Oil palm is an important commercial crop in Malaysia where Malaysia is the second largest producer and exporter of palm oilin the world. In order to meet the increasing demand for palm oil, elite oil palm planting materials with higher palm oil yield are the desirable planting materials. Hence, the oil palm plantation companies have incorporated in vitro micropropagation technique through somatic embryogenesis in producing elite oil palm. However, low embryogenesis rate has hampered large production of elite oil palm ramets. In this study, proteomic technology was deployed to compare protein expression and identify differential expressed protein between high and low proliferated embryogenic lines of oil palm tissue culture. From the study, total protein of oil palm young and old leaves was extracted using an optimized trichloroacetic acid/acetone precipitation protocol followed by polyethylene glycol (PEG) fractionation to isolate low abundance proteins. Then, the extracted proteins were separated on two-dimensional (2D) gel electrophoresis and protein profiles between the high and low proliferated embryogenic lines were compared. Total of 40 differentially expressed protein spots were isolated from the 2D gel for mass spectrophotometry (MS/MS) identification. However, only 26 out of 40 protein spots were identified and just 8 of the identified protein spots were isolated from young leaves. Quantitative real-time PCR were conducted on 17 proteins candidates to study on the relationship between the protein and mRNA expression level. There was 29% of the 17 proteins’ expression showed linear correlation with their mRNA expression. These proteins candidates were highlighted for further validation in the future.

Brassica napus is a commercially important crop worldwide and its use is quickly increasing due to its beneficial oil products and biofuel demands. Yield can be lost through infection by a fungal pathogen, Leptosphaeria maculans, the causal agent of stem canker (blackleg). An early indication of the presence of stem canker is a lesion (leaf spot) on the cotyledons or early leaves. The leaf spot stage of the disease was used in this work to ascertain if biological control agents applied both individually and in combination decreased the lesion area and also to quantify the amount of L. maculans DNA present using quantitative polymerase chain reaction (qPCR). The natural production of antibiotics by some bacteria is a commonly found form of antagonistic biological control. Bacillus amyloliquefaciens and Pseudomonas chlororaphis spp. aureofaciens 30.84 evaluated in this work both produce antibiotics and were assayed for their ability to provide control of Leptosphaeria maculans. Known active strains and field isolates of Bacillus and Pseudomonas were tested as potential biocontrol agents in vitro and then used in in planta assays. The in planta assays using bacterial isolates applied individually indicated that all the bacteria gave statistically significant control of L. maculans at the leaf spot stage. Those isolates with highest activity were further evaluated in combination, to determine if improved control of leaf spot occurred. Firstly, however, it was important to confirm the two bacteria would be compatible and antibiotics would be produced. To this aim, an in vitro assay using mutant Chromobacterium violaceum confirmed Pseudomonas chlororaphis spp. aureofaciens upregulated antibiotic production using acyl-homoserine lactones, signalling molecules. Consequently, it was vital that the Bacillus applied with it did not produce lactonase which would denature these molecules. PCR was used to confirm the enzyme was not present. It was, however, shown using in planta assays that combinations of Bacillus and Pseudomonas did not halt the infection or growth of L. maculans, but appeared to lead to increased lesion size. Colonisation of the cotyledons by the bacterial biological control agents applied onto the cotyledons was monitored by washing recovery, serial dilution, plating and colony counting along with qPCR of the DNA. All bacteria colonised successfully when applied individually. However, the populations decreased from the quantity at time zero when they were applied in combination, indicating they were unable to colonise the cotyledons successfully under those circumstances. To quantify Leptosphaeria infection, the concentration of ergosterol, a fungal sterol, was quantified to measure the colonisation of cotyledons. Concentrations were assessed using high performance liquid chromatography (HPLC). This assay was not successful no free ergosterol could be detected. This was probably due to L. maculans either having small amounts of ergosterol in its cell membranes, or having most of the ergosterol esterfied and unsuitable for quantification using this method. Polymerase chain reaction (PCR) was used to ascertain the presence of fungal hyphae within asymptomatic regions of cotyledons. It was found that the fungal DNA was detected within all areas of the cotyledon irrespective of whether the leaf spot could be seen. This result highlights the unreliability of the common method of visually assessing the presence and/or severity of L. maculans infection using leaf spot area. To monitor the populations of bacteria and the fungus in real time, DNA was extracted from the cotyledons and quantified using quantitative PCR (qPCR). The amount of L. maculans DNA isolated decreased when the BCAs were applied individually, and increased when the BCAs were applied in combination (when compared with the amount isolated from the control cotyledons). These results confirmed earlier, non-molecular assessments. To provide a benchmark for biocontrol activity, fungicides used in the control of leaf spot on oilseed rape were tested under the standard experimental conditions. Whilst control was obtained, it was not as effective as when used in the field, probably due to the formulations being optimised for field conditions. Fungicides targeted at wheat pathogens were also tested for control against L. maculans. Field application rates of these fungicides were not successful, as all damaged the epidermis of the cotyledon, resulting in death of the plant. Application of ¼ field rate still induced epidermal damage in all cotyledons except those sprayed with Q8Y78 (now called Refinzar®), where a necrotic lesion could be seen without pycnidia, at day 15 after inoculation.

