Search

The carbon sink potential of temperate forests plays a central role in climate change mitigation strategies, and soil organic carbon sequestration can be achieved through afforestation and reforestation. Yet, the main factors responsible for influencing the dynamics of long-term forest carbon stabilization within the soil are poorly understood. This study investigates how different forest management practices affect the carbon sequestration potential within the soil organic surface horizon (Litter, Fragmented and Humic) under second rotation Picea sitchensis plantations in the UK. Fieldwork activities were carried out in two experimental sites of upland Britain to collect samples related to soil carbon quantity, carbon quality and the dynamics of fine root turnover. Two separate experiments were carried out. The first was on a pre-existing experimental site (Forest of Ae) to assess differences between conventional stem-only harvest, whole-tree harvest and fertilization. The second experiment was designed on an existing trial (Clocaenog forest) to compare a stand with no interventions in the overstory or understory since the research area was established in 2002 (Control), and one stand in transformation to continuous cover forestry (irregular shelterwood). At the Forest of Ae, results revealed that fertilization practices had a significant, positive effect on soil carbon storage within the L horizon (conventional harvest p < 0.01, whole-tree harvest p < 0.01). Brash retained on site at the time of harvesting had a significant, positive effect on soil carbon storage within the F horizon (conventional harvesting p = 0.03 and fertilization p = 0.01). Results also suggest that soil nitrogen concentration can be used to predict the soil carbon storage of each organic horizon (adjR2= 0.931). Also, the fine root necromass within the 15 to 30 cm soil depth is significantly higher (p = 0.02) in the fertilized treatment when compared with whole-tree harvest, although this does not affect the carbon storage within the H horizon. At Clocaenog forest, transformation to irregular shelterwood had a highly significant, positive effect on soil carbon storage within the soil H horizon (p < 0.01). Soil nitrogen concentration, C:N ratios and available nitrogen all consistently point towards a higher presence of nitrogen in the Control treatment which could be responsible for SOC and N mineralization in the H horizon. Overall, the study shows that forest management decisions do affect C storage in the organic soil horizons of commercial forest plantations in upland Britain. These dynamics need to be taken into account in C and GHG balances and guidelines for soil protection.

Mathematical models of tree diseases often have little to say about how to manage established epidemics. Models often show that it is too late for successful disease eradication, but few study what management could still be beneficial. This study focusses on finding effective control strategies for managing sudden oak death, a tree disease caused by Phytophthora ramorum. Sudden oak death is a devastating disease spreading through forests in California and southwestern Oregon. The disease is well established and eradication is no longer possible. The ongoing spread of sudden oak death is threatening high value tree resources, including national parks, and culturally and ecologically important species like tanoak. In this thesis we show how the allocation of limited resources for controlling sudden oak death can be optimised to protect these valuable trees. We use simple, approximate models of sudden oak death dynamics, to which we apply the mathematical framework of optimal control theory. Applying the optimised controls from the approximate model to a complex, spatial simulation model, we demonstrate that the framework finds effective strategies for protecting tanoak, whilst also conserving biodiversity. When applied to the problem of protecting Redwood National Park, which is under threat from a nearby outbreak of sudden oak death, the framework finds spatial strategies that balance protective barriers with control at the epidemic wavefront. Because of the number of variables in the system, computational and numerical limitations restrict the control optimisation to relatively simple approximate models. We show how a lack of accuracy in the approximate model can be accounted for by using model predictive control, from control systems engineering: an approach coupling feedback with optimal control theory. Continued surveillance of the complex system, and re-optimisation of the control strategy, ensures that the result remains close to optimal, and leads to highly effective disease management. In this thesis we show how the machinery of optimal control theory can inform plant disease management, protecting valuable resources from sudden oak death. Incorporating feedback into the application of the resulting strategies ensures control remains effective over long timescales, and is robust to uncertainties and stochasticity in the system. Local management of sudden oak death is still possible, and our results show how this can be achieved.

There has been growing interest in the use of plant biomass, particularly secondary cell walls, as a sustainable feedstock for second generation biofuels. However, the feasibility of converting cellulose and other cell wall carbohydrates into biofuels and other chemicals is hindered by the hydrophobic phenolic polymer, lignin, which makes the secondary cell wall inherently recalcitrant to breakdown and hampers enzymatic hydrolysis. Secondary cell walls with altered composition naturally occur in xylem fibres of 'Lord Lambourne' apple trees infected with Apple Rubbery Wood associated Virus (ARWaV). However, the development of symptoms has not been described in detail and the mechanism by which ARWaV modifies the secondary cell wall has never been studied. In this study, a detailed morphological and biochemical assessment of symptoms was performed during symptomatic wood development in branches infected with ARWaV. Symptomatic xylem was characterised by fibres with very thick secondary cell walls and overall, contained a third less lignin and a two-fold higher levels of soluble phenolics, whilst the total cellulose and hemicellulose content remained unchanged. These compositional modifications resulted in a two-fold increase in the glucose released from symptomatic xylem digested with cellulase. Using a systematic biological approach the molecular mechanism that determines secondary cell wall alterations during symptom development, specifically poor lignification was investigated. Proteomic and metabolomics analyses together demonstrated that the first committed stage of lignin biosynthesis, involving the conversion of phenylalanine to cinnamic acid via phenylalanine ammonia lyase, was disrupted in symptomatic xylem. RNA-sequencing analysis was also used to examine transcriptomic changes associated with symptom development. However, gene expression patterns were largely inconsistent with the biochemistry of symptomatic wood and other omics analyses indicating a potential tissue-sampling bias. Functional analysis experiments of apple MYB and NAC transcription factors in the Arabidopsis hypocotyl are also described, revealing potentially novel roles for MYB83 during secondary cell wall formation. Overall, the experiments performed in this study provide a comprehensive analysis of symptom development in the xylem of branches infected with ARWaV.

Mango (Mangifera indica L.) is an economically important fruit crop grown in the tropics. This crop species is popularly consumed as fruit in Malaysia. Once ripening is initiated, the process proceeds at a fast rate making postharvest life short. Excessive softening during ripening is a major challenge in the postharvest storage of fruits as it renders the fruits unfit for long term storage leading to heavy postharvest losses. The improved storage of mango fruit would greatly enhance the economic potential of this crop. Hence, an in-depth understanding of the ripening-related events is essential to facilitate the development of strategies to improve fruit quality and reduce post-harvest losses. Fruit softening during ripening involves the trafficking of cell wall polymers and enzymes. The Rab (Ras related proteins in brain) GTPase family are key players in vesicle trafficking. Therefore it is important to understand the linkage between the Rab (Ras related proteins in brain) GTPases and the differential softening rate in fruit varieties for effective postharvest management, hence this research. The first part of this research was conducted to characterize the ripening process of the mango varieties according to their postharvest quality attributes. The study was carried out on 'Chokanan' (CK), 'Golden phoenix'(GP) and 'Water lily'(WL) as exemplar mango varieties for which there are limited number of studies at the postharvest and molecular level respectively. Significant increase (P < 0.05) in the soluble solid concentration (SSC), ethylene production, respiration rate and weight loss coupled with significant decline in titratable acidity (TA) and fruit firmness occurred as ripening progressed. Significant differences were also found among the mango varieties. The analysis revealed that 'Chokanan' (CK) had greater fruit firmness (P < 0.05) than 'Golden phoenix' (GP) and 'Water lily' (WL) mango varieties. Multivariate analysis separated the unripe and ripe fruits according to their physicochemical attributes. The ripening stages (unripe and ripe) as defined based on the measured postharvest parameters were selected for further studies. Characterization of the mango Rab (Ras related proteins in brain) GTPase family by comparative analysis was performed. The study took advantage of the publicly available databases and transcriptome datasets to identify and conduct comprehensive comparison of the mango Rab (Ras related proteins in brain) GTPase family. A total of twenty-three members of the mango Rab (Ras related proteins in brain) GTPase family with similarity to those obtained from Arabidopsis thaliana and tomato (Solanum lycopersicum) were identified. Sequence similarity analyses and identification of conserved motifs, diagnostic of specific Rab family and subfamilies enabled the bona fide assignment of the deduced mango proteins. A transcriptomic approach by RNA-sequencing (RNA-seq) was performed to investigate the molecular basis of mango ripening using two ripening stages (unripe and ripe) and two mango groups with contrasting firmness (P < 0.05). It is worth pointing out that this is the first experiment reported on Southeast Asian mango varieties employing the RNA-sequencing (RNA-seq) approach. Pairwise comparison between the ripening stages (unripe and ripe) of Chokanan ('CK') and Pool ('P') mango groups identified 9,765 and 13,651 differentially expressed genes (DEGs) (adjusted P value < 0.05; log2 fold change (FC) > 1 or log2 fold change (FC) < -1) respectively. On the other hand, comparison between mango groups at the same ripening stage identified 18,258 and 10,521 DEGs at the unripe and ripe stage respectively. Genes involved in the metabolism of energy, sugars, hormones and cell wall were differentially expressed. Notably, the Rab (Ras related proteins in brain) genes were also detected as differentially expressed suggesting the involvement of vesicle trafficking during ripening. Interaction analysis showed that the proteins involved in vesicle trafficking and cell wall softening were interconnected providing further evidence of the involvement of the Rab (Ras related proteins in brain) GTPases in fruit softening. The expression of ten genes evaluated by both RNA-sequencing (RNA-seq) and reverse transcription quantitative polymerase chain reaction (RT-qPCR) showed a good correlation (R2 = 0.769) indicating a good consistency between both techniques and the reliability of the RNA-sequencing data. Correlation analyses showed a significant relationship (P < 0.05) between the expression level of the RabA3 and RabA4 genes and fruit firmness at the unripe stage of 'Chokanan' (CK), 'Golden phoenix' (GP) and 'Water lily' (WL) suggesting that the differences in the Rab gene expression level may play an important role in the contrasting firmness of these varieties. The expression levels of these genes in other mango varieties were also analysed by reverse transcription quantitative polymerase chain reaction (RT-qPCR) but no consistent regularity was found suggesting the contribution of other factors to bring about softening in the varieties. In summary, these findings have provided insights into the molecular mechanisms underlying mango ripening and lay a foundation for the exploration of novel genes towards future development of strategies to improve fruit quality of mango and other non-model fleshy fruits.

Strawberries are a valuable fruit crop for the UK and worldwide. The UK berry market was worth £1.2 billion in 2016, with strawberries as 50% of this market. One of the major threats to the industry is the water-borne disease strawberry red core, caused by the oomycete pathogen Phytophthora fragariae. One way to increase the resilience of the industry to this pathogen is breeding for genetic resistance in plants. To do this effectively, a strong understanding of the pathogen, including identification of avirulence genes is required. To investigate this, ten isolates of P. fragariae and three isolates of the related raspberry pathogen Phytophthora rubi were sequenced with the Illumina MiSeq system. PacBio sequencing was used on an additional isolate of P. fragariae, BC-16, to produce an improved reference assembly of 91 Mb in 180 contigs. Following assembly of these genomes and gene prediction through RNA-Seq guided and ab initio methods, effector genes were identified. Further investigations utilising orthology analysis, variant calling and differential expression analysis allowed for the identification of candidate avirulence genes for races UK1, UK2 and UK3. A very strong candidate for the avirulence gene in the UK2 race was identified as an RxLR effector named g27513 in BC-16. Further investigations did not identify clear cis or trans DNA sequence polymorphisms causing the variation in expression across races. Three of the identified races (UK1, UK2 and UK3) clustered into a single population with low levels of nucleotide diversity and a mixture of clonal and sexual reproduction which may possibly be undergoing recovery from a recent genetic bottleneck. The candidate genes provide future targets for identifying avirulence genes to aid in effector guided breeding approaches to produce disease resistant strawberry plants. This work also provides resources for further investigations of this pathosystem and the Phytophthora genus as a whole.

