The African oil palm (Elaeis guineensis Jacq.) is a highly valued oil producing perennial crop with a productive lifespan of about 25 years. Although benefiting from a long productivity period, oil palm genetic improvement is a slow and tedious process which requires between 10 to 12 years to complete one selection cycle. As such, marker-assisted selection (MAS) is an invaluable tool for yield improvement in oil palm. In particular, MAS could be used to facilitate efforts to increase the unsaturated fatty acid content of palm oil by introgression of desired alleles from the American species, E. oleifera which produces highly unsaturated oil. In order to help achieve this, high density genetic linkage maps were constructed for a commercial Deli dura (maternal) x Yangambi pisifera (paternal) breeding population (P2) and a Colombian E. oleifera (maternal) x Nigerian E. guineensis (paternal) interspecific hybrid population (OxG). The P2 and OxG mapping populations were screened with approximately 700 oil palm SSR primer-pairs and genotyped with a 4.5K customized oil palm SNP array to identify informative markers. The P2 and OxG populations consisted of 87 and 108 palms, respectively. Genetic linkage maps were first constructed for the individual parental palms of the mapping populations and followed by integration of the two parental maps. A P2 integrated map with 1,331 markers spanning 1,867 cM over the 16 linkage groups was constructed, representing the 16 chromosome pairs in oil palm. This study for the first time reports the genetic map for the Colombian E. oleifera, although the map only comprises of ten linkage groups with 65 markers spanning 471 cM. The Colombian E. oleifera map was also successfully integrated with the Nigerian E. guineensis parental map, resulting in a partial integrated map for OxG. The genetic maps and the available phenotypic data were successfully used to identify 22 quantitative trait loci (QTLs) associated with various yield components (YC) in the P2 population and 12 QTLs for fatty acid composition (FAC) in the OxG population. The QTLs identified for FAC include the total unsaturation levels via iodine value (IV), myristic (C14:0), palmitic (C16:0), palmitoleic (C16:1), stearic (C18:0), oleic (C18:1) and linoleic (C18:2) acids. On the P2 integrated map, QTLs for YC were associated with mean bunch number (MBN), mean fruit weight (MFW), oil/bunch ratio (OTB), oil/wet mesocarp ratio (OTWP), oil/dry mesocarp ratio (OTDP), mean mesocarp weight (MPW), wet mesocarp weight (WPWT), kernel yield (KY), mean kernel weight (MKW), mean shell weight (MSW), shell to fruit (STF), total oil (TOT), oil yield (OY) and dry mesocarp weight (DPWT). The closely linked markers demonstrated significant allelic effects associated with the YC and FAC phenotypes analysed. The genetic effects (estimated by G Model) for the identified QTLs can be ranked from high for C16:0, C18:1 and IV (ranging from 2.16 – 2.46) to medium for OTWP, DPWT, MPW, WPWT, OTB, MFW, OTDP, MBN and STF (0.50 – 2.14) and low (< 0.5) for KY, MKW, MSW, C18:2, C18:0, C16:1 and C14:0. The three major QTLs for C16:0, C18:1 and IV were also successfully cross-mapped on two interspecific BC2 populations, which adds confidence on the association of the markers with the traits concerned and reflecting their potential utility in a MAS programme. This study also identified candidate regulatory genes and transcription factors (TFs) within the QTL confidence intervals by aligning to the oil palm (EG5) genome build. A set of five candidate genes (HIBCH, PATE/FATB, BASS2, LACS4 and DGAT1) and a TF (WRI1) were identified within the QTL confidence interval associated with genetic effects for C16:0, C18:1, C14:0, C18:0 and IV in LGOT1, which was supported by the significant differential expression patterns observed for the candidate genes and TF in RNA sequencing (RNA-seq) and real-time PCR (qRT-PCR) experiments. The RNA-seq and qRT-PCR experiments included palms from OxG and two independent interspecific backcross populations. Clear differential expression patterns were observed for some of the genes and their putative isoforms, which requires further validation in future studies. The high-density SNP and SSR-based genetic maps developed in this study have greatly improved marker density and genome coverage in comparison with the first reference map based on AFLP, RFLP and SSR markers. The improved maps with reduced gap between markers were aligned to the EG5 genome build, which proved useful for mining of candidate genes associated with the QTLs from the targeted regions. The closely linked markers and candidate genes associated with FAC and YC provide a good starting point for other genetic improvement studies in oil palm including whole genome association mapping studies. The candidate gene approach as used in the present study is useful for identifying the potential causal genes linked to QTLs. Finally, the markers closely linked to specific traits, specially IV, C16:0 and C18:1, MFW, MPW and OTDP have great potential and should be prioritized for further validation in the effort towards their adoption for MAS to introduce greater unsaturation and improve oil yield in commercial oil palm.

