Striga hermonthica (Scrophulariaceae: Rhinanthoideae) is aparasitic weed on sorghum and millet in Africa. It has not been possible, so far, to breed varieties of these crops immune to striga. Variation in many floral and vegetative features and in seed coat ornamentation indicates a diversity of genotypes within populations of hermonthica. The colour and structure of hermonthica flowers and their production of nectar are adaptations for cross-pollination by "long-tongued" insects like butterflies and moths; the floral biology of the species promotes outbreeding. Evidence for a gametophytic system of self-incompatibility was obtained for plants from Sudan using fluorescence microscopy to study the behaviour of pollen on stigmas. Plants grown from seed samples of hermonthica populations from Ethiopia, Sudan, Nigeria,Niger, Upper Volta, Mali, Ghana and Ghambia were tested and were also found to be self-incompatible. Crosses made between plants from different countries and from different host species were found to be compatible and set seed. Because there are no physiological barriers to gene exchange, variability is maintained throughout the range of the species by obligate outbreeding. There is much variation in the response of a host variety when tested, not only against different samples of hermonthica seed from different localities, but between repetitions using the same seed sample. This variability occurs in controlled conditions and in sick plots, as well as in the field. It indicates that bulk samples of striga seed are also variable for genes determining the host-parasite relationship. This brings into question the effectiveness of the standard techniques used for screening crops for resistance to the parasite. Evidence for the breakdown of resistance to striga was obtained from field observations in Sudan.

In the field crops are subject to a wide variety of biotic and abiotic stresses. In order to manage crop protection effectively it is important that we understand not only the way plants respond to these stresses, but the way in which these responses interact. High levels of fertilisers and pesticides are often applied to maintain soil nutritional status and prevent disease in modern intensive farming systems. Potassium (K) is an essential element for plant growth and development, and is required for a wide variety of processes within the plant. These processes can be broadly divided into biophysical processes such as stomatal opening and cell extension and biochemical processes such as protein synthesis and enzyme activation. K starvation has been shown to lead to increased levels of the stress hormone jasmonate (JA) and related compounds in Arabidopsis thaliana plants which in turn modulates the plant’s defence against herbivorous insects and probably other pests or pathogens (Armengaud et al., 2004; Troufflard et al., 2010). In order for these results to be applicable to agriculture it is important to assess whether crop plants respond to K in a similar manner as the model plant. In this project the effect of K-deficiency on growth, metabolite concentrations, transcript levels and pathogen susceptibility of barley were investigated. Plants were grown in full-nutrient (control) or K-free hydroponic culture. The physiological, biochemical and transcriptional effects of K-deprivation were accessed over a time course of 20 days. Roots and shoots from plants grown in K-free nutrient solution had significantly lower K concentration than those grown in the control solution after 3 and 6 days respectively. A significant reduction in growth was seen as early as 6 days after K withdrawal. K-starvation led to a slight decrease in nitrogen metabolism, while hexose sugars strongly accumulated. By day 9 a significant increase in the expression of JA marker genes was seen in plants grown in K-free nutrient solution. Thus, despite possible differences in downstream events an induction of JA biosynthesis in response to K-deficiency occurs in both Arabidopsis and barley. Detached leaf segments were used to assess the effect of K-deficiency on infection of barley by two fungal pathogens with different strategies for nutrient acquisition. K-deficient barley plants were less susceptible to the biotroph Blumeria graminis f. f. sp. hordei (powdery mildew) and more susceptible to the hemi-biotroph Rhynchosporium secalis. Treatment of detached leaves with methyl-jasmonate (Me-JA) also led to less B. graminis infection, but had no effect on the R. secalis infection, indicating that JA increase in response to K-deficiency influences B. graminis but not R. secalis infection. The study therefore provides strong evidence that the effect of K-deficiency on pathogen susceptibility is determined by the JA-sensitivity of the pathogen.

