including juvenile root traits, and grain Zn concentration of a panel of 36 Indian diverse wheat genotypes to explore the potential for site specific trait selection for hostile soils and characterise the baseline effect of genotype (G), site (E), and genotype x site interaction (G*E) under a wide range of soil conditions. Mean grain yields ranged from 1.0 to 5.5 t ha-1 at hostile and non-hostile sites, respectively. G*E interactions affected many yield and component traits, which support the value of site-specific traits selection for hostile soils. The mean grain Zn concentration of 36 genotypes ranged from 25 to 35 mg kg-1. Despite a relatively small overall contribution of G to the overall variation in grain Zn concentration, biofortifying wheat through breeding is likely to be effective at scale given that some genotypes (e.g. Kharchia 65) performed consistently across diverse soil types. Root angle and lateral root traits were associated with grain yield and some mineral composition traits. The second aim of this thesis was to study the performance of eight amphidiploids derived from Thinopyrum bessarabicum, a tall wheat grass, for yield, yield components and grain Zn concentration under saline soils. Reduction in GYD in amphidiploids were less than in Indian genotypes under saline soils and grain Zn concentration ranged from 36-43 mg kg-1. The third aim of this thesis was to explore wild wheat relatives, non-relatives and their derivatives to increase the genetic diversity for grain Zn concentration. The mean grain Zn concentration of 225 wild wheat accession ranged from 47 to 178 mg kg-1. Notably, Amblyopyrum muticum, derived amphidiploids and double haploid lines could be useful sources of grain Zn variation that can be used in breeding programmes to increase the grain Zn concentration in modern wheat varieties to alleviate the dietary Zn deficiency.

Sclerotinia sclerotiorum is a necrotrophic fungal pathogen with a worldwide distribution and a wide host range, including many economically important crops. The control strategies for this pathogen and related species include using fungicides, biological control agents and cultural practices such as crop rotations. However, the genetic diversity and the long term survival structures (sclerotia) of this pathogen, combined with the recent discovery of the related species S. subarctica in England and the need for growers to implement integrated disease management strategies means that new control measures need to be sought. Biofumigation, using green manures which are macerated and ploughed into the soil, may be a useful new control approach in an integrated programme. Microcosm and in vitro experiments clearly showed that volatiles released from biofumigation crops have a direct inhibitory effect on the mycelial growth and carpogenic germination of S. sclerotiorum sclerotia. The most effective biofumigation crop for inhibiting carpogenic germination varied depending on whether the volatiles released from the biofumigant crops were in direct contact with the sclerotia when the most effective crop was Raphanus sativus ‘Terranova’, or in the vapour phase when the most effective crop was B. juncea ‘Vittasso’. Carrot root inoculations showed that the number of sclerotia produced on carrot roots was significantly affected by S. sclerotiorum isolate. However, the results also showed that the weight of individual sclerotia produced by different isolates was influenced by carrot accession, but not by S. sclerotiorum isolate. Additionally, the carrot plant and detached leaf inoculations showed significant differences in the rate of lesion progression of S. sclerotiorum on different carrot accessions, indicating differences in susceptibility to the pathogen. S. subarctica microsatellite haplotypes identified in this research were shown to be shared between Scotland and Norway, and between crop plants and meadow buttercup. However, the English population did not share any microsatellite haplotypes with any other population, and analysis indicated that this S. subarctica population in England may be isolated and inbred.

