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Supramolecular chemistry deals with systems made of distinct chemical species which, when put together, have different properties than each individual component. These species are often not bonded in a covalent or ionic sense, but are based on host-guest chemistry. Mechanically interlocked molecules (MIMs) and handcuff rotaxanes in particular, which are systems containing multiple covalently bonded macrocycles, through which a rod is threaded then stoppered, are an example of such species. MIMs have wide ranging applications in nanoscale electronics, systems which mimic biology, and many others. Since its recent discovery, pillar[5]arene has been used extensively in MIMs due to its interesting host guest properties, and this work deals with handcuff rotaxanes containing it, as well as perylene diimide (PDI), tetrazine, and imidazole groups. The feasibility of the synthesis of a three-membered PDI cofacial stack or a 'triple decker handcuff rotaxane', using a templated, clipping method, utilising interactions between PDI cores and between pillar[5]arenes and imidazole groups, is investigated. The difficulty in this lies in the synthesis of a 'linker' that can connect two pillar[5]arene macrocycles and also the PDI core of the macrocycle based component of the handcuff rotaxane. Various methods of amine alkylation, amide coupling and ether synthesis were explored to connect the functionalised pillar[5]arenes together, but due to the difficulties with pillar[5]arene syntheses and purifications they were all unsuccessful in either of those steps. However, novel pillar[5]arene-based species were successfully synthesised in this part of the project and fully or partially characterised. Next, a simpler cofacial stack of a PDI and a tetrazine based on handcuff rotaxane topology was attempted but was unsuccessful due to the low solubility of pillar[5]arenebased species in solvents required for the tetrazine forming reaction. However, during this part of the project two new functionalised pillar[5]arenes were synthesised and characterised and attempts at optimising these syntheses were made. Finally, a handcuff rotaxane containing only one PDI species was successfully synthesised and characterised. Its properties were probed using cyclic voltammetry, spectroelectrochemistry and electron paramagnetic resonance spectroscopy and compared with similar handcuff rotaxanes previously synthesised in the group. The lack of stacking species in this handcuff proved a previously postulated hypothesis that the synthesis method here described only requires templating between the host's macrocycles and the threading guest. This does however, lower the yields relative to species with additional molecular recognition sites. The thus far described part of this work explored and celebrated the organic synthesis of supramolecular structures, while the second part focuses on spectroscopic analysis of supramolecular systems. The systems in question are the collagen-tannin matrices found in leather, and more specifically in deteriorated leather book bindings from the Natural History Museum. As such the two parts of this thesis are only related due to dealing with supramolecular structures and should be interpreted separately. This second project explored a leather acidic deterioration process known to conservators as red rot. Red rot affects leather book bindings from the late 19th and early 20th centuries and causes them to become dry and reddish, or in advanced stages crumble into a dark powder. This project set out to explore health and safety aspects of red rot dust using various spectroscopic techniques and suggest further necessary tests. This was evaluated using Inductively Coupled Plasma analysis (Optical Emission Spectroscopy and Mass Spectrometry), in comparison with permissible heavy metal content in samples as defined by a commercial certification body, OEKO TEX. For the tested samples, it was found that arsenic, cadmium and lead were not within the permissible limits and hence caution when handling these items is recommended. Furthermore, this work aimed to understand more about the red rot deterioration process by comparing undeteriorated and deteriorated leather samples with Fourier Transform Infrared spectroscopy and Scanning Electron Microscopy. No features present in red rot but absent in other types of deterioration were found, however, this work recommends gas chromatography as another technique that might achieve this. Finally, this work attempts to quantify the degree of deterioration of bindings suffering from red rot through an FTIR peak ratios. Such a ratio is explored and found to relate to visually assessed levels of degradation. However it is not certain that this is a red rot specific ratio and not a general degradation ratio. This work allowed for health and safety recommendations to be made to the museum, as well as for a deeper understanding of the red rot deterioration process to be obtained.

Zinc deficiency affects over 17% of the global population. Risk deficiencies of up to 96% have been reported in Sub Saharan Africa, mostly due to increased poverty levels and high dependence on cereal diets with low bioavailable zinc. In Africa, although wheat provides up to 20% of dietary energy, cultivated wheat is inherently low in essential micronutrients such as grain zinc (Zn) and iron (Fe), and the genetic variability is relatively narrow. Genetic biofortification of food crops is considered a sustainable and cost-effective approach for alleviating mineral nutrient deficiencies. Wheat progenitors and wild relatives are considered as potential sources of genetic variation for crop improvement. Inductively coupled plasma mass spectrometry (ICP-MS) was undertaken to determine the natural variation in grain Zn and selected essential mineral nutrients (Fe, Ca and Se) of wheat wild relative accessions, in order to identify novel sources of genetic variation. Accessions from the genus Triticum, Aegilops, Thinoprum, Amblyopyrum and Secale were screened. Results showed a wide variation in grain Zn, Fe, Ca and not Se. Triticum urartu and Amblyopyrum muticum accessions showed the highest grain Zn and Fe, whilst Thinopyrum species showed the highest Ca concentration. A preliminary study of 48 pre-breeding introgression lines (doubled haploids) derived from T. urartu and Am. muticum also showed a wide variation in grain Zn, Fe, Ca and not much in Se. Selected T. urartu and Am. muticum doubled haploid (DH) lines were also phenotyped under two contrasting soil types, to investigate the effects of soil type on grain Zn, Fe, Se and Ca concentration. One soil type was characterised by higher Zn, Fe, and lower pH (Chitedze soils), and the other soil type was characterised by lower Zn, Fe and higher pH (Ngabu soils). Analysis of variance (ANOVA) revealed a ~two-fold higher grain Zn concentration in low pH, higher Zn soils compared to high pH, lower Zn soils. Variation in grain Zn concentration was associated with the genotypes, soil type, and the interaction between soil and genotypes. Grain Fe concentration was influenced by genotypes and soil type only, grain Se was highly influenced by soil type whilst grain Ca was independent of soil type but highly influenced by genotypes and partly by the interaction between genotype and soil type. Two high-Zn DH lines (DH-348 and DH-254) were selected, and crossed with three Malawian wheat varieties (Kadzibonga, Kenya nyati and Nduna), to transfer the Am. muticum and T. urartu chromosome segments potentially increasing grain mineral concentration in the DH lines. From the crossing program, 41 Malawian wheat/Am. muticum and 11 Malawian wheat/ T. urartu BC1F3 introgression lines were generated. A field based phenotyping study of the 11 Malawian wheat/T. urartu and the 37 Malawian wheat/ Am. muticum alongside three Malawian wheat, DH-348, DH-254, Paragon, Pavon 76 and Chinese Spring showed high yields and 11-30 mg kg-1 improvement in grain Zn in 11 introgression lines, above the three Malawian wheat varieties and Chinese Spring and Paragon. These lines also showed 8-12 mg kg -1 improvement in grain Fe than Nduna and Kenya nyati, whilst four lines showed a 6-10 µg kg -1 Se concentration improvement above paragon and the three Malawian checks. Across the four experiments, grain Zn showed strong and significant positive correlations with grain Fe concentration. Grain Ca moderately and significantly correlated with grain Zn and Fe, whilst grain and straw Zn, Fe, Ca and Se showed positive and low significance or positive but insignificant associations. Grain Zn and Fe also showed significant negative correlations with TKW/yield.

The resistance of cv. Cougar to Zymoseptoria tritici has been investigated in detail, involving Quantitative trait loci (QTL) analyses to map the resistance, various physiological measurements to investigate the mechanism of resistance and transcriptomic analyses to identify candidate resistance genes. To map the resistance in cv. Cougar, QTL analyses utilised visual septoria tritici blotch (STB) assessments, chlorophyll fluorescence measurements & hyperspectral reflectance measurements. Additionally, these physiological measurements were used to map other sources of resistance from both cv. Cougar and cv. Scout and to predict future STB disease within a growing season. Utilising a set of near isogenic lines (NILs) for the source of resistance in Cougar, and two incompatible Z.tritici isolates (HT-22/IPO323), transcriptomic analysis characterised the conserved incompatible wheat-Z.tritici transcriptome and identified candidate resistance gene(s) at the location identified on chromosome 4D. The Cougar resistance mechanism was investigated using a range of techniques including chlorophyll fluorescence measurements, hormone, carotenoid and xanthophyll enzyme quantification, superoxide and hydrogen peroxide accumulation, stomatal behaviour, stomatal morphology and Z.tritici spore germination rates. These techniques were used to investigate the effect of compatibility by utilising a Z.tritici isolate which has overcome the Cougar resistance (508, compatible) and an avirulent isolate (HT-22, incompatible). STB assessments and hyperspectral reflectance measurements mapped the cv. Cougar resistance to chromosome 4D in 2018, with a breakdown of this resistance in 2019, likely due to the evolution of pathogen genotypes with virulence to cv Cougar. NPQI (Pheophitinization of chlorophyll a to phaeophytin) was the best index at mapping the resistance to chromosome 4D and was unique to this QTL. This study also demonstrated the broader application of chlorophyll fluorescence and hyperspectral reflectance measurements in identifying novel sources of resistance, with indices such as D2 (chlorophyll fluorescence), ND705 (chlorophyll content) and ARI (anthocyanin content) tightly correlating with septoria tritici blotch (STB) disease in a manner consistent with previous studies. Transcriptomic analysis identified 3 candidate resistance genes at the location identified on chromosome 4D, with upregulation of protein kinases, F-box proteins and cytochrome P450 proteins amongst the main transcripts associated with incompatibility. Resistance was associated with a photoinhibitory and photoprotective mechanism involving both the qI and qE components of NPQ and a change in carotenoid composition reflected by changes in xanthophyll enzyme expression and a decrease in superoxide accumulation. Additionally, changes in SA, JA and 7 ABA content was associated with the Cougar defence response. Preformed defence traits such as stomatal morphology, behaviour and spore germination rates were not associated with compatibility. These results demonstrate that the major source of resistance in cv. Cougar resides on chromosome 4D and likely involves a form of effector triggered immunity which induces a photoinhibitory and photoprotective resistance mechanism involving altered carotenoid and hormone metabolism.

In Indonesia, approximately 505-kilo tonnes of fresh cacao pod husk (CPH) are discarded annually as a primary waste by-product during cacao production. Although they can be directly applied as fertiliser or animal feed, most of them are left on farms, causing environmental issues that could reduce cacao productivity. In the meantime, CPH contains bioactive compounds, including phenolics and anthocyanins, which have promising antioxidant activity. Therefore, recovering bioactive compounds from CPH by solvent extraction is a promising sustainable way to both avoid waste and valorise it as a new renewable resource. The aim of this research was to study how the processing parameters can maximise the extraction yields and consider process efficiency when designing a flowsheet of CPH valorisation. A systematic extraction research was studied to understand the influence of material pretreatment (drying and size reduction), solvent type, and different heating methods (conventional and microwave) on extraction yields. How other system variables (extraction time and temperature, solvent concentration and solvent-to-feed ratio) interact within conventional and microwave heating was also investigated to maximise yields. The work presented in this thesis can first demonstrate that CPH contained up to 107.3 mg GAE/g dw of phenolics including 0.37 mg Cy3GE/g dw of anthocyanin with good antioxidant activity (up to 4.6 mg TE/g dw or ~ 94% radical scavenging). Phenolic and anthocyanin compounds were concentrated in CPH epicarp layer, while antioxidant was found maximum in CPH endocarp layer. Solvent type and material pretreatment (size reduction and drying) were very influential in maximising the extraction yields. Size reduction enhanced the phenolic and anthocyanin yields significantly but had no significant effect on the antioxidant activity of extract. Phenolic compounds, including anthocyanins, were highly extracted in aqueous ethanol (50% iii (v/v) ethanol/water) due to their similar solubility based on Hansen Solubility Parameter (HSP) value. However, the highest antioxidant activity was found in the ethanolic extract (100% (v/v) ethanol) due to protic solvent effect. In terms of the heating method, microwave has been regarded as a promising extraction method due to its volumetric and selective heating, which allows for rapid heating and increased yield. A comparison of MAE and CSE at a similar heating rate (by neglecting microwave volumetric heating) demonstrated no differences in optimum extraction time, solvent concentration and solvent-to-feed (S/F) ratio for both methods but a difference in extraction yields. The best time to extract bioactive compounds was 5 min because a longer extraction time resulted in lower bioactive yields. In contrast, extraction temperature had varying effects: increasing temperature can increase the phenolic yields while decreasing anthocyanin and antioxidant yields. MAE at 60 °C had 5% higher phenolic yield than CSE, which was attributed to a selective heating effect. Meanwhile, extracting anthocyanin and antioxidant compounds was favoured at low temperature (50 °C) to prevent degradation despite no selective heating effect. Additionally, the CPH solid residue from the extraction process still has a potential to be valorised into other valuable products, such as bio-oil, non-condensed gases and activated carbon, due to its proximate and lignocellulosic contents. This study, therefore, can be used as input data in the preliminary engineering design of CPH valorisation flowsheet to select an efficient process and assess its viability. The usage of CPH as new resource material for the production of high-value products has the potential to increase its economic value while reducing waste.

Phytohormones regulate virtually every aspect of plant growth and development. The interaction between auxin and cytokinin determines the vascular pattern in the root. One key node of crosstalk between these hormones, involves cytokinin promoting the transcription of the auxin efflux transporter PIN-FORMED 7 (PIN7). However, the mechanism by which this occurs is not known. A forward genetic screen to identify novel loci regulating PIN7::PIN7:GFP in the root identified a number of mutants. One of them, in a mutant called 56B2, is in the promoter of the CYTOKININ OXIDASE/DEHYDROGENASE 5 (CKX5) gene. In this project the phenotype of this mutant was characterised in detail. It has been shown that in addition to mis-expression of PIN7 in the root tip, this mutant also shows reduced sensitivity to cytokinin and defects in organ formation in both lateral roots and leaves. It was demonstrated that CKX5 is expressed in the root vascular cylinder, lateral root primordia, and the shoot apical meristem. These are all regions consistent with the phenotypes that was observed in 56B2. To test whether the mutation in the CKX5 promoter causes mis-expression of CKX5 in root tips, reporter lines were developed for CKX5 with either wild-type or 56B2-like promoters. Surprisingly, these showed no difference in CKX5 levels in the root meristem. Then variation in natural accessions has been looking and two closely related lines (Kardz 1 and 2) that differ from each other with exactly the same substitution present in 56B2 were identified. It has been shown that several of the phenotypes present in 56B2 are shared with Kardz-2, but that CKX5 levels are not altered in the root tip. As cytokinin is known to be transported from shoots to root via the phloem, the results are consistent with a hypothesis in which cell non-autonomous regulation of CKX5 causes the root phenotype shown in 56B2. A series of experiments were presented that could explore this further.