The apple industry in the UK produces half a million tonnes of fruit a year; its most economically important disease is apple scab caused by the fungal pathogen Venturia inaequalis. Mixing cultivars with differing resistance to the pathogen, in the same orchard, has been shown to reduce the levels of apple scab. In this study we investigated the population genetics and epidemiology of apple scab in mixed cultivar orchards. Using molecular techniques, populations of V. inaequalis differed on the hosts present in an orchard, this difference remained over time. This indicates a "super race" of the pathogen that can infect all of the cultivars present has not emerged and become dominant, therefore making the concept of mixed cultivar orchards more feasible. The lack of emergence of a super race might be, in part, due to asexual conidia spores forming a proportion of primary inoculum as opposed to being purely from sexually produced ascospores. Conidia accounted for 20-50% of the primary inoculum in the orchard studied. The importance of conidia is likely to be heavily dependent on local conditions. For a reduction in levels of apple scab in a mixed cultivar orchard it is important that the cultivars present have differing resistance. Comparing scab populations on a number of desert and cider cultivars showed that populations on cider cultivars are most different. An assembled V. inaequalis genome is presented and was used to align isolates from different cultivars within the same orchard. Looking at differences between these isolates has indicated that there is a lack of mating occurring between isolates from the different cultivars present within the same orchard. This indicates that mating is most likely initiated between isolates on the same leaf. The findings of this thesis could contribute to apple orchard practises, regarding apple scab control, in the short, medium and long term.

Sweet chestnut Castanea sativa has been regarded as a Roman archaeophyte in Britain since the eighteenth-century AD. This research re-examined that thesis, collecting new evidence from genetic, dendrochronological, archaeological and historical analyses, using archived specimens, published reports, peer review and novel fieldwork. The main research and original fieldwork focused on England and Wales, within a British, Irish and continental European context. Sweet chestnut landscapes were identified as ancient inclosures, ancient coppice woods, historic boundaries, historic gardens, historic deer parks and designed parklands, historic formal avenues, and more recent high forest and production coppice. Genetic analysis determined that the oldest British sweet chestnut trees/stools derived from parts of France, Spain, Portugal, Italy and Romania. Some of these sources were refugia during the Last Glacial Maximum for sweet chestnut and other nut-bearing trees (oak, hazel, beech). Innovative clonal analysis verified individual tree and stool antiquity for the first time. Modern (post-AD 1800) trees and coppice in Britain were genetically differentiated from ancient trees and coppice; historic garden trees (from the 12th.-13th. centuries AD) originated in N Portugal and N Spain; and Welsh sites differentiated from Irish and English sites. Dendrochronological analysis discovered that sweet chestnut tree ring series replicate oak reference chronologies, so archaeological specimens of sweet chestnut wood can now be precisely dated. Several iconic ancient trees were dated accurately for the first time, the oldest from AD 1640. Archived specimens purported as 'Roman' 'sweet chestnut' were re-examined and rejected as neither. No pre-AD 650 sweet chestnut finds could be verified as grown in Britain. The earliest written record of sweet chestnut growing in Britain was from AD 1113. Other 12th. century AD records evinced nut growing and coppicing: these sites pre-date their written record, possibly by several centuries. Overall, no evidence was found for the 'Roman introduction' thesis. Further research should focus on finding sweet chestnut pollen and wood specimens amenable to dating.

Malaysian carambola (Averrhoa carambola L.) B10 variety is one of the promising exotic tropical fruit traded in the global market. The alarming demand for carambola was stimulated by its unique shape and flavour, increasing health consciousness and great potential in fresh-cut industry. Nevertheless, carambola is a highly perishable commodity that greatly impairs its postharvest quality and long term storability. Therefore, investigations were carried out to verify the potential of putrescine (PUT), spermidine (SPD) and spermine (SPM) as a postharvest dip treatment for maintaining quality, reducing chilling injury (CI) and extending the storage life of carambola. Carambola at Index II was dipped in different concentrations (0.0, 0.1, 1.0 and 2.0 mM) of PUT, SPD and SPM, and then stored at 3oC (±0.5), with 85-90% RH. Physicochemical changes and fruit quality attributes were made at harvest, 7 day intervals for 28 days of cold storage plus 6 days at 22±1oC for shelf life. PUT treatment effectively lowered the weight loss, maintained peel color (L*, C*, ho), retained higher firmness, reduced the rate of respiration and ethylene emission, suppressed the degradation of soluble solid content (SSC) and titrable acidity (TA) throughout shelf life. Moreover, PUT-treated fruit substantially suppressed the advancement of dominant softening enzymes in carambola such as β-galactosidase (β-gal), polygalacturonase (PG) and pectin methylesterase (PME). The softening enzymes activity trends in PUT-treated fruit were concomitant with less apparent changes in flesh firmness. Accordingly, the applied PUT treatment significantly reduced CI symptoms in carambola. Lipid peroxidation levels (MDA) and membrane leakage activity were declined in fruit treated with PAs, and the reduction was more distinct in fruit treated with PUT. This study demonstrates that the influence of PUT on postharvest quality and protection of cell membrane against chilling damage was more profound at the highest concentration (2.0 mM). Ascorbic acid (AA), total antioxidant (TAA) and total phenolic contents (TPC) were enhanced to greater levels in PAs-treated fruit, while control fruit experienced significant losses of these bioactive compounds throughout chilling storage. Highest SPM concentration (2.0 mM) exhibited the best results on increasing TAA through an increment of TPC. On the other hand, AA content was increased with the lower concentration of SPD (1.0 mM). Exogenously supplied PUT induced tremendous endogenous PAs accumulation in carambola tissue, particularly free PUT and SPD concentrations. Such responses suggest that PUT may stabilize and protect cellular membrane integrity against chilling stress. In general, the increment of endogenous PAs with PUT treatment induced stress tolerance mechanisms in carambola during cold storage. An attempt to identify unknown genes sequence of SAMDC, ADC, ACS and ACO in carambola was carried out. In line with this, an efficient extraction protocol of RNA isolation from carambola mesocarp tissue was optimized. CODEHOP features were exploited to design degenerate oligonucleotide primers and RT-PCR approach was utilized to attest degenerate primer specificity. Phylogenetic trees revealed the sequenced products of SAMDC, ADC, ACS and ACO in carambola exhibited close evolutionary relationship with protein sequences present in muskmelon, peach, tobacco and sweet oranges respectively. These present findings throw light on the potential of PAs particularly PUT at a dose of 2.0 mM for 5 min could be an effective means for maintaining postharvest quality and protection against CI, with a net increase in shelf-life of B10 carambola.

Strawberry plants produce one of the highest quantities of soft fruits in the UK. The plants are grown in fields and glass houses where the environment is hard to completely control. There are a variety of biotic and abiotic stresses that affect the plants' production rate, lifespan and the quality of the fruit. It is possible to mitigate these stresses, but first they must be detected as early as possible. Drought, or water deficit, is an environmental stress which impacts the plants' productivity. The stress can be monitored by looking for visible signs, but detection by a person can occur too late. Using technology could improve the detection before a person can see the signs. One such technology is hyperspectral imaging. Hyperspectral imaging has the potential to detect certain features in plants by examining their reflectance spectrum. In this work, a spectral range from visible to near-infrared will be used to record reflectance changes from plants during drought experiments. The data collected in this thesis comprises strawberry plants undergoing drought conditions. Initial inspection of the data suggests that a difference in reflectance may exist throughout this time period, but the data is noisy and changes subtle: using whole-plant measures may not be as accurate as selecting individual leaves. Also, particular leaves may be more suited to hyperspectral inspection than others. Therefore, the work in the rest of the thesis focuses on automatically selecting suitable quality leaves from which to derive hyperspectral measures. Leaf locations are selected automatically by combining 2D spatial information and select wavelengths from the hyperspectral data to extract leaf features (leaf centres and vein patterns), and this information is used to initialise a level set shape model to segment the leaves. The results from the 2D segmentation are evaluated, and results suggest clearly visible leaves can be segmented well automatically. However, it is hypothesised that further information is required to select the best possible leaves for analysis from the set of segmented leaves, so 3D plant information is then incorporated into the approach. The orientation of leaves, and shadows, are likely to influence the spectral signatures, and occluded leaves are undesirable. Therefore, the leaf orientation, position and height are taken into consideration when selecting leaves for measurement. To do this, 3D surface models are created from multiple digital images captured at the same time as the hyperspectral data. The hyperspectral data is then mapped onto the model and suitable leaves are identified based on their orientation, height and distance from the centre of the plant. This allows for selection of a subset of leaves as sources of hyperspectral measurement for each plant. This approach, from segmentation to leaf selection and measuring, is built into a fully-automated pipeline, and evaluated. The resulting leaves are selected from the other time points in the time series data, and the spectral signatures are compared to the initial manual inspection. The automatically selected leaf data show similar spectral responses to the manual approach. The challenge of detecting changes in these spectral profiles is investigated and discussed.

Brazil is the world's sixth largest cocoa producer with 270,000 tonnes of cocoa produced per year. In a world with an increasing demand for chocolate, but with agriculture threatened by climate change, the chocolate industry is worried about a possible shortage of cocoa. Furthermore, growing cocoa is a main cause of deforestation. However, in the state of Bahia, Northeast Brazil, cocoa is grown in traditional agroforests called 'cabrucas' which maintain a forest cover. Cocoa, an understorey crop, is planted under the shade of native Atlantic Forest trees and exotic fruit trees introduced by the farmers. These cabrucas have high conservation value but very low cocoa yield. In my thesis I investigate the factors limiting cocoa yield and how to increase yield in cabrucas. I explore the role of shade trees and the nutrient dynamics in litterfall. Finally, I explore the risk that climate change could represent for cocoa production in the future by looking at the effects of an unexpected drought caused by an El Niño Southern Oscillation (ENSO) event between November 2015 and May 2016. My study is based on data collected in permanent transects in 32 randomly chosen cabruca farms in Barro Preto a municipality of Bahia over a period of three years. I also established littertraps in 10 cocoa farms where I intensively studied nutrient dynamics and cocoa yield per tree over 12 months. My results showed that unproductive trees, low cocoa tree density, high shade cover and high cocoa mortality due to drought were the main factors limiting cocoa yield in cabrucas. Surprisingly, adding fertilisers to the cocoa trees did not increase yield. This suggests that there is no nutrient deficiency in cabrucas. In the farms, I found 69 species of shade trees for an average density of 125 ± 32 trees per hectare. Half of the species of shade trees were Atlantic Forest species of conservation value. The litterfall experiment showed the shade tree species and the quantity of litterfall produced, can affect the number of cocoa pods per tree. In cabrucas, a higher number of cocoa pods was found on cocoa trees under shade trees than under no shade. Finally, I showed that the exceptionally severe ENSO-related drought caused 80% loss in yield and 11% cocoa tree mortality in Barro Preto. Climate models predict an increased frequency of strong ENSO events in the future. Farmers in Bahia are not prepared to face regular drought events. The 2015/16 drought affected the dynamics of cocoa production in Brazil: it accelerated the decrease of extensive wildlife-friendly cocoa production in Bahia whereas it increased the development of cocoa production in intensive low shade plantations in the state of Pará. This suggests that climate change could be a threat to traditional cocoa agroforests in Bahia. Developing wildlife-friendly certification schemes and Payment for Ecosystem Services to internalise the value of forest conservation and to encourage farmers to maintain their shade trees could save cabruca systems from going extinct.