Phytoplasmas are wall-less, non-culturable, phloem-limited bacterial pathogens that belong to the Mollicutes. They cause many diseases in lots of plant species (wild and cultivated) belonging to many different plant families, resulting in significant losses in important crops, and economically damaging epidemics worldwide. Phytoplasmas infect major cultivated crops such as many annual crops, fruit trees, grapevines and palms, which makes control of these diseases a priority, and the first important step for management is efficient and effective phytoplasma diagnosis. Detection of phytoplasmas is difficult because of their irregular distribution within the diseased plants and low concentration inside infected plants. In the last two decades most research toward the detection of phytoplasmas has used nucleic acid-based techniques such as PCR, which is used to amplify regions of phytoplasma genomes existing inside infected plants. However, most routine diagnostics has moved from general PCR to real-time PCR, due to the improved sensitivity and reduced risk of contamination due to the use of a closed system for product detection. Also the method can be developed into a semi-quantitative method. In this project the aim has been to improve the specificity and reliability of phytoplasma diagnostic techniques by using primers that detect specific genes in phytoplasma genomes, and designing new universal primers for conventional and real-time PCR. This has involved developing new assays for 16Sr groups II, III, V, VI, XI, and XII, to facilitate analysis of changes in levels of different phytoplasmas in mixed infections. In addition, this work has involved the evaluation of LAMP (loop mediated isothermal amplification) diagnostic assays for different phytoplasma groups (I, II, III, V, VI, X, and XII) and also validating a rapid DNA extraction method and whether this is effective for all plant species (i.e. Madagascan periwinkle versus Napier grass and other grasses). The second main objective was to investigate the rate of evolution of phytoplasma genomes. For this, infected plants (of phytoplasma groups 16SrI, II, III, VI, and X) were grafted onto fresh plants at 3-4 month intervals throughout the project. Once the phytoplasma had re-established, DNA was extracted and a range of genes including 16S rRNA, secA, tuf, and rp were amplified and sequenced. The aim was to determine whether there was any evidence of genome evolution over time. However, the results suggested that in these genes at least, the rate of change due to point mutations and/or insertion of potential mobile elements (PMUs) was slow, with no sequence changes being detected over the three years of study.