Concerns about climate change and energy supply security have led to a focus on using biofuels to replace oil-based fuels in the transport sector. Second generation biofuels (SGBs), which are produced from lignocellulosic material such as wheat straw, are currently being developed. This project investigated wheat straw supply for SGB production, focusing on the use of dual-purpose cultivars (DPCs) that are optimised to provide for both food and SGB markets. The project consisted of: agronomic assessment of cultivars and management practices for traits associated with a DPC; economic assessment of the value of these DPCs to farmers and costs of straw delivery; life cycle assessment for quantifying environmental burdens associated with straw production from DPCs; and a farmer survey for quantifying current straw supply and potential future straw supply should a new market for straw emerge. Agronomic trials did not identify any outstanding candidates for use as DPCs from currently grown wheat cultivars or any management practices that would benefit DPC traits. Economic assessment found that straw production costs were lower than the straw price but the overall straw gross margins were much lower than grain gross margins suggesting that grain yield would not be traded off against increased straw yield. Transport costs were slightly lower with the use of DPCs. Environmental burdens for straw production were found to be lower than in other studies but the allocation process had a large influence. From the survey, 50% of respondents were willing to increase straw yields but even with a very generous price of straw, 21% of respondents would not supply additional straw. The work suggests that straw availability is lower than some current estimates and there is only limited scope to increase straw yield through cultivar selection.

In the developing endosperm of bread wheat (Triticum aestivum), seed storage proteins are produced on the rough endoplasmic reticulum (ER) and transported to protein bodies, specialised vacuoles for the storage of protein. The important gluten proteins of wheat are transported to the protein bodies they are stored in by two distinct routes. One route consists of vesicles that bud directly off the ER, while the other involves transport through the Golgi (Arcalis et al, 2004). In plants, the RabD clade mediates ER to Golgi vesicle transport (Batoko et al, 2000). Available sequence information for Rab GTPases in Arabidopsis, rice, Brachypodium and bread wheat was compiled and compared in phenetic trees. Partial genetic sequences were assembled using the first draft of the Chinese Spring wheat genome. A suitable candidate gene from the RabD clade (TaRabD2a) was chosen for down-regulation by RNA interference (RNAi) and an RNAi construct was used to transform wheat plants. Using real time PCR, all four available RabD genes were shown to be knocked down in the developing endosperm of transgenic wheat. The transgenic grain was found to produce flour with significantly altered processing properties when measured by farinograph and extensograph. SE-HPLC found that a smaller proportion of HMW-GS and large LMW-GS are incorporated into the glutenin macropolymer in the transgenic dough. Lower protein content but a similar protein profile on SDS-PAGE was seen in the transgenic grain

The primary aim of this project was to identify and characterise Fusarium species associated with the basal rot of Allium species and internal fruit rot of sweet peppers in the UK. The secondary objective was to develop quick molecular markers to identify Fusarium oxysporum f. sp. cepae (FOC) causing onion basal rot. Isolates representing diverse Fusarium species taken from onions, garlic, shallot and leeks obtained from different production and processing sites in the UK were collected. F. proliferatum was found for the first time to be a causal agent of onion basal rot in the UK, but F. oxysporum was by far the most common species and F. oxysporum isolates belonged to at least two different genotypes based on a sequence comparison of several “housekeeping” genes, and overall, appeared to be polyphyletic. None of the housekeeping genes studied correlate with pathogenicity. Secreted in xylem (SIX) genes offer more promise for the specific identification of F. oxysporum formae speciales (Lievens et al., 2009a) and a homologue of the SIX7 gene was found only in a few FOC isolates suggesting that SIX7 is not absolutely necessary for pathogenicity. Whole genome sequencing of a FOC isolate was carried out in order to understand pathogenicity and identify novel effector genes. This work revealed the presence of further homologues of published SIX genes, namely SIX3, SIX5 and SIX9. The presence of SIX3 and SIX5 has only been reported from F. oxysporum f. sp. lycopersici previously. Additionally, screening of eleven new candidate effector genes suggested that FOC isolates have different gene sets which correspond to the continuous variation of aggressiveness found within the FOC population. Fusarium lactis, F. proliferatum and F. solani were identified in association with internal fruit rot of sweet pepper obtained from three different production sites in the UK.