Conventional intensive agriculture is largely reliant on high agrochemical inputs and has resulted in damaging environmental impacts including large scale biodiversity loss. More environmentally sustainable agricultural production methods are required. Ecological intensification is an approach which aims to sustainably increase production by using biodiversity-derived ecosystem services and replacing agrochemical inputs where possible. This can be achieved through modifying agricultural management practices to support ecosystem service-providing beneficial species. This thesis investigates the ecological intensification of commercial apple orchards in the UK. Apples are one of the most economically and nutritionally important fruit crops globally and their production relies upon a number of ecosystem services including pollination, pest regulation, and soil fertility services. Alleyway cover crops were trialled as a novel management practice which has the potential to improve a number of orchard ecosystem services. Three different cover crop species mixtures, all based on perennial legumes but each with a different rationale, were compared to a standard mown-grass control. Growing cover crops in the alleyways was provided improved habitat quality for beneficial species, attracting greater numbers of natural enemy taxa including predatory beetles, parasitoids, and active-hunting spiders, without increasing the abundance of crop pests. Greater numbers of pollinators were also observed in alleyways sown with cover crops. Despite the greater numbers of beneficial species recorded in the cover crop treatments, no increases in pest regulation or pollination services were detected and no change in production was observed during the timescale of the study. A second potential benefit of alleyway cover crops is the production of mulch material. Traditionally, organic mulches were used in orchards to help supress weeds underneath the trees, increase soil nutrients, and retain soil moisture, however many of these functions have now been replaced by agrochemical inputs. The cuttings from alleyway cover crops can provide an in-situ source of mulching material. Alleyway cuttings were compared to two traditional mulch materials, compost and straw, and a standard no-mulch control. Alleyway cover crop cuttings boosted numbers of earthworms and enhanced leaf litter decomposition, whilst the traditional straw and compost mulches improved some soil fertility measures including soil organic matter and moisture when compared to the control. In the final study of the thesis, the importance of pollination is quantified and the methods used to assess pollinator dependence and pollination deficits are tested, with recommendations made about the scale at which these experiments should be carried out. Following pollinator exclusion apple yields were found to fall to 55% whilst supplementary hand pollination led yields to increase to 167% of current ‘open’ pollination rates, showing that pollination deficits existed in the study orchards. This study also highlights the importance of pollination for fruit quality, a key deciding factor of a crop’s economic value. Alleyway cover cropping was found to have positive effects on ecosystem service providers both above and below ground. Even relatively inexpensive cover crop mixtures, combined with a reduction in mowing frequency and increase in mowing height, were found to increase numbers of beneficial species. The findings demonstrate the potential benefits of this multi-purpose habitat management method.

Conditions during the autumn (propagation phase), when plants are developing and flowers are initiated, impact upon subsequent fruit production in strawberry (Fragaria x ananassa Duch.). Little is known about the best conditions in which to propagate strawberries, particularly for newly released cultivars from breeding programmes which often struggle to fulfil their yield potential when cropped in a commercial environment. The research presented in this thesis therefore aimed to examine the impact of crop management during the propagation phase on transplant growth, yield potential and the subsequent cropping performance of new Junebearer and Everbearer strawberry cultivars. Five experiments were conducted between September 2013 and 2016 to examine the impact of tipping date, daughter plant position and nitrogen concentration, winter chill accumulation, temperature and light intensity during plant propagation. At the end of the propagation phase for each experiment, a destructive harvest was carried out to analyse treatment effects on transplant growth and yield potential. In the following season, remaining plants were then cropped under conditions designed to replicate a commercial growing system so treatment effects on yield, yield components and cropping profiles could be determined. The results of the experiments confirmed that conditions during the propagation phase impact on the cropping performance of strawberry and showed that there is the potential improve strawberry yield by improving crop management during this important phase. Results also demonstrated that cropping profiles could be manipulated to enhance valuable early-season strawberry yield, which is an important goal in the soft fruit industry at present.

At present, the global population is increasing, while soil and fresh water resources for crop production are declining. It is important to adopt sustainable practices to optimise the use of limited natural resources without compromising the environment, and to enhance continuous production in the long term. The rapid growth of UK strawberry industry has been achieved through the precision use of varieties, nutrients and polythene tunnels. This intensive production has caused significant environmental impacts especially Greenhouse Gas (GHG) emissions from the production. Strawberry powdery mildew (Podosphaera aphanis) is a major fungal disease affecting strawberry production worldwide particularly in polythene tunnels. The disease can result in yield losses of up to 70% of the crop. A ruleQbased system was used in the field trials to predict high risk days of P. aphanis development, taking into account the optimal environmental conditions conducive to conidial germination and disease development. The results (Chapter 3) showed that the use of this prediction system achieved satisfactory control of P. aphanis in commercial strawberry production, with reduced fungicide applications compared with commercial spray programme. The results were consistent in two consecutive years and on different varieties. In addition, it was suggested that the use of the prediction system may also lead to lower GHG emissions associated with fewer fungicide applications, thereby benefit strawberry growers both environmentally and economically. Results from 2014 & 2015 silicon fertigation trials showed that the use of a silicon nutrient via the fertigation system reduced the strawberry susceptibility to P. aphanis and twoQspotted spider mites (Tetranychus urticae Koch) in two consecutive years on different varieties (Chapter 4). In both years, crops received the silicon nutrient only without fungicides had both lower rate of epidemic (r) and lower value of Area Under the Disease Progress Curve (AUDPC) (r = 0.0036, AUDPC = 475 in 2014; r = 0.001, AUDPC = 267 in 2015) compared with the untreated control (r = 0.0042, AUDPC = 662 in 2014; r = 0.0011, AUDPC = 281 in 2015). Silicon also delayed the epidemic buildQup in the silicon nutrient only treatment for approximately two weeks compared with the untreated control. Crops from the silicon nutrient plus fungicides treatment had lower susceptibility (r = 0.0012 in 2014; r = 0.0004 in 2015) than those from the fungicides only treatment (r = 0.0017 in 2014; r = 0.0005 in 2015) suggesting that the silicon nutrient may also enhance fungicides performance in reducing the epidemic buildQup when used together. Moreover, the presence of T. urticae on strawberry leaves was significantly lower (P < 0.001) in plants treated with the silicon nutrient than those without. In addition, initial results suggested that silicon may play a positive role in raising °Brix of strawberry leaf petiole, improving pollen viability, and influencing the length of flower receptacle and stamens. Maltmas Farm has a wide range of semiQnatural habitats that provide food and nesting resources for wild pollinators. Hoverflies, bumblebees and solitary bees were found to be the main wild pollinators that pollinate commercial strawberries at Maltmas Farm (Chapter 5). The number of pollinators in tunnels or open fields significantly correlated with the abundance of strawberry flowers (P < 0.05). Pollinator presence also differed between groups throughout the day and over the seasons. Hoverflies appeared early in the day and were abundant in summer months; bumblebees and solitary bees were present most of the day and throughout the season, whereas honeybees were only active in sunny days. Temperatures, relative humidity and cloud coverage also affected pollinator presence. In addition, pollinator activity was not significantly (P > 0.05) affected by the application of the silicon nutrient via the fertigation system. The integrated use of the prediction system (to reduce fungicide applications and subsequent GHG emissions), the silicon nutrient (to reduce crop susceptibility to P. aphanis and T. urticae), and sustainable farmland management (to encourage the presence of wild pollinators) could help strawberry growers to achieve a more sustainable production.

Minimal processing of fresh-cut pineapple (Ananas comosus L.) is time and labour consuming as it has thick inedible skin and large crown. Liberation of cellular contents at the site of wounding can promote the growth of microorganisms and limit the storage life of fresh-cut pineapple. Therefore, ultrasound treatment at different power input and exposure time was used to investigate its effectiveness on the storage life of fresh-cut pineapple. To determine the antimicrobial effect of ultrasound on the proliferation of spoilage microorganisms three different ultrasound power inputs (17, 25 and 29 W) and treatment times (5, 10 and 15 min) during 7 days of storage at 7 oC were applied on co. Josapine. The application of ultrasound at the power input of 25 and 29 W for 10 and 15 min, respectively, inhibited the growth of mesophilic, lactic acid bacteria and yeast and moulds. On day 5, it was found that 29 W for 15 min treatment resulted in the lowest growth of mesophilic, lactic acid bacteria and yeast and mould counts. However, changes in the proliferation of spoilage microorganism were observed among samples treated at 25 W: 10 min, 25 W: 15 min and 29 W: 10 min. The storage life of ultrasound treated fresh-cut pineapple was extended by 2 days in comparison to those washed in distilled water (dH2O). The ideal ultrasound power input (25 and 29 W) and treatment time (10 and 15 min) were then used to study the effect of treatment on the production of intracellular ROS and extent of oxidative damage in fresh-cut pineapple. Increments in ROS concentration when exposed to ultrasound treatment negatively correlated with populations of mesophiles, lactic acid bacteria and yeast and mould. Higher ROS contents may have induced disease resistance in fresh-cut pineapple. However, increments in power input and treatment time to 29 W and 15 min resulted in the oxidation of polyunsaturated fatty acid (PUFA) as indicated by higher malondialdehyde (MDA) content during cold storage. Ultrasound treatment also invoked oxidative stress and induced defence mechanisms in fresh-cut pineapple by regulating phenolic metabolism and recycling of ascorbate concentration. Induction of phenylalanine ammonia lyase and inhibition of polyphenol oxidase and polyphenol peroxidase activity in fresh-cut pineapple upon exposure to ultrasound treatment resulted in higher total phenolic concentration. Similarly, the redox state of ascorbate as indicated by lower concentrations of dehydroascorbic acid was better maintained following ultrasound treatment due to the induction of monodehydroascorbate reductase and dehydroascorbate reductase activity. Likewise, the total antioxidant capacity of fresh-cut pineapple treated at 25 W for 10 was found higher in comparison to other treatments during 5 days of storage at 7 oC. The effect of ultrasound treatment on the physico-chemical and physiological changes in fresh-cut pineapple was also assessed in this study. Ultrasound treatment at 25 W for 10 min retained 98% of initial firmness and did not result in changes in the juice leakage, colour parameters, soluble solid concentration and titratable acidity in regards to control after 5 days of storage. Meanwhile, the increment of ultrasound power input and treatment time to 29 W and 15 min had resulted in the lowest SSC concentration with the highest volume of juice leakage and respiration rate in fresh-cut pineapple during 5 days of cold storage. In conclusion, an ultrasound treatment at 25 W for 10 min optimally inhibited the growth of spoilage microorganisms and extended the storage life for 2 days. Higher reduction of spoilage microorganisms was achieved when the ultrasound power input and treatment time was increased to 29 W and 15 min but it caused higher accumulation of ROS which reduced the nutraceutical concentration of fresh-cut pineapple following 5 days of cold storage.

Among the Fragaria species, the cultivated strawberry Fragaria × ananassa (2n=8x=56) is the most economically valuable crops. After harvest, they are extremely perishable, have a short shelf life, and are susceptible to mechanical injuries and physiological decay due to loss of tissue integrity, sensitivity to fungal diseases, and have a large surface area, which lacks an outer protective rind. Therefore, maintaining high nutritional values in the berry fruit whilst maintaining high fruit quality requires an understanding of the genetic and environmental effects on each trait, and how different traits are associated with each other. Mapping traits on the linkage map using a Quantitative Trait Loci (QTL) approach is the first step to identify the underlying gene(s) and to explore their effects and interactions. It will improve our understanding of the genetic control of measured traits and facilitates molecular marker development. Therefore, it can be used to improve plant-breeding efficiency at the molecular level, which significantly reduces the breeding time and cost of phenotyping. The overall aim of this study was to characterise the variation in quality traits among the F1 mapping progeny derived from a cross of Redgauntlet x Hapil (RGxH) strawberry cultivars. These traits include total soluble solids (TSS), titratable acidity (TA), fresh weight, surface colour, firmness, and phenolic content. This thesis presents two areas of work. First, using a novel high-density single nucleotide polymorphism (SNP) linkage map, phenotyping plant characteristics of RG x H progeny enabled the detection of QTL linked to traits associated with shelf life (at 4 °C). Subsequent QTL analysis highlighted 47 QTL linked to quality traits associated with three post-harvest days in two sequential seasons (2013 and 2014). Among them, three major QTL for fruit lightness (L*value) and TSS/TA ratios were detected in 2013, whereas 17 major QTL were detected in 2014, of which three accounted for >30 % of phenotypic variance. Study results provided additional data on the genetic architecture of fruit quality traits across shelf life at points relevant for strawberry breeding. However, it is still necessary to confirm the stability of the identified QTL resulting from the study findings. Second, the study evaluated the flavour profiles of seven genotypes of the RGxH F1 strawberry population and their parental lines in order to assess correlations between sensory and instrumental data. Ten trained sensory panellists rated strawberry puree samples on day 1 and day 5 of storage. Thirty attributes were evaluated, including odour, taste, flavour, mouth sensation and aftertaste. Gas chromatography systems were coupled with the solid-phase micro extraction (SPME) method to determine volatility of organic compounds. The results showed a clear separation between desirable attributes, which correlated with most day 1 samples, and undesirable attributes, which correlated with most day 5 samples. Furthermore, the results confirmed the role that volatile compounds (mainly esters, terpenes and aldehydes) and some physical traits (mainly TSS, TA and their ratios) play in sensory perception.