Root system architecture (RSA) is a dynamic system of root network capable of adapting to changes in soil environment such as decline in soil moisture and nutrient deficiency. RSA responses to different nutrient concentration levels provide a unique system to study interactions between plants and their soil environment and the effect of different nutrient levels on root development. Wild (Lactuca serriola) and domesticated (Lactuca sativa) lettuce root systems have contrasting RSA and therefore populations developed from these two contrasting parents provide unique resources to explore root traits between cultivated and domesticated crop species. Wild lettuce has a deeper root system with capability to exploit deeper soil horizons for nutrients and water while the domesticated lettuce possesses a shallow root system capable of acquiring resources mostly from the topsoil. Although there are clear RSA differences between wild and domesticated lettuce grown under normal soil condition, an understanding of the effect of different phosphorus (P) levels on RSA is lacking. P is one of the most important macronutrients for most crops after nitrogen, especially used as one of the building blocks of nucleic acid, phospholipids and many metabolites. Furthermore, P is often immobilised in the soil, therefore understanding the optimal uptake of P through RSA is important. The present study aims to provide a better understanding of the effect of crop domestication on root traits by evaluating lettuce RSA, specifically the contrasting features of wild and domesticated lettuce, in response to a wide array of P levels. Specifically, the root systems of lettuce parental lines, wild lettuce (Lactuca serriola acc. UC96US23) and domesticated lettuce (Lactuca sativa cv. Salinas) were evaluated using agar-based and paper-based root phenotyping methods. This was followed by the QTL analysis of the lettuce parental lines and an recombinant inbred lines (RIL) mapping population derived from the cross of the two lettuce parental lines. The present study also explored the use of x-ray microcomputed tomography (μCT) to visualise the undisturbed lettuce RSA in 3D. The agar-based root phenotyping method utilised vertical agar-filled petri dishes at five different P levels (0, 6, 312, 625 and 1250 μM P) and images of the roots were obtained through a flatbed scanner and analysed in silico. Seven RSA traits showed significant difference (P≤0.049) between lettuce parental genotypes × P levels interaction. The subsequent multiple comparison tests implied that the wild lettuce showed significant enhanced primary root (PR) growth (P < 0.001) while domesticated lettuce significant showed enhanced lateral roots (LR) formation (P < 0.001), especially at very low and high P levels. The paper-based root phenotyping method utilised vertical paper pouches and images were obtained through simple DSLR camera setup, and then analysed in silico. The results showed significant mean differences (P≤0.006) between the parental genotypes in most of the measured traits. The trait means of domesticated lettuce were consistently higher than the wild. Additionally, the correlation tests revealed strongest significant correlation (r ≥ 0.82, P < 0.001) of similar trait classes (i.e. lateral-lateral, primary-primary and global-global root traits), suggesting similar growth mechanisms between highly related traits. The confirmation of significant genotypic differences in previous experiments led to the QTL mapping of the traits using an F8 RIL mapping population. From multiple QTL mapping (MQM) analysis, six QTLs and a putative QTL were obtained, mostly clustered in a hotspot in linkage group (LG) 1. The traits were mainly of the primary and global root traits. The primary root length (PRL) in this hotspot was driven by wild lettuce, which may imply association of domestication QTL in lettuce rooting depth as opposed to interval mapping (IM) or multiple QTL mapping (MQM) analysis. Using a non-parametric Kruskal-Wallis (KW) QTL analysis, 48 QTLs were identified, in which some clustered at hotspots (i.e. LG1, LG4, LG5 and LG8) dominated by lateral root traits. These clusters of trait loci may imply similar mechanisms control similar growth-related traits. The overall differences seen between wild and domesticated lettuce RSA have provided an understanding of the effects of domestication on RSA traits. The present study showed some deviation in P adaptation between the parental lines, suggesting the novel domestication QTL identified particularly in LG1 which relates to the PRL. The outcome of this study could potentially be applied in identifying RSA traits that should be maintained or selected in other species, particularly the underutilised crops, during improvement process. Development of improved varieties with superior root traits such as deep rooting system, may pave the way for more sustainable agricultural practice thereby reducing dependency of crops on inputs such as chemical fertilisers and excess water. The results obtained from the present study were obtained from 2D images, which may not entirely represent the 3D architecture of the roots in the soil. The utilisation of x-ray microcomputed tomography (μCT) in visualising the lettuce RSA in a preliminary study have shown interesting ‘umbrella-shaped’ root architecture, which cannot be clearly identified in experiments using 2D images. The study could be potentially expanded to explore more traits, especially using 3D-related root traits, to better understand the lettuce RSA, particularly responses towards different P levels.