Current sugar beet varieties vary widely in their canopy architecture; some have a distinctively prostrate canopy angle whilst others are much more upright. Radiation use efficiency (RUE) is the amount of biomass accumulated per unit of light intercepted by the crop. In crops such as rice and wheat, where canopy architecture has been quantified, canopy angle has been shown to significantly influence light interception and RUE. This project quantifies canopy architecture and assesses its effect on RUE and yield of sugar beet. A combination of controlled environment and field experiments were conducted to classify varieties into canopy types according to petiole angle and assess the impact of canopy angle on light interception, photosynthesis and biomass accumulation in the crop. Prostrate canopy types were demonstrated as having the greatest canopy expansion rate and to intercept more light across the season than an upright or intermediate canopy type. However, despite intercepting the most light, this did not lead to the greatest sugar yield. This research shows evidence that prostrate canopy types have lower rates of photosynthesis, and that the canopy is acclimated to shaded conditions indicative of the overlapping nature of the leaves within and between rows. Upright canopy types had the greatest RUE of total biomass later in the season and could be suited to a later harvest due to potentially more efficient light interception at lower sun angles. Furthermore, the upright canopy angle was demonstrated as advantageous to the crop during hot and droughted weather conditions, when it retained more of its canopy. Intermediate canopy types had the greatest photosynthetic potential under optimal conditions. This trait can be associated with high carbon assimilation throughout the summer months in the absence of significant plant stress leading to high total biomass RUE. The Intermediate 2 variety also showed favourable biomass partitioning to the roots later in the season and this also resulted in high sugar yields. However, the Intermediate 1 variety, with similar canopy architecture yielded less and had a lower RUE. This variety was from a different breeder which may indicate that genetic traits, other than canopy architecture, are also important in determining yield and RUE. To investigate the relationship between canopy angle, RUE and yield a canopy manipulation experiment was conducted. The high yielding intermediate variety was made upright, prostrate or left as a control. Canopy manipulation had no effect on final sugar yield and the upright treatment had a higher RUE in 2022 which was a result of less proportional canopy loss and better tolerance during the drought between July and September 2022. Therefore, biomass partitioning, and high levels of photosynthesis are important traits to select for high RUE and sugar yields. However, further research is required to understand the interaction between canopy angle and RUE in winter months and water stressed conditions. Overall, the findings from this have shown that sugar beet varieties can be classified into canopy types according to their petiole angle. Canopy angle is not as important as photosynthetic rate and biomass partitioning for high RUE and sugar yields. The impact of canopy angle on drought tolerance and harvest timing should be explored by breeders in the future.

Rhizoctonia solani is a necrotrophic soil-borne plant pathogen species complex, of which anastomosis group (AG) 2-1 causes devastating disease on oilseed rape (OSR, Brassica napus). It is frequently isolated from arable crop fields where it affects establishment and yield via pre- and post-emergence damping off, hypocotyl and root rot. Genetic resistance to R. solani AG2-1 has not been observed and long-lived sclerotia, plus a broad host range allow the pathogen to survive in the soil for many years. Here, the interactions between Rhizoctonia solani AG2-1, its crop host OSR and the model organism Arabidopsis thaliana were explored. Variation in responses to R. solani were observed between commercial OSR varieties and gene expression data showed that susceptibility was associated with auxin and abscisic acid signalling, and the MYC2 branch of jasmonate signalling, while reactive oxygen species, ethylene signalling and the ERF/PDF branch of jasmonate signalling were associated with increased tolerance. This was supported by inoculation of A. thaliana defence mutants and microscopy using Jas9:VENUS and IAA2pro:GUS lines. Further investigations into the role of auxins in R. solani AG2-1 - A. thaliana interactions showed that R. solani was able to differentially affect the root architecture of WT and aux1 transport mutants. Experiments showing the effects of 2,4-D, PAA and NAA demonstrated that PAA was able to restore gravitropism in aux1. R. solani produced both IAA and PAA when grown in broth culture and growth stimulation was observed when R. solani was grown in broth with low concentrations of exogenous PAA. Analysis of gene expression markers (GEMS) from a previous genome wide association study (GWAS) provided further evidence for the involvement of auxins, jasmonates and ethylene in the defence responses of OSR to R. solani AG2-1. Corresponding A. thaliana candidate gene mutants were inoculated with R. solani AG2-1 under experimental conditions to identify potential susceptibility genes. Two of these were taken further and B. rapa TILLING line resources were developed. This thesis increases understanding of the defence pathways involved in resistance and susceptibility to R. solani AG2-1, examines the influence that R. solani has on the root architecture of auxin mutants, and provides candidate gene TILLING line resources for future work.

Oil palm (Elaeis guineensis) is renowned as the golden crop of Malaysia and Indonesia for its' high yields per hectare of land compared to other oil crops globally. Malaysia contributes 25.93% of the world's palm oil supply with export revenue of RM73.25 billion in the year 2020. As with any other crop, oil palm faces challenges, such as pests and diseases in sustaining the oil palm plantation industry. In Malaysia, four Ganoderma species are commonly found in the oil palm plantations, whereby G. boninense (isolate PER71), G. zonatum (isolate POR69) and G. miniatocinctum (isolate 337035) are associated with high incidences of basal stem rot (BSR) disease, with the former being the most pathogenic of all species. The fourth species, G. tornatum (isolate NPG1) is a saprophyte. Besides being causal agents of BSR, G. boninense and G. zonatum are also causal agents of upper stem rot (USR) disease in Malaysia. For decades, studies have been conducted to understand the mode of infection and epidemiology, genetic diversity, and discover ways to curb these diseases from spreading to adjacent trees or new plantings. Most studies focused primarily on the host and host-pathogen interactions but not on the pathogen itself. Understanding the pathogen is essential and that too at the molecular level. With continuous developments in DNA sequencing technologies, PacBio single molecule-real time (SMRT) offers long reads with high accuracy to decipher many organisms. Although there are many extraction protocols available for Ganoderma species, the high molecular weight of good quality nucleic acid is a prerequisite of SMRTbell library construction. Therefore, the first objective of this study was to extract high quality genomic DNA for the four Ganoderma species required for PacBio sequencing. This study described modified DNA extraction protocols for G. boninense, G. zonatum, G. miniatocinctum and G. tornatum, and an RNA extraction protocol for G. boninense. The modified salting out DNA extraction protocol was suitable for G. boninense and G. miniatocinctum, while the modified high salt low pH protocol was suitable for G. tornatum. These modified nucleic acid extraction protocols were able to produce high quality DNA and total RNA of ~140-160 µg/g and ~80 µg/g of mycelia, respectively. As for G. zonatum, the Boehm protocol was the most rapid and efficient protocol with a yield of 208.95±4.52 µg DNA per gram of tissue. In the second objective, using the PacBio (Sequel platform) sequenced long read data, two draft genomes G. boninense the most pathogenic species, and G. tornatum, a saprophyte were assembled. The diploid aware assemblers FALCON and FALCON-Unzip phased assembled the two Ganoderma genomes generating ~67 Mbp and ~76 Mbp size genomes with 297 and 246 contigs for the former and latter species, respectively. Next, gene prediction was performed using four gene prediction pipelines on these two genomes, and MAKER2 was selected as the best pipeline generating 19,851 and 23,989 gene models, respectively. In the third objective, molecular markers were identified to distinguish pathogens from non-pathogens in oil palm plantations. This was performed using the four assembled Ganoderma genomes (454 sequencing technology). Species-specific simple sequence repeats (SSRs) were mined from the four Ganoderma genomes based on BUSCO (Benchmarking Universal Single-Copy Orthologs) and ortholog analysis. One hundred SSRs were synthesized and screened against the four Ganoderma species. Based on the screening results, 13 SSR markers were evaluated on 20 Ganoderma isolates collected from four states in West Malaysia. Data from the absence and presence of amplicons from the 25 Ganoderma isolates generated a phylogenetic tree. However, these 13 SSR markers were not able to distinguish the pathogenic isolates/species from the non-pathogens. Therefore, published internal transcribed spacers (ITS) were also used for species identification. For isolates with low quality ITS sequences, new ITS primers were designed based on the assembled G. boninense genome (PacBio) from this study. Molecular markers, together with morpho-taxonomy were able to facilitate the identification of Ganoderma isolates from West Malaysia. In the fourth objective, G. boninense culture was grown in limited carbon (C) and nitrogen (N) medium. This starved environment with minimal simple sugar and sawdust was to mimic as closely as possible to the field conditions. In response to the starved condition, differentially expressed genes (DEGs) in numerous metabolic pathways were identified, with four significant pathways explored in this study. The results provided first insights into possible genes that were up- and down-regulated in the pathways, namely secondary metabolite biosynthesis, carbohydrate metabolism, glycan metabolism and mycotoxin biosynthesis. A cocktail of enzymes was released by G. boninense to be associated with the degradation of cellulose, hemicellulose, lignin and pectin. The DEGs involved in the mycotoxin biosynthesis pathway are of interest, as they have not been reported in Ganoderma species. In the fifth objective, using comparative genome analysis genes associated with pathogenicity between the two Ganoderma species were identified. A workflow to detect small secreted proteins (SSPs) was used on the Ganoderma gene models of G. boninense and G. tornatum. A total of 18 candidate SSPs were identified in G. boninense, predicted to be involved in numerous functions associated with host-pathogen interactions. This study reported on optimized nucleic acid extraction protocols for four Ganoderma species that were meant for PacBio sequencing. This study also reported on novel genes that were differentially expressed during C-N starvation in four metabolic pathways of G. boninense. The 18 candidate SSPs associated with pathogenicity in G. boninense have not been reported yet. Further investigation on these genes needs to be verified in a wet lab to confirm their presence in the pathogen.

Higher methane yields from the anaerobic digestion (AD) of Sargassum muticum could improve the process energy balance and make its use during AD more economical and energetically favourable. Previous research showed that after 28 days of AD, methane yields from S. muticum were low (17% of the theoretical yield). This thesis aims to identify the causes of the low methane yield. Biochemical methane potential tests of freshly harvested, rinsed, and freeze-dried (FD) spring and summer S. muticum sampled over three years delivered yields of 27-39% and 24-32% of the theoretical, respectively. FD samples were extracted with water or with 70% (v/v) aqueous methanol (MeOH); methane yields per gram volatile solids of the extracted samples were higher than the untreated FD samples by up to 19.1% and 26.6%, respectively. Proximate, ultimate, and biochemical analyses showed that untreated FD biomass contained ash contents of 24.2-28.1% dry weight, with total dietary fibre representing 49.8- 67.4% of the organic fraction. Water- or MeOH-extracted spring and summer biomass were higher in total dietary fibre content (75.3-82.8% of the organic fraction) and lower in soluble dietary fibre (SDF) and phenolic content than the FD samples. Indices calculated for bioconversion of the biomass to methane were negatively correlated with the SDF and phenolic contents. Water-extracted spring biomass had lower SDF content than the FD and water- extracted summer samples and produced higher methane yields. The aqueous MeOH extract of S. muticum was examined after repeated extraction (×9) with 1% polyvinylpolypyrrolidone (PVPP). The PVPP-treated extract was 93.7% lower in phenolic content (Folin-Ciocalteu assay) and 24.4% higher in protein content than the untreated extract, with no significant difference in the lipid contents. MeOH-extracted biomass combined with the PVPP-treated extract produced 85.7% higher methane yields than when combined with untreated MeOH extracts. Membrane filtration of the untreated MeOH extract yielded a high molecular weight (MW) (≥ 5 kDa) fraction, which contained 90.7% of the total phenolic content of the extract. It inhibited methane yields by 41.9% when combined with MeOH-extracted biomass; however, since the methane yields of the extracted biomass remained low (≤ 32% of the theoretical, an increase from ≤ 27%), recalcitrance of the total dietary fibre also represents a limiting factor. Improving methane conversion of the residual fibre fraction after phenolics' extraction is required to utilise this biomass in a biorefinery approach efficiently.

Food insecurity and malnutrition are driven by food system challenges. Bioscience provides a strong foundation to address these challenges. Reversible epigenetic changes, including histone acetylation, are emerging as an important regulatory junction between genomic, transcriptional, translational, and metabolic responses. Histone acetylation is mediated by histone acetyltransferases (HATs) that catalyse the transfer of an acetyl group from acetyl-CoA to lysine residues within histones. HATs are recruited to loci by sequence specific transcription factors (TFs) to ultimately affect gene expression. The aim of this project was to investigate the role of two Arabidopsis thaliana HATs; HAC4 (AT1G55970) and HAC5 (AT3G12980) in plant homeostasis. Using yeast twohybrid assays, novel TFs interacting with HAC4 and HAC5 were identified. Among them, Auxin Response Factor 2 (ARF2) stood out as a HAC5 specific interactor. The loss-of-function mutants of both HAC5 and ARF2 have increased responses to abscisic acid (ABA), a phytohormone known to regulate plant growth and stress responses. Additionally, they show enhanced defence responses against the necrotrophic fungus Botrytis cinerea and delayed dark-induced senescence. Through transcriptomic analysis we uncovered that HAC5 and ARF2 act together in the regulation of dark-induced senescence, by regulating both common and unique genes.

Cherry tomatoes play an important part in the human diet as they have a high content of nutritional component, including ascorbic acid, carotenoids and total phenolics. This study aimed to investigate how postharvest techniques, temperature, light irradiation and Modified atmosphere packaging (MAP) affected nutritional quality of cherry tomatoes, and to identify the strategies to preserve their quality. Three temperatures (5, 15, 20°C) were examined to evaluate the effect of temperature on cherry tomatoes. A storage temperature of 15°C was found to inhibit weight loss and the decrease of lycopene, s-carotene and lutein content when compared with 20°C, whereas a low temperature (5°C) caused chilling injuries, such as pour colour development, and inhibited the increase of lycopene and s-carotene content compared with 15 and 20°C. The effect of postharvest red/far-red (ratio 0.89) and blue light irradiation on fruit quality was also investigated. The results showed that red/far-red light inhibited weight loss, inducing colour changing from green to red, and increased the content of lycopene, b-carotene, and total phenolics compared to darkness. In contrast, blue light induced weight loss, and had little effect on colour change and the content of ascorbic acid, lycopene and total phenolics compared to darkness. The influence of the combination of red/far-red light and modified atmosphere packaging on fruit quality was also examined. The results showed that the combined treatment effectively extended shelf-life of cherry tomatoes by delaying ripening as indicated by the delayed increase of respiration and colour change from green to red, reduced weight loss, and increased the content of lycopene and s-carotene. The role and mechanism of red/far-red light in the regulation of carotenoid biosynthesis were explored. Results showed that gene Phytoene synthase (PSY), Zeta carotene (ZDS) and Chloroplast lycopene beta cyclase (LCY-b) and were overexpressed in fruits treated with red/far-red light during storage compared to the darkness. Moreover, red/far-red light induced expression of 1-aminocyclopropane-1- carboxylate synthase 2 (ACS2) during the first 25 days of storage, Ripening inhibitor (RIN) during the first 28 days and Elongated hypocotyl 5 (HY5) during the whole period of storage. This provided a hypothetical model of red/far-red light in the regulation of carotenoid biosynthesis.