Breadfruit (Treculia africana) is a member of the taxonomic family Moraceae, genus Treculia and a multipurpose tree crop of Southeast Nigeria. The desire to study breadfruit was instigated by a paradoxical situation observed in Nigeria. First, there is high and increasing demand for the crop. Second, it is a well-known and appreciated traditional component of Souteastem Nigerian farming systems. Third, however, high demand for the crop does not seem to be leading to an increase in cultivation and production of any of the varieties. Finally, instead of increasing supply, it is listed as an endangered species. The need for increased planting of the crop has been emphasized by many authors, but there appears to be no increase in breadfruit cultivation. The research therefore investigates this apparent paradox with the aim of understanding the reasons for limited planting of both traditional and improved breadfruit varieties in Southeast Nigeria. Data were collected via a survey questionnaire, 38 key informant interviews, 16 focus group discussions and 21 in-depth interviews. A total of 260 farmers were randomly selected from 13 communities in two states of Southeast Nigeria for the study. Data collected were analysed using descriptive statistics, Z statistics and logistic regression analysis. The study found that breadfruit planting appears to be at subsistence level with an increased number of the trees in the last 10 years relative to the number in the previous 20 years and that this is due to an increase in the number of farmers growing the crop and that adoption of improved varieties is poor. The study revealed that breadfruit plays important roles in the livelihoods of the farmers including its use for household food security, income generation, snacks, a source of firewood, fodder and traditional medicine, and in sociocultural activities. It was also found that the major reasons for limited planting of breadfruit were lack of access to new breadfruit (NBF) planting material, high cost of NBF and lack of awareness of the existence of NBF varieties, fear of increased risk of bush fires, drudgery relating to breadfruit depulping and cultural norms that allow the free collection of breadfruit in farm fields. The study indicates that the farmers' characteristics associated with NBF adoption at 5% level of significance were their breadfruit consumption frequency (monthly intake), extension contact and educational level while sourcing of fodder and medicinal importance were associated with planting more of their traditional trees.

Postharvest tools have long been developed for minimising postharvest stresses and preserving fruit quality. However, increasing evidence points towards the role of abiotic stress in improving the bioactivity and nutraceutical value of fruits. This study was an investigation into the effects of postharvest stresses on the bioactive content of the tropical fruits carambola (Averrhoa carambola), dragonfruit (Hylocerues sp.) and mangosteen (Garcinia mangostana). The fruits were subjected to stresses induced by cold storage at 6 °C along with exposure to four different levels of one of the stress hormones salicylic acid (0, 0.1, 1, 2 and 5 mM) and methyl jasmonate (0, 0.01, 0.1, 0.2 and 0.5 mM). Physicochemical responses of all three fruits to the postharvest stresses along with changes in the antioxidant activity were assessed throughout the shelf life of the fruits. The goal was to characterise physiological and biochemical associated stress responses of the tropical fruits, and to evaluate the potential of using these stress responses for enhancing fruit quality.

Many wild and underutilised plants contribute to food and nutrition. However, overexploitation due to ever increasing demand for wood products has frequently led to declines in populations of these species. Enhanced knowledge of the status of such species is necessary for livelihood security and conservation of these valuable species. The present study considers an underutilised and threatened species of Bangladesh, namely wild mango (Mangifera sylvatica Roxb.). Although this wild mango is one of the genetically closest species to the common mango (Mangifera indica L.) research is very limited and mostly focused on wood quality and phylogenetic relationships. Therefore, this study investigated the conservation potential of wild mango considering its contribution for food, nutrition and livelihoods. To do so, an assessment was made of the current and future distribution of the species, which is a crucial first step towards mitigation and management of future species losses or habitat shifts. The study characterized fruit quality by profiling morphological, nutritional and medicinal values. Finally, farmers’ preferences, and the agroforestry potential of this unutilized native fruit species were explored. The study conveyed five key messages: 1. Wild mango may become extinct under future climate change scenarios so it is high time to start thinking about conservation initiatives. 2. Wild mango is a small sized mango with a large kernel in relation to other Mangifera species which provides significant nutritional and medicinal advantages that can contribute to nutrition and health of local people. 3. Wild mango fruit kernels producing a butter which has the potential to be used as a Cocoa Butter Alternative (CBA) thus providing new market potential. 4. Wild mango is a considered as a food for wildlife but local people are also appreciative of the taste and colour of the fruits and consume them. The unripe fruit is also sold to the pickle industry and can generate income during the fruiting season. 5. The crown architecture of wild mango is similar to other popular agroforestry species (M. indica, Artocarpus heterophyllus and Acacia auriculiformis). Therefore, urgent conservation initiatives are required to evaluate its potential as a new native agroforestry tree species. It is concluded that these attractive properties of wild mango could be promoted by a coalition of land use planners, climate change policy makers, government or non-government organizations, commercial breeder, potential investors (chocolate, butter, nutraceuticals, flavourings), food industries, food technologists, minister responsible for foreign direct investment in Bangladesh and Bangladesh forestry department to promote more widespread cultivation of this wild fruit species to realise its full potential.

Blackcurrant (Ribes nigrum L.) is a perennial shrub grown for its black piquant berries, rich in a variety of nutrients, phytochemicals and antioxidants. Blackcurrants are commercially grown in 21 countries mainly across temperate zones of Europe, Russia, and New Zealand and to a lesser extent North America. The berries can be harvested by hand and consumed raw, however the main market lies within the mechanically harvested crop used for processing. Demand for juices, and fruit juices in particular, continues to rise mainly due to increasing consumer awareness of the health benefits of a balanced diet. The rich nutritional content of blackcurrant makes it a desired commodity for production of juice and other innovative products. Breeding of new blackcurrant cultivars is dominated by the processing industry and the emphasis in recent years has been to increase the nutritional value of the crop. New berry fruit cultivars in the UK have recently focused more on fruit quality traits than agronomic characters (Brennan and Graham, 2009), and the main quality traits of blackcurrant have been associated with antioxidant, colour and flavour properties. Quality-focused breeding is challenging due to long timescales and low precision as quality traits are complex, show continuous variation, polygenic control, genes of small effects and strong influence by the growing environment; additionally, blackcurrant is a minor crop with no reference genome and existing sequence annotation is based on homology to Arabidopsis. In this study high throughput phenotyping, and metabolome and transcriptome profiling analysis contributed to a comprehensive overview of blackcurrant physiology and regulation during fruit development. Combination of a novel correlation platform and database mining of metabolite and transcript abundances contributed to identification of genes associated with anthocyanin content in blackcurrant and provided functional gene annotation for Ribes sp. Sixty three genes were identified as having major roles in blackcurrant anthocyanin accumulation with putative functions of catalytic proteins, transporters and regulatory proteins; a number of cytochrome P450 family proteins were also implicated. Moreover, a range of proteins with unknown functions in Arabidopsis were shown to correlate strongly with flavonoid accumulation in blackcurrant. The developed approach for functional gene orthology annotation (genes with similar functions) can also be utilised for several other (~200) traits analysed in this study and can provide a functional systems biology platform for other woody perennial species with no reference genome. In parallel, mapping population analysis and a new high-density quality-specific genetic linkage map and quantitative trait loci association with major quality compounds such as anthocyanins, sugars, organic acids and other polyphenols were developed. This contributed to the identification of significant associations between 28 quality traits and 978 markers present on genetic linkage map and created a functional tool for future quality-orientated blackcurrant breeding. The genetic linkage map assisted further functional annotation of several new Ribes SNP based markers obtained through GbS technology through their association with quality traits for which polymorphism can be analysed using existing blackcurrant genomic resources. Integration of functional candidate genes identified in fruit ripening analysis and on genetic linkage map with several blackcurrant genomic resources formed a platform for assisting further developments in quality-orientated blackcurrant breeding at The James Hutton Institute. This platform provides a holistic view of the mechanisms that underlie fruit compositional quality and may provide a means for germplasm selection with no prior phenotypic information. Knowledge and tools developed in this study can be further developed with new developing genomic technologies.

Date Palm (Phoenix dactylifera L. Family: Arecaceae; sub-family: Poaceae) is thought to be the oldest fruit tree grown in the Sultanate of Oman and is a major crop in terms of the number of trees and their distribution. Dates are widely considered to be a strategic source of food security as well as an important cash crop, and have always been looked upon as a key source of stability for oasis agro-ecosystems. Several insect and mite pests and plant pathogens attack Date Palm trees. The Dubas bug, Ommatissus lybicus DeBergevin (Homoptera: Tropiduchidae), has been considered the key pest of Date Palm plantations in Oman for 40 years due to the total area infested, the severity of infestations and the scale of the crop losses. Current control programmes for Dubas bug are reliant on chemical pesticides, applied by air and from the ground over an area ranging from 12,000-20,000 ha annually. These pesticides are currently the only feasible control measure against this pest, although research is underway on bio-control technologies. The cropping environment resulting from traditional Date Palm cultivation - high planting density, high temperature and humidity, topography of the plantations, intercropping and variability in cultivars and plant height - has an influence on pest and disease incidence and also affects the control options available. The present research attempts to determine the effects of technical, environmental and biological factors on the control of Dubas Bug in order to develop a more integrated control strategy. Data have emerged from this study on: 1) optimal spray droplet spectrum and application rates for improved coverage and placement of spray deposits, including under leaf deposition; 2) information on how Dubas bug daily movement can influence control efficacy; 3) on the selective use of insecticides against Dubas bug at economic threshold levels as a supplement to other IPM methods, including cultural practices such as thinning to maintain optimal distances between trees, irrigation management, the removal of old leaves including pruning cuts and surrounding tissues that may support and harbour Dubas bug.

The susceptibility of citrus fruits to microbial pathogens, especially green and blue moulds, is one of the difficulties that face citrus fruits suppliers to keep these fruits in good condition for consumers. Therefore, there is an urgent need for a safe and efficient method to preserve them during transportation and storage. This study focused on searching for a bacterial strain that have antifungal activity against moulds that attack citrus fruits. Environmental samples were screened for microorganisms with antifungal activity against Penicillium fungi that were isolated from infected lemon fruits. Twenty out of 500 isolated bacterial strains showed inhibitory activity against Penicillium, 16 of these strains were excluded from further study because they belonged to the genus Bacillus which has been widely studied as a bio-agent in the biological control. The results of phenotyping and the genotyping characteristics on the other active strain (4 isolates) proved that they were Pseudomonas koreensis. These four isolates differed in their antifungal activity, isolate B had the best suppression activity either with or without living cells (in concentrated spent media) which was mainly linked to the difference in lytic enzyme production capability (protease, chitinase and others). In addition, the active strain was able to produce siderophores and biosurfactants which could take part in the suppression activity. The antifungal activity in broth culture is produced during the log phase of the bacterial growth. The primary characterization of the antifungal activity showed it was heat sensitive, and not stable against pH changes (especially raising the pH), was sensitive to the treatment with proteinase K and appeared to have a molecular weight >3000 Da which suggested a protein nature for the active molecule. In addition, Tn5 mutagenesis was employed to identify the gene(s) that is responsible for the inhibition activity, the obtained results from one of the mutants showed that the antifungal activity may be linked in some way to the acquisition of iron, making it unavailable for the fungal growth.