Agricultural production is at the mercy of uncertainties driven by climate change, as a result of this most of the major and minor crops are under threat of crop failure due to the severity of its effects on ‘crop fertility’. Plant reproduction is regarded as highly sensitive to such climatic changes, especially under high temperatures stress. Therefore, a key strategy to adapt to ever-increasing global temperature is by improvement and promotion of underutilised crops, one such future crop and the main focus of our research is bambara groundnut (Vigna subterranea [L] Verdc.). The present research was aimed at investigating the effect of temperature stress on plant reproduction, however, there is very limited data on how bambara groundnut genotypes differ in their response to temperature stress with respect to plant reproduction. Therefore, the focus of this research was a systematic study to establish firstly a guide to the reproductive development and, to quantify the impact of high temperature stress on floral development, pollination to fertilization and pod set in bambara groundnut. The main methodology applied to establish the first guide to bambara groundnut flower development and pollen formation was through advanced microscopy techniques (fluorescence and scanning electron microscopy [SCM]). Later, the effect of short duration high temperature stress surrounding flowering time (pre- and post-anthesis) in seven bambara groundnut genotypes (IITA-686, S19-3, AHM-753, Uniswa red, Getso, and DipC), was investigated by applying three days of high temperature stress (36/33°C, day/night) at 100% flowering, before the temperature was returned to control conditions (28/22°C) and maintained until pod harvest. Phenotypic characteristics such as flower morphology, pollen viability and pod set, between control and heat stressed groups, were some of the traits observed to assess the effect among the seven genotypes. RNA sequencing experiment was designed and executed to obtain differential gene expression data under high temperature stress, however breakdown of a freezer prevented the successful completion of the experiment. Firstly, a scale of bambara groundnut flower development was established based on flower size as a unit of measurement, from stage 8 to stage 13, which corresponds to floral organ differentiation and flower opening, respectively. Pollen architecture and development (micro-sporogenesis and micro-gametogenesis) was documented using fluorescence microscopy and SCM. And this study is the first one to link flower phenology to the stages of pollen development through morphological data. Secondly, the effect of short duration high temperature stress was evaluated, it showed that the effect on in vitro pollen germination was significant (p < 0.05) and was seen within 24 h of the application of the heat stress (HT-1) in all genotypes, and correspondingly pod set was significantly (p < 0.05) reduced during heat stress. The genotypes IITA-686, AHM-753 and S19-3 recovered, pollen viability relatively faster and produced pods when the plants were returned to control conditions after heat- stress, in contrast to Uniswa red and Getso, where pod set was severely affected. We could conclude that like most of the legumes bambara groundnut pollen is sensitive to high temperature stress, with temperatures 36/33°C producing significant effects on pollen viability, and also display acclimation capability, when returned to control conditions. We advocate that selection for breeding should start at male gamete level, through in vitro pollen germination to determine tolerant and sensitive genotypes, and the prospects of bambara groundnut pollen thermo-tolerance should be evaluated. Many research experts are considering bambara groundnut as a future crop based on its agro-ecological, cultural, genetic and nutritional importance. This research is one step in contributing to the knowledge of this future crop. This study serves as a guide for future researchers interested in flower development and variation in the process observed within and between bambara groundnut genotypes. Assessing pollen thermo-tolerance can give a direct indication of crop success/ seed yield under heat stress and the methodology is not limited to only temperature stress, that is it could also be adapted in photoperiod, drought and water stress. Investigation of other forms of stress tolerance could ultimately contribute to the development of future crop which could cope with future climatic anomalies.