Oilseed rape (Brassica napus) is a commercially important agricultural crop susceptible to damage from invertebrate herbivores, such as caterpillars, aphids and slugs. Plants can detect the presence of invertebrates via physical contact, tissue consumption, and on recognition of compounds in saliva. Plant retaliation includes the production of proteinase inhibitors to impair gut function and the accumulation of phenylpropanoids and potentially toxic glucosinolates to decrease plant palatability. Previous work has shown that a component of sunlight, ultraviolet-B (UV-B) radiation, can regulate defence related responses in a manner similar to that of pests and the plant wound-response hormone, Jasmonic acid (JA). The molecular basis behind UV-B- enhanced plant defence against invertebrates, however, remains elusive. This project aims to better understand invertebrate resistance in oilseed rape along with the genetic and metabolic basis of UV-B-enhanced defence against two agricultural pests, the grey field slug and caterpillars of the Diamondback moth (Plutella xylostella). UV-B treatment of B.napus and Arabidopsis thaliana has been found to enhance their resistance to these pests, and gene expression analysis of B.napus identified several genes similarly regulated by UV-B radiation, JA application, and/or slug or Plutella grazing. It is thought that these genes are important in UV-B enhanced plant resistance. Transgenic Arabidopsis lines over-expressing three of these oilseed rape genes have been generated to evaluate their role in UV-B-mediated defence. If found to be more resistant to pests, these lines will serve as ‘proof of concept’ that manipulation of the UV-B response pathway in members of the Brassica family could be used to develop new invertebrate resistant varieties.

The aphid transmitted Polerovirus Turnip yellows virus (TuYV) was found to be widespread with high incidences in oilseed rape (OSR) across Europe. UK, France, Germany and Poland all having >90% TuYV incidence in some OSR crops. From the 179 whole TuYV genomes sequenced in this study the phylogenetic analyses indicated three distinct genetic groups in the UK, two of which were also detected in Europe. These three genotypes were also distinct from the original sequenced TuYV-FL. These groups are proposed to be distinct species due to their genetic distance based on the most variable gene ORF5 and phylogenetic analyses of ORF1, ORF3, ORF4 and ORF5. Mixed TuYV infection was uncommon and only two plant samples had genetically distinct isolates. Whole genome analysis also provided valuable information on two recombination hotspots located within TuYV genes ORF3 and ORF5. Investigation into the epidemiology of TuYV revealed many weed and crop species as hosts, including sugar beet, which it was previously thought not to infect. TuYV isolates detected infecting weed plants in the UK were successfully transmitted to OSR. Previously undescribed hosts, verbascum, geranium, teasel, spear thistle, dock and previously described hosts in the Brassicaceae, Compositae and Lepidium families were found in the UK. A full-length infectious clone of a UK isolate of TuYV has been produced, this will allow further assessment of TuYV in the future. The infectious clone was able to cause systemic infection of TuYV and was aphid transmissible. The Arabidopsis thaliana gene knock-out study did not reveal a single eIF gene or gene linked to virus movement or silencing that could provide extreme broad-spectrum resistance. The gene eIF(iso)4G.1 was able to give a broad-spectrum quantitative resistance, and the potential of eIF3D.2 as well as sucrose symporters SUC1 and SUC2 as candidates for extreme TuYV resistance were discovered. This understanding of the epidemiology and diversity of TuYV is being used to develop strategies for control.