The use of crop protection products (CPPs) is essential to improve crop production levels and feed the rising global population. Safety testing of CPPs is also essential to ensure that their use does not adversely affect human health or the environment. Currently, laboratory-based studies typically over-estimate the environmental persistence of CPPs in the environment. The inclusion of environmental variables that are currently omitted from laboratory studies, such as non-UV light, could reduce the disparity between laboratory and field degradation studies. The inclusion of light resulted in a significant reduction in extractable parent compound for benzovindiflupyr, chlorotoluron, prometryn, imidacloprid, and fludioxonil compared to dark conditions. In contrast, a significantly slower rate of cinosulfuron transformation was observed under light compared to dark conditions. In a separate experiment, terminal restriction fragment length polymorphism showed that under light conditions, the soil surface (0-3 mm) harboured distinct phototroph, bacterial and fungal communities compared to the underlying bulk soil (3-12 mm), or dark incubated soil. 454 pyrosequencing revealed that light selected for diazotrophs at the soil surface, including Nostoc punctiforme, in addition to heterotrophic bacteria, particularly within the phylum Firmicutes. Metatranscriptomic analysis showed that light also selected for actively transcribing photosynthetic eukaryotes at the soil surface, such as Chlorophyceae and Saccharomycetes, in addition to heterotrophs, such as Nostocaceae. Finally, light selected for major soil functions such as photosynthesis, and reduced the alpha and beta diversity of predicted protein coding regions at the soil surface. This work has important implications for CPP regulatory studies and soil surface management practices.

The detection of plant diseases is an important part of commercial greenhouse crop production and can enable continued disease and pest control which will ultimately lead to the economical benefit as well as the significant reduction in use of chemical and biochemical treatments. A plant subject to infection typically releases exclusive volatile organic compounds (VOCs) which may be detected by appropriate sensors. A set of experiments were designed, constructed and conducted at University of Warwick in which the state-of-the-art gas sensors namely Electronic Nose (EN) and Field Asymmetric Ion Mobility Spectrometry (FAIMS) were employed to sample the VOC profiles in order to detect powdery mildew-infected and spider mite-infested tomato plants in a non-destructive manner. The data acquired from the EN and FAIMS devices was analysed using Principal Component Analysis, Linear Discriminant Analysis, Support Vector Machines and Artificial Neural Networks. Both EN and FAIMS proved to be able to distinguish between healthy and infected tomato plants with desirable accuracy when coupled with an appropriate data analysis technique. A review of the literature on plant diseases, destructive and non-destructive plant's disease detection tools as well as VOC sampling procedures and instrumentation will be given throughout this thesis. Moreover, the latter part of this thesis presents the master-slave synchronisation of identical chaotic dynamical systems using the open-plus close-loop (OPCL) control method. The study is mainly concerned with the behaviour of the synchronisation of chaotic dynamical systems in respect to an added bias and in the case of mismatch of parameters of master and slave systems. The link between the external bias and the synchronisation error generated as well as between the value of parameters mismatch and the synchronisation error is examined and discussed. The usability of the newly proposed approaches is assessed by the aid of two applications. The first application demonstrates that a weak bias acting on Nano-mechanical resonator shows the linear correlation with the synchronisation error and, consequently, the bias can be estimated via this error. The second application is related to the synchronisation of the cantilevers commonly found in ENs and Atomic Force Microscopy (AFM). It is suggested to use a novel scheme of coupled master{slave cantilevers and, estimate the difference in cantilever-surface interactions in master oscillator and in slave oscillator via measuring the synchronisation error. The scheme is particularly useful for using the master cantilever as a control and the slave cantilever as a unit device which measures surface properties. The study shows that by calculating the error of synchronisation, a precise measurements can be conducted when two cantilevers leave the synchronous region, that is when they de-synchronise. Thus, this thesis also contributes to the understanding of de-synchronisation of nano-scale chaotic systems (Nano electromechanical Systems) in respect to the addition of an external bias and/or parameters mismatch by outlining the possible applications.