Beans are seeds of leguminous plants and are rich in macronutrients and micronutrients such as polyphenols predominantly phenolic acids and flavonoids that may have health benefits arising from their antioxidant and other properties. Beans, especially from underutilised legumes, may play an important role in future world food supply. However, there has been limited investigation into the nutritional composition of underutilised beans compared with commercial beans such as soya bean. Therefore, this study aimed to improve the extraction, identification and quantification methodologies for characterizing soluble free, conjugated and insoluble bound phenolics from underutilised beans using high performance liquid chromatography (HPLC) and liquid chromatography – mass spectrophotometry (LC-MS). Six underutilised beans (adzuki bean, black eyed pea, bambara groundnut, lablab bean, mung bean, pigeon pea) were found to possess a comparable amount of antioxidant activity to commercial beans and this showed positive correlation with their phenolic compounds. Optimisation revealed that 80% methanol was most suitable for extracting soluble phenolics compared with 80% acetone and acetate buffer, although subsequent HPLC profiling showed strong similarities among all three solvents. Alkaline hydrolysis for 5 mins followed by SPE partitioning on soluble extracts and alkaline hydrolysis for 1 h followed by acetonitrile salting out liquid-liquid partitioning on residue were the optimum procedures for estimating the conjugated phenolics and releasing the bound phenolics. The methods showed better recovery, were more solvent friendly and had shorter drying times than ethylacetate liquid-liquid partitioning. Using 20 phenolic standards, more phenolics were detected by LC-MS than HPLC. Black eyed pea had the most diverse soluble phenolics profile (n=13), followed by adzuki bean and bambara groundnut (n=11) whilst soya bean exhibited the most diverse bound phenolics profile (n=7), followed by pigeon pea and adzuki bean (n=5). Five phenolics were found at the highest concentration in bound extracts from adzuki bean (consist of gallic acid at least 5-fold higher than in soya bean), bambara groundnut (consist of protocatechuic acid at least 160-fold higher than in soya bean), lablab bean (consist of p-coumaric acid at least 3-fold higher than in soya bean), black eyed pea (consist of ferulic acid at least 0.5-fold higher than in soya bean), soya bean (sinapic acid) and others were found at highest concentrations in soluble extracts from different beans. In conclusion, this study has achieved its objectives by developing the comprehensive profiling of phenolics for underutilised beans with optimised extraction methodologies and analysis techniques. The outcome was that underutilised beans are potential alternative resources to commercial beans since they possess higher concentrations of, and more diversified, phenolics than soya bean. This is the first report of optimised extraction methodologies and analysis techniques for the comprehensive analysis of phenolics in underutilised beans. It has generated phenolic profiles from the application of the optimised methodologies and produced useful reference databases for future studies and serves to create an awareness of the potential of underutilised beans as alternative food resources.

Self-incompatibility (SI) is an important genetic mechanism that angiosperms utilize to reject "self' pollen. In Papaver rhoeas (poppy) Sl is controlled in an allele-specific manner by a single locus with multiple haplotypes; each haplotype encodes male (PrpS) and female (PrsS) S-determinants. PrsS-PrpS interaction triggers Sl, stimulating cation channel activity and increases in cytosolic free Ca2+ ([Ca2+]i), triggering a signalling network involving actin cytoskeleton alterations and programmed cell death (PCD). PrpS was recently functionally transferred into self-compatible, highly diverged Arabidopsis thaliana. Transgenic Arabidopsis pollen expressing PrpS-GFP was shown to undergo a "Papaver-SI-Iike response", involving actin and PCD when challenged by recombinant PrsS. Here we investigated function of PrpS in several other heterologous model systems, including Arabidopsis mesophyll protoplasts, yeast, barley and mammalian HeLa cells. Although more work is needed on some of these systems, data were obtained suggesting that PrpS is functional in mammalian HeLa cells. A key finding was that HeLa cells expressing PrpS , when exposed to cognate PrsS, exhibited transient increases in [Ca2+]i and inward cation currents; actin reorganization and decrease in cell adherence. These data suggest that: PrsS-PrpS interaction can recruit endogenous components in HeLa cells to achieve a biological response.

Despite the success of breeding for high-yielding varieties during and since the ‘Green Revolution’, there are still an ever increasing number of people who suffer from malnutrition, due to both inadequate calorie intake and ‘hidden hunger’ from insufficient essential nutrients. There are also adverse impacts of such high-input, intensive agriculture on the wider environment. It is necessary therefore to focus breeding efforts on improving nutrient uptake and composition of crops, as well as improved yield. Roots have been an under-utilised focus of crop breeding, because of difficulty in observation and accurate measurement. Furthermore, genetic diversity in crop roots may have been lost in commercial varieties because of the focus on above-ground traits and the use of fertilisers. Techniques which can accurately measure phenotypic variation in roots, of a diverse range of germplasm at a high throughput, would increase the potential for identifying novel genetic loci related to improved nutrient uptake and composition. The aim of this PhD was to screen at high throughput in a controlled-environment, the roots of an array of Brassica napus germplasm. The validity of the system to predict field performance, in traits including early vigour, nutrient composition and yield was assessed. Genetic loci underlying variation for the root traits were also investigated. A high throughput screen of the mineral composition of a mutagenised B. rapa population was also conducted, with the aim of identifying mutants with enhanced mineral composition of human essential elements, particularly magnesium. It has been demonstrated that root traits in the high throughput system can predict field performance, particularly primary root length which has the greatest ‘broad-sense heritability’ and relates to early vigour and yield. Lateral root density on the otherhand was found across the studies to relate to mineral composition, particularly of micro-nutrients. Genetic loci underlying root traits, and enhanced magnesium accumulation have been identified, and have potential for use in breeding Brassica with improved mineral nutrition.