Oil palm is the main commodity crop cultivated in Malaysia and has made significant contributions to the economies of Malaysia and Indonesia. However, there is a major problem in oil palm, the basal stem rot (BSR) disease caused by Ganoderma boninense. This is a serious threat to the oil palm industry as it reduces oil palm yield and shortens the economic lifespan of the crop. In order to control this disease, this present study evaluated the efficacy of Trichoderma spp. as a biological control agent (BCA) through the application of different types of bioorganic fertilizers at selected oil palm estates in Palong, Pahang and Tanjung Karang, Selangor with different palm ages and soil types. Trichoderma spp. was produced on large scale through the submerged fermentation method. Conidial seed culture resulted in higher Trichoderma spp. count from the bioreactor (6.32 log cfu/ml) in comparison to mycelial seed culture (4.95 log cfu/ml) and this was statistically significant (P<0.001). Trichoderma spp. was then mixed with biochar as the carrier at different ratios; 1:0.5 (B50%), 1:1 (B100%) and 1:2 (B200%) for ease of handling and long term storage. For oil palm field applications, Trichoderma-biochar (T-biochar) formulations were added into organic fertilizer, Living Organic Fertilizer (LOF) as the final products at concentrations of 0% (T1/T6), 5% (T2/T7), 10% (T3/T8) and 20% (T4/T9). The viability of Trichoderma spp. in the carrier and biofertilizer was monitored for up to 24 weeks. It was found that B100% was the best formulation for biochar with Trichoderma populations between 5.00-6.00 log cfu/g while there was no significant difference for the Trichoderma spp. count in biofertilizers at 10% (T3/T8) and 20% (T4/T9) formulations (around 5.00 log cfu/g). In the oil palm plantations, the treatments were divided into two bioorganic fertilizer treatments, 1) Fortified Living Organic Fertilizer (FLOF) with customised N, P and K formulations; Treatments T1 to T5 and 2) LOF; Treatments T6 to T10 with different percentages of Trichoderma spp. (0, 5, 10 and 20%). Populations of microorganisms including bacterial, fungal and Trichoderma spp. were monitored for up to 24 months. Even though Trichoderma spp. count fluctuated over time and between treatments (between 4.00-5.00 log cfu/g), there was a significant difference in treatment T9 (20% Trichoderma in LOF) as it had the highest Trichoderma spp. populations at both Palong and Tg Karang plantations. Total bacterial and fungal populations were not significantly different (P≥0.05) at both locations. The soil pH at both locations was acidic whereas the electrical conductivity (EC) in Palong was low, below 0.10 dS/m. Nutrient analyses on soil and leaf samples revealed that the nitrogen, phosphorus and potassium (N, P and K) levels were correlated with the fertilization regime at both estates. Generally, the disease incidence (DI) for BSR disease at Palong was low (below 13.0%) and can only be noticed in few treatments (T1 to T6) with T1 (FLOF control) showed an increment in DI at 20 and 24 months (12.5%). In comparison, at Tg Karang, high DI was recorded for all the treatments especially T8 (10% Trichoderma in LOF) and T10 (Grower's standard practice; GSP) with DI of 29.2% and 25.0% respectively at 24 months. Palong plantation also recorded a low percentage of palms with the disease at 5.2% and 3.5% for control and Trichoderma treatments respectively whereas the percentage increased between 3-6 folds at Tg Karang. Additionally, while no recovery was recorded for control palms, seven palms from the present Trichoderma treatments were found to have completely recovered from BSR disease (two and five palms at Palong and Tg Karang respectively). Subsequently, Trichoderma spp. and other fungal communities in the rhizospheres of healthy, asymptomatic and symptomatic palms were identified through Sanger sequencing method. This is the first study that reported and evaluated the structure of fungal communities in oil palm rhizospheres over the course of BSR disease. Trichoderma spp. were present in rhizosphere soils at Palong and Tg Karang but with different distributions across the different symptoms. However, only healthy palms retained unique Trichoderma spp. T. asperellum was detected between all the symptoms which indicates that this species might be indigenous to the soil or from residual bioorganic fertilizer applications. Analysis of the fungal-ITS (internal transcribed spacer) DNA region revealed that healthy palms at Palong were similar to each other with 8 common genera. Asymptomatic and symptomatic palms had four and one common genera respectively. In contrast, the fungal communities were distinct across all samples at Tg Karang and ectomycorrhizal fungi (ECM) was absent in asymptomatic and symptomatic palms. Regardless of soil types, it was observed that Ascomycota was the dominant phyla in healthy and asymptomatic palmss. Conversely, symptomatic palms were dominated by Basidiomycetes which suggested a shift in the fungal community. Furthermore, ITS DNA of Trichoderma spp. and Ganoderma spp. in the palm rhizospheres was quantified via quantitative real-time Polymerase Chain Reaction (qPCR). The quantity of Trichoderma and Ganoderma DNA was not significant between the different symptoms, but Ganoderma DNA was detected ten-fold higher in symptomatic palms. Comparison between the Palong and Tg Karang plots showed that the quantity of Ganoderma at Tg Karang was also ten times higher than at Palong. For Trichoderma, the quantity was similar at Palong and Tg Karang which was between 0.020-0.035 ng/µl. Overall, this research revealed that Trichoderma spp. had biocontrol activity in mature oil palm estates infected with Ganoderma spp., but the effects were influenced by biotic and abiotic factors. Such impacts on Trichoderma populations should be studied further. This study also provides evidence on the changes of the fungal communities in oil palm rhizosphere soils with regards to BSR disease. Further evaluation needs to be conducted to elucidate the role of other fungal communities that could co-exist with Trichoderma as a biological control agent for the control of BSR disease in oil palm.

This thesis examines portrayals of homes and gardens in magazines, advice books, public health discourse and government propaganda in mid-twentieth-century Britain, analysing representations of healthy domesticity inside and outside the home, and in transition between the two. Taking an environmental perspective, it explores the implications of the association of housewives with hygiene and care for choices in shopping, the home and the garden. Vegetables were regarded as essential to health yet might still have soil on them. Waste, when converted into compost, was seen as a component of healthy soil, yet whilst in the process of decay had associations with risk to health. This thesis explores the tensions between two different understandings relating to health, namely that fresh vegetables grown in soil were nutritious, and that germs might hide unseen in dirty soil and might pose a risk if ingested. It attends to alternative voices advocating a cyclical and local approach to waste management and vegetable production but argues that they did not significantly impact the dominant cultural association between housewives, the indoors, and hygiene. Chapter one demonstrates how considering soil in the domestic space connects perspectives from multiple disciplines. Chapter two explores the construction of boundaries in the domestic space, between the indoors and the outdoors, the clean and the dirty. Chapter three focuses on the procurement of vegetables, analysing choices that were made between different purchasing options, and domestic growing in the garden or on the allotment, assessing how far concepts of protection from germs influenced these choices. Chapter four explores waste, both as rubbish and as sewage, and the ways in which practices were influenced by the construct of the ideal hygienic home. This thesis thus makes a significant contribution to histories of domesticity, gender and the environment that can inform current debates relating to climate breakdown.

Regional adaptation and end-use potential for dry common beans (Phaseolus vulgaris L.) provides an opportunity for sustainable innovation in the UK agrifood system to support the 'Great Food Transformation' required for addressing global problems in nutrition and environmental degradation caused by food production. In this work, molecular genetic methods were applied for both responsive and strategic disease resistance breeding objectives of the Warwick dry bean breeding programme. This includes confirming predictions by J Taylor for genetically distinct sources of recessive halo blight resistance in two P. vulgaris accessions from Africa using an allelism test in one example and genotyping-by-sequencing to map resistance in the second example. In response to a novel virus outbreak in trial fields, this research applied high throughput sequencing for viral diagnostics and detected the pathogenic potyvirus Bean yellow mosaic virus (BYMV) using total RNA sequencing and metagenomic analyses. A 1.5 Mb mapping interval was defined for a major effect recessive resistance locus to BYMV in the Warwick pre-breeding material on P. vulgaris chromosome 3. Furthermore, whole genome resequencing of parental lines revealed polymorphisms in candidate genes for both halo blight resistance (HB4.2 locus defined by Tock et al., 2017) and the novel BYMV resistance mapped here, as well as providing insights into the relatedness of one parent lines to an English heirloom variety, Ireland Creek Annie. Additionally, through the lens of consumer behaviour research, consumer attitudes towards pulses and interest in adding homegrown white haricot beans to the UK diet, particularly as a dry ingredient, was investigated. The methods applied to provide this foundational evidence include a systematic literature review examining perceptions and attitudes to pulses, and an online consumer behaviour experiment that investigated effects of packaging country-of-origin and cooking-time messages had on consumer perceptions of dry white haricot beans.

The cabbage aphid, Brevicoryne brassicae L., is a Brassica specialist, and is among the most damaging pests of vegetable Brassica crops, causing significant yield losses due to direct feeding damage, virus transmission and crop contamination. It is normally managed using synthetic chemical pesticides. However, with emerging reports of insecticide-resistant B. brassicae clones and withdrawal of insecticides from the market because of environmental concerns, there is a need for alternative, sustainable approaches. In this project, a novel Integrated Pest Management (IPM) system was developed and evaluated, combining partially aphid resistant Brassica accessions with entomopathogenic fungi (EPF). In recent years it has been suggested that host plant resistance and biological controls such as EPF may interact favourably, resulting in greater than additive control. It was hypothesised that partial host plant resistance may extend the window of opportunity for successful EPF infection resulting in significantly higher levels of control. Through pre-selecting and screening a range of Brassica accessions, partially resistant accessions were identified which limited B. brassicae population development by approximately one third. Assessment of aphid life history traits showed that partial resistance significantly reduced the rate of juvenile aphid development, aphid weight and adult reproduction. Laboratory bioassays of 10 isolates of EPF showed that all were pathogenic to B. brassicae adults but were largely ineffective against nymphs with the exception of one isolate of Akanthomyces dipterigenus, which was highly virulent to nymphs. Experiments indicated that this may have resulted from faster germination and growth compared to other isolates. In experiments where B. brassicae were reared on partially resistant Brassica accessions and treated with the EPF A. dipterigenus or Beauveria bassiana, it was found that partial host plant resistance caused nymphs to become significantly more susceptible to infection by B. bassiana relative to nymph cohorts on more aphid-susceptible plants. Combining partial resistance with A. dipterigenus caused a significant increase in aphid population control as a result of a plant x EPF interaction. The results of this study demonstrate the potential of this combined IPM strategy, with the effects of partial resistance upon B. brassicae able to activate or improve EPF virulence to aphid nymphs, which appear to be the primary challenge for aphid control using EPF.

The field pea (Pisum sativum) is an important legume grown for human and animal consumption. In the UK, growth is restricted to eastern England and Scotland, which has led to intensive production and yield declines of up to 40 %. This is attributed to a build-up of fungal and oomycete pathogens involved in the pea foot rot complex (PFRC); Fusarium solani forma speciales (f. sp.) pisi (FSP), F. oxysporum (FO), Didymella pinodella (DP) and Aphanomyces euteiches. Knowledge regarding the genetics, dynamics, and control of these pathogens, in particular for DP, is limited. Therefore, the main aims of this project were to characterise selected PFRC pathogen isolates through multilocus sequencing, better understand PFRC pathogen virulence, dynamics and interactions, and identify biofumigant crops that can suppress PFRC pathogens. Sequencing and multilocus phylogenetic analysis of both DP and F. solani (FS) isolates revealed the lack of diversity within DP isolates from the UK and other countries, while UK FS isolates clustered within a previously published clade of FS isolates from a variety of legume hosts, which challenges the notion that FS formae speciales are specific to single plant species. Positive relationships between pathogen inoculum concentration, pea foot rot disease development and plant mortality were established for FO, FSP and DP using a test-tube based assay, and for DP a glasshouse-based assay. A further test tube assay revealed the additive nature of interactions between FO, FSP and DP when coinoculated in terms of disease development in pea. Preliminary qPCR analysis of root colonisation in this experiment successfully quantified DNA for each of the three pathogens. Biofumigant crop varieties, particularly species of Brassica juncea and Eruca sativa, significantly reduced and inhibited mycelial growth of FO, FSP, DP and AE invitro and significantly supressed DP foot rot in a pot-based glasshouse experiment. Overall, this research has contributed substantial knowledge regarding the phylogeny, disease development and interactions of PFRC pathogens, and the potential of biofumigation as a management strategy.

Zymoseptoria tritici, a fungal pathogen of wheat and the causal agent of Septoria Tritici Blotch (STB), is a particular challenge to wheat production on a global level, causing severe crop losses. As the site of photosynthesis, the chloroplast plays a crucial role in energy balance and trade-off between growth demands and response to environmental stresses and it is gaining an ever-growing attention due to its multilayered involvement in disease response and downstream signalling. However, very little is known regarding wheat resistance responses to Z. tritici and the involvement of chloroplastic photoprotection. In the following thesis, I present data indicating the importance of photoprotection, through non-photochemical quenching (NPQ), in disease resistance of wheat plants against virulent and avirulent Z. tritici isolates. This study presents novel data on wheat plants with increased, "primed" photoprotection resulting in enhanced tolerance towards virulent and avirulent isolates. Plants were over-expressing the photoprotective chloroplastic protein PsbS and maintained a greener phenotype and reduced pycnidia upon inoculation with virulent strains of Z. tritici. Stb6, which encodes a wall-associated kinase protein that confers resistance to Z. tritici isolates expressing the corresponding AvrStb6 effector, has recently been cloned. In this study, I also used Stb6 near-isogenic lines and present findings on the association between the photoinhibitory component of NPQ, qI, and the avirulent isolate IPO323, at 24 hours after inoculation. Transcriptomic analysis also revealed the importance of the oxygen-evolving complex and photosystem II antenna proteins in resistance responses. In contrast, avirulent Z. tritici had no effect on photoprotection; however results indicated a potential virulent strategy that exploits the photosynthetic repair machinery. Also, this study presents early findings on interactions and potential mechanisms of effector-triggered susceptibility from Z. tritici, utilising necrotrophic effectors from another foliar wheat pathogen, Parastagonospora nodorum. This study represents an important contribution to our understanding of chloroplastic responses to the important pathogen Z. tritici and suggests putative mechanisms of photoprotective, chloroplastic defence. Understanding and incorporating chloroplastic mechanisms into breeding programs could help develop more productive crop plants with a novel durable genetic resistance to plant pathogens.

Previous studies suggest that genetic variation in grain yield potential in wheat is associated with grain sink strength under favourable conditions, which is mainly determined by grain number. Even in suboptimal conditions, increasing grain sink strength raises yield potential and attainable yield in wheat. Therefore, the elucidation of novel grain number traits such as fruiting efficiency (FE, ratio of grain number to spike dry weight at anthesis) and grain dry matter partitioning in wheat is crucial for genetic gains and food security. However, the physiological and genetic basis of these traits is not fully understood. The objectives of this study were, using a winter wheat KWS panel, to identify novel grain number and partitioning traits for increased harvest index and grain yield, and to determine marker-trait associations and candidate genes through a genome wide association study. The association panel of 138 KWS winter wheat genotypes was phenotyped for grain number and partitioning traits in field experiments at anthesis and physiological maturity in two seasons near Cambridge, UK. A subset of eight genotypes representative of field variation for FE was grown in the glasshouse under well-watered conditions at the University of Nottingham, UK in two years for analysis of flag-leaf gas exchange traits and their association with grain number traits and grain yield. To examine if specific plant organs and stem internodes were competing with the spike at anthesis, samples were taken in the field and glasshouse where the plants were separated into their component parts (ear, stem (including stem internodes), leaf sheath and leaf lamina). Results showed genetic variation in grain yield correlated with grain number and harvest index in the field experiments. The increase in grain number amongst genotypes was associated with an increase in FE. The stem internode component which was competing most with spike growth was the stem-internode 3 as indicated by a negative association between stem-internode 3 partitioning index and spike partitioning index, suggesting reducing stem-internode 3 length could increase spike dry matter at anthesis. Fourteen traits were analysed in a genome-wide association study and 78 putative marker-trait associations were identified, while 50 potential candidate genes were suggested. These included the GNI-1 gene on chromosome 2A for Fruiting efficiency, a known gene associated with increased grain number, and NFYB4 for spike partitioning index, a gene associated with increased spikelet fertility on chromosome 1A. Next steps include validating the associations and developing markers for these key traits to incorporate into plant breeding programs.