The potential for viruses to be causing the plateau in the yield of UK wheat (Triticum aestivum) was investigated. Mechanical inoculation of Cynosurus mottle virus to wheat cv. Scout and cv. Gladiator caused 83% and 58% reduction in the number of grains produced, highlighting the potential of viruses to cause disease and yield loss. Viruses historically detected in cereals in the UK were not found to be prevalent following real time reverse transcriptase polymerase chain reaction testing of 1,356 UK wheat samples from 2009-2012 using eleven assasys developed in the project. This included an assay for Cynosurus mottle virus, which was based on its complete genome sequence which was obtained for the first time in this project. Viruses detected were Barley yellow dwarf virus-MAV (6 samples) (BYDV-MAV), Barley yellow dwarf virus-PAV (6 samples) (BYDV-PAV) and Soil-borne cereal mosaic virus (12 samples) (SBCMV). There was a higher prevalence of viruses in the south, thought to be due to warmer temperatures which benefitted insect vectors and the molecular processes of infection. Viruses were most commonly detected in the variety JB Diego, perhaps because this variety has no known resistance to viruses. The low prevalence of known viruses could also have been because they were outcompeted or replaced by previously unknown ones. Next generation sequencing was used to test 120 samples from an organic site, including wheat, weeds and insects, to search for novel viruses. Testing of twelve storage regimes for insect traps using BYDV-PAV infected Sitobion avenae for recovery of PCR amplifiable RNA using 18S rRNA and BYDV-PAV assays found that 0.5 M EDTA was the most successful regime which was therefore used in the collection of samples for sequencing. Known viruses such as BYDV-PAV were detected along with some additional potentially novel viruses (eight possibly novel viruses or strains of viruses with four in wheat). One such virus was apparently present in 25% of all wheat samples tested, making it potentially very significant. This could be important for unlocking the yield potential of wheat because it could be a cryptic virus which is highly prevalent. In order to control the spread of viruses their methods of transmission must be understood, therefore testing of seeds and resulting plants from Cynosurus mottle virus infected material was done. Tests did not detect the virus, therefore it was concluded that seed transmission does not occur. However, further tests are required. In conclusion this study indicates that known viruses are not currently a major problem for UK winter wheat. However, novel viruses that are a problem may be detected in the future perhaps by next generation sequencing. Additonal viruses from abroad would add to the threat. The impact of all viruses in wheat may be greater in the future due to climate change.

Plants growing in arid regions often suffer from high shoot temperatures, low shoot water concentrations, low turgor pressures, and high salinity in the rhizosphere. To investigate which traits confer tolerance on plants in these areas a range of genotypes was studied. These included Local (an uncharacterized landrace grown in south western Pakistan), Soorab-96 and Awaran-2002 (both elite cultivars developed by ICARDA and commercially grown in Pakistan), and Optic (an elite European cultivar). Measurements on germination, growth, and yield suggested that landrace Local is significantly least affected by high salinity (p<0.05) compared with lines Soorab-96, Awaran-2002 and Optic. Further investigations on ion profiling established that landrace Local could maintain low Na+/K+ ratios. This appeared to arise from Local’s ability to prevent Na+ accumulation in the roots and shoots by enhanced exclusion or efflux or both. Probably this unique characteristic of landrace Local helped in maintaining its photosynthetic efficiency, plant water status, and stomatal conductance, which resulted in its better performance and survival in high salinity. There was no evidence that high tissue solute concentrations, high proline levels or life cycle strategies played a role in salt stress tolerance. In addition, there was no evidence that osmotic stress was responsible for the observed suppression of growth in any of the genotypes. The main conclusion from this study is that for glycophytes (which do not complete a full life cycle above 100 mM NaCl; this includes all of the world’s major crops), it is the ionic component of salinity stress that impairs growth processes and yield, not the osmotic component. Further research on salinity stress in crops should focus on understanding the processes that control ionic balance rather than osmoregulation. There is some evidence that long term exposure of plants in the preceding generations to moderately high salt concentrations (e.g. 100 mM NaCl) improves barley halotolerance in succeeding generations, i.e. halotolerance has a transgenerational, epigenetic basis, but there was also evidence that the improved halotolerance in the Local genotype was partly genetic. In another series of experiments the importance of short periods of high leaf temperatures (Tleaf) on photosynthetic efficiency of barley genotypes Local, Optic, and Soorab-96 was investigated. In all three genotypes light saturated carbon dioxide assimilation rates (Asat) and the carboxylation coefficients (CO2, a measure of the efficiency of CO2 fixation) in the fourth fully expanded leaves were equally suppressed to approximately 20 % of their pre-treatment levels immediately after a short period of heat stress (Tleaf > 40.0 ± 0.5 °C for 20 minutes). Parallel measurements using a range of techniques confirmed that the suppression of Asat and CO2 was not attributable to changes in the light harvesting capacity (leaf absorptance and chla excitation spectra), maximum quantum efficiency of PSII (PSII, Fv/Fm), and to stomatal conductance (gs). It is unlikely that the suppression arose from damage to the electron transport chain¸ or to the capacity to develop or maintain non-photochemical quenching (NPQ, which is dependent on the transthylakoid pH), but these possibilities cannot be dismissed. LC-MS and enzymic analysis of leaf metabolite levels showed that the pools of metabolites feeding into RuBisCO are not affected by heat stress whilst those of the metabolites flowing away from RuBisCO were significantly depleted. The implication is that short periods of heat stress severely impairs RuBisCO, RuBisCO Activase, or processes close to the carboxylation step. Five days after heat stress Asat and CO2 had significantly recovered to approximately 40 % (p<0.05) of their pre-stress levels in landrace Local, but no significant recovery was observed in any of the elite lines including those distributed by ICARDA for arid land production. These findings provide evidence that thermal damage may play a significant role in yield suppressions in arid regions and that there is a genetic basis for thermotolerance in barley.

