The ability to perform nucleic acid-based detection of plant pathogens away from conventional laboratory facilities has the potential to be beneficial in situations where results are required very rapidly or where resources and access to laboratory equipment are limited. Methods for use in such situations must combine sensitivity and specificity with rapid and simple workflows. The aim of this project was to investigate aspects of on-site testing for plant pathogens by developing detection methods for a range of target species. Detection methods based on loop-mediated isothermal amplification (LAMP) exhibit characteristics which make them potentially suitable for on-site testing. LAMP-based methods were developed for detection of plant pathogens with three potential non-laboratory testing scenarios in mind: testing during plant health inspection (assays for Phytophthora ramorum, P. kernoviae and Guignardia citricarpa); testing to assess inoculum levels in the processing of plant products (an assay for Botrytis cinerea); and testing in under-resourced settings (assays for Cassava brown streak virus and Ugandan cassava brown streak virus). In developing these detection methods, attempts were made to address some of the specific requirements of potential end-users of the tests in each case. For testing in the context of inspection, a particular emphasis was placed on the need for simple, rapid methods for nucleic acid extraction. As well as investigating the use of rapid extraction methods in conjunction with LAMP, work was also carried out to investigate how on-site nucleic acid extraction using lateral flow devices could be integrated with current field and laboratory testing for P. ramorum.

The potyvirus Turnip mosaic virus (TuMV) is a major constraint on the cultivation of a wide range of plant species worldwide. It causes significant economic losses in brassica species such as Chinese cabbage (Brassica rapa), which is one the most important vegetable crops in the world. The B. rapa line RLR22 has broad-spectrum resistance to TuMV, which is undefeated. Many recessive resistances against plant viruses in the Potyvirus genus are based on mutations in plant eukaryotic translation initiation factor 4E (eIF4E), or its isoform eIF(iso)4E . B. rapa has three eIF4E genes and three eIF(iso)4E genes. Segregation following a cross between RLR22 and the TuMV-susceptible R-o-18 line of the closely related B. rapa ssp. trilocularis revealed the resistance was due to a recessive gene, retr01 that was epistatic to a dominant gene, ConTR01. My research revealed that retr01 is BraA.eIF(iso)4E.a and that ConTR01 is probably BraA.eIF(iso)4E.c. It also showed that the highly sought after broad-spectrum resistance to TuMV is due to a novel, recessive, natural mechanism, based on the mis-splicing of BraA.eIF(iso)4E.a in B. rapa. This results in a range of eIF(iso)4E splice variants, the most common of which retained the whole of intron 1 and appears to be non-functional for the virus. As the susceptible parent in the original cross, R-o-18, was a different sub-species to RLR22 (B. rapa var. pekinensis, Chinese cabbage), the genetic inheritance of resistance was also investigated in crosses with Chinese cabbage lines; F2 segregation ratios were consistent with those predicted for the single recessive gene (retr01 ). Yeast two-hybrid interactions between the viral protein genome-linked (VPg) of TuMV and eIF(iso)4E from B. rapa seem to be TuMV isolate-specific. Aphid transmission experiments to investigate the complementation of an eIF(iso)4E Arabidopsis thaliana knockout line with B. rapa BraA.eIF(iso)4E.a confirmed the earlier results from mechanical inoculation of these plants. The inability of TuMV to access multiple copies of eIF(iso)4E in Chinese cabbage and the broad-spectrum of the resistance, suggest it may prove to be durable.

The onion thrips, Thrips tabaci (Thysanoptera, Thripidae) is a polyphagous pest of Allium crops in the UK and considerable effort and expenditure is employed in its control. Despite this, overall understanding of the biology and behaviour of T. tabaci is poor and this project addresses some of these deficiencies in knowledge. The relationship between T. tabaci development and temperature was investigated using linear and non-linear descriptors. The most accurate descriptor was a non-linear logistic curve. A forecasting system was developed to predict population trends in the field using field temperature data to estimate the progression of development over time. It was not possible to predict field population trends accurately and possible reasons for this are discussed. The effect of temperature and of leaf quality on behaviour was examined. A range of different behaviours were identified, classified and shown to have a direct relationship with both temperature and leaf quality. The potential for such information to help to explain and predict patterns of behaviour seen in the field is discussed. The diel periodicity of the intra-plant distribution of T. tabaci was examined and a clear pattern identified. A high proportion of adults were located on exposed portions of host plants in the early afternoon. An experiment was conducted, focusing on this potential window of vulnerability, using a novel control technique involving irrigation. No significant control of thrips was achieved, but further investigations into the potential of such strategies are recommended. Field populations of T. tabaci were monitored between 2004 and 2008. Throughout this period thrips were most numerous in late summer and overwintered as adults. The monitoring data were examined in light of what has been learnt about T. tabaci biology and behaviour in this study. Recommendations are made about future work on forecasting and control.

No description available.

Despite the existence of an extensive literature on the morphology, autecology, utilisation, and eradication of Pteridium aquilinum, relatively little research has been done on the Pteridium-grassland ecosystem of Scottish rough grazings. This study is a systematic and semi-quantitative investigation of the influence of Pteridium competition on its associated vegetation and soils, based on field and soil laboratory techniques. It is postulated that the differential response of moorland species to varying degrees of bracken dominance and the modification of soil morphological and chemical characteristics by the dominant plant species is partly responsible for the well-known association of Pteridium aqutlinum with Festuca-Agrostis - brown forest soil ecosystems. This hypothesis is tested in the field in three contrasting upland environments in Scotland. The influence of varying densities of bracken on three facets of the vegetation - soil association is examined: (I) the characteristic particularly the biomass, of the ground vegetation as a whole (2) the species composition of the herb layer and (3) the morphological characteristics of the soil. The degree of dominance of bracken is defined in a semi-quantitative manner and correlated with indices of the vigour of the ground vegetation and its species composition. A classification of common dry moorland species, according to their response to Pterldlum competition is produced. The association of Ptertdlum aqutltnum with soils of brown forest soil morphology is studied and the importance of the rhizome system In modifying the physical characteristics of the soil and the distribution of organic matter in the profile demonstrated. The tendency of bracken to modify the morphological characteristics of podsolised soils is shown. Subsequent laboratory analysis substantiates the morphological evidence of the relationship between Pteridium-dominated vegetation and soil type. By revealing the differences in nutrient status between bracken soils and podsolised heath soils and the seasonal variation In nutrient levels, the efficiency of Pteridium in cycling nutrients through the ecosystem Is suggested. The ability of Pterldium to release phosphate from inorganic sources in the soil is demonstrated by laboratory experiment, anomalously high available phosphate levels in the subsoil of bracken soils having been revealed by routine analysis. Laboratory experiment also suggests that the modification of iron pans by Pteridium rhizomes may have a chemical as well as a physical component. The evidence of Pteridium's Influence on vegetation and soil characteristics allows preliminary comment to be made on the ecological significance of bracken eradication schemes.

Field, glasshouse and laboratory experiments and field surveys were done in Western Australia to develop control strategies for various non-persistently aphid-borne viruses of grain legumes, celery and carrots and for the fungally-transmitted lettuce big vein disease (LBVD). In a range of legumes, extreme resistance to Alfalfa mosaic virus (AMV) was found in Vicia faba cv. Ascot, Hedysarum coronarium cv. Grimaldi, and Lens culinaris IL5480, to Cucumber mosaic virus (CMV) in Lathyrus cicera ATC80521, L. clymenum C7022, Ornithopus sativus cv. Cadiz, and V. sativus cv. Languedoc, and to Pea seedborne mosaic virus (PSbMV) in all accessions and varieties of Cicer arietinum and L. culinaris and some of L. sativus and most pasture legumes tested. No sources of extreme resistance to Carrot virus Y (CarVY) was found to carrot germplasm. The first reports of seed transmission of AMV in Vicia faba and of CMV in Pisum sativum, V. faba, V. narbonensis and eight pasture legumes were made. No evidence for the seed transmission of CarVY was found. Plants of V. faba infected early with AMV recovered while plants infected later incurred yield losses (up to 45%). In contrast, plants of C. arietinum infected with AMV when young were killed. L. culinaris plants infected with AMV and CMV suffered high yield losses (up to 90%) dependent on the age of plants when they were infected. Plants of lettuce infected with LBVD when young often failed to form ‘hearts’ but leaf symptoms were mild, whereas later infected plants had more severe leaf symptoms. Spatial patterns of disease spread were monitored and implications for disease control discussed for CarVY and LBVD. The incidence of CarVY in carrot crops was often high in a wide selection of varieties grown throughout Australia. CarVY was determined to have a wide host range within the Apiaceae family but not in other plant families. No evidence for reservoirs of CarVY was found in species other than carrot, despite extensive surveys of known Apiaceous hosts. CarVY was readily transmitted by a wide range of aphid species in a non-persistent manner. Control strategies for Celery mosaic virus (CeMV), by instigation of a ‘celery free period’ and LBVD by combining resistant lettuce varieties and plastic mulch were demonstrated. New control measures for AMV, CMV, PSbMV and CarVY were also discussed.

Researchers decided to explore whether diatomaceous earths (DEs) might meet the grain protection demands of rural households. These inert dusts are non-toxic to mammals but deadly to insects absorbing the wax from the insect’s cuticle which leads to water loss and death. Following laboratory studies, promising commercial DEs were trialled collaboratively by researchers and farmers as grain protectants in Zimbabwe. Protect-lt and Dryacide applied at 0.1%w/w were as effective as the synthetic conventional insecticide, Actellic Super dust, in limiting insect damage on stored maize, sorghum and cowpea grains for periods of eight months. However, laboratory studies revealed that the devastating larger grain borer now spread throughout many African countries was more tolerant to DEs than the storage pests found in Zimbabwe. This initiated the testing of DEs in combination with other products. Higher DE application rates of 0.25%w/w, a DE-pyrethroid combination and a local African DE were successfully tested by farmers in Tanzania. During this work the importance of the link between a potential technology such as DEs and the wider post-harvest service provision context became clearer. This led to the exploration of this context using: an enquiry approach to learn about post-harvest decision making amongst diverse rural households; and an experimental learning process to empower farmers. As the nature of the different stakeholders within the agricultural innovation system and their information requirements became more central to the work, the importance of the patterns of interaction amongst them and associated attitudes was repeatedly revealed. A learning alliance of key post-harvest stakeholders was established to explore and test opportunities for stakeholders to work together differently to help overcome institutional and other constraints.