The garden, or hortus, was a core component of ancient Roman life. Over several centuries, the hortus underwent a complex process of evolution in Roman thought and space, beginning life as a small, humble plot used to grow vegetables for the table, and growing into a powerful symbol of social display in the early Imperial period. Yet despite mounting scholarly interest in this space, and extensive investigations by Wilhelmina F. Jashemski and other teams in the field, a misconception persists relating to the Imperial decline of the urban agricultural hortus and the supposed low contribution of its produce to local life. Such suppositions have led to scholarly interest being weighted towards the recreational garden, namely those owned by the elite. As such, the academic value of the agricultural hortus, as an important social tool, and a key source of economic and nutritional income, remains undervalued. In response, this thesis undertakes an interdisciplinary analysis of thirty-two productive horti in Regions I and II of Pompeii, investigating the social, economic, and nutritional contribution of these spaces and their produce to the local population through an analysis of related archaeological, archaeobotanical, paleonutritional, and pictorial remains. Grounded in ancient literary receptions of the hortus, including the hortus' ability to reinforce and define collective Roman identity and memory, agricultural garden development and use in Pompeii is linked to recent social, economic, and geographical developments in the city, namely the growing commercialisation of Roman urban centres. This includes the first quantification of archaeobotanical assemblages from Campania, allowing hypothetical yields of selected domestic and commercial properties and their monetary and nutritional outputs to be produced, alongside a novel application of spatial syntax analysis of commercial and domestic properties, uniquely uncovering the intricate relationship between garden placement, crops, and use in the city. The Roman hortus' complex process of evolution is found to culminate in a phenomenon of twenty-three new agricultural gardens created in the city's final years, prior to its destruction in the AD 79 eruption. This phenomenon is found to be a direct response to the geographic and economic challenges, commercial opportunities, and elite social agendas discovered in previous chapters, and serves to underpin the persistent nutritional, social, and economic power of the hortus right into the city's final days.

The Clustered Regularly Interspaced Short Palindromic Repeat (CRISPR)/CRISPRassociated nuclease 9 (Cas9) system has become the most widespread method to produce edited plants with improved traits. A DNA-free genome editing approach was developed using the plant virus vectors Potato virus X (PVX) and Tobacco rattle virus (TRV) to deliver and express Cas9 and sgRNAs. Splitting two Cas9 orthologs was explored to avoid viral instability due to the delivery of large transgenes. Manipulating flowering time in crops is a long-term goal in plant biotechnology. To achieve this, targeted genome edits were introduced in the SD flowering Nicotiana tabacum var. Maryland Mammoth FLOWERING LOCUS T 4 (NtFT4) gene. The expression of the split Cas9 was corroborated in N. benthamiana leaves and in vivo activity was validated in N. tabacum protoplasts by edition of the PDS gene. A single transcription unit was constructed encoding the Cas9 and the sgRNA flanked by ribozymes. Mature sgRNAs were detected after self-cleavage of the ribozymes, enabling them to guide the Cas9 to the NtFT4 target sites. Genome editing was found in N. tabacum leaves inoculated with TRV full-length or split Cas9, with frequencies between 3.03% to 0.29%, depending on the enzyme and target site. A delay in flowering time was observed in some plants, however other factors, such as strong viral symptoms, cannot be discarded. Cas9 protein was detected only in inoculated leaves with TRV-full-length SpCas9, and TRV or PVX vectors expressing the SaCas9 C-terminal end, while Cas9 mRNA was found in all inoculated leaves. Even though systemic symptoms of TRV viral infection were seen, full-length or split SpCas9 mRNA was not found, while weak expression of full-length and N-terminal SaCas9 mRNA was observed. In contrast, SaCas9 C-terminal mRNA was detected strongly in TRV systemic leaves, whilst weak expression was found in one PVX systemic leaf sample. Thus, a cargo below 1.3 kb is suggested for viral stability. To obtain fully edited plants, shoots from inoculated tobacco leaves with the different viral constructs were regenerated, but only non-edited plants were found. In summary, this work demonstrates that viral-mediated genome editing is feasible. Improvements to this system, such as the use of newly developed Cas enzymes, are also discussed and may prove useful in generating crops with new desirable agronomical traits.

Greenhouse whitefly (Trialeurodes vaporariorum) are a major global pest, causing direct damage to >850 plant species and transmitting viral plant diseases. Management of T. vaporariorum is increasingly difficult because of widespread pesticide resistance. Many greenhouse growers rely on biological control agents to maintain T. vaporariorum. However, biological control agents are slow acting and variable in their efficacy, resulting in subsequent application of chemical insecticides when pest populations become unmanageable. There is an increasing drive to use integrated, multiple pest control strategies, limiting chemical application and increasing the use of sustainable alternatives. Entomopathogenic fungi (EPF) have the potential to be used as one of these alternative control methods, but EPF efficacy is highly variable between applications. Co-application of a chemical insecticide with an entomopathogenic fungus can result in improved pest control, assist resistance management, target multiple pest species and increase the range of environmental conditions over which control is effective. Combining chemical and biological pesticides has the potential to result in both positive and negative interactions, so it is important to understand how mixture components interact. Positive interactions result in synergism, whilst negative interactions cause antagonism and a reduction in pest control. In this thesis, EPF with potential to control T. vaporariorum were identified through a series of laboratory in vitro and in vivo tests. Co-application of a mixture of selected EPF and the chemical insecticide spiromesifen were evaluated in laboratory based bioassays. Using an ecotoxicological MixTox model, complex interactions between the EPF and insecticide were described; depending on the EPF and the concentrations applied, mixtures resulted in additivity, synergism or antagonism. The types of interactions were influenced by temperature and applications of a low concentration of spiromesifen with EPF resulted in additive mortality of T. vaporariorum in greenhouse trials. By understanding of the complex interactions between components of integrated pest management strategies, optimised approaches can be developed to control pests.

Take-all disease, caused by the soil-borne ascomycete fungus Gaeumannomyces tritici, is one of the most important root diseases of wheat in the UK and worldwide. The fungus invades the roots and destroys the vascular tissue, hindering the uptake of water and nutrients from the soil. Current control methods include crop rotation, later sowing of crops at risk and the use of partially effective fungicide seed dressings. Closely related species in the Magnaporthaceae family, such as Gaeumannomyces hyphopodioides, occur naturally in arable and grassland soils and have considerable potential to suppress take-all disease. In vitro assays revealed that the direct interaction between G. tritici and G. hyphopodioides is unlikely to play a significant role in take-all control. Co-inoculation bioassays demonstrated that effective take-all control is achieved when G. hyphopodioides colonises the root system before G. tritici. Detailed microscopy analyses revealed that G. hyphopodioides produces chlamydospore-like structures in the root cortex, which could also play a role in the infection cycle. Furthermore, the analyses confirmed previous findings that G. hyphopodioides induces physical plant defence responses such as cell-wall lignification. A dual RNA sequencing experiment of G. tritici infected and G. hyphopodioides colonised roots further highlighted this defence induction and revealed extensive transcriptional reprogramming in wheat following G. hyphopodioides colonisation. Taken together, these findings indicate that induced plant resistance is responsible for take-all control by G. hyphopodioides. Despite the clear upregulation of several defence pathways, plant bioassays revealed that G. hyphopodioides colonisation alone does not adversely affect wheat health. Finally, an improved protocol for virus-induced gene silencing (VIGS) in wheat roots was developed, which could facilitate the functional validation of candidate G. tritici resistance/susceptibility genes in wheat. This PhD project provides novel information regarding wheat responses to G. hyphopodioides and G. tritici infection, and provides vital data which could inform future biocontrol strategies against take-all disease in wheat.

Perennial crops, such as oil palm (Elaeis guineensis Jacq.) have a long breeding cycle (typically 20 years per cycle) and inherently heterogeneous populations. Oil palm is the most productive and traded vegetable oil globally compared to other oil crops such as soybean, rapeseed etc, but it has only undergone four generations of selection since breeding started 80 years ago. No doubt genome-enabled biology in oil palm breeding is crucial yet genetics and crop improvement have been actively pursued in research but with limited deployment in the industry. Further, the oil yield has stagnated for many years, hence the realistic approach of genome-based breeding is needed. High resolution genetic map maximizes discoveries of recombination events and thus empowers comparative genomic and quantitative trait locus (QTL) studies. The present study aims to develop multiple ultra-dense linkage maps using high density marker panel and integrate these with physical genome map of oil palm. To improve the current genome assembly, more of the previously unplaced genomic scaffolds can now anchored to chromosomes using mapped markers from the genetic maps. Linkage maps generated using three populations contained 11,421 transferable markers - consolidate each and the total maps span, on average, 1,355.64 cM with the lowest average marker intervals of 0.04 cM. These are by far the densest linkage maps reported in oil palm. The creation of a consensus linkage maps from combinations of different mapping populations provides essential information about the consistency of marker order and genetic distance among oil palm populations, while increasing map precision and resolution. The published oil palm physical genome size is 657.98 Mb while the assembled scaffolds add up to 1.53 Gb. The coverage of the assembled physical genome still leaves more than 60% to be fully covered. The estimation of genome-wide recombination rates revealed varying degrees of genetic exchange across different populations and between chromosomes. The integration of the high-density linkage maps with the published oil palm genome could potentially improve the current genome for utilisation in oil palm improvement programmes. The outcome of this study has significantly improved the assembly of oil palm genome by anchoring more genome sequence scaffolds to chromosomes, resulting in 1.2 Gb equivalent to extension of 79% of the publicly available genome version. The creation of the most complete genome map within palm species here, allows comprehensive comparative genomic studies. Applications of genome information in oil palm breeding through genome-wide association study (GWAS) and genomic selection (GS) and their combinations will pave the way for crop improvement not only in oil palm but also the exploration of economically important traits within palm species generally.

Oil palm (Elaeis guineensis Jacq.) contributes 35% of global vegetable oil and has become the most important oil crop in the world. It occupies only 7% of total global oilseed-harvested land with 10 times more oil yield per hectare of cropland than any other oil crop. To further improve the superior oil yield, enormous efforts have been put into selective breeding programmes in the last eight decades. Nevertheless, the breeding progress of oil palm, like other perennial crops, is extremely slow (typically 12 years per breeding cycle) and costly. In this study, major QTL (quantitative trait loci) for trunk height (THT) and correlated yield traits were discovered in low trunk increment breeding populations using single nucleotide polymorphism (SNP) and simple sequence repeat (SSR) markers. Further understanding of the correlation between THT and oil yield traits, and the effect of cumulative positive alleles of QTL can significantly increase the success rate of multiple trait integration through MAS to produce high-yielding oil palms with low height increment. This compares to an estimated 1% probability of success using conventional breeding methods. Furthermore, illegitimacy in breeding crosses and commercial seed production can be a common problem, if mismanagement happens in controlled pollination (given that oil palm is a naturally outcrossing species) and seed processing. For perennial crops such as oil palm, the illegitimacy problem can easily badly effect a 12-year breeding cycle and illegitimacy can lead to a 25-year yield reduction in commercial planting. Therefore, a practical genomic SNP-based legitimacy testing method with accuracy >97% was developed as a standard quality control procedure for seed purity in breeding and commercial seed production. The method has also successfully addressed the inaccuracy and inefficiency of the conventional fruit census test for contamination. The overall objectives of this study and findings are reported in the thesis.

Bambara groundnut (Vigna subterranea (L) Verdc), is an exemplar neglected African grain legume that thrives under strikingly contrasted environments relative to other grain legumes. Originating in West Africa, its distribution spans across aridity gradients from tropical dry climates in Senegal and Kenya, respectively, down to arid and semi-arid regions in sub-Saharan Africa. This is on soils more or less poor in nutrients and formed under variable pedoclimatic conditions. In these contrasting habitats, it is generally agreed that bambara groundnut has diversified due to domestication from its wild relative, Vigna subterranea var. spontanea (Harms) Hepper, as a result of steady changes through natural and artificial selection. Bambara groundnut is a close relative of cowpea (Vigna unguiculata) and morphologically fits into the same niche as groundnut (Arachis hypogaea L.). The wide distribution in natural environments and ability to tolerate both biotic and abiotic stresses better than cowpea and groundnut, make bambara groundnut an interesting model for examining diversification in response to ephemeral soil water resources. Although important, comprehensive variation assessment on below ground (root) traits in bambara groundnut have not been pursued. The hypothesis was that by focusing on naturally occurring genotypic variation in root system architecture and rooting distribution, bambara groundnut genotypes from dry agroecologies with periodic drought stress had developed root system traits that improved water foraging in deeper soil depths over time. This could be visualised and quantified using a low-cost polyvinyl chloride column (PVC) phenotyping system and image analysis. To test this hypothesis, morphological variability in root system architecture was characterized in eight bambara groundnut parental lines of varying geographic origin (Gresik, LunT, IITA-686, DodR, S19-3, Tiga nicuru, Ankpa-4, DipC1). The experiment was conducted over two seasons (2018 and 2019) under fixed rainout shelter at the Crops For the Future-Field Research Center (CFF-FRC) in Semenyih, Malaysia. Results revealed that in deeper (60-90cm) soil depths, genotypes S19-3 and DipC1 from drier regions of Sub-Saharan Africa had longer tap roots and greater root length distribution. Bambara groundnut genotypes from wetter regions in Southeast Asia and West Africa (i.e., Gresik, LunT, and IITA-686), on the other hand, had shallower and more branched root growth closer to the soil surface. Genotypes generally displayed two extremes in root foraging patterns and branching habits i.e., deep-cheap rooting in genotypes sourced from dry regions and shallow-costly rooting in genotypes adapted to higher rainfall areas with shallow soils. Next, the natural genotypic diversity revealed in the eight genotypes was then investigated to detect adaptive changes in tap root length and root length density in response to periodic drought stress. Genotypes were grown in PVC columns in well-watered and 30-day drought stress (DS) treatments for two seasons (2018 and 2019). DS significantly (P < 0.05 - < 0.001) reduced average shoot height, number of leaves, and delayed flowering in 2018 and 2019. In 2018, the average root-to-shoot ratio was significantly higher (P < 0.001; 22%) under DS treatment. On average tap root length at 55 days after emergence (DAE) i.e., end of 30-d DS, was reduced by 14% and 22% in 2018 and 2019, respectively, and by 5% and 11% at 105 DAE (50-days of DS recovery) in 2018 and 2019, respectively, with some genotypes in 2018: DodR (55 DAE); LunT and Ankpa-4 (105 DAE) and in 2019: IITA-686 (105 DAE), increasing to measurements comparable to the well-watered (WW) treatment. In 2018 and 2019, root length density in the DS treatment was associated with significant grain yield advantage (R2 = 0.27 and R2 = 0.49) in 2018 and 2019, respectively. This indicates that the various agroecological conditions to which bambara groundnut has been exposed in its natural setting may have induced phenotypic differentiation to adapt to ecotypic conditions, which may help offset the impact of adverse events like regular drought stress. When looking for superior genotypes, ecotypic distinction can be an interesting aspect to remember. Finally, root traits such as tap root length and root length density in the 60-90cm soil layer were shown to be beneficial in screening and selecting superior lines from a bambara groundnut population. The population was derived from a cross between two parental lines i.e., S19-3 (maternal) × DodR (paternal). Across replicates, 100-seed weight had the lowest average repeatability (0.62), while high repeatability values were observed for root length density in the 60-90cm soil depth (0.99). Under DS environment (50-d of DS recovery), root length density in the 60-90cm soil depth was strongly correlated (P < 0.05 - P < 0.001) with shoot traits such as number of leaves (r = 0.69), shoot dry weight (r = 0.78), and shoot height (r = 0.67). This indicates that shoot traits are useful traits that can also be used as proxies to make estimations of root length density. According to a regression analysis, root length density in the 60-90cm soil depth was associated with grain yield (R2 = 42%; P < 0.001). According to biplot analysis, the top three bambara groundnut lines in terms of yield under drought stress were 'Line12', 'Line35', and 'Line41'. Overall, the work provides a novel and in-depth examination of bambara groundnut below-ground (root trait variation) and its role to drought tolerance. According to this research, bambara groundnut possess differential deep root foraging and density patterns with two extremes i.e., deep-cheap rooting in the genotypes mainly sourced from dry regions and a shallow-costly rooting system in genotypes suited to higher rainfall areas. Farmers have inadvertently selected for these variations over time due to their effect on yield in both dry and wet conditions. Drought tolerance breeding for bambara groundnut will more likely accelerate as a consequence of a better understanding of root systems and foraging patterns. Selected high yielding lines from the S19-3 (maternal) × DodR (paternal) cross i.e., 'Line12', 'Line35' and 'Line41' - all exhibiting deep and extensive rooting in deeper soil depths, will be advanced as part of the current Future Food Beacon: Bambara Groundnut breeding (BamBREED) research project. Elite lines generated from this breeding programme could be registered as improved varieties and released to the general public for cultivation in drought-prone areas. This is projected to boost dietary diversity and significantly increase the nutritional value of people's diets.