Rice (Oryza sativa L.) provides up to 50% of the total calories consumed in countries such as India, Madagascar and Nigeria. As a crop, rice can require significant fertiliser inputs to maintain the required yields. Additionally, climate change has increased the need for rice varieties with improved drought resistance, tolerance to pests and more efficient acquisition of nutrients from soil. One major fertiliser input for rice is phosphate; reducing phosphorus (P) fertiliser use would have environmental and economic implications. Root traits linked to P acquisition in crops include shallow root angle, lateral root proliferation and increases in root hair length and density. Two T-DNA knockout alleles with reduced gravitropic response, Osaux1-1 and Osaux1-2, were used to investigate the influence of shallow root angle on P uptake. OsAUX1 is a rice ortholog for the Arabidopsis thaliana gene AUX1, which controls lateral root growth and gravitropic response. The wildtype and mutant rice plants were grown in soil and non-destructively imaged using X-ray micro Computed Tomography (X-ray CT). In Chapter Three, visualisation of rice roots in soil using X-ray CT was optimised by determining the ideal soil moisture content that would produce the best images. Water in soils has a similar X- ray attenuation density to that of plant roots and can influence segmentation of roots from soil in X-ray CT images. It was found that soil at nominal field capacity (ca. 3 days of drainage) produced the best contrast between soil fractions (organic matter, minerals and pore space) and root material. In Chapter Four, the impact of X-ray dose on root growth was quantified because the experimental design included repeated scanning of the same sample (Chapter Five). It was found that even under repeated scanning, the X-ray doses involved in this work (ca. 15 Gy per sample) did not significantly affect the root architecture and overall plant growth in rice cultivars used. In Chapter Five, Osaux1-1 and Osaux1-2 retained the agravitropic phenotype that was observed on agar-based systems when plants were grown in loamy sand soil. However, when subject to various soil P concentrations and distributions (Chapter Six), Osaux1-1 had similar gravitropic response and P uptake as wildtype. It was unclear what role gravitropism and topsoil foraging played in P uptake for these rice cultivars, if any. OsAUX1 could be linked to P uptake as well as responses to soil P concentration and distribution. Under uniformly low soil P wildtype had a shallower root system distribution than Osaux1-1. Of most interest were the results when sufficient soil P was sequestered to the top 4 cm of the soil column and low P was maintained in the bottom 6 cm. Under these conditions, wildtype took up more overall P, had almost twice the biomass, twice the total root length and twice the surface area when compared to Osaux1-1. This provides evidence that OsAUX1 can be linked to adaptation to P stress and distribution of P in soil through control of fine root characteristics and not necessarily its impact on gravitropic response. Chapter Seven describes the investigation into the impact of OsAUX1 on sub-architectural effects of the root system that could influence P uptake. It was determined that OsAUX1 was involved in root hair density and elongation under varying P availability for agar grown plants. In comparison to wildtype, Osaux1-1 had significant variation in root hair phenotype that seemed unrelated to a P stress response. In flooded environments, root hairs influence the potential for root:soil contact that is integral to P uptake in rice paddies which have reduced soil conditions and mass water flow that can transport plant available soluble P. This reinforces the potential for an interaction between OsAUX1 and P uptake in paddy rice.

A three-year study on the practice of ratooning of sorghum was conducted in Eastern Kenya (1999 to 2002), with emphasis on the stem borer (Chilo partellus) and covered kernel smut (Sporisorium sorghi Ehrenberg Link). Ratooning is the practice of stimulating tillering by cutting the old straw after harvest (Doggett, 1988). A six season on-station experiment in Machakos District showed the practice of ratooning short duration sorghum increased the reliability and yields in comparison to a direct sown with yield ranges of 1630-1778kg/ha and 0-148kg/ha, respectively. The higher number of heads and stems per unit area meant the ratooned crop had higher level of stem borers per unit area than the direct sown crop and when infected with covered kernel smut was a greater source of inoculum. Unlike the incidence of CKS, the number of stem borers had little correlation with the numbers in the previous season’s crop; there was no upward trend to the number of stem borers per stem during the experiment suggesting factors other than the presence of a sorghum crop have a stronger influence on the population. Yield loss was an interaction between cultivar*incidence of stem borers * stage of infestation * rain quantity and distribution, but rain was the most important factor. An on-station trial in Kitui (2001-2) found the ratooned crop outperformed the direct sown crop in yield by a factor of three and non-cutting of stems produced a similar yield to cutting back stