Plant performance under reduced water availability has traditionally been assessed as drought resistance and more recently as water use efficiency (WUE). An extensive body of work has been established over the past 15 years where the natural variation of water use efficiency has been studied in the model species Arabidopsis thaliana (Arabidopsis). At the same time, a substantial degree of criticism has arisen with respect to the use of drought resistance and WUE as measures of plant performance, due to the lack of relatedness of these parameters to reproductive performance, i.e. yield. The work in this thesis is centered on understanding the physiological and genetic basis of water use and water productivity as alternative measures of plant performance under the context of reduced water availability. The first part of this study describes an extensive assessment of the natural variation of water use and water productivity in Arabidopsis in relation to numerous key physiological, phenological, and developmental parameters. Furthermore, this work concisely relates plasticity of key traits to historical climatic variation. A fundamental aspect of this work was the clarification that it is possible to estimate long term water use to a high degree of accuracy based on short term water use, i.e. soil drying rate, and flowering time. Flowering time was demonstrated to be the predominant driver of vegetative performance and water use, however it appeared to be genetically uncoupled from reproductive performance. This is in contrast to previous work that suggests WUE, measured as the ratio of C12 to C13 isotopes (δ13C), is positively associated with flowering time. Additionally, it was demonstrated that multiple commonly employed proxies of reproductive performance including total biomass, WUE, and flowering time, were not sufficient at predicting seed yield in Arabidopsis across multiple environments. The second part of this study involved the genetic dissection of water use and productivity related traits in Arabidopsis through a quantitative trait loci (QTL) mapping study and a genome wide association study (GWAS). QTL mapping using a recombinant inbred line (RIL) population developed from the ecotypes Col-0 and C24 revealed two key flowering time genes, FLOWERING LOCUS C (FLC) and FRIGIDA (FRI), as key regulators of water use. It was demonstrated that a combination of non-functional alleles of both FLC and FRI reduced long term water use via a shorted life cycle, which is again in contrast to previous work relating to the genetic dissection of WUE in Arabidopsis. Crucially, it was observed that reduced water use mediated in this fashion did not detrimentally impact upon reproductive performance. GWAS was employed subsequent to the QTL mapping in order to identify candidate genes underlying the variation for productivity as a unique trait and also as a factor of water use, i.e. water productivity. GWAS identified multiple promising candidate genes that potentially underlie the heritable genetic variation for flowering time, water use, and water productivity.

With increasing prevalence of Wireless Sensor Networks (WSNs) in agriculture and hydrology, there exists an opportunity for providing a technologically viable solution for the conservation of already scarce fresh water resources. In this thesis, a novel framework is proposed for enabling a proactive management of agricultural drainage and nutrient losses at farm scale where complex models are replaced by in-situ sensing, communication and low complexity predictive models suited to an autonomous operation. This is achieved through the development of the proposed Water Quality Management using Collaborative Monitoring (WQMCM) framework that combines local farm-scale WSNs through an information sharing mechanism. Under the proposed WQMCM framework, various functional modules are developed to demonstrate the overall mechanism: (1) neighbour learning and linking, (2) low-complexity predictive models for drainage dynamics, (3) low-complexity predictive model for nitrate losses, and (4) decision support model for drainage and nitrate reusability. The predictive models for drainage dynamics and nitrate losses are developed by abstracting model complexity from the traditional models (National Resource Conservation Method (NRCS) and De-Nitrification-DeComposition (DNDC) model respectively). Machine learning algorithms such as M5 decision tree, multiple linear regression, artificial neural networks, C4.5, and Naïve Bayes are used in this thesis. For the predictive models, validation is performed using 12-month long event dataset from a sub-catchment in Ireland. Overall, the following contributions are achieved: (1) framework architecture and implementation for WQMCM for a networked catchment, (2) model development for low-complexity drainage discharge dynamics and nitrate losses by reducing number of model parameters to less than 50%, (3) validation of the predictive models for drainage and nitrate losses using M5 tree algorithm and measured catchment data. Additionally modelling results are compared with existing models and further tested with using other learning algorithms, and (4) development of a decision support model, based on Naïve Bayes algorithm, for suggesting reusability of drainage and nitrate losses.

The research demonstrates that Three-Dimensional Variable-Density Groundwater Flow models such as the SEAWAT model can be effectively used for design of subsurface drainage systems for controlling salt concentration in the root zone on salt affected irrigated land. The SEAWAT model was used to optimize subsurface drainage design to ensure that the salt concentration of the groundwater at the base of the root zone does not exceed pre determined levels instead of the conventional approach of maintaining the groundwater at a predetermined water table level. The study was carried out on a conceptual uniform homogenous block of irrigated flat field of shallow water table depth of 0.5 m and salt concentration of 7200 mg/l with impermeable layer at 20 m deep and impermeable field boundaries. Using the model, spacings were designed to be used as design criteria for subsurface drainage system to maintain salt concentrations of 6000, 5000 and 4000 mg/l at the base of the root zone and water table depth of 0.8 m from the soil surface. The results showed that over a wide range of irrigation water quality and aquifer hydraulic conductivity the optimum drain spacing using SEAWAT was, depending on irrigation water quality and aquifer hydraulic conductivity, wider by between 3 and 50 % and the amount of drain discharge reduced by 1 and 27 % than would be recommended using conventional design equations. It was concluded that Three-Dimensional Variable-Density Groundwater Flow models are better for designing effective drainage systems than Conventional drain spacing design equations such as Hooghoudt.

The disposal of biosolids poses a major environmental and economic problem. Agricultural use is generally regarded as the best means of disposal. Although the impact on soil ecosystems remains uncertain. Biosolids can improve soil properties by supplying nutrients and increasing organic matter content but there is also a potentially negative impact arising from the introduction of heavy metal contaminants into soils. It is widely acknowledged that the bioavailable fraction, rather than total metal content, is indicative of plant metal uptake and toxicity. The bioavailable metal fraction in turn is dependent on soil properties. Therefore, the overall aim of this work was to determine the bio-geochemical factors that control the dynamics of trace element bioavailability in soils that have been subject to the disposal of sewage sludge for over 100 years. Three main investigations were undertaken. In order to determine the current metal composition of the site and identifying the geochemical factors that control the dynamics of metals bioavailability, thirty -eight fields, from a dedicated sewage sludge disposal site for over 100 years, were sampled for both soil (bulk and rhizosphere) and plant. Special attention was devoted to determining soil properties that govern metal partitioning between different metal pools (i.e. total, isotopically exchangeable, Ca(NO3)2-extractable and free ion activity). In order to identify the best estimate of plant uptake and toxic response, a pot experiment was carried out to compare the effects of Zn on plant growth in soils recently spiked with Zn and soils historically amended with biosolids to identify soil properties that best predict metal uptake and subsequent phytotoxicity. The effect of biosolids on soil microorganisms was assessed. Terminal restriction fragment length polymorphism, a fingerprint molecular technique, in combination with multivariate data analysis were used to relate soil microbial diversity and community structure to metal accumulation and bioavailability. High levels of contamination, exceeding the current limits for the use of biosolids in agriculture, were observed in the studied soils reflecting extensive long-term biosolid application. Enrichment factors in relation to background levels in the area were greater than 5 and followed the trend Cd>Cu>Zn>Pb>Ni. Copper and Cd exhibited extremely high enrichment levels, up to 106 and 151 respectively. Except for Pb, the isotopically exchangeable pool of the studied metals (E-value) was mainly controlled by the total metal content in soil, accounting for more than 90% of the variation in E-values. Lead lability was primarily controlled by the total P, LOI and Fe oxides. Metal labilities expressed as % of total metal content were < 40% for the five studied elements following decreasing order of Cu > Cd > Zn ≈ Ni > Pb. Apart from Pb, all the bioavailability estimates (total, E-values, Ca(NO3)2-extractable and free ion activity) correlated strongly with metal concentration in plant, accounting for more than 70% of the variation in plant concentrations. Ca(NO3)2-extractable provided the best estimate out of the four measures of bioavailability, accounting for 87, 77, 87 and 83% of the variation in plant concentration of Ni, Cu, Zn and Cd respectively. The results of the pot trial showed that 67-90% of the added Zn remained isotopically exchangeable after 3 months of Zn addition, suggesting that rapid adsorption processes take place, followed by a slow aging process that cannot be detected over the period of the experiment (3 months). The speciation of soil solution showed that Zn was present mainly (80% on average) as free ion indicating the low affinity of this metal to complexation by dissolved organic matter. An antagonistic relationship was observed between Zn and Cd suggesting that greater Zn availability suppressed Cd uptake by plant. Although Zn addition increased Cd concentration in the soil solution, Cd transfer factor was simultaneously inversely correlated with Zn concentration in soil solution. The free ion activity model (FIAM), based on the biotic ligand model (BLM), accounted for 94% of the variation Zn concentration in plant. Cadmium appeared to play an important role in competing with Zn for uptake. A simple regression model utilising soil total Zn, soil organic matter and soil pH accounted for 88% of the variation in plant uptake. This indicates the possibility of using soil properties that are measured routinely as input for prediction of plant uptake. The results of the Zn phytotoxicity test indicated that the intensity of the exposure (i.e. free ion activity) was the key quantity in the context of predicting plant toxic response, describing 80% of the variation in the response of barley growth to Zn toxicity. Only labile Zn from the quantity based extraction was able to describe the toxic response explaining only 46% of the variation. The study of the effect of biosolids on soil microorganisms showed that soil total Zn concentration could be adopted as a good indicator of the overall (historical) biosolids loading. A biosolids loading, equivalent to 700 – 1000 mg kg-1 Zn appeared to be optimal for maximum bacterial and fungal diversity. This markedly exceeds the maximum soil Zn concentration of 300 mg kg-1permitted under the current UK Sludge (use in agriculture) Regulations. Redundancy analysis (RDA) suggested that the soil microbial communities had been altered in response to the accumulation of trace metals, especially Zn, Cd, and Cu. Based on the findings of this thesis, it can be concluded that (i) the estimation of metal speciation, both in the solution and solid phase is a key factor in determining the bioavailability and thus, has greater chemical and biological significance than soil total metal content; (ii) the maximum beneficial effect of biosolids on soil microbial diversity occurred at a metal (Zn) concentration well in excess of current regulations governing application of biosolids to agricultural land. This indicates that soil microbial diversity is unlikely to be determining factor for regulatory limits for biosolids disposal to agricultural lands.

Nematode infection is one of the major causes of disease in young sheep. Selective breeding of genetically nematode resistant sheep is an alternative method for controlling the nematode infection. This process could be simplified if loci that account for nematode resistance can be identified. MHC is one of the candidates and several studies have confirmed the association between MHC alleles and nematode resistance. The aim of this study is to establish the role of MHC class II genes in nematode resistance in Texel sheep. Thus, it can help endorse the usefulness of the MHC class II genes as a genetic marker of nematode resistance and extend the knowledge of the mechanism of resistance against nematodes. This study has been focused on three main areas; 1) description of MHC class II gene diversity, 2) description of haplotype and linkage disequilibrium pattern at MHC class II genes and 3) the association of MHC class II genes and nematode resistance. Sequence-based typing was applied to characterise MHC class II allelic diversity in 235 Texel lambs. The haplotype and linkage disequilibrium patterns were deduced from pedigree information. Finally, the association between MHC class II haplotypes and nematode resistance (FEC and IgE activity against L3) were investigated using a MIXED model approach. MHC class IIa genes were diverse in Texel, consistent with previous studies reported in sheep. The most polymorphic locus among MHC class IIa genes was DRB1. A total of 21 distinct DR-DQ haplotypes were obtained and strong linkage disequilibrium exhibited between DR-DQ genes. There were also statistically significant associations of specific haplotypes and nematode resistance in this population. The work in this thesis confirms the likely importance of MHC genes in regulating resistance against gastrointestinal nematodes, thus supporting the use of MHC as a genetic marker of nematode resistance in selective breeding. Sequence-based typing system for MHC class IIa has been established in this study.

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No description available.

In many developing countries, those people who work the land as food producers are also the ones who most suffer from food insecurity. While many studies look at the power dynamics within the food system at the global level and the role played by transnational companies in particular, this investigation starts at the local level to look into the reasons behind the high levels of food insecurity among farmers. Specifically, it analyses how the relationship between the domestic food producers and the state in Tanzania has affected food security in rural areas, in particular in farmers' households. The question it asks is: How has the relationship between the state and farmers shaped food security in rural Tanzania since its independence? A qualitative approach has been employed: farmer interviews were conducted in 8 villages located in two regions of Tanzania - Coast and Kilimanjaro - and supplemented by interviews with state officials and civil society representatives. The villages surveyed in the Coast region suffer from arid conditions and are isolated from the main road that connects Dar es Salaam to Morogoro, while the villages studied in the Kilimanjaro region are on the slopes of the mountains around the town of Usangi, far from the touristic and commercial centres of Moshi and Arusha. Through interviews with farmers in these villages, the qualitative approach of this research offers a contextualised insight into food insecurity, the problems of the agricultural sector and farmers' attitude towards the state and its policies. The interviews with state officials and representatives of civil society were employed to investigate both current agricultural policies and officials’ attitude towards small scale farmers. This thesis makes an empirical contribution to the literature on food security and state-farmer relationships. I argue that the mixture of agricultural policies implemented by the state over the years have done little to improve the livelihoods of small scale farmers that live in isolated rural areas. One of the reasons why this is so is that the policies are not framed around the needs of small scale farmers (despite them being the great majority of the farmers in the country), and hence are not welcomed positively by the communities. The results of this study identify a reciprocal distrust between the state and farmers as one of the main causes of policy failure and unsatisfactory improvements in food security in rural areas. On one side, state officials see small scale farmers as inefficient and wish for the agricultural sector to be driven by medium and large scale farmers. On the other side, most farmers tend to dismiss state officials' advice as inadequate to the reality of farming. In general, farmers see the state as a distant entity, with which they have little contact and which they do not trust. I argue that the controversial relationship between the Tanzanian state and farmers is historically grounded and has a direct link with food insecurity amongst farmers for two main reasons. First, it affects the framing, objectives and implementation of agricultural policies, which thus fail to support small scale farmers. Second, it hinders the ability of farmers to successfully cooperate and/or create a coherent farmers' movement to improve food security and address their challenges at state level. Farmers' discontent is perceived in their alienation to politics, and in their distrust towards a state that has historically not been able to address their challenges nor improve their condition.