Effects of whole essential oils (EOs) and their constituent compounds (EOCs) on the fermentation activities of rumen microbes and the biohydrogenation (BH) of n-3 polyunsaturated fatty acids (PUFA) were evaluated in four in vitro experiments and one feeding trial . In all the in vitro experiments, rumen fluid was collected from Hartline x Texel cross cull ewes. A basal feedstock comprising of 70:30 grass hay and concentrate was formulated, milled (1mm screen) and then supplemented with 32.5 g oil/kg (40% oil from ground whole linseed and 60% from fish oil). In the first experiment using 15 EOCs, anethole and 4 - allyanisole which were the most effective EOCs reduced the BH of 18:3 n-3 by 22.2% and 26.4%, respectively. But, at 300 mg/L there was a concomitant substantial inhibition of tot al volatile fatty acids (VFA). In the second experiment, out of 10 whole EOs, anise and cassia oils which were the most effective EOs reduced the BH of 18:3 n-3 by 58.2% and 54.3%, respectively. However, protection was accompanied with significant suppress ion of VFA at 300 mg/L. In the third experiment using varying doses (0, 100, 200 and 300 mg/L) of 4 - allylanisole, anethole, anise oil and cassia oil, it was observed that at 200, 4 - allylanisole, anethole and anise oil maintained best balance between satisfactory protection of n-3 PUFA and minimal disruption to VFA concentration. In the fourth experiment , six Hartline x Texel cross lambs were used. Three of the lambs were randomly assigned to the untreated basal diet (BDG) and the remaining three lambs were offered diet with anise oil (AOG ). Rumen fluid collected from each of the BDG and AOG was used in in vitro batch culture system. The AOG maintained higher concentrations of PUFA and lower concentration of stearic acid. Results of these studies indicate that dietary addition of selected EOs and EOCs represent a potential effective strategy to optimize the fatty acid composition of ruminant food products (to be confirmed) . However, whole EOs are more effective than EOCs.

In der Broschüre werden Anbau, Umweltwirkungen und Verwertungsmöglichkeiten des Miscanthus erläutert. Miscanthus, auch Chinaschilf genannt, ist eine sehr massenwüchsige Pflanze, die zur Familie der Süßgräser gehört. Die Pflanze ist ein bedeutender Rohstoff für die stoffliche und energetische Verwertung. Unter den Standortbedingungen Sachsens gedeiht Miscanthus gut und liefert wirtschaftliche Erträge. Die Broschüre richtet sich an Landwirte als Rohstoffproduzenten, aber auch an Nutzer und Verarbeiter des nachwachsenden Rohstoffs.

Phoma stem canker is a disease of oilseed rape (Brassica napus) caused by closely related plant pathogens Leptosphaeria maculans and L. biglobosa. It is an economically important disease, causing annual yield losses of approximately £770 million worldwide. When colonising oilseed rape, L. maculans and L. biglobosa exist in close proximity on the leaf, competing for resources as they move through the main leaf vein and into the stem. Fungicides are commonly used to decrease severity of phoma stem canker on oilseed rape. However, the efficacy and longevity of active chemicals is under threat from evolution of resistance in pathogen populations and government legalisation. Moreover, it has been suggested that both L. maculans and L. biglobosa differ in their sensitivity to azoles, and important class of fungicides that are used to control the disease through the inhibition of lanosterol 14-α demethylase (erg11, CYP51). This project aims to further understand the role that fungicides have in controlling phoma stem canker by investigating their efficacy against L. maculans and L. biglobosa in crops, in vitro and in planta. In field experiments, established in Cambridgeshire across four cropping seasons, the fungicide mixture penthiopyrad (SDHI) plus picoxystrobin (QoI) was as effective at controlling phoma leaf spotting and phoma stem canker in winter oilseed rape as prothioconazole (DMI), suggesting that both fungicides could be used to reduce phoma stem canker symptoms. The two pathogens differed in their growth rates in vitro, with L. biglobosa growing faster than L. maculans when untreated or treated with lower fungicide concentrations. Fungicide sensitivity assays suggest that L. maculans and L. biglobosa are both sensitive to DMI, SDHI and QoI fungicides and that differences between the species are minor. Prothioconazole and penthiopyrad + picoxystrobin had a similar efficacy on oilseed rape cotyledons colonised with either L. maculans or L. biglobosa. There was no difference between species on prothioconazole treated plants, although there was a difference between L. maculans and L. biglobosa when treated with 20 μg/ml penthiopyrad + picoxystrobin. Heterologous yeast expression of LmCYP51B and LbCYP51B with fungicide sensitivity testing of the yeast transformants suggests that LmCYP51B and LbCYP51B are similarly sensitive to azole fungicides flusilazole, prothioconazole-desthio and tebuconazole. These findings are supported by homology protein modelling, which predicts that LmCYP51B and LbCYP51B are structurally very similar, specifically at the azole-binding site. In conclusion, fungicides are still an effective control method for reducing phoma stem canker symptoms caused by Leptosphaeria species in the UK, and a useful tool to in the sustainable production of oilseed rape.