Zymoseptoria tritici, a fungal pathogen of wheat and the causal agent of Septoria Tritici Blotch (STB), is a particular challenge to wheat production on a global level, causing crop losses of up to 50% in some cases. Genetic resistance presents an effective way of controlling STB in wheat, with numerous resistance loci having been identified. Stb6, which encodes a wall-associated kinase-like protein and confers resistance to Z. tritici isolates expressing the corresponding AvrStb6 effector, has recently been cloned. However, many questions regarding Stb6-mediated resistance remain unanswered. The global frequency of avirulence AvrStb6 alleles in modern Z. tritici populations remains unknown. The role that AvrStb6 plays in Z. tritici pathogenicity, the nature of its interaction with Stb6 and the mechanism by which Stb6 confers resistance are also yet to be elucidated. In the following thesis, I present data indicating a dramatic shift in the frequency of virulence AvrStb6 isoforms in modern Z. tritici populations, relative to previous studies. Transient expression of fluorophore-tagged Stb6 and AvrStb6 in the tobacco species Nicotiana benthamiana also revealed that AvrStb6 localises to the apoplast. Stb6 displays an unusual cellular localisation pattern, being present in both the plasma membrane but also identified in the cell wall and in hectian strands adjoining the two. Expression of Stb6 in N. benthamiana induces a kinase-dependent cell death phenotype, which is independent of the co-receptor BAK1. I also report on the identification of candidate protein interactors for Stb6 and AvrStb6. Both interactors are predicted to be chloroplast-localised. These findings present an intriguing hypothesis as to the possible mechanism of Stb6-mediated resistance. This study therefore represents an important contribution to our understanding of evolutionary genetics in a plant pathogen, provides a putative mechanism for AvrStb6 in pathogenicity and has also potentially identified a completely novel resistance mechanism for an immune receptor protein. Research such as this plays a role in helping develop more productive crop plants with improved genetic resistance to pathogens.

Biochar creates a resistant soil carbon pool that is carbon-negative, provides long-lasting improvements in soil fertility and serves as a net withdrawal of atmospheric carbon dioxide stored in highly stable soil carbon stocks. The enhanced nutrient retention, improved soil fertility and water holding capacity of biochar-amended soil not only reduces the total fertilizer requirements, but also the climate and environmental impact of croplands with generally increased production. I hypothesized that biochar increases plant growth by ameliorating negative soil physicochemical, and enhancing microbial, properties with special relation to nutrient availability and contributes actively to modify ecosystem gas exchange. Moreover, I hypothesized that the rate of biochar application influences the rate of biochar surface oxidation, nature and mineralization of functional groups, when it was added to soil for a long period of time in a controlled environment. The present study focused on determining the potential of a wood-based, high temperature (1100°C) biochar, to increase strawberry plant growth and ecosystem gas exchange in topsoil and its influence on soil quality. The results discussed in this thesis were obtained from a long-term investigation conducted under controlled conditions and is novel because of its duration (18 months), and because of the use of biochar derived from demolition wood. There is currently much interest in utilising biochar as a soil amendment for increased soil health and for carbon sequestration and European and International voluntary standards for biochar safety are under review in the UK post-Brexit. All work on biochar to date, has utilised biochar from virgin wood or agricultural residues. To the best of my knowledge, this is the first study to quantify effects of biochar derived from demolition wood on soil health. The importance of this is twofold; firstly, the stock of virgin wood for biochar production is limited, therefore it is important to be aware of any dangers of 'diluting' virgin wood with unapproved feedstock during production, and secondly, it is possible that biochar from such feedstocks might be acceptable for restoration programmes of already contaminated land. Biochar (0, 2.5, 5, 10 and 15% w/w) was mixed with topsoil, added to 14 L pots and maintained in a growth room at 20/16°C (16 hours day/night) and 50 % relative humidity for 18 months. Pots were either planted or left bare and soils in planted and unplanted pots were regularly sampled for microbiological and soil chemical determinations and plant growth measured. Biochar addition did not affect strawberry shoot growth or carbon or nitrogen content, but the 2.5% addition of biochar slightly increased root biomass, whilst the highest concentration (15%), reduced biomass relative to the 2.5% amendment, but not to the control. In the strawberry shoot, K, P, Zn, Cu, and As concentrations increased with biochar addition, while Pb content decreased with increasing rate of biochar compared to the control. Other than these, none of the shoot or root elements analysed exhibited clear biochar-driven trends. Neither leaf conductance nor leaf temperature were affected by biochar amendment. However, biochar amendment generally reduced ecosystem respiration (Re), net ecosystem exchange (NEE), gross ecosystem exchange (GEE) and soil enzyme activities. Biochar had no effect on microbial biomass nitrogen and carbon. CO2 and CH4 fluxes in soil were generally reduced by biochar amendment, but presence or absence of strawberry plants had no effect. However, soil water content, pH and Olsen P concentrations all increased with biochar amendment, as did soil nitrate concentrations in unplanted soils (but not as markedly in the presence of plants). Bulk density of the soil deceased in line with increasing biochar addition. Results from FTIR analysis showed that when this high temperature wood biochar was applied to soil, due to microbial and plant mediated transformation, it becomes more aromatic because of the loss of aliphatic and labile compounds and broadening of aromatic bands. The maximum number of functional groups (aliphatic, aromatic and carbohydrates) was recorded in the control soil (0 % biochar) both with and without plants. Aromatics (C-C and CH) were more prevalent than oxygen containing compounds (carboxyl and carbonyl), or aliphatic compounds and there were very few hydrocarbons. Shifts in the spectra for all wave numbers were observed in planted biochar-amended soils compared to control (0 % biochar). After 12 months, a marked decrease in spectral bands between 500 and 4000 cm−1 was noted in treatments with 2.5 %, 10 % and 15 % biochar. Overall, the use of biochar made from demolition wood ought to be avoided in agricultural settings. However, in contaminated areas, concentrations up to the lowest used in this study may be beneficial if pH changes or improvements in bulk density are desired.

Wheat yields are stagnating or declining in many regions of the planet, requiring efforts to improve the light conversion efficiency, i.e., radiation use efficiency (RUE). RUE is a key trait in plant physiology because it links light capture and primary metabolism with biomass accumulation and yield. High-throughput phenotyping (HTP) was used among a population of field grown wheat with variation in RUE and photosynthetic traits to build predictive models of RUE, biomass and intercepted photosynthetically active radiation (IPAR). The use of remote sensing models predicted RUE with up to 70% accuracy compared to ground truth data. Wheat yield can be defined as the product of solar radiation intercepted throughout the crop cycle, radiation use efficiency and harvest index. Photosynthesis is a central component of RUE but normally measured in the upper layers of the canopy where light conditions are saturating. Significant relationships were found between light saturated photosynthetic rates measured at initiation of booting in the top, middle and bottom layers of the canopy and yield. These findings indicate that there is an opportunity for yield improvement if we consider the requirements of photosynthesis in the middle and bottom layers of wheat canopies where conditions are not light saturating. The study of photosynthesis in the field is constrained by low throughput and lack of integrative measurements at canopy level. Partial least squares regression (PLSR) modelling was used to build predictive models of photosynthetic, biophysical and biochemical traits at the top, middle and bottom layers of wheat canopies. The combined layer model predictions performed better than individual layer predictions. Using HTP allowed us to increase phenotyping capacity 30-fold compared to conventional phenotyping methods and our models can be used to screen varieties for high and low RUE. There is clear consensus in the physiological and breeding communities that improving RUE will be key to boost wheat yield. In the previous years of RUE research little has been explored on the role of root biomass accumulation and its interaction with aboveground biomass accumulation, RUE and yield. Strong positive associations were found between above and belowground biomass accumulation with RUE and root biomass during the vegetative period, and negative associations between yield components and root biomass accumulation, suggesting there is a coordination between roots and shoot in the vegetative period to maximize growth. However, if too much energy is invested in root biomass this will have an effect in decreasing aboveground biomass during grain filling. More research will be needed to explore new hypothesis in the field that accounts the effect of root biomass in canopy RUE and yield.

The horticultural industry in sub-Saharan Africa (SSA) has witnessed unprecedented growth in recent years, fuelled by increased demand for temperate fruits and vegetables in the European market. In Uganda, the introduction of Non-Traditional Agricultural Exports (NTAEs) in the post-civil war era (mid 1980s onwards) as an export diversification strategy was met with limited success attributed to agronomical, logistical, and institutional challenges that resulted in a relatively small and fragile horticultural industry, serving a limited market specialised in the ethnic/exotic food trade. However, in recent years, increased demand from the diaspora has created new opportunities for Uganda´s ethnic/exotic horticultural exports in a buoyant industry that has increased fourfold over the last two decades. Meanwhile, this renewed opportunity is threatened by EU/UK legislation targeting the introduction and spread of organisms considered harmful to the environment. The threat is manifested in the interception and destruction of consignments found to be infested by (regulated) organisms (notably the false coddling moth (FCM)). While being common to all SSA countries infested by the FCM, interceptions have been particularly high for Uganda over the last seven years, a period coinciding with the boom in its horticultural industry. Based on an instrumental case study design consisting of semi-structured interviews, document reviews, and participant observations, this research investigates the cause of interceptions in the Ugandan Horticultural Export Supply Chain, (fresh fruits & vegetables) and their relationship to the concept of transparency, which is increasingly core to agri-food chains. In line with the Global Value Chain (GVC) approach (Gereffi, 1999; 2005), it examines the response and outcomes resulting from attempts to comply with international public standards governing agricultural supply chains. Findings indicate that a combination of environmental (e.g., regulatory), people (e.g., literacy levels of Outgrowers), process (e.g., bureaucracy) and technological (e.g., lack of IT infrastructure) factors working together as inhibitors of transparency are to account for the rising wave of interceptions. Uganda´s response to interceptions, described in this study as the regulated integration (backwards) of supply chain relationships through the mandatory registration of producers is yielding results. This is in terms of enhanced capability development and supply chain transparency in a process described by the GVC literature as process upgrading. In so doing, the research contributes to the literature on supply chain transparency while suggesting a renewed focus of GVC research on the role of public standards (as opposed to private governance) in the upgrading and integration of developing countries in the world economy. The research is limited by the lack of a quantitative approach to validating findings that are essentially qualitative in nature. Future research involves the validation of transparency inhibitor matrix for the prioritisation of improvement initiatives in a quantitative study as well as an investigation of opportunities for improving Uganda´s phytosanitary certification process with distributed ledger technology.

Plant hormones are organic substances that influence specific physiological processes, such as floret fertility, and move throughout the plant. Previous studies suggest that genetic variation in grain number in cereals is associated with hormones such as cytokinin, which is crucial in controlling cell division and lateral meristem activity. This has been demonstrated in cereals when QTLs linked with reduced expression of cytokinin oxidase/dehydrogenase (OsCKX2) increased grain number in rice and wheat. However, how hormones regulate grain number traits such as fruiting efficiency (FE, ratio of grain number to spike dry weight at anthesis) and grain dry matter partitioning in wheat is not fully understood. The objectives of this study were, using a high biomass spring wheat panel, to identify novel grain number and partitioning traits for advancing harvest index and grain yield, and to determine how they are influenced by spike hormones. Finally, to understand the genetic regulation of these traits, using a bespoke target sequence capture strategy, to generate SNPs and establish molecular markers for the hormonal traits. A high biomass association panel (HiBAP II) of 150 CIMMYT spring wheat genotypes was phenotyped for grain number and partitioning traits in the field under irrigated conditions and spike hormone levels were sampled at anthesis in two seasons in NW Mexico. A subset of 10 genotypes representative of field variation for FE was grown in the glasshouse under well-watered conditions at the University of Nottingham, UK in three years for detailed hormonal analysis at GS49 (late booting) and 65 (anthesis). To test if certain plant components and stem internodes were competing with the spike at GS49 and GS65, destructive samples were taken where the plants were separated into their constitutive parts. Results showed genetic variation in grain yield correlated with grain number in both the glasshouse and field experiments, and grain yield correlated with harvest index in the field experiments. The increase in grain number amongst genotypes was associated with an increase in FE. The stem internode traits which were competing for most with spike growth was stem internode 2 leaf sheath, suggesting reducing internode 2 leaf sheath length could increase allocation of assimilates to the spike at anthesis. The results also identified novel genetic variation in spike hormones and found associations between higher levels of cytokinins and increases in grain number and yield at both GS49 and GS65 in the glasshouse and field experiments. The genetic variation in spike cytokinins also correlated across the glasshouse and field experiments. Twenty-six traits were analysed in a genome-wide association study and 213 putative marker-trait associations were identified, while 53 candidate genes were suggested including one candidate gene on chromosome 1B for spike cytokinins zeatin riboside and isopentenyladenosine at anthesis, which, in Arabidopsis, codes for an auxin efflux carrier protein PIN3 that is regulated by cytokinins. The next steps include validating the markers through developing KASP markers to be deployed in wider germplasm and using the genetic information from this study to improve traits in plant breeding programmes.

Bambara groundnut (Vigna subterranea (L) Verdc) is an underutilised African legume commonly known for its resistance to harsh environmental conditions such as drought, and equally known for its high protein content, and thus, having the potential to aid in the pursuit of food security as the climate is constantly changing. As an underutilised crop, Bambara groundnut has been relatively poorly researched in comparison to other more conventional crops such as maize, wheat, soybean, or rice. To help Bambara groundnut farmers and breeding programs achieve the development of varieties with better agronomical potential, a better understanding of the physiological and genetic mechanisms, in relationship to drought resistance, is needed. A series of experiments under controlled glasshouse conditions were conducted in order to gain a better understanding of the responses of Bambara groundnut to drought. Drought is defined as when the level of water content in the soil is below a healthy threshold for plants to continue normal physiological and biochemical processes. A selection of genotypes was assessed over a period of three years, in 10 L pots, and an Association Genetics Panel was assessed over one season in 5 L pots. Additionally, the transcriptome of a sub-set of 4 genotypes was studied through RNA-sequence, and a genome wide association study was conducted over the association genetics panel. A combination of these approaches allowed to have a better understanding on a series of physiological mechanisms where two main approaches were detected, such as, drought tolerance and drought avoidance. For drought tolerance, several genotypes, such as DodR, S19-3, and TN, showed a higher conservation of their canopy, their efficiency of the photosystem II, relative water content in leaves, and a warmer canopy under drought conditions. Additionally, genes related to several osmo-protectant compounds, and cuticular waxes were differently expressed in response to drought. For drought avoidance, several genotypes, such as UnisR, Kano2, Kano3, and Gresik, showed a faster and higher rate of leaf senescence, lower efficiency of the photosystem II, lower percentage of relative water content in leaves, and a cooler canopy temperature. However, the recovery rate when irrigation was re-introduced, was significantly higher than the drought tolerant genotypes. Additionally, in the case of Gresik, genes related to stomatal conductance were differently expressed in response to drought. These findings will help stepping forward in the Bambara groundnut research by narrowing research objectives in future efforts through a selection of specific physiological traits and genes, and subsequent adaptation into breeding programs by marker assistant selection, or gene editing.

The conservation and use of plant genetic resources (PGR) is subject to a range of international treaties and conventions, but these have not resolved controversies over rights of access to seeds, control over new crop varieties or biodiversity conservation. This thesis examines the role of CGIAR, a publicly-funded body that manages 11 international genebanks, within these debates. The thesis explores how the role of, and strategy for, public international agricultural research (IAR) has evolved in the light of changes in governance of the global agri-food system (1990 - 2012). The research takes CGIAR as its central case study, using archival research and key informant interviews to examine the relationship between CGIAR's mandate to provide 'global public goods' (GPGs) and its policy decisions on the management of plant genetic resources (PGR) and intellectual property. It examines how different understandings of GPGs fitted with or challenged dominant discourses about future agri- food systems, and whose interests have been served by CGIAR's changing understandings of its role. The research finds that there were multiple and vague understandings of the GPG concept across CGIAR and its donors; and that this ambiguity was critical in CGIAR's policy choices on PGR management. The evidence shows that CGIAR's ostensible policy goals on the management and use of PGR remained remarkably stable over time. It explains this stability by demonstrating how ambiguity over the GPG concept enabled particular narratives about how science contributes to development outcomes to remain dominant. It finds that an over-focus on the global aspect of its GPG mandate undermined opportunities within CGIAR to consider the different publics that IAR should serve, and the range of goods they might need. This framing of CGIAR's public goods mandate resulted in a policy alignment with dominant, market-based, paradigms of agricultural development, to the neglect of opportunities for the exploration of alternative pathways to development.

Salad onions (Allium cepa L. or Allium fistulosum L.) are a high value UK vegetable crop consumed for their immature bulbs, green leaves and distinctive flavour. Producing a crop with little variation is key to attaining maximal yields and economic returns. However, high levels of in-field crop variability, where individual plants or crop areas can vary significantly in size, distribution and quality, are regularly reported by salad onion growers. Current knowledge as to what causes this variability is limited. Therefore, improving our understanding of the nature of this variability provides an opportunity for growers to implement actions that will enhance crop uniformity. Field scale-monitoring trials undertaken within UK commercial salad onion crops identified plant performance as being associated with seed depth, soil surface strength and soil moisture; all factors considered to have greatest influence during early crop development. Controlled environment investigations revealed that sowing depths of 5- 20 mm, with low to moderate compaction, support good seedling development. Larger seeds were also found to possess enhanced vigour, improving seedling establishment. Under field conditions, a moderate sowing depth (~25 mm) and the rolling of seedbeds provided the greatest crop establishment and marketable yields. Additionally, spatial variability of soil texture was shown to have a significant influence on growth, with a higher clay content having a deleterious impact on crop performance. This project has identified early crop development as a key phase in which variability can be introduced to salad onion crops, identifying potential opportunities for new strategies that maximise crop uniformity and yields.

Hevea brasiliensis, the Par`a rubber tree, is the primary source of natural rubber (NR). NR is harvested through the wounding, or tapping, of rubber trees, and the collection of the latex that flows from the wound. Serial tapping and ethylene stimulation can boost the yield of latex harvested after each tapping, though the mechanisms that underpin this increase in yield have not been fully characterised. This study has generated whole-genome transcriptome and methylome datasets, in order to explore the regulatory mechanisms that underpin latex production in response to tapping and ethylene stimulation. Analyses show key patterns of differential expression across genes of functional significance, including a large number of genes under the control of endogenous-ethylene, whose transcriptional response to tapping is enhanced by exogenous ethylene. This includes numerous DNA methylation relevant genes, indicating an epigenetic role in latex production, and therefore prompting the generation of bisulfite-seq libraries. Collectively, these experiments will provide great insight into the mechanisms underpinning latex production.

Phosphate is a vital macronutrient yet its availability is often a limiting factor which hinders plant growth. A large proportion of phosphate in soils is organic phosphate (Po) which is inaccessible to plants, it needs to be in its inorganic orthophosphate (Pi) form to be accessible. When grown in Pi deficient conditions plants have adapted numerous phosphate starvation responses (PSR), such as an alteration of their proteome and secreted root exudates, to improve their Pi efficiency. Roots will secrete various compounds such as Purple Acid Phosphatases (PAP) and RNases into the surrounding soil to improve the accessibility of Pi from Po sources for plants to utilise. The majority of research on plants molecular responses to Pi deficiency has been performed on Arabidopsis thaliana, with various crop species responses being largely uncharacterised. To gain insight into how the crop species Brassica rapa responds to Pi stress they were grown hydroponically and a PSR was induced. The plants root and shoot proteomes were analysed with mass spectrometry to determine proteomic responses to Pi starvation. When Pi starved, the root exudates displayed a significant increase in abundance of various proteins, including secreted PAPs, RNases, and lipid remodelling proteins which could help to improve the accessibility of Pi and improve Pi uptake efficiency. The root and shoot proteomes also displayed an increased abundance of various phosphatases as well as various proteins involved in phosphate transport, lipid remodelling, and signalling. These changes in protein abundance have not been documented before in response to Pi starvation in B. rapa, therefore provides valuable insights into which proteins play a role in improving Pi efficiency in B. rapa, providing new and interesting candidates that we could utilise to further improve a plants efficiency in Pi deficient conditions.

Overpopulation of the planet, climate change and the limitations in the available arable land are undoubtedly among the major problems of modern era that threaten global food security. Crop losses due to diseases in the field caused by plant pathogens account as one of the most daunting obstacles for food security in the 21st century. Engineering plants with durable resistance against pathogenic microbes is arising as a key strategy for sustainable food production. We aimed to unravel novel pathways for robust plant production and minimise crop losses to pathogenic infections by elucidating the role of uncharacterised "truncated" receptors in plant immunity. "Truncated" TIR-NB (TN) proteins are structurally similar to NLR immune receptors, without the LRR domain. Increasing evidence show that TN proteins may be important players in plant immune responses, possibly due to the role of the TIR domain. A transcriptomics study (Lewis et al., 2015) on Arabidopsis thaliana when challenged with the pathogenic bacteria Pseudomonas syringae pv. tomato (Pst DC3000) showed rapid upregulation of 4 TN genes from the same genetic locus: AT1G72920, AT1G72930, AT1G72940, and AT1G72950. RT-q-PCR confirmed that A. thaliana TN genes AT1G72920 and AT1G72940 are upregulated specifically in response to Pst DC3000, but not to the mutant strain Pst DC3000 hrpA that cannot deliver effectors, or in response to any of the other biotic and abiotic stresses tested. Analysis of TN promoter regulation showed that Pst DC3000 effectors HopQ1-1, HopAl1, HopB1, AvrPto, HopF2 and HopAB2 correlate with TN promoter induction when co-expressed in protoplasts. A study by (Mine et al., 2018) using chromatin immunoprecipitation (ChIP) showed that ERF6 transcription factor (TF) binds on AT1G72920 and AT1G72940 promoters, and suggests that more ERFs may regulate TN expression. Yeast expression vectors were generated with promoter AT1G72940 and versions of it with mutations on three motifs for TF recognition, to facilitate large scale yeast-one-hybrid screenings of a transcription factor library, to identify candidates that mediate TN promoter regulation. Pst DC3000 assays on knockout plants missing the TN locus did not reveal significant differences to wild type plants, possibly due to functional redundancy. A range of A. thaliana lines were generated, selected and characterised for constitutive and inducible overexpression of AT1G72940 to facilitate immunity assays and high-throughput experiments that can elucidate the role of AT1G72940 in plant immunity. Characterisation of overexpressing AT1G72940 lines showed that protein AT1G72940 is not detected beyond the early plant developmental stages, suggesting epigenetic silencing of transgene expression and/or protein degradation in adult plants. Preliminary results of Pst DC3000 bacterial growth indicate susceptibility to infection of the same plants when compared to wild type, which is inconsistent with the lack of protein detection. Nevertheless, the generation and selection of A. thaliana transgenic plants for AT1G72940 with many combinations of different promoters and tags offers many possibilities for future work in the field.

An indoor environment that does not detrimentally affect our health and is comfortable to spend time in should be considered a fundamental human right. Previous studies have shown that various species of indoor plants are able to remove pollutants, including those shown to be both prevalent and harmful in indoor environments and contributors to poor Indoor Air Quality (IAQ). However, a lack of consensus exists on whether plants are able to improve IAQ in real dynamic environments with complex and everchanging ventilation, indoor sources and occupant numbers. Additionally, the processes underlying pollutant removal in plants are evidently equally complex, with numerous environmental parameters and likely physiological traits influencing species' removal ability. In terms of Indoor Environmental Quality (IEQ), relative humidity regulation and control are vital for both occupant comfort and reductions in disease transmission - the latter ever more relevant with the current pandemic. However, humidity control indoors through mechanical systems is energy intensive, thus, exploration of plants as a passive technique is worthwhile. The focus of this study was to investigate a representative range of houseplants - with differing metabolisms, leaf types, and sizes - for their potential to improve indoor environments through pollutant removal (namely, CO₂ and NO₂) and relative humidity regulation under differing environmental conditions and experimental scales. Alongside this, the study looked to address some of the inherent issues with plant-pollutant removal experiments in literature, namely, pollutants tested at much higher concentrations than what is typically measured in indoor environments. For CO₂ removal, both studied experimental scales (leaf and chamber scale) drew the conclusions that for measurable removal supplementary lighting is required (at ~ 22 200 lux), and to elicit room scale concentration changes the number and density of plants offered by a green wall is necessary. At typical indoor light levels (0 - 500 lux), little potential is offered for CO₂ removal, however, respiration rates were equally found to be negligible in terms of increasing CO₂ concentrations at the room scale. The type of growing media (GM) was found to have a significant influence, with peat GM contributing to a greater reduction of CO₂. Additionally, substrate moisture content (SMC) was deemed to have a negligible effect, especially when removal rates were extrapolated to the room scale. All studied plant types were able to reduce NO₂ concentrations representative of a polluted urban environment to varying degrees at typical indoor light levels (0 - 500 lux). Few statistical differences were measured between differing environmental factors at the single plant scale namely, GM type, light level, and substrate moisture content. This research suggests that approximately five plants in a small, unventilated office could provide broadly similar health benefits in terms of life years saved, as are estimated to result from clean air policies in urban areas. As a method for measuring low VOC concentrations to improve the current plant-pollutant experimental methodology, little potential was offered by solid phase micro extraction (SPME) as a technique over what has been previously utilised, the gas-tight syringe. Moreover, we found that plant species which assimilated the most CO₂ also contributed most to increasing relative humidity (RH) namely, Hedera helix and Spathiphyllum wallisii 'Verdi'.

Colonisation of the root surface, or rhizoplane, is one of the first steps for microorganisms within soil to become established in the plant microbiome. However, the timing and relative contributions of processes, such as microbial movement, attachment, and proliferation to colonisation are not well characterized. This limits our ability to comprehend the complex dynamics of microbial communities in soil. The aim of this thesis was to develop a set of experimental and theoretical frameworks that can be used to isolate and quantify key microbial processes involved in rhizoplane colonisation. A model plant and bacterial system, consisting of Pseudomonas fluorescens isolate SBW25, transformed with a fluorescent marker plasmid, and Lettuce (Lactuca sativa) was selected for characterisation. A liquid microcosm system was developed which enabled inoculation of plants with bacterial suspensions and manipulation of the plant following treatment. Using this system, a framework for the independent quantification of bacterial attachment and proliferation on the root surface was developed. This allowed previously indistinguishable components of the colonisation process to be independently quantified. The timing and spatial distribution of colonisation in a granular environment was further analysed through the live imaging of plants grown in transparent soil. A chemotaxis assay was developed for the measurement of bacterial movement in transparent soil in response to plant root exudate. Data from chemotaxis assays was used to construct a model of bacterial diffusion and convection in soil. These novel characterisations of bacterial movement, attachment to the root surface, and proliferation offers new insight into the timing of rhizoplane colonisation by Pseudomonas fluorescens SBW25. The techniques and analyses developed in this thesis could be applied to many different combinations of plants and microorganisms. Potential applications include the selection of microbial traits which improve maintenance of targeted isolates in agricultural systems, and the development of biological fertilizers.

The grasses are one of the largest and most diverse families within the angiosperms and make up to 70% of all crops grown. Domestication of wild ancestors of the major cereals involved artificial selection of agronomically important traits like tillering. Plant architecture in the grasses is influenced by the initiation and outgrowth of axillary meristems that determine the number of reproductive organs formed. Inflorescence architecture has also been a major selection trait in human domestication of cereal crops and is determined by a complex genetic network of meristematic transcription factors. The RWP-RK transcription factors are a family of developmental regulators that are tightly expressed in reproductive tissue and are implicated in early embryogenesis across the plant kingdom. We've found that ectopic expression of zygotic the RWP-RK genes TaRKD1-7D and OsRKD3 leads to increased tiller number, inflorescence size and seed weight in wheat and rice respectively. Interestingly, we also see greater increases of these traits in conditions of lower nitrogen availability. Through extensive bioinformatics analysis we hypothesise that ectopic expression of these transcription factors upregulates pluripotency factors, specifically cell cycle regulators, histones, histone methylation factors and meristem determinacy genes like trehalose phosphate synthases. This increases meristem formation and indeterminacy by creating and maintaining stem cell niches that determine plant architecture. This is a novel strategy for manipulating yield determining traits across a range of cultivars and cereal crop species.