Phytoplasmas are plant pathogens that are small prokaryotic, wall-less bacteria causing significant diseases in hundreds of plant species globally. They have been named as distinct ‘Candidatus phytoplasma’ species and belong to the Mollicutes. These microorganisms are non-cultivable plant pathogens (obligate), so their diagnoses are primarily achieved by molecular techniques. In infected plants, they inhabit phloem tissues (sieve cells) and they are transmitted between plants by insects (phloem feeders) such as those in the orders Cicadellidae, Psyllidae and Fulgoridae. Phytoplasmas have extremely small genomes and also have very low levels of the nucleotides cytosine and guanine. Polymerase Chain Reaction (PCR) has been developed and employed for investigating phytoplasmas in their hosts, and such techniques have been advanced through the use of nested PCR and real-time PCR to improve the diagnosis of phytoplasmas with low titre in their different hosts, and also to be able to identify the different taxonomic groups of the pathogens. In addition, real-time PCR can be used to quantify phytoplasmas in the infected plants or insects. The purpose of this project was to concentrate initially on 16S rRNA, leucyl tRNA synthetase and secA based PCR assays and test these on periwinkle plants containing phytoplasmas from six taxonomic groups, 16SrI, II, III, V, VI and X. Work also focussed on transmitting the six phytoplasma strains between periwinkle plants and other host plants such as Napier grass, oil palm, and tomato plants through dodder shoots. Cuttings were taken from mother plants, that are all from the same periwinkle genetic background, to enable the propagation of new plants containing isolates from the six groups. These were treated with different potential control strategies, and conventional and real-time PCR and (Loop-mediated isothermal amplification) LAMP were used to test the levels of phytoplasma in these plants following treatments to determine the efficacy of the different control treatments. In more detail, the control strategies being tested included altered nitrogen fertilization regimes, treatment with salicylic acid, and UV-C pulse treatments. As a consequence, phytoplasma titre of different phylogenetic groups were affected by the application of different nitrogen fertilizers and different amounts, and this showed the potential for use of various nitrogen sources as a control method for phytoplasma diseases. Furthermore, this research has shown that UV-C light can be applied to phytoplasma-infected plants to enhance the resistance characteristics of plants against phytoplasma and reduce phytoplasma titre within diseased plants. Through applying different control approaches against phytoplasma infected plants, it has been shown that low concentrations of salicylic acid application had an optimal significant effect on phytoplasma quantity and reduced infection on diseased periwinkle plants. However, a high concentration of the same solution produced a negative effect and phytotoxicity on periwinkle plants.