The cultivated strawberry (Fragaria × ananassa Duch.) is the third most economically important fruit crop. In recent years the withdrawal of many fungicides and soil fumigants have made the sustainability and profitability of this crop more challenging. To overcome these challenges, plant breeders aim to improve upon existing cultivars and to release new ones with higher yield, better fruit quality and more disease resistance. Through Quantitative Trait Mapping, markers linked to genetic variants associated with traits of economic and agronomic importance can be identified through and molecular markers such as simple sequence repeats (SSRs) and single nucleotide polymorphisms (SNPs), can be used to improve plant breeding efficiency at the molecular level, which significantly reduces the breeding time and cost of phenotyping. In this thesis the following work is described: a correlation analysis of plant characteristics and fruit quality traits; the saturation of an existing SSR-based linkage map; the development of a high density consensus SNP-based octoploid strawberry linkage map, and the identification of quantitative trait loci (QTL) linked to two key plant attributes, fruit quality and powdery mildew resistance. In addition, the most closely linked SSR markers were identified and validated in a wider strawberry germplasm using firmness as an example study. Moreover, the physical locations of expansin genes and SNP markers associated with firmness QTLs were investigated. The purpose of this analysis was to find out if QTLs associated with fruit firmness overlapped the positions of expansins, genes known to be important in controlling fruit firmness.

The research described in this thesis focussed on the potential effect of ethylene produced under severe water deficit conditions (SWD) on the concentration of phenolic compounds in fruit and leaves of commercial strawberry (Fragaria x ananassa Duch.). An increased ethylene production rate was detected in green fruit and leaves at midday of the second day of wilting in response to SWD. The stress-induced rise in ethylene production was successfully inhibited by applications of aminoethoxyvinylglycine (AVG) and subsequently re-instated by 1-aminocyclopropane- 1-carboxylic acid (ACC) or replaced by abscisic acid (ABA) in fruits. Initially, fruit total ellagic acid concentration increased along with ethylene production but conclusive evidence for the causal role of ethylene in the accumulation of individual phenolics in fruit from the inhibition, re-instatement and replacement of the ethylene signal was not obtained. The quantitative expression of selected genes in leaves was investigated, and a significant reduction in the relative expression of FaACS1 (coding for ACC synthase), an increase in FaACO1, FaACO4 (coding for ACC oxidase) expression and no change on the expression FaPAL (coding for Phenylalanine ammonia lyase) was observed. Increased leaf ethylene production rate was likely due to increased expression of genes regulating ACC oxidase activity. However, no evidence was found from these genetic studies to confirm the role of stress-induced ethylene production in accumulation of phenolics in fruit or leaves.

There is a growing global urban appetite for fresh fruit and vegetables, particularly fruit. There is a further recognised need for agri-food systems that support human health, ecological integrity and social justice (Morgan and Sonnino 2010). This thesis explores the current possibilities and challenges of regenerative agri-food systems through the case of the urban apple. With the lens of political ecology, the thesis presents a relational interpretation of the spaces, natures and relations of the urban apple through considering the practices and the guiding logic of the corporate and agro-ecological urban apple in Hackney, London. The methodological framework, informed by relational geographies, supports a situated and place-based understanding of the corporate and agro-ecological logics through attending to practices in place. The thesis draws upon a number of semi-structured interviews and participant-observation with representatives involved in the production, distribution and trading of the urban apple. As the case of Growing Communities demonstrates, citizens can be supported in practicing more healthy, ecological and just ways of growing, trading and consuming food through agro-ecological communities of practice. Currently, such communities remain politically marginalised, particularly at national government levels. A political framework that fosters physical, economic and political space for regenerative agri-food practices and systems is considered key. The city-region is recognised as a ‘space of possibility’ and ‘space of action’ (Gibson-Graham and Roelvink 2011) in the scaling-out regenerative agri-food practices and systems. This needs to be supported by multi-scalar, cross-sectoral, participatory and co-productive processes (Jennings et al. 2015; Moragues-Faus and Morgan 2015; Jégou and Bonneau 2014), prioritising space for community-led, place-based practice.

This study investigated the simulated impact and vibration tests on bruise damage and quality of the British strawberries from winter and summer cultivations. The actual transport of food products was also monitored for the vibration and temperature levels in the city and highways. The winter cultivation produced a superior overall quality of 'Elsanta' and 'Sonata' strawberries compared to the summer cultivation. 'Sonata' fruits were more sensitive to vibration damage in the summer cultivation. The packed strawberry punnet of 250 g was tested in impact and vibration tests. The maximum drop height at 750 mm gave a significantly larger wet bruise level of around 40% than other drop heights (p.0.05). The simulated vibration investigated the three frequencies and three exposure times plus control. The vibrated fruits from the most severe of 5 Hz (1.1 g) for 150 sec had significantly higher wet bruises (50-60%) than for other treatments (p.0.05). The bruise damages increased for both simulated tests after storage at 10°C, 70±5% RH for 3 days. The EC value gave a significantly stronger correlation with wet bruise and severity score as compared to puncture, compression and respiration rate measurements (p.0.01). The EC method is suggested for use as a rapid indicator and a predictor for the bruise assessment of strawberries. The vibration and air temperature levels in the refrigerated truck and semi-trailer were monitored. The overall peak frequency of power density was often found at 10-14 Hz. The vertical vibration was the dominant direction during the road transport. The rear-top position gave a stronger root mean square acceleration value. A gradual increase of vibration level occurred after the first drop in city distribute as well as for a smaller load. The range of temperature during food transport was around 2 to 8oC with a set point at 3°C.

Bitter pit is an important physiological disorder of many apple cultivars where the low uptake and poor distribution of calcium within the cortex of apples pervades. Controlled atmosphere storage and application of 1-MCP (SmartFreshSM) can delay the onset of bitter pit symptoms by delaying maturity and senescence; however, significant losses may occur in long-term stored apples. It is hard to detect internal bitter pit using external examination alone. Previous studies have focused on improving pre-harvest prediction and curative treatments before harvest. Present prediction models are based on history of orchards, mineral analysis 2-3 weeks before harvest and quality assessments and monitoring over storage time. This study aimed to identify a greater understanding of the storage potential of fruit based on destructive standard quality assessments, biochemical and molecular analysis, also a non-destructive monitoring method by chlorophyll fluorescence at the point of harvest and monitoring during storage for developing more reliable prediction models to improve storage management. The role of free and conjugated calcium in maintaining cellular integrity and the relationship between biochemical and fluorescence changes and development of bitter pit were investigated. A diagnostic model based on comparison of changes of ascorbic acid during storage was developed. Another diagnostic model based on changes in the proportion of calcium oxalate content during storage in comparison with harvest was developed to identify samples with higher propensity to bitter pit. Also chlorophyll fluorescence was investigated as a non-destructive method for monitoring fruit during storage and prediction models for detecting changes in the maturity of fruit and developing bitter pit and reduction of fluorescence during storage as an alert to identify incidence of bitter pit were developed. Furthermore, changes in gene expression profiles of a limited number of genes like calmodulin showed the differences in patterns of transcripts between apples suffering from bitter pit and healthy apples. All the suggested methods have potential of being commercialised and applied practically to improve apple fruit store management. It would be possible to build a multi variate model for predicting the onset of bitter pit development in apple by combination of two or more suggested diagnostic tools.

African Walnut (Tetracarpidium conophorum- Mull. Arg) is a perennial climbing shrub which grows mainly in the Western region of Africa. It is found mainly in Nigeria, Gambia, Sierra Leone, Gabon, Equatorial Guinea and Cameroon as well. The nuts are encased in pods which may contain between 2 to 5 nuts. The seed is enclosed in a hard shell-like case. The nuts are commonly processed by boiling or roasting and consumed as a snack or used as soup thickener. In ethnobotanical medicine, the nut extract is extensively used in decoctions for treatment and/or management of common and chronic ailments such as malaria, dysentery, high blood pressure, diabetes and cancer. The nuts are generally exposed to high temperatures (25 – 37 °C) and relative humidity (RH) which increases susceptibility to fungal contamination and nutrient degradation, hence, raising concerns over product quality and safety. Experiment simulating the common retail postharvest storage and processing practices was conducted to: (i) determine the effects on the fatty acid profile; (ii) assess the impact on the fungal population contaminating the nut shells at different maturity stages, and potential mycotoxigenic implications; (iii) evaluate the cytotoxicity of four extract of the nut on lung cancer (A549) cells; and finally (iv) assay the total phenolic content and profile potential individual phenolic components of the nut. Results indicated the presence of essential and non-essential fatty acids namely; palmitate, oleate, stearate, linoleate, arachidate and α-linolineate with α-linolineate being the most abundant (1.1 – 8.2 mg/g freeze-dry weight). Boiling and roasting generally improved the concentration of the fatty acids best when nuts are cold stored at 5 °C for maximum of 10 days. Potential mycotoxigenic species - Aspergillus section Nigri, Aspergillus flavus/Parasiticus, Fusarium spp. and Penicillium spp. - were frequently isolated from cultured shell pieces of stored nuts. When compared with unprocessed nuts, roasting completely prevented fungal contamination in shell pieces from nuts in the non-stored (NSN) group at early maturity stage, while boiling significantly reduced the level of contamination to about 58 % (P < 0.05). Simulating open market conditions caused 100% fungal contamination in all boiled samples and roasted samples at early maturity. Mycotoxin analysis using Yeast Extract agar (YES) and High Performance Liquid Chromatography (HPLC) - Fluorescence detector (FLD) showed that Aflatoxins - G1 (AFG1), B1 (AFB1), G2 (AFG2), and B2 (AFB2) were produced by 20 isolates with both AFG1 and AFB1 being predominant at concentration ranges 4 – 32,200 and 4 – 22,700 ng/g plug weight, respectively. No Ochratoxin A (OTA) was detected. Phenolic component analysis indicated unprocessed (20.79 ± 1.0 mg gallic acid equivalent per gram freeze-dry weight – GAE/g FDW) samples showed the highest value for total phenolics while both boiling (9.90 ± 1.8 mg GAE/g FDW), and roasting (9.32 ± 2.7 mg GAE/g FDW) reduced the amount by more than 50 % when compared with unprocessed. Potential individual phenolic compounds were unambiguously separated using high performance liquid chromatography – diode array detector (HPLC-DAD). There were no differences between chromatograms of defatted and non-defatted unprocessed, roasted and boiled samples. Cytotoxicity evaluation showed no decrease in cell densities in plates treated with extracts from unprocessed nuts at all concentrations. Diethyl ether-ethyl acetate (10 µg/mL) and n-butanol (1000 and 500 µg/mL) extracts of roasted nuts as well as dichloromethane and water (1, 10 µg/mL) of boiled nuts caused a non-significant decrease of < 10 % in cell densities when compared with the phosphate buffered saline-media control. However, all extracts showed no cytotoxic effect on the A549 cells African walnut is basically produced at subsistence level in Nigeria, but considering the presence of desirable fatty acid profile and phenolic compounds, need for increased industrial scale production is herein recommended. Although fungal attack and potential mycotoxin risk on the nut may be high, retail processing by roasting has prospects to greatly accentuate the risk. Cold storage of the nut may help to improve the shelf life although it may not be cost effective for local farmers in Nigeria and Africa, however, it provides opportunity for export business. Although the nut extracts showed no cytotoxic effect on A549 lung cancer cell lines, there is need to investigate further to confirm it non-cytotoxicity activity on other cancer lines and normal cell lines.