With growing demand for increased crop yields, mitigating losses due to abiotic and biotic stresses is of paramount importance. A new fungicide with a novel mode of action effective in wheat against the pathogen responsible for Septoria tritici blotch (Zymoseptoria tritici), has recently been released by Corteva Agriscience. Inatreq™ active (active ingredient fenpicoxamid) is the first commercially available picolinamide fungicide. Preliminary observations of this fungicide suggest that it may also have biostimulant-like properties, unrelated to its fungicidal activity. The aim of this study is to further characterise the fungicidal activity of Inatreq when applied as a curative application, using traditional and image-based assessment techniques. This work also aims to characterise the beneficial non-fungicidal effects associated with the application of Inatreq, and to begin to understand the mechanisms underlying this activity. It was found that when the curative efficacy of Inatreq was compared to a panel of commercially available fungicides also used to manage Septoria tritici blotch, it performed excellently, outperforming all alternatives. This work was also used to validate an imagebased assessment tool against traditional manual scoring methods. This tool aims to eliminate the influence of bias from the process of scoring disease severity and was found to be reliable and accurate, providing more consistent scores, that were more specific in the mid-range of disease severity, and closer to the accepted ground truths than traditional methods. Inatreq application was associated with improvements in biomass accumulation, a reduction in stomatal conductance and improvement of water use efficiency, in both wellwatered plants and plants experiencing drought. These effects were observed in controlled environment growth room conditions, as well as in a large-scale glasshouse trial, across multiple wheat varieties. These effects were also observed in the model plant species A. thaliana. However, this conserved response was not observed in A. thaliana plants that had mutations in their abscisic acid (ABA) signalling and biosynthesis pathways. RNA sequencing data revealed an array of biological processes and genes that were upregulated following the application of Inatreq, with many related to ABA, stomatal regulation, and a variety of other stress responses, providing targets for future research. The findings of this project highlight the amenability of Inatreq to a variety of crop protection strategies, as well as characterising its biostimulant-like activity. This research utilised a range of phenotyping technologies, as well as developing some bespoke tools, with a particular emphasis on low-cost phenotyping approaches with wider applicability.

Field beans are an up-and-coming crop in Irish agriculture, helping to reduce imports of feed protein and encouraging a home-grown source for cattle feed. Since the introduction of the protein grant in 2015 as part of the Common Agricultural Policy (CAP) greening scheme, the area of field beans sown in Ireland has increased rapidly. However, due to their unpredictable year on year variation in yield, field beans have not yet reached their full potential in Irish agriculture. A better understanding of their growth and development as well as management of the crop for full yield potential is essential to encourage growers to avail of the added benefits of having field beans in their crop rotations. This thesis outlines research which aimed to develop a better understanding of the agronomy and physiology of field beans in the temperate Irish climate, to gather information and create advice for Irish growers on the best way to grow and manage field beans. This was achieved through three years of field experiments from 2017-2019, where different sowing dates, seed rates and varieties were used to vary the canopy size. Through this canopy manipulation, the variation in leaf green area, pods per unit area and seeds per unit area was evaluated in order to identify the key components of yield in field beans. Throughout this research, several parameters were studied. This thesis outlines the results of this study on the effect of sowing date, seed rate and variety on the growth and development of the field bean crop in a temperate climate. The results of this study found that even though field beans show great variability in yield from year to year, with the correct sowing conditions and management, they have the potential to produce high yields in the Irish climate. Using a broad range of seed rates from 10 - 80 seeds per square metre over six sowing dates, the response of field bean yield to these factors could be thoroughly studied over three years. In 2017, yield in this study was found to be 6.2 t ha-1, which was close to the national average yield for field beans of 6.7 t ha-1 (Teagasc, 2018). Yield was found to be the lowest in 2018 when it dropped to 2.5 t ha-1 due to lower-than-average rainfall from pre-flowering to harvest. The October sowing date generally yielded highest for the winter sown treatments and February/March for the spring sown treatments, coinciding with the current recommendations for sowing field beans in Ireland by the Department of Agriculture, Food and Marine (DAFM). However, with the variation found in crop establishment over the three years of study, yield was examined and presented against plant populations instead of seed rate. The general trend showed that as plant populations increased, yield increased. This led to the study of the economic plant population in field beans for Ireland, which we believe to be the first to report. The economic plant population for the spring variety was between 24 - 38 plants per square metre and 13 plants per square metre for the winter variety. This study concluded that yield and profit will not improve by sowing at higher plant densities. Further study into the components of yield in field beans found a strong relationship between pod number and final yield. It was generally found that pod number closely related to the Green Area Index (GAI) of the crop during the pod development phase of growth, which led to the hypothesis that light interception during the pod development phase determined pod number and thereby yield. A supplementary experiment was carried out to support this, where shades were erected over the plots, reducing the intercepted radiation by c.60%. This found that when light was reduced during the reproductive phase, there was a 27% yield reduction, resulting from a 38% reduction in pod number. With green area strongly relating to pod number per square metre, it can be concluded that radiation intercepted during the reproductive phase is crucial for the determination of pod number which in turn is a driving factor in final yield of field beans. Crops like cereals and oilseeds have been studied to determine management strategies for fertilisers and spray treatments throughout the season. Field beans are a relatively new, up and coming crop in Irish agriculture and the knowledge behind field bean management in Ireland is being trialled. This study found that green area in field beans is strongly related to leaf fresh biomass. From this, we hypothesised that leaf fresh biomass can be used as a predictor of GAI and in turn be used by growers as a tool in canopy and overall crop management throughout the season. A model was created using the relationship between leaf green area and leaf fresh biomass, resulting in the equation y = 0.0021x - 0.0734. Using an independent field bean data set and the equation from the model, results showed a strong correlation between measured leaf green area and predicted leaf green area with an R2 = 0.92 and RMSE of 0.38. The greater understanding of yield components and the driver of final yield in field beans will lead to further studies in this area and a greater understanding of this potentially high yielding crop in temperate climates. Overall, the findings in this thesis are a foundation for further research in field beans and other protein crops in Irish agriculture.

White rust (WR) (caused by the oomycete Albugo candida) inflicts significant yield decline in brassica crops across the world. It is a particular problem in countries like India, where resource poor farmers cultivating oilseed mustard (Brassica juncea) suffer between 30-60% yield losses per year. Breeding for host resistance is the most effective and environmentally friendly way of protecting brassica crops from WR. Rapid evolution of the pathogen highlights the need to efficiently map multiple resistance genes for combined integration into cultivars. Here we present novel methods for achieving this, with an emphasis on directly mapping from undeveloped genebank populations. In this work, the application of Whole Genome Resequencing (WGS) and Bulked Segregant Analysis (BSA) proved to be highly effective for rapidly mapping sixteen major effect white rust resistance (WRR) QTLs across five geographically diverse Brassica rapa genebank populations, including a landrace and a wild species. This includes a QTL mapped on chromosome 6, containing a WRR allele that provides resistance to Donskaja-virulent UK race 2 isolate AcBjDC. WGS for all QTLs has been scrutinised, allowing identification of various polymorphic candidate WRR genes. WRR was also explored in the Brassica oleracea EBH527 x A12DH mapping population, where a previously fine-mapped ACA2 locus contains a recessive race non-specific resistance. A CRISPR-Cas9 knockout of the primary candidate (a GDSL Lipase) yielded no alteration to susceptibility and WGS of the two parents has since been used to identify other potentially causal mutations within the region. WGS-BSA was also applied here to map a dominant resistance locus in tight-linkage to ACA2 from segregating recombinant line EH177. Finally, Oxford Nanopore Technology long-read sequencing was used to produce high-quality genome assemblies for race 2 isolates AcBj12 and AcBjDC, augmented with Illumina reads. The AcBj12_ONT assembly provided a 30 % improvement in contiguity relative to previous efforts using PacBio data. Comparative genomics that included Donskaja-virulent isolate Ac2v was used to document allelic variation in "CCG" class effectors that provides a platform for future identification of the Avr elicitor. Collectively, methods presented here enhance rapid identification of loci and candidate genes for the benefit of global brassica production.

Germinating embryos release gibberellins (GAs), which act on aleurone cells to promote the expression of hydrolytic enzymes via the transcription factor (TF) GAMYB. GAs promote the degradation of DELLA proteins, which in the aleurone results in the upregulation of GAMYB expression. Although it is known that DELLAs negatively regulate GAMYB activity, the molecular mechanisms underlying this response are currently unclear. Recent studies have demonstrated that DELLAs do not contain a DNA-binding domain and they regulate transcription by acting as coactivators or corepressors of TFs. It was therefore hypothesised that the regulation of GAMYB by DELLA may be indirect, by working in a complex with other TF/TFs. A yeast two-hybrid (Y2H) screen of the wheat aleurone cDNA library revealed that wheat DELLA protein, RHT-1, interacts with different classes of TFs. Two TFs were selected for further analysis: INDETERMINATE DOMAIN 11 (TaIDD11) and ETHYLENE RESPONSE FACTOR 5 (TaERF5). The interactions between RHT-1 and TaIDD11 and TaERF5 were confirmed in Y2H assays and in planta. Reverse genetics approach was applied to understand the roles of identified TFs in the regulation of GA response. TaIDD11 was found to be a positive regulator of GA-mediated growth and floral transition, as the Taidd11 (triple knockout mutant) displayed reduced growth and delayed transition to flowering. The transcript levels of GA3ox, GA20ox and GID1b, the genes positively regulating GA biosynthesis and signalling, were enhanced in the mutant, which resulted in enhanced levels of bioactive GA1. The TaERF5 has a close paralogue in wheat (TaERF5a), which shows high level of conservation and is hypothesized to have redundant function. Genome editing using CRISPR/Cas9 was applied to generate sextuple Taerf5 Taerf5a mutant, and the Cas9-free T3 seeds are now awaiting phenotypic analysis. Together, this study identified a novel component of GA signalling that regulates GA-mediated growth and development, possibly via interaction with RHT-1.

Fusarium head blight (FHB) is a devastating fungal disease of barley and other small-grain cereals worldwide, caused by a complex of toxigenic Fusarium spp. and non-toxigenic Microdochium spp. This disease causes detrimental yield losses, reduces grain quality and leads to mycotoxin contamination of grain. Fusarium avenaceum, which is frequently isolated from small-grain cereals, causes FHB disease in the cooler climes of Northern and Central Europe. This is a species associated with significant production of enniatin (ENN A, A1, B and B1), moniliformin (MON), and occasionally, beauvericin (BEA) mycotoxins. Although no maximum levels of ENNs, BEA and MON have been legislated for until now, their toxic effects in combination with high contamination levels in food suggest that they may pose hazards to human health. The aim of this study was to determine whether UK isolates of F. avenaceum cause Fusarium seedling blight (FSB), Fusarium foot rot (FFR) and FHB in UK barley, and if so, how aggressively. A further aim was to ascertain the mycotoxin range and impact on quality and safety during the milling and malting processing of barley grain. New separation conditions of liquid chromatography with tandem mass spectrometry (LC-MS/MS) were developed to detect and quantify BEA, ENNs and MON in barley grain. The limit of detection (LOD) and limit of quantification (LOQ) for the mycotoxins ranged from 0.1-0.9 µg kg-1 for ENN A and MON and 2.0-4.0 µg kg-1 for ENN B1 and MON, respectively, with a relative standard deviation (RSD) of less than 10%. The most common mycotoxins found in 223 survey samples from commercially grown UK malting barley collected between 2007 and 2011 were ENN B, B1 and A1, in that order; however, BEA and ENN A were not detected. ENN B had the highest incidence of 100% in 2007 and the lowest incidence of 68.5% in 2011, with mean concentrations of 3072.9 and 1977.9 µg kg-1, respectively. MON was quantified only in samples from 2010 and 2011, with incidence rates of 10.1% and 15.5% and concentrations of 5.1-45.3 µg kg-1. There were five regions within the UK, South, East, Midlands and North of England and Scotland. Year and region had a significant interaction on ENN A1 and B1, but there was no significant interaction in ENN B. The incidence of ENN A1, B and B1 were higher average concentrations in East of England compared with other regions in the UK. In vivo and in vitro experiments were conducted as a series to determine the aggressiveness and mycotoxin profiles of UK isolates of F. avenaceum. The study used artificial inoculation with nine isolates of F. avenaceum on the barley varieties Moonshine and Quench. There was significant variation between F. avenaceum isolates in their ability to cause FSB and FHB diseases and mycotoxin production. Fa225, Fa40, Fa219 and Fa75 were found to be more aggressive in causing FSB and FHB diseases and more toxigenic because these isolates produced ENN A1, B and B1 under both in vitro and in vivo experimental conditions. Fa235 and Fa55 proved to be moderately aggressive, whereas Fa248, Fa210 and Fa74 produced the lowest FSB and FHB symptoms and the lowest levels of ENN A1, B and B1 concentrations in in vitro experiments, and they only produced ENN B and B1 under in vivo experimental conditions. ENN B had the greatest concentrations in inoculated barley heads, ranging from 690 to 7510 µg kg-1 in vivo, followed by ENN B1 and A1; however, BEA and ENN A were not detected, and not all isolates produced ENN A1. It is worth noting that the level of ENN B was significantly higher in vitro, ranging from 2030 to 81850 µg kg-1, followed by ENN B1 and A1; however, BEA and ENN A were not detected. The barley cv. Moonshine was more resistant and accumulated fewer mycotoxins than cv. Quench did. MON was not quantified in in vivo experiments; however, all isolates of F. avenaceum produced MON under in vitro experimental conditions. A field experiment was conducted to determine the severity of FHB caused by individual F. avenaceum isolates, the fate of mycotoxins during the milling and malting barley processes and the impact of individual isolates on the quality of malting barley. Disease assessments revealed a significant variation between the isolates of F. avenaceum in causing FR and FHB diseases. Isolates of F. avenaceum Fa40, Fa225, Fa219 and Fa75 showed more severe FR and FHB disease and were capable of producing ENNs A1, B and B1, but BEA and ENN A were not detected. Fa235 and Fa55 were moderately aggressive, whereas Fa248, Fa210 and Fa74 produced the lowest FR and FHB symptoms and the lowest levels of ENN B and B1 concentrations under field conditions. ENN A1, B and B1 ranged from 63.6 to 148.9, 20.5 to 245.8 and 63.6 to 148.9 µg kg-1, respectively, and the barley cv. Concerto was more resistant than cv. Propino, accumulating fewer mycotoxins. A significant positive relationship was found between the total amount of F. avenaceum DNA and the quantified mycotoxins. The yield quality, specific weight (SPW), thousand-grain weight (TGW) and germinative energy of barley were significantly reduced following inoculation with F. avenaceum isolates. Three inoculated samples by isolates of F. avenaceum were chosen to investigate the fate of ENNs during milling, bread making and malting barley processing. Analysis of the pilot mill fractions identified a significant difference between the proportions of ENN A1, B and B1 and between varieties. ENN A1, B and B1 were higher in bran fractions and lower in flour, which slightly higher in the barley cultivar cv. Propino. The final baking at 237 °C for 15 minutes resulted in a further decrease in ENN B, B1 and A1, ranging from 13.9% to 41.2% of their initial levels in the barley flour used as raw material. During malting barley processing, steeping removed 4.0%-37.0% of ENNs B, B1 and A1; however, ENNs were significantly increased during the period of germination. At the kilning stage, approximately 33.8%-77.7% of ENNs B, B1 and A1 were reduced after the rootlets were discarded. The barley cv. Concerto and cv. Propino were micro-malted and subjected to malt and wort analysis of quality parameters. Infection of barley grain by F. avenaceum can be correlated with increased friability and wort colour, lower amylase activity, a greater proportion of FAN and decreased wort viscosity. Thus, the quality of malt production, which is used in the brewing industry, could be reduced. Current research findings suggest that UK isolates of F. avenaceum are significant seedling blight, FR and FHB disease-causing fungi of commercial UK barley varieties and are capable of reducing yield and malt quality. Hence, research efforts should be pursued to provide tools to improve strategies aimed at controlling the infection of F. avenaceum, subsequently reducing levels of this class of mycotoxins in barley grain and their products.