In der Broschüre werden Anbau, Umweltwirkungen und Verwertungsmöglichkeiten des Miscanthus erläutert. Miscanthus, auch Chinaschilf genannt, ist eine sehr massenwüchsige Pflanze, die zur Familie der Süßgräser gehört. Die Pflanze ist ein bedeutender Rohstoff für die stoffliche und energetische Verwertung. Unter den Standortbedingungen Sachsens gedeiht Miscanthus gut und liefert wirtschaftliche Erträge. Die Broschüre richtet sich an Landwirte als Rohstoffproduzenten, aber auch an Nutzer und Verarbeiter des nachwachsenden Rohstoffs.

Holding approximately 89,000 Tg of organic carbon, tropical peatlands are one of the largest pedological sinks of carbon (Page et al., 2011). Waterlogged conditions in undisturbed peatlands reduce heterotrophic respiration and provide environments in which organic matter accumulates (Moore et al., 2013). However, from 1990 to 2010, the forest cover in the peatlands of South East Asia fell from 77% to 36%; at this rate of decline, all of the undisturbed peatlands are likely to have disappeared by 2030 (Li et al., 2007; Koh et al., 2011; Miettinen et al., 2011). Land-use changes in these ecosystems can have important consequences for carbon (C) budgets (Page et al., 2002; Hooijer et al., 2010). Recently a number of studies have been carried out on tropical peatlands (e.g. Couwenberg et al., 2010; Hergoualc'h and Verchot, 2011; Hirano et al., 2012; Jauhiainen et al., 2005, 2012; Li et al., 2007; Melling et al., 2005; Page et al., 2009), but some parts of the C budget are yet to be quantified. In order to fill these gaps in our knowledge, the goal of this work was to assess heterotrophic and total soil respiration, litterfall, litter decomposition and evaluate peat properties in an intact peat swamp forest, a transitional logged drained forest and an oil palm plantation located on the same alluvial peat plain. This in-situ research lasted two years, and heterotrophic and total soil respiration were separated using the trenching method. Our results from the carbon dioxide flux monitoring in the three land uses showed that the trenched plots provided a good proxy for heterotrophic respiration. The annual integrated total soil respiration was lower in the intact and drained forest than in the oil palm plantation, at 20.2 ±3.4, 18.7 ±1.1 and 26.4 ±1.7 Mg C ha-1 y-1, respectively. A similar pattern was seen in the heterotrophic respiration for the same land uses, 9.6 ±7.7, 15.7 ±1.0 and 22.9 ±2.0 Mg C ha-1 y-1, respectively. When extrapolated to the landscape, the percentage of heterotrophic 4 respiration appeared to have significantly increased following drainage, even before the conversion to oil palm, with percentages of 47.6 ±10.1, 83.9 ±7.3, 86.6 ±1.9 for intact forest, drained forest and oil palm plantation, respectively. The average litterfall in the three land uses was not significantly different, at 26.3 ±4.1, 23.2 ±4.2 and 18.6 ±3.5 kg dry litter ha-1 d-1 respectively. Overall, the C fluxes results produced in this thesis point towards a negative C balance (i.e. net ecosystem loss of C) for the drained forest, a pronounced negative C balance for the oil palm plantation and a near neutral balance for the intact forest. Other relevant findings in the study were: (1) the impacts of N fertilizer application in the oil palm plantation lasted only a few days and were unlikely to have significant consequences on the annual C budget; (2) concerns over the diurnal variability of carbon dioxide fluxes are not particularly pertinent in these tropical peatlands; and (3) the principal soil property affected by drainage and land-use change was the abundance of logs in the soil. In summary, the results produced in this thesis represent noteworthy data about the C budget and C dynamics in tropical peatlands and will help decision making by policy makers and land managers for sustainable use of these ecosystems.

In einem Anbauversuch wurden auf einem leichten, trockenen Standort acht unterschiedliche Fruchtfolgen mit Energiepflanzen hinsichtlich ihrer ökologischen und ökonomischen Auswirkungen untersucht. Ertraglich schnitten Anbausysteme mit Mais, Futterhirsen (Sorghum) und Zuckerrüben am besten ab. Diese drei Fruchtarten erzielten auch hohe Deckungsbeiträge. Wintergetreidepflanzen erreichten nur ein mittleres Ertragsniveau, zeigten aber die geringsten Ertragsschwankungen. Zweikultursysteme mit Mais und Sorghum erreichten zwar höhere Erträge, waren jedoch nur geringfügig wirtschaftlicher. Auch hinsichtlich ökologischer Kriterien konnte festgestellt werden, dass mit geringfügigen Maßnahmen wie Zwischenfruchtanbau, Blühstreifen oder Stickstoffreduzierung am Gewässer eine nachhaltige und vielfältige Landnutzung möglich ist.