Hazelnuts are mostly non-dormant at harvest but develop seed dormancy after a few days of storage. The seeds have been classified as recalcitrant since they cannot be stored for more than one year under ambient conditions. Cryopreservation has not been satisfactory so an alternative protocol is required. To test for recalcitrance, chilled non-dormant seeds (control) were compared with gibberellic acid (GA3) treated seeds during 6 weeks storage at 5°C or at ambient temperature. Control seed moisture content (MC) was 14-15% compared with 20% for GA3 treated seeds. No change in viability was noted until the end of 6 weeks at ambient temperature, when infection proliferated. Reduced germinability, associated with increased leachate conductivity, was noted on all treatments and controls, with ambient temperature storage most harmful for seed viability. This supports classification of hazel seeds as recalcitrant. However, orthodox behaviour could be induced by reducing seed moisture to <6%, showing survival for more than 3 years at -20°C with acceptable germinability and producing healthy seedlings. Pathogen tests show that 6 weeks chilling to break seed dormancy may activate the seeds’ internal protective mechanisms, thereby reducing infection and enabling germination and healthy seedling establishment. The link between seed viability and protection from free radicals and pathogens was examined. Antioxidant activity in hazelnut seed associates (such as endocarp, funiculus and testa) was found to be much higher than in the seed embryo, perhaps indicating that hazel seeds have natural protective mechanisms within the pericarp. Antioxidant activity of seed associates increased during chilling, indicating their role in protecting the seed. Nevertheless, TTC test revealed that seeds acclimatised to ii < 6% MC and stored at 5°C for 45 weeks showed viability loss due to damage of the embryonic axes, probably caused by free radicals. Initial tests to stabilise seed moisture content showed that reduction in seed moisture did not impose dormancy and seed moisture content (MC) stabilisation resulted in > 80% germination but many abnormal seedlings. Dormancy reversibility was tested by treatments T1 (one period at 15°C) and T2 (two periods at 15°C), designed following a consideration of the natural environment. Both resulted in reduced germination, delayed seedling emergence, increased abnormal seedlings, reduced seedling height and decreased internode numbers. To test the role of temperature in reduced seed performance, non-dormant hazelnuts were held at either 5°C or at ambient temperature for up to 6 weeks. Seeds from both sets exhibited high viability, but germinability was significantly decreased in the ambient temperature set, associated with increases in leachate conductivity and infection. Work in this thesis has confirmed that dormancy was broken by chilling, with gradually increasing germination as chilling time was increased. Germination increased with increase in chilling and reduction in infection. No infection was recoreded after 6 weeks chilling. It is most likely that protective agents are produced causing suppression of infection. In these experiments it was observed that not all germinated seeds produced healthy seedlings, suggesting that germination tests without observation of seedlings may give an incomplete assessment of germination success. Assessment using the Tetrazolium test (TTC) was found to be much more dependable and it was also possible to detect damage to specific tissues that might result in unhealthy seedlings.

The western flower thrips, Frankliniella occidentalis (Pergande), is an increasing problem in UK strawberry crops. The use of polythene tunnels has provided a more favourable environment for the pest, and pesticide-resistant strains have resulted in control failure. There is a need for improved knowledge of thrips biology and for additional control methods that can be integrated with natural enemies in order to make thrips management programmes more robust. The distribution of, and damage caused by, F. occidentalis was investigated to improve monitoring and decision-making, and the viability of using traps as a control was tested. Over 74% of adult thrips on plants were in flowers. Twice as many adult thrips were found in mature flowers at the top of the plant compared to those at the side. The distribution of larvae between flower and fruit stages varied with thrips density. All stages of flower and fruit were susceptible to damage but thrips larvae caused more damage than adults per individual, so the distribution and numbers of larvae between fruit stages best predicted the timing of damage. The predatory mite Neoseiulus cucumeris Oudemans reduced damage by feeding on thrips larvae. Economic crop loss occurred at five adult thrips per flower in the absence of N. cucumeris, but up to about 11 adult thrips per flower with good mite establishment. Adult F. occidentalis females overwintered on strawberry and on weeds, resulting in more thrips in second-year than in first-year crops. Mass trapping using blue sticky roller traps caught sufficient adult thrips to reduce fruit damage by 55-68% and increased grower returns by an estimated £2.2k per hectare. The addition of the F. occidentalis aggregation pheromone, neryl (S)-2-methylbutanoate, to the traps doubled the trap catch, but a visual stimulus was essential for trapping. (R)-lavandulyl acetate reduced trap catch, suggesting that it is not part of the aggregation pheromone.

Sown flowering strips can benefit beneficial arthropod groups (pollinators and natural enemies) on farmland and enhance the delivery of arthropod-mediated ecosystem services in crops. However, not all flowering plants may be useful for beneficial arthropod taxa, as differences in floral traits associated with nectar accessibility (e.g. nectar-holder depth) determine resource use. Therefore, increasing the number of distinct floral traits in flower mixes may be an effective way to manage multiple arthropod-mediated ecosystem services in farmland. Here, the response of pollinators and natural enemies in cider-apple orchards to three functionally-distinct flower mixes ('open-nectar plant' mix, 'concealed-nectar plant' mix, and a third 'multi-functional' mix that contained all species in distinct mixes), sown in flowering strips between rows of trees were assessed, and compared to areas under existing management (mown grass), as well as the effects on arthropod-mediated ecosystem services (pollination and pest control) in orchards. Observations of flower visitation revealed a dichotomy in floral resource use by beneficial arthropod groups, with pollinators more abundant in plots sown with the concealed-nectar plant mix, whereas natural enemies were more abundant in plots sown with the open-nectar plant mix. When mixtures were combined, plots sown with the multi-functional mix attracted both suites of beneficial arthropods. Although effects of flower strips on ecosystem service delivery (yield, pest pressure) were less clear, there was some evidence that flower strips influenced service provision (increased predation of sentinel prey), and the abundance of key taxa (Andrena solitary bees). The link between visitation by andrenids during blossom in spring and fruit set was the clearest link found between beneficial arthropods and yield in cider-apple orchards. This thesis provides clear evidence that a trait-based approach to designing flower mixes enables sown flowering strips to support beneficial arthropod taxa and enhance multiple ecosystem services in cider orchards, and quantifies the important role that beneficial arthropods play in supporting crop production.

Podosphaera aphanis which causes powdery mildew of strawberry is of economic importance in strawberry production in United Kingdom as it affects yield and fruit quality. Silicon has been shown to reduce the severity of a number of plant diseases. In strawberry, the mechanism of suppression against powdery mildew remains uncertain. Therefore, it has been suggested that supplying silicon would help strawberry plants to absorb silicon and improve resistance against the pathogen. The silicon based wetter Omex SW7 was used and three different concentrations of silicon wetter were applied on the leaves of the strawberry plants (foliar application). Each treatment was applied at three different timings. Enhanced level of silicon was quantified by the Autoclave Induced Digestion (AID) method. Whilst the main study has used the variety Elsanta, other varieties have also been used. It was observed that the weekly application (total 5 sprays) of 3 different concentrations of Omex SW7 on leaves showed significantly (P<0.05) higher silicon concentrations compared to application 3 times in weeks 1, 3 and 5 or twice in weeks 1 and 5. Microscopic observations showed that weekly application of standard, high and very high concentrations of Omex SW7 significantly (P<0.05) increased the number and length of leaf hairs on both the upper and lower surfaces of strawberry leaves. The different varieties of strawberry used showed morphological changes in the leaves with regard to the density and length of leaf hairs. Untreated leaves from Rhapsody had no hairs on the upper leaf surface, but a low density of hairs was observed after treatment with the high concentration of Omex SW7. In this study, Omex SW7, a silicon based wetter was applied to the roots of strawberry plants (root application) and silicon accumulation and physical changes in leaves were assessed. Strawberry variety Elsanta was used in this experiment. Results revealed that weekly application (total 5 applications) of 2 different concentrations (standard and high) of Omex SW7 to roots showed significantly (P<0.05) higher silicon concentrations compared to application 3 times in weeks 1, 3 and 5 or twice in weeks 1 and 5. It was found that the weekly application of two different concentrations of Omex SW7 showed significantly higher (P<0.05) leaf hair numbers and significantly (P<0.05) longer leaf hair length on both the upper and lower surfaces of leaves compared to application 3 times in weeks 1, 3 and 5 or twice in weeks 1 and 5. The effect of foliar application of silicon and potassium carbonate to limit P. aphanis infection was examined in a field trial under polythene tunnel at Wisbech. Treatments were arranged in a randomised block design of 3 replicates. There were a total of 18 plots. There were six treatments and all treatments were applied to the strawberry variety Sonata. Results revealed that application of silicon based wetter Omex SW7 onto the leaf surface does result in accumulation of silicon in the leaves. The application of Omex SW7 has stimulated an increase in the number and length of leaf hairs in strawberry plants. Results showed that germinating ascospores and colonies were present in all plots before the trial was sprayed. Treatments with standard and high Omex SW7 significantly (P<0.05) reduced the number of germinating ascospores and colonies in this trial. However, Potassium carbonate alone gave some reduction in the number of colonies and germinating ascospores. Moreover, potassium carbonate mixed with silicon based wetter Omex SW7 significantly (P<0.05) reduced the number of germinating ascospores and colonies.

Monilinia laxa is the causal agent of brown rot disease on stone fruits, and also causes blossom wilt and twig canker. The common practice used to manage this disease is through fungicide treatments, especially during the flowering and fruiting period. However the demand to reduce fungicide input has been increasing and there is a growing number of reports of M. laxa strains that are resistant to fungicides. This study is based on the development of biological control agents (BCAs) as an alternative strategy for disease control using either existing BCA products or new indigenous isolates from UK orchards. Efficacy of exotic commercial BCAs against M. laxa was investigated using in vivo tests on cherries and plums. Serenade partially inhibited M. laxa while the other four BCA products (BioPK, BoniProtect, Prestop and Trianium) had no effect against the pathogen. Indigenous BCAs were isolated from healthy leaves, intact fruits and mummified fruits of cherries and plums collected from orchards in Kent. A total of 217 isolates were screened against two strains of M. laxa in a series of in vitro tests using a dual culture technique. From these tests, 12 isolates were selected for further screening. The final screening based on in vivo tests on cherries and plums narrowed these down to two isolates with good potential for development. They were further tested under post-harvest conditions by dipping cherries and plums in suspensions of cells of the individual control agents and storing treated fruit under standard storage conditions. The two BCAs did not control brown rot on cherries under these conditions, and the low incidence of natural infection by M. laxa in plums also meant that significant control could not be demonstrated. The two BCAs were identified as Bacillus amyloliquefaciens/subtilis (isolate B91) and Aureobasidium pullulans (isolate Y126). Their modes of action were investigated. Bacillus sp. B91 was shown to produce soluble and volatile organic compounds which inhibited M. laxa, while A. pullulans Y126 apparently competes with the pathogen for nutrients and did not produce inhibitory compounds. The capability of B91 and Y126 to grow and survive at low temperatures was studied. Bacillus sp. B91 was shown to be a mesophillic bacterium that could grow at 10-25°C but suffered significant mortality at 0 and 5°C, while A. pullulans Y126 was both mesophilic and psychrotolerant because it grew between 0-25°C, although 20°C was the optimum temperature. Once all nutrients were removed, Y126 was able to survive for several weeks in all test temperatures (0-25°C) but showed significant mortality at 25°C. The capability of B91 to survive at 20 and 25°C was higher than low temperatures (0-15°C). Molecular studies were used to show that M. laxa populations on mummified fruits were likely to be responsible for fruit rot infection in the same orchards the following season. Geographical origin and host also influenced the population structure of M. laxa. Field trials were conducted in which mummified fruits were either treated with a commercial fungicide (Indar) or BCAs to investigate whether these treatments would significantly reduce sporulation of the pathogen in the field thus reducing the infection load in the spring. Spraying in Winter alone was not sufficient to significantly suppress sporulation of M. laxa but the efficacy was improved when the control agents were applied in Spring either as a single spray or in combination with a Winter spray. Sprays of Indar or A. pullulans Y126 greatly suppressed sporulation on mummified fruits if the fruits were treated on both occasions. It was concluded that the two novel, indigenous BCAs have potential to control M. laxa but more research is necessary to develop these two potential BCAs for field use.

Orchards are biodiversity hotspots, home to a wide range of organisms including epiphytic bryophytes and lichens. However, the area of the UK given over to orchards has become considerably reduced; these habitats are under threat. In response to this, Traditional Orchards are now included as a priority habitat in the UK Biodiversity Action Plan. Local Habitat Action Plans have been produced. It is important that the factors which cause orchards to be such biodiverse habitats are understood in order to facilitate the management of newly planted and restored orchards. Surveys across 7 orchards were carried out, six in Hertfordshire and one in Cambridgeshire. A total of 141 apple trees were surveyed. Epiphytic bryophyte species were recorded, and in 7 of the surveys the cover of individual species was also included. 26 species of epiphytic bryophyte were recorded. There was a high level of similarity in species composition between the orchards, however this was much reduced when relative species cover was taken into account. In order to assess the overall diversity in order to compare orchards, the optimal number of trees to sample was found to be 10. Within the same orchard, significant differences in number of bryophyte species per tree and bryophyte cover were found between two varieties of apple tree, Ashmead's Kernal and Newton Like. This was accompanied by significantly different bark pH and nitrogen concentrations. However, pH was found to be of low importance in explaining the distribution of epiphytic bryophytes on Bramley trees across orchards. In vitro experiments found that low pH inhibited spore germination and growth in the species Brachythecium ve!utinum, Rhynchostegium confertum, Orthotrichum affine and Bryum capillare. High concentrations of nitrogen inhibited spore growth but not germination in the species Orthotrichum affine. The in-depth surveys of Bramley trees showed that across orchards, tree structure, as determined by management, explained about 10% of the observed variation in bryophyte cover. Within that, trunk girth and distance to nearest neighbouring orchard trees were the most important factors. Site was found to be the strongest influence on epiphytic bryophyte distribution in the orchards.

Studies on natural regeneration and bark production in Prunus africana were carried out in Kenya to provide basic information required to develop guidelines for sustainable utilization and conservation of the species. The objectives were: to analyse patterns of population structure; to develop an understanding of the effect of herbivory and disease infection on natural regeneration; and to assess available quantities of ecological sustainable bark yield per tree and characteristics that could influence it. The results showed that the population density is relatively low and a high proportion of trees are greater than 20 cm diameter. Prunus africana was most abundant along forest edges and on forest patches. The average density of trees was 6 trees/ha. The spatial pattern was clumped, and linked to gap creation. Size structure suggests that Prunus africana's recruitment is episodic and is dependent on canopy openings. Disease infection and herbivore damage was higher closer to parent trees where seedling density was high, and decreased with increasing distance away from the parent trees. Mortality of seedlings in Prunus africana is very high; the number of seedlings present at each stage decreases as the seedlings develop from one stage to another. This evidence is consistent with the Janzen-Connell model describing the spacing out of recruitment (away from parent trees) through the action of density- or distance responsive herbivores or pathogens. However, the hypothesis is too simple to determine the final recruitment pattern in Prunus africana. Populations of Prunus africana growing in open habitats have thicker bark compared to those in closed canopy forests. The mean bark yield per tree was 75.81 kg in closed canopy forest and 73.38 kg in open farmland. Tree diameter and bark thickness are the best estimators of bark yield. However, variability in tree form between different habitats may require separate equations for accurate predictions. The ability of Prunus africana to withstand bark damage offers the potential for sustainable harvesting. It is recommended that a full-scale inventory and resource assessment of Prunus africana be done in Kenya and harvesting regulations and quotas should be developed and enforced to achieve sustainability. To promote the recovery of Prunus africana populations in harvested area, interventions should include opening the canopy around, and clearing the undergrowth beneath seed bearing trees. More research work is necessary to assess the correlation between bark production and bark quality; the influence of tree-fall gaps on spatial patterns of recruitment; the best sustainable bark harvesting techniques; minimum exploitable diameter and intervals for sustainable bark harvesting in Kenya.

Early Coffea arabica associations with timber shade trees Eucalyptus deglupta or Terminalia ivorensis and service tree Erythrina poeppigiana were studied on-farm in Costa Rica (640 m a.s.l.; rainfall 3516 mm yr"1). Tenninalia ivorensis stem diameter, crown projection and shading were higher than for E. deglupta. Coffee plant growth was higher in uniformly than in locally fertilised plots, and higher under E. deglupta but was not influenced by timber shade tree proximity. Coffee produced more benies under E. deglupta. Coffee and timber tree fine roots (diameter< 2.0 mm) predominated in the coffee fertilisation strip compared with on the opposite side or in coffee inter-rows. Coffee RLD (fine root length density) was evenly distributed in 20 cm topsoil but tree RLD predominated in the first 10 cm. Coffee and E. deglupta RLD increased progressively from 2 to 5-year-old associations, with coffee RLD concentrating close to the coffee trunks and tree RLD in the inter-rows. Interspecies nutrient competition was low although T. ivorensis was the potentially stronger competitor with coffee and coffee the stronger competitor than trees . Daily coffee water uptake was lower under timber trees than in full sun or under E. poeppigiana. Both coffee and tree transpiration was restricted in the dry period by an air vapour pressure deficit (VPD) threshold level, while the plants followed the photosynthetic photon flux density and VPD pattern in the wet season. Daily water uptake ranged from 0.38 -1.73 litre m-2 of foliar area for coffee and from 47 -104, 44-119 and 13 -90 litre per tree for Eucalyptus deglupta, T. ivorensis and Erythrina poeppigiana, respectively. In the dry period there was evidence of water competition between shade trees and coffee plants. Eucalyptus d eglupta was a more promising timber shade tree to be associated with coffee than T. ivorensis.

Different modifications, namely hexanolylation, acetylation, thennal modification and silylation by trimethoxy vinyl silane (VTMS,) and by 'Y-methacryloxy propyl silane (TMPS) were applied to impart decay resistance to Corsican pine sapwood, which is a non-durable wood. The possible mechanisms by which the modifications impart decay resistance to the wood were also investigated. The silanes applied in this study showed completely different reactivity so that the vinyl group of VTMS remained un-reacted and the vinyl group of TMPS reacted (but its sHanol was not very reactive). The decay resistance of the modified woods were assessed by soft rot, brown rot and white rot fungal tests. The decay resistance against basidiomycetes and soft rot fungi was improved by all the wood modifications applied in this study, but the wood treated with methanolic solutions of the silanes did not show complete decay resistance against brown rot fungi. The failure of the silanes to impart complete protection of wood against brown rot fungus (c. puteana) was attributed to the restriction of the silanes in penetrating into the cell wall. In the soft rot tests, VTMS modified stakes showed high decay resistance but TMPS modified wood showed a moderate decay resistance. This was attributed to the uneven distribution of TMPS in wood. An industrially acceptable treatment method (by using aqueous solutions of silane instead of methanolic solutions and pressure treatment instead of vacuum treatments was established). The perfonnance of the silane treated wood was assessed by field tests. The method worked well with TMPS (the wood showed significant decay resistance in the test) but it didn not work with VTMS. Since both anhydrides (hexanoic and acetic anhydride) used in this study, showed nearly the same perfonnance against C. puteana and soft rot fungi, it was concluded that the improvement in decay resistance against the brown rot fungi and soft rot depends on the WPGonly. Heat treatment above 200°C was recognised to be an effective treatment in improving the decay resistance of wood. It was shown that heat treatment temperature plays a more important role in the improvement of decay resistance than the treatment time. Heat treatment at 250°C for 2 hours, imparted complete decay resistance to the wood against basidiomycetes and soft rot. No significant difference between decay resistance of heated wood post-extracted and heated wood without any extraction against basidiomycet and soft rot fungi was obtained, suggesting that extractable fungicidal is not the reason for the improved decay resistance. In addition to the decay tests, dimensional stability, pore cell wall pore accessibility and hygroscopicity of the modified wood were also studied to find the mechanism by which the modification imparts decay resistance to the wood. It was suggested that hexanoylation and acetylation reduces hygroscopicity so that not enough water is available for the diffusion of brown rot degrading agents into the cell wall, while lignin substitution might be the main reason for the improved decay resistance against white rot fungi. For heated wood, a good correlation between a reduction in FSP and WL due to decay was obtained. Thus, it was suggested that a reduction in the hygroscopicity of wood could be the main reason for the improved decay resistance. By using the Hailwood Horrobin model it was shown that a reduction in poly-molecular adsorption of heated wood is the main reason for the reduced hygroscopicity. Since good correlation between an increase in the lignin content and a reduction in the poly-molecular sorption was obtained, a reduction in the hygroscopicity of heated wood was suggested to be due to a reduction in the swelling of the wood cell wall in which micro fibrils were placed in a matrix of condensed lignin and the hemicellulose residue, rather than a reduction in the hydroxyl groups of wood. Lignin modification is thought to be the main reason for the reduced hygroscopicity.

The Forestry Authority, as the country's leading authority on forestry practice, has Design Guidelines which aim to offer designers sound relevant and appropriate advice on the theory, process and practice of forest landscape design. The guidelines therefore represent the FA's vision of how designed Britain's forest landscapes should appear. The aim of this study is to rigorously evaluate the advice offered in the FA's guidelines in relation to the FA's objective to offer an aid to design. A literature review and series of interviews with those responsible for the advice explores the motivation behind the introduction and development of the guidelines. The review concludes that the unusual circumstances surrounding the inception of guidelines are likely to have resulted in the advice having a strong forestry bias, a weak theoretical framework and to be offering advice that is divorced from other land-use interests. An analysis of the nature and contents of the guidelines and the subsequent critical discussion suggests that the advice is not always complete, consistent, logical or relevant. The concept of an alternative approach to offering forest landscape design guidelines is tested through both a postal questionnaire and a field survey. The findings for the postal questionnaire suggest that the FA's advice is generally well used and found useful but that it is at times limited and fails to respond to the needs of the current user group. The findings for the field survey show that enough evidence exists to support the concept and further investigation along these lines. The study concludes by making 20 recommendations for changes or additions to the FA's current advice, which address the issues raised by the research findings. These recommendations are offered as a framework within which alternative advice could be further developed.

Ground based forest inventory surveys can provide highly accurate measurements of tree and stand characteristics, but are time-consuming and costly, and therefore typically limited to number of sample plots.  Estimating tree and stand characteristics from digitised aerial photographs can provide measurements from the whole stand, but is less accurate.  The goal of this study was to evaluate the application of scanned, stereo aerial photography and digital photogrammetry in combination with tree crown delineation techniques to measure tree and stand characteristics in two sites in Scotland, Rosarie and Leanachan forests.  Existing medium-resolution scanned images of true colour aerial photographs (1:10,000) were used to derive Digital Elevation Models (DEMs) of the forest canopy and digital orthophotographs.  Tree crown delineation techniques were used on the derived digital orthophotographs and tree crown measurements including crown area and coordinates of each crown were derived.  The DEMs in combination with Digital Terrain Models (DTMs) derived from digital contour maps, were used for the estimation of tree and stand heights.  Equations derived from regression analysis of individual tree measurements on the ground, and the orthophotographs from Rosarie forest, were used for the estimation of tree and stand characteristics of both sites. For Rosarie forest the estimations of stand top height, basal area, stand volume stand biomass and stand density (~23.7%) were similar with the ground measured stand characteristics (±10%), where as for Leanachan forest the estimations were less accurate due to the non-optimum illumination conditions during the acquisition of the aerial photographs. The level of accuracy achieved in this study is adequate for measuring tree and stand characteristics, if the acquisition conditions of aerial photographs are optimal.  Higher level of accuracy may be possible, but requires more accurate DTMs, possibly derived using active airborne remote sensing sensors.

Annual losses of nitrogen from existing glasshouse crop production substrate systems could be as high as 600 kg ha 1, using an average of 30% drainwater containing a nitrate-nitrogen concentration of 200 mg 1". The use of nutrient recirculation systems such as nutrient film technique (NFT) helped to reduce nutrient losses to the environment but the commercial area of NFT has decreasedd ue to high initial capital costs, concernso ver diseaset ransmissionw ithin the system and an absence of recent research and development. Most substrate systems rely on the provision of liquid nutrient feeds at every watering. This study examines clinoptilolite which is able to selectively store, supply and exchange cations with plant roots. The use of the naturally-occurring volcanic aluminosilicates pumice and clinoptilolite zeolite in the intensive production of edible and ornamental protected crops, tomatoes, sweet peppers and standard carnations was studied. Pumice from Sicily, Italy and clinoptilolite (84-87%) from Beli Plast, Bulgaria were used in the experiments. The management of the pumice and unloaded clinoptilolite systems involved provision of all the plant growth nutrients via a drip irrigation system. In comparison, the nutrient-loaded clinoptilolites were examined using only water in the irrigation cycles which allowed relatively unimpeded cation exchange to take place between the clinoptilolite and the surrounding solution, thus providing nutrients for plant roots. The total cation exchange capacity of clinoptilolite was measured as 132.0-158.3 meq 100g'', compared with 1.8 meq 100g-' for pumice. Unloaded clinoptilolite irrigated with nutrient-balanced liquid feeds gave yields and quality equivalent to those of tomatoes, peppers and standard carnations grown on rockwool, pumice and peat / peat alternatives. For the first nine months of an eighteen month experiment, the yield and quality of standard carnation flowers from high nutrient-loaded clinoptilolite matched those from pumice receiving liquid feeds at every watering. Thereafter, lower concentrations of available nitrogen and, to a lesser extent phosphorus, limited production by up to 25%. Drainwater nutrient concentrations were, however, extremely low and reduced the potential pollution risk to the surrounding environment. Drainwater nitrate-nitrogen concentrations of below 10 mg 1'' were measured, compared with 100-300 mg 1.1 for pumice. Drainwater potassium concentrations were also comparatively low at < 20 mg 1'' for clinoptilolite and 200 mg 1" for pumice. Phosphorus concentrationsi n the drainwater did not exceed1 2 mg 1.1c, omparedw ith a maximum of 70 mg 1'1 in drainwater from pumice. The inclusion of phosphate rock (apatite) in with the clinoptilolite provided a source of phosphorus available to plants and the dissolution of apatite was regulated by the rate of absorption of phosphorus and calcium by plants. In all the experiments, clinoptilolite adsorbed ammonium-nitrogen and potassium, releasing calcium and sodium. However, concentrations of sodium released into the root zone were not harmful to plant growth. The average nitrate-nitrogen concentration of new, fully-expanded carnation leaves was 51.7% lower than the target levels. The nutrient loading of nitrogen and phosphorus regulated the overall yield of the crops evaluated in the experiments. The use of nutrient-loaded clinoptilolite to produce commercial crops and reduce environmental pollution by regulating the concentration of nutrients in the drainwater over long periods of time is further explored in the study.

The study aimed to provide quantitative information on the ecology of short fallow systems in southern Cameroon, and their socio-economic value to farming communities of that area. Results from this study will lead to recommendations for the design of appropriate conservation and management decisions and plans that will improve the productivity and guarantee the sustainability of shortened fallows in the area. The specific objectives of the present research were to assess species diversity as impacted by fallow age and fallow type, both during the fallow phase as well as during the subsequent cropping period, and to evaluate the productivity of some key fallow trees identified by local farmers that could be components of productive agroforests. To address these objectives, field activities included ethnobotanical surveys throughout 15 villages of the study area, vegetation surveys of fallows and food crop fields at Mengomo (over two years), and monitoring of about 100 fruit trees at Kaya (during 19 months). Analyses of the results showed that local farmers of the study area do have an extensive knowledge of their environment. Using a common criterion - the fallow duration - they were able to distinguish short, medium and longfallow systems (of respectively, <6, 7-10, and >10 years old) as well as the characteristics and constraints associated with their agricultural management. The effect of the resource use intensity was particularly evident on the availability and distribution of short and long fallows across the three study resource domains. About 174 useful plant species were identified, from which nearly 58 % were collected in fallows of less than 10 years old. Most frequently mentioned useful species that farmers collect from all fallow classes included 'wild' fruit trees and forest species. The present study revealed that species and functional diversity were significantly associated with vegetation structure and plant community composition in 5-7 years old fallows under different land use intensity regimes. The ordination analyses showed a clear pattern of distribution of species along a gradient of resource use intensity: recurrent Chromolaena odorata-dominated fallows (reflecting high land use intensity) were clearly separated from fallow sites that had been forests in the previous cropping cycle (corresponding to relatively lower land use intensity). The pattern of the responses of maize, groundnut and cassava to the three fallow types did not differ over the two years of the study, all crops producing higher yield in fields established after clearing C. odorata-dominated fallows than in fields following bush fallows. Coula edulis, Dacryodes edulis, Irvingia gabonensis and Ricinodendron heudelotii were recorded at very low density values in fallow lands of the study area (< 10 individuals of more than 10 cm dbh ha⁻¹), suggesting the need to develop preferential management of regeneration for these species. Apart from leaf flushing, flowering and fruiting phenology of these species was seasonal, with irregular flowering/fruiting observed for some D. edulis and I. gabonensis individuals over the two years of monitoring. Fruiting was concentrated between July and October (and up to January for R. heudelotii), coinciding with the rainy season. An individual of C. edulis, D. edulis, I. gabonensis and R. heudelotii produced, on average, 236±48 fruits (9.6±2.1 kg fresh weight in 2001, 335±94 fruits and 10.9 ±2.9 kg in 2002), 235±94 fruits (12.5±5.1 kg in 2001 and 801±246 fruits, 51.4±16.0 kg in 2002), 547±212 fruits (71.8±24.9 kg in 2001 and more than 2002 fruits, 133.3±30.0 kg in 2002), 2018±467 fruits (72.2±16.4 kg in 2001), respectively. Regression analyses showed that tree size parameters were correlated with fruit production for some species, but generally, do not explain an important pat of the production data of the study species (r² < 60%).

The effects of crown pruning of Vitellaria paradoxa C.F. Gaertn (karité) and Parkia biglobosa Gacq.) Benth. (néré) on above and below-ground interactions with associated crops of Pennisetum glaucum (L.) (millet) and Sorghum bicolor (L.) Moench (sorghum) were investigated as well as the use of the pruned material as mulch on soil fertility and millet production in an agroforestry parkland system in Burkina Faso. Three treatments of crown pruning (total-pruning, half-pruning and no-pruning) were applied to karité and néré. The area under each tree was divided into four concentric tree influence zones before pruning the trees (Zones A : up to 2 m from the tree trunk, B: up to half of the radius of the tree crown, C: up to the edge of the tree crown and D: up to 2 m away from the edge of the tree crown). Millet production under these zones and outside was assessed over two years' cropping seasons and sorghum over one cropping season. Crop production was analysed in relation to tree transpiration, light transmission, root distribution and soil fertility. Investigation on the use of the pruned material as mulch involved assessment of its decomposition and nutrient release patterns, its effects on soil properties and crop production and the existence of allelopathy in it. The results showed that tree crown pruning had significant effect on associated crop production. Total-pruned trees gave the highest crop production due to the reduction by crown pruning of the effects of large tree crowns on PAR transmission below crowns and rates of transpiration by trees. Root niche differentiation also occurred in which fine root length density of trees was reduced and crop roots dominated the upper soil layer due to crown pruning and as a consequence crop production of up to eight fold higher was achieved under total-pruned trees than under unpruned trees. Soil was more fertile closer to the tree trunks than outside treee crowns and therefore crop overall performed better under Zone B than outside tree crowns. The higher production of crop under Zone B than under Zone A, the zone closer to the tree trunk, may be due to lower light intensity and more intense competition for water and nutrients between trees and crops under Zone A. Pruned leaf litter of néré decomposed and released nutrients faster than karité. However, the slow rate of decomposition of karité leaves was beneficial to crops perhaps in terms of protecting the soil against excessive heat, surface runoff and erosion and due to the achievement of good synchrony between nutrient release from decomposing leaves of karité and crop nutrient demand. As a consequence of these, millet grain yield was increased by 120% and total dry matter by 43% by applying leaf litter of karité as mulch. The results of the laboratory allelopathy experiments were, however, contradictory to the field experiment. Leachate of karité showed more depressive effect on crop seed germination compared with néré. It was argued that this may be due to the fact that allelopathic effects under natural conditions are mediated by environmental conditions and decomposers community and therefore can show different results from the laboratory. Due to the results of the pruning and mulching experiments it was concluded that karité was a more suitable tree species than néré for semi-arid agroforestry parkland systems. Since the period of three years of the present study was too short to evaluate the effect of pruning on the overall productivity of the system it was finally recommended that the monitoring is continued over a longer period to determine if complete recovery of fruit production or an optimum compromise between fruit arld crop production could be achieved before conclusions are made whether pruning is beneficial or not.

When maintaining the biodiversity and ecological integrity of forests is a goal of management, a primary requirement is to assess the status, condition, conservation value of each forest, and change in forest conditions over time. GIS procedures were used here to compare different map-based surveys and look in detail at changes in woodlands of the Snowdonia National Park, North Wales, from 1970 to 2000. The maps from the 1970s and 1980s generated by Silsoe College did not compare well with the map from the 1990s produced by the Forestry Commission and no meaningful changes could be measured. This was attributed to difficulties with comparison of different interpretations and classification schemes used by the two organisations. A series of landscape surveys using the same minimum mapping unit, classification scheme, and methodology in general is needed. The potential changes in broadleaved and scrub woodland area were modelled based on the two most extreme climate change scenarios, termed the Low and High scenarios. Temperature and rainfall models formed the basis for logistic regressions of woodland type and distribution. A declining trend in probability of presence for both woodland types from the present sites was shown under the UKCIP98 High climate change scenario. The results emphasized the conceptual difficulties in using fragments of woodland within the realised niche rather than the fundamental niche as the basis for environmental modelling of plant community distributions. GIS based models were generated to address the key question in the biodiversity action plan process of where should new woodland be created or plantations restored. Ecological criteria were developed to identify the priority areas for native woodland expansion taking into account of the requirements for successful woodland expansion from the nature point of view and specific policy aims. The results were interesting and suggested that there is ample land potentially suitable in Snowdonia for new native woodland. The models could be used to aid decision-making for new native woodland in the National Park. A further extension of GIS-based modelling was developed for the prediction of individual NVC types and BAP priority woodland types. The environmental spaces occupied by the fragments of NVC woodland types currently present in Snowdonia were defined and used as templates to produce maps of potentially suitable sites for the occurrence of each NVC type. The results were not as clear-cut as had been hoped because of overlaps in the predicted occurrences of various woodland types. Independent verification of the predictions using non-spatial data for 24 sites revealed that the model produced was very poor. This was not, however, a fault of the modelling but a reflection of the fact that some of the environmental data were at too coarse a scale and that NVC types are not solely determined by environmental factors. In spite of some weaknesses in the data, the use of GIS for modelling these scenarios proved useful. Nowadays, forest policies in Wales, Europe and elsewhere are changing rapidly to meet modified global, national, and local objectives. GIS is, and will increasingly be so, proving to be a useful and flexible tool for translating forest policy into practical application on the ground.