Self-incompatibility (SI), a type of intraspecific reproductive barrier occurs widely in flowering plants and helps to avoid inbreeding and protects the genetic diversity of a population. When the pollen lands on a self-pistil, SI will prevent fertilization; when the pollen lands on the pistil of an unrelated plant, fertilization will not be affected. SI consists of two types: Sporophytic SI (SSI) and gametophytic SI (GSI). In GSI it is the haploid genotype of the pollen itself that controls the pollen phenotype. Transgenic studies in Petunia have shown that the pistil phenotype is determined by a stylar ribonuclease (S-RNase). In the fertilization process, Slinked F-box genes/SLFs that are expressed in pollen work together with S-RNases to determine the outcome of a pollination. Recently up to 20 SLF genes have been reported at the S-locus in Petunia, but the exact role of individual SLFs in controlling the phenotype is still not clear. Part of this project aims to investigate SLF expression between two closely linked varieties of Petunia hybrida, which have different phenotypes. A combination of RT-PCR and qRT-PCR using specific primers were used to determine the expression patterns of individual SLF genes in these two varieties. The results of RT-PCR and qRT-PCR indicate that all SLFs express in these two varieties, and most SLFs share significant differences in the expression levels comparison between these two closely linked varieties of Petunia hybrida. The partial DNA sequences of SLFs in these two varieties are proved that is identical. Therefore, the different expression level of SLFs might is the cause of the different SI between these two closely linked varieties of Petunia hybrida. The finding of this part of this project might be able to provide some evidence in the evolution theory of SI plants. On the other hand, there are only two SLFs expression analysis papers been published to date from Kao et al. (2004) and Hua et al. (2007), which indicated SLFs express in pollen tube, pollen and anther of Petunia by RNA gel blot analysis and RT-PCR, but there is no paper to show the expression pattern of SLFs using GUS or GFP analysis. This project also aims to explore the promoter analysis of SLF genes that have recently been identified as part of a genome sequencing effort of Petunia inflata. The genomic sequence data were used to characterize the promoter regions to identify shared pollen promoter elements such as those identified for the gene LAT52 (a tomato pollen gene). Promoter fragments of three selected SLFs were cloned and used to prepare SLF promoter:GUS fusion constructs. Agrobacterium-based transformation was performed to transfer these constructs into Petunia hybrida. The GUS assay was used to test the SLF expression pattern in Petunia. The result of GUS analysis indicates SLF3 is expressed in pollen of stamens, which is consistent with the findings from Kao et al. (2004) and Hua et al. (2007). This part also provides a good attempt in other transformation experiments to use the SLF promoter of Petunia inflata. In addition, the results of both these two parts of this project support each other: the expression of SLFs in Petunia shows an exponential growth during the maturation of pollen.

Phytic acid (PA) is the main source of phosphorus storage in plants. Since the molecule has a negative charge, it creates complexes with important minerals such as Cu, Zn, Co, Mn, Mg, Fe and Ca. It is therefore regarded as an antinutrient because monogastric animals do not have the necessary enzymes to break the bonds. This leads to major issues such as micronutrient deficiencies in the population, all the unused phosphorus is excreted and eventually reaches water bodies causing eutrophication. Up to 60-85 % of P from soil is stored as PA in grains, hence all this P is removed from the soil at harvest and this removed P has a cost, which has been estimated in billions. Hence, even small reductions in the PA concentrations could represent more efficient and nutritious crops as well as important money savings. In this study we analysed wheat samples grown in a hydroponic system and evaluated the effect of P and Zn treatments on its concentration in leaf and grain (Chapter 2). Treatments had significant effect over PA and other mineral concentrations in grain and leaf samples. We observed significant relationships between leaf and grain PA and mineral concentrations indicating that some predictions could be made from a single and simple analysis in leaves. In Chapters 3 and 4 we describe a huge variability in PA concentrations in diverse genotypes and environments. We found significant differences between the genotypes, environments and their interactions. Moreover, phytate to mineral molar ratios were calculated and the potential impact over the bioavailability of Ca, Fe and Zn is discussed. The results obtained here highlight the importance of PA determination as an important trait to be looked at when breeding or searching for mineral enhanced varieties. As we observed, some genotypes with high concentrations of Fe and Zn had also high concentrations of PA. High PA ratios will inevitably affect the bioavailability of Fe and Zn. A great amount of work has been done over the past years, but there are still gaps of knowledge to be filled, such as the transport and loading of P into seeds, the genetic control of P translocation from vegetative tissues to seed, the heritability of P and PA traits, among others. This work aims to set the basis for further and more specialized studies looking into developing new low phytate varieties.

Cereal crops are highly vulnerable to heat stress. Pollen development is particularly susceptible to high temperatures, with prolonged periods of exposure resulting in male sterility and yield loss. With global temperatures set to rise, yield losses are predicted to increase, warranting further investigation into the role of phytohormones in controlling wheat reproductive development and responses to abiotic stress. Various phytohormones have important roles in regulating many aspects of plant development, in particular pollen development and are also implicated in regulating heat stress responses. This project aimed to investigate the role of phytohormones in wheat development and the heat stress response. A stable heat stress assay was initially developed specific for hexaploid wheat var. Cadenza. It was found that conditions of 4 days at 33/26°C d/n 80% humidity was enough to induce a significant loss of grain set when the stress was applied at meiosis or unicellular pollen stages. Utilising this assay, an RNAseq and global hormone analysis was performed on accurately staged anthers after either control or heat stress conditions. The results reveal the complex interplay of phytohormones in controlling pollen development, the changes that occur in response to heat treatment and the genes underlying these changes in accumulation. The reverse genetics approach of TILLING was used to identify gain-of-function mutants which are insensitive to auxin and ethylene in Cadenza. Auxin-insensitive Aux/IAA mutants showed partial male sterility and increased sensitivity to heat stress, in addition to striking defects in lateral roots, root hairs and agravitropism. This project defines an optimised heat stress assay for Cadenza which can be applied to investigating the heat stress response using reverse genetics or endogenous application of hormones. It also demonstrates an application of TILLING as a method to dissect complex signalling pathways and determine their role in development and abiotic stress tolerance of hexaploid wheat.

The global population is predicted to reach 9.1 billion in 2050 and the current rate of genetic progress in wheat yields is not sufficient to meet future demand. Nitrogen fertiliser is a key determinant of yield and represents a significant cost for the grower and has environmental impacts through nitrate leaching and N2O emissions. Therefore, there is need to develop wheat cultivars with improved Nitrogen-Use Efficiency (NUE; grain dry matter yield per unit of N availability). NUE is divided into two components, N-uptake efficiency, and N-utilization efficiency. Developing cultivars which have higher grain yield but use N efficiently may allow farmers to maximise income and minimise the pollution risk by reducing N fertilizer application. Due to wheat selection in plant breeding for high grain yield under high N fertility conditions, genetic diversity of modern wheat for NUE traits is reduced. Therefore, exploration for novel sources of genetic variation for NUE is needed. Landrace-derived lines which provide novel sources of genes could be used by plant breeders to improve NUE of modern bread wheat. The overall objective of the present project is to investigate favorable physiological traits for N-use efficiency in wheat landrace-derived lines and their genetic regulation. Two field experiments at the Bunny field station, two glasshouse experiments and one hydroponic experiment were conducted at the University of Nottingham. The current work can be divided into four main components. (i) quantifying the genetic variation for above-ground biomass, grain yield, NUE and its components in landrace-derived lines and modern bread wheat cultivar Paragon; (ii) Identifying novel physiological traits determining genetic variation in biomass, NUE and NUE components; (iii) exploration of root system architectural traits for improved N-Uptake efficiency (NUpE; above-ground N uptake / N available) of wheat landrace-derived lines compared to modern wheat; and (iv) identifying marker-trait association (MTAs) for the NUE traits. The experimental programme utilized a Nested Associated Mapping population of 286 genotypes comprising landrace-derived lines plus the elite bread wheat parent Paragon. These genotypes were assessed for biomass, grain yield, NUE traits and physiological traits under a moderate N stress condition in the field in two seasons. In subsets of germplasm, NUE traits including leaf photosynthesis traits were assessed in 14 landrace-derived lines and Paragon under HN and LN conditions in two glasshouse experiments; and root seedling architecture traits were assessed in 30 landrace-derived lines and Paragon under HN and LN under controlled-environment hydroponic conditions. Significant variation for most of the traits was identified among wheat genotypes where modern bread wheat Paragon had higher grain yield and generally shorter plant height compared to landrace-derived lines. Higher grain yield of modern elite bread wheat Paragon was due to improved harvest index compared to the landrace-derived lines. Lower NUE in landraces was therefore mainly due to lower harvest index as expected because the landraces were not bred for grain yield potential. Three lines (PxW396-62, PxW349-31 and PxCIM47-113) had higher NUpE than Paragon under moderate N stress conditions. In the glasshouse experiments, two lines (PxW223-89 and ParxPfau-59) under HN showed significantly later onset of flag-leaf senescence than Paragon associated with N-utilization efficiency (NUtE; grain yield DM/above-ground N uptake) and one line (PxW420-32) under LN conditions. However, under both, HN and LN conditions, generally, senescence traits were not well correlated with each of yield and biomass in the glasshouse experiments. This was also the case in the field experiments. These results indicated the grain yield of the NAM lines was mainly limited by sink rather than source in the experiments in the present study. In the glasshouse experiments, NUtE of modern wheat Paragon was higher than most landrace-derived lines mainly related to harvest index. Generally, NUpE explained more of the genetic variation in NUE than NUtE in the project experiments. Significant variation in root system architecture traits was identified in landrace-derived lines compared to Paragon, with landrace-derived lines showing higher expression for seminal root number, average primary root tip angle, total primary root length, average lateral root length and seminal root angle under N limitation compared to Paragon. A trend for a correlation was found between primary root tip angle and N-uptake efficiency in the field experiments (r=0.36, P=0.054). There was also a trend for a positive correlation between average primary root length and each of grain yield and NUE (r=0.33, P=0.07). Total lateral root length was also positively correlated with biomass (r=0.38, P=0.03) and there was a trend for a positive association between average lateral root length and biomass (r=0.33, P=0.07). Present results suggested that seedling root architectural traits could potentially be used as selection criteria for selecting genotypes for higher NUpE at maturity. Genome-Wide Association Study (GWAS) was carried out on the phenotypic data in the field experiments for the NAM population. In 2017, a total of 127 MTAs, including co-located MTAs, with a - log10 P-value of greater 4 were detected which explained from 5 to 15 % of the phenotypic variation. Major marker-trait associations (MTAs) were identified for anthesis date/ harvest index on chr 1A, grains m-2/1,000 grain weight on each of chr 1D, 2A, 2D and 5A, NUE/grains m-2 on chr 2B, NUE/AD/NDVI senescence rate/grain yield on chr 5A and AD/ NDVI senescence rate on chr 5A. In 2018, a total of 52 MTAs, including co-located MTAs, with a - log10 P-value of greater 4 were detected which explained from 4 to 10 % of the phenotypic variation. Major MTAs were identified for NDVI at anthesis/NDVI senescence rate on chr 2A and grain yield on chr 3B. Overall, the strongest co-localized genomic region was identified on chromosome 5A at 503137755 bp associated with four traits (grain yield, anthesis date, NUE and NDVI senescence rate). The genomic co-location of loci 503137755 bp with these four traits suggests a pleotropic effect of the 5A Vrn-A1 gene underlying these traits. A promising novel MTA for grain yield and NUE was identified on chr 3B. To our knowledge, the present work is the first published study in bread wheat that reports GWAS results on N-use efficiency in wheat crop using landrace-derived lines.

Climate change threatens crop production globally and in Europe hotter and drier summers are predicted which will result in a reduction in crop yields due to increasingly limited water availability. A sufficient supply of water is crucial to maximising crop yield because dry matter accumulation is directly proportional to water use in many environments, as solar radiation drives both photosynthesis and transpiration. Water use efficiency (WUE) has been studied in many of the major crop species including rice, wheat and maize, as they are grown in a wide range of climates, including those with poor water availability. From this research more WUE varieties of wheat have been developed to enable production in areas where water is limiting. This highlights that understanding crop WUE is a useful endeavour and that research should be undertaken in less studied crop species. One such species is sugar beet which is usually either irrigated or grown in climates with sufficient water availability. As water availability becomes increasingly limited it would be beneficial to understand how sugar beet uses water to inform crop management and identify traits for breeders linked to greater WUE to make the crop more resilient. This thesis explores WUE in sugar beet from the leaf to the crop level in controlled environment room and polytunnel experiments to understand how the plant uses water. The three studies presented in this thesis have enabled sugar beet WUE to be characterised and have highlighted the anisohydric behaviour of the species. The first controlled environment study showed that sugar beet has fast stomatal responses compared to spinach which resulted in a similar level of intrinsic water use efficiency (WUEi), despite reaching higher rates of stomatal conductance (gs). The high rates of gs could be linked to the transient wilting of the crop in the field and the concurrently high rates of CO2 uptake and assimilation suggests wilting may not be detrimental to yield. Scaling up from the leaf level to the crop level, sugar beet were grown in large boxes in a polytunnel and exposed to four different irrigation regimes. Reduced water availability increased WUE (except in cases of extreme water limitation) and no acclimation (defined as permanent changes in physiology opposed to short term changes such as reduced leaf gas exchange) to water deficit was evident as the plants responded similarly to repeated drought. Full recovery was observed after drought and the sugar beet showed an ability to continue to photosynthesise, even under severe water deficit, which is likely attributed to its anisohydric characteristics. The most significant finding of the study was that varietal differences in WUEi and associated traits were evident, including a lower stomatal density, which could possibly be linked to canopy architecture. Following on from these studies, diurnal WUEi in sugar beet was characterised to identify when the crop is most and least WUE during the day, and if water deficit affected this response. It was shown that WUEi declines later in the day as light, and therefore assimilation, declines faster than gs. Water deficit increased WUEi and decreased the magnitude of the diurnal change in WUEi, as gs and A were reduced. The variety with greater WUEi in the second study also had higher WUEi in this study, but this did not lead to a greater dry matter WUE (WUEDM) in any of the experiments which may be due to small biomass sample sizes. Diurnal fluctuations in leaf water content were also evident, although the plants did not wilt due to diurnal changes but did under water deficit, however the diurnal changes in temperature and VPD were not as great as those observed in the field due to limitations of the growth chamber. Overall, the results show that sugar beet is a highly resilient crop species which is partly attributed to its anisohydric characteristics. Additionally, the difference in WUEi between commercial sugar beet varieties shows greater WUEi can be selected for without detriment to yield, as shown in the polytunnel experiment, and should be explored by breeders to develop varieties which will yield consistently well for growers as the climate changes.