Over the last three decades, concern about food safety and the management of natural resources has increased. Instigated by the previous EU pesticide review, (EU 91/414) carrot growers in particular have been hit by the revocation of several post-emergence herbicides. There is real concern among growers that this may impair profits. To identify alternative weed control strategies, a modelling framework capable of simulating the impact of alternative weed management strategies on long-term weed population dynamics, was proposed. Scentless mayweed (Tripleurospermum inodorum) was chosen as model weed species. The system represented in ECOSEDYN (Effects of Cultural control and climate On SEedbank DYN For each component model in ECOSEDYN the literature was reviewed to identify the best mathematical representation and then the model was parameterised. To improve accuracy of model projections and address gaps in knowledge, field experiments were conducted in two areas: soil cultivation, and plant growth and reproduction. The results of the cultivation experiments revealed that key assumptions in models for weed seed re-distribution are incorrect. The experiments focusing on plant growth and reproduction resulted in a novel approach to the modeling of biomass increase, flowering and seed shedding where the different processes were quantitatively and temporally linked using Beta functions. amics), comprises a six-year crop rotation: one year of carrot and five years winter wheat and repeated four times. The weed management strategies consist of combinations of cultural control measures (sowing time and crop maturity time). In addition, the interaction of climate with the cultural control measures was assessed by implementing two future climate scenarios, (‘No change’ vs ‘Heating up’) based on weather data over the last 18 years. The results of the ECOSEDYN simulations showed that, regardless of the prevailing climate, choosing a fast maturing carrot cultivar is by far the most important factor in maintaining the weed seedbank low. In addition, the risk for higher seedbank levels in the long-term under ‘Heating up’ climate is largest if carrot is continuously sown late.

MYB90 and MYB75 are two MYB transcription factors that regulate anthocyanin biosynthesis in Arabidopsis. Prior to this study a microarray experiment indicated that MYB90 was required for senescence associated anthocyanin biosynthesis. The role of MYB90 during senescence was investigated using a MYB90 knockout insertion mutant, IM28. Gene expression studies at different time points during the development of the seventh rosette leaf showed that MYB90 regulates anthocyanin biosynthesis genes and MYB75 during senescence. The absence of MYB90 expression reduced photosynthetic performance at two time points during development. Analysis of anthocyanin and flavonoid content showed that there was reduced anthocyanin biosynthesis in the absence of MYB90 expression. The role of MYB90 and MYB75 during high light stress was investigated by analysing the photosynthetic performance and anthocyanin content of high light treated IM28 and MYB75 RNAi plants. MYB90 is required for increased resistance during high light stress, which reflected anthocyanin levels. However, there was eventual compensation for the absence of MYB90 expression in prolonged high light stress. MYB75 was also required for increased resistance to high light stress, but this was not reflected in the anthocyanin levels. The spatial and temporal regulation of MYB90 and MYB75 was investigated using transgenic plants containing promoter: GUS fusions. MYB90 promoter activity was mainly localised to vascular tissue during senescence and low nitrogen/high glucose treatment. MYB75 showed differential tissue specificity in different treatments. The transcriptional regulation of the MYB90 promoter was analysed using promoter deletion GUS: fusions. A senescence specific activation region and a repressor region of the promoter were identified.

Concerns regarding carbon emissions, increasing demands on water supplies and environmental pollution have meant that the European protected horticulture industry is being challenged to develop more sustainable greenhouse climate management systems. These new systems can however potentially impact on pest and disease (P & D) pressures and the efficacy of biological control agents (BCAs). This thesis aimed to use a combination of experimental work and simulation models to compare novel and traditional greenhouse climate management scenarios in Spain and the Netherlands using two model P & D systems. These were Oidium neolycopersici (powdery mildew) and its BCA, Bacillus subtilis, on tomato, and Tetranychus urticae (the two-spotted spider mite) and its BCA, Phytoseiulus persimilis, on ornamentals. Experiments showed that latent period, disease development and sporulation of Oidium neolycopersici were strongly influenced by temperatures between 10-33°C and that the control efficacy of B. subtilis was significantly influenced by temperature and humidity in the ranges 10-33°C and 50-95% RH. The functional response of P. persimilis was found to be significantly affected by ambient humidities of 57-99% RH, with predation highest at 85% RH and lowest below 76% RH. These results, in combination with existing data, were used to construct dynamic P & D models. A greenhouse climate model, based on observed temperatures in European greenhouses, was constructed to provide data on the diurnal and seasonal variation in temperature and humidity for different climate management scenarios. The predictions from the P & D models allowed climate control regimes in different greenhouses in Spain and the Netherlands to be identified, which minimised P & D pressures and maximised the efficacy of the BCAs. The implications of these findings for greenhouse climate management are discussed.