Tropical forested peatlands are a major carbon store and are a significant source of global carbon dioxide (CO2), methane (CH4), and nitrous oxide (N2O) emissions. While the role of environmental variables, including temperature and water table depth have been relatively well studied, uncertainty remains in the extent to which plant roots regulate greenhouse gas (GHG) fluxes and peat biogeochemistry. This study examined the role of roots, and root inputs of carbon and oxygen in regulating fluxes from peat under two dominant plant species, Campnosperma panamensis and Raphia taedigera, a broadleaved evergreen tree and canopy palm, in San San Pond Sak wetland, in Bocas del Toro Province, Panama. A combination of in situ and ex situ experiments were performed between February 2015 and August 2017. Small scale variation in GHG fluxes and peat biogeochemistry was measured at two distances within the rooting zones of C. panamensis and R. taedigera. Peat organic matter properties were assessed using Rock-Eval 6 pyrolysis. Results indicated significant variation in CH4 but not CO2 fluxes at different distances within the rooting zone, with CH4 fluxes subsequently linked to measures of the overall size of the available organic carbon pool (S2). Rock-Eval pyrolysis data was used to construct a three-pool model of organic matter thermostability which indicated significant differences in organic matter composition between peats derived from different botanical origins, in addition to a high level of heterogeneity within the rooting zone. Changes in GHG production and peat biogeochemical properties in response to the addition of root exudate analogues were assessed in an ex situ anoxic incubation experiment. A combination of organic acids and sugars, identified as common forest plant root exudate components, were added over a two week period to peats derived from C. panamensis and R. taedigera. GHG fluxes varied significantly between treatments but not by peat botanical origin, and were associated with significant changes in soil properties including, pH and redox potential, thereby demonstrating a link between plant root carbon inputs, peat properties and GHG fluxes. In situ mesocosms were used to assess the effects of root exclusion on peat biogeochemistry and GHG fluxes. Partial and full root exclusion significantly reduced dissolved oxygen concentrations and was associated with greater root necromass. Full root exclusion increased CH4 fluxes five-six fold compared to partial root exclusion, equivalent to an 86 - 90% reduction in CH4 oxidation, demonstrating the important role of root inputs of oxygen in mitigating CH4 efflux from tropical peat. A 13CO2 pulse labelling experiment was conducted using both R. taedigera, C. panamensis, and Symphonia globulifera, a second broadleaved evergreen tree species, to demonstrate a direct link between plant photosynthesis and CH4 fluxes, and identify aspects of the bacterial and fungal community associated with the turnover of labile carbon. The extent of 13C enrichment of CH4 differed significantly between plant types (palms vs broadleaved evergreen trees), as did the extent of net CH4 efflux. Phospholipid fatty acid (PLFA) biomarker analysis indicated both peat types were dominated by Gram negative bacteria. There was strong 13C enrichment of Gram negative bacteria, supporting their previously proposed role as important decomposers of labile carbon. Collectively, these results demonstrate that root inputs of carbon and oxygen can strongly regulate tropical peatland GHG fluxes, and that the extent of regulation can vary significantly between tropical wetland plant species from contrasting dominant plant types. This is particularly important in understanding regulatory processes in a globally significant carbon store and understanding possible consequences of land use change in the tropics.

The development and analysis of crop models of differing complexity is presented, ranging from a simple, static, empirical model, to more complex, dynamic, mechanistic models. Two models, an existing mechanistic model (Sirius) and a new mechanistic model of more intermediate complexity (Intermediate), were developed and analysed using relatively detailed field-level observations. In contrast, two new simpler models, an empirical and a mechanistic model, were developed using relatively coarse farm-level observations. Analysis of the existing mechanistic model (Sirius) revealed that a number of model variables and cultivar-specific parameters were redundant and did not contribute to model performance. The results of this analysis informed the development of mechanistic model of more intermediate complexity (Intermediate), although this was also indicated to contain redundant variables and parameters. Vernalisation simulation was one aspect of the models that was consistently identified as an area of redundancy. These reduced models are a product of the data used to generate the reduced model - in this work, simplified versions of the models were identified that were capable of maintaining the ability to predict differences in cultivar growth and development under different nitrogen treatments. Careful consideration needs to be given to the application of the reduced model, to inform the data used in the reduction. Automated, comprehensive model reduction techniques, such as the one employed here, have the potential to be important tools in reducing unnecessary model complexity, and associated uncertainty, for an application. This unnecessary complexity can act as a barrier to application, analysis and understanding. An empirical (Simple-EMP) and simple mechanistic (Simple-MECH) model were additionally developed to predict wheat yield at the farm-scale, using farm-level observations. The empirical model produced more accurate predictions of wheat yields than the mechanistic design, which was hindered by the monthly time step necessitated by the driving meteorological observations and the lack of traditional mechanistic model input observations. The farm-level survey data from which these models were developed is collected annually, and suggestions for further development of these models are made, including (i) incorporating newly available data on fertiliser application to replace the existing proxy, and (ii) exploring the potential to obtain additional data traditionally required by crop models, primarily the timing of important management decisions, for example, sowing and harvest dates.