Degradation of terrestrial habitats with high conservation value has resulted in strategic efforts to cease or reverse their declines. Broad habitat management can restore ecological processes and large herbivores can provide ecological function in some terrestrial systems. Following years of decline and fragmentation, owing to factors such as cessation of traditional practices, lowland heathland has become an internationally important habitat with strategic protection. Free-ranging grazing aims to assist in mitigating such losses to habitat and vegetation communities, but quantifying the grazing regime and its associated impacts is necessary to ensure protection of these vulnerable systems. Reviews of herbivore impacts on lowland heath provide detailed evaluations and recognise the absence of experimental assessments and baseline monitoring. This research aimed to assess ecological activity and impacts (herbage removal, trampling and dunging) of horses and cattle on a lowland heath system to determine their influence on changing vegetation and to inform grazing management. This mixed regime is commonly adopted for restoration of semi-natural habitats but a failure to understand the separate vegetation impacts can be detrimental for the system as a whole. Behavioural activity was quantified using scan-sampling assessing spatial and temporal variation in behaviour, habitat selection and niche overlap, spatial occupancy and diet. A factorial design was set up to quantify the impacts of herbage removal, trampling and dunging to vegetation separately. Assessments vegetation community composition and architecture in treatment and control areas were undertaken. Analyses incorporated non-parametric and general linear models. Animals utilised their environments in different ways, varying for feeding and showed high habitat selectivity, based on physiology and foraging strategy primarily. Herbage removal strongly influenced vegetation architecture and heterogeneity owing to selection for graminoids and the plants’ competitive traits; effects on other plants were not as well defined due to minimal abundance. Trampling modified the vegetation structure due to reduced canopy density maintaining colonising gaps, but increased graminaceous cover and showed a capacity for lateral expansion. Dunging regime was highly influential for enhancing plant architecture and modified vegetation composition based on nutrient availability and competition. Worming regime was influential on architectural parameters and may be due to retarded dung degradation; further research is required. The findings contributed knowledge to lowland heath grazing management, validating the use of mixed regimes at low densities, for generating vegetation heterogeneity, for the control of dominating plants and for understanding the impacts of different animal-management practices. Expanding the reach of this research to comparable systems is necessary to develop the knowledge of grazing-management impacts. The work addressed an absence of experimental evaluation on these systems and also illustrated the importance of separately quantifying the impacts of large herbivores.

This thesis investigates the development of regional agri-food systems and their supply chains to understand how they affect the sustainability of rural regions. It argues that the existing dichotomies of alternative-local and conventional-global do not provide a sufficiently nuanced understanding of the dynamic transitions and interactions that occur in regional agri-food systems. Deploying and extending socio-technological systems theory, the thesis explores the interaction between nested levels of sectoral and general agri-food regimes and reconstructs the emerging logics of interaction. Against this background, it analyses how alternative agri-food supply chain innovations evolve and assesses their various degrees of success. The meat, dairy and horticultural sectors in SW Wales are investigated as case studies, using a mixed methodological approach combining secondary data analysis and interviews with key stakeholders and supply chain actors. The research finds three sub-sectoral systems with highly differentiated socio-technological configurations and equally diversely configured niches. Using the socio- technological systems framework the: socio-technological configuration, degree of system stability and the future transitional pathways of the each sub-sectoral system is examined. This framework also creates the basis for an assessment of how likely their innovations are to be adopted or absorbed by the conventional agri-food system in SW Wales. The thesis finds that meaningful interactions occur not only within each sub-sector and betweentheir niches but also between sub-sectoral systems. The thesis ultimately provides a nuanced analysis of SW Wales’ agri-food systems that shows the complexity of regional food systems and critiques possible sustainable responses from public policy. It demonstrates that a socio-technical regime perspective can uncover the manifold relations between local and regional agri-food innovations and the dominant, multi-layered agri-food system. This constitutes a major empirical and conceptual contribution to the debates on sustainable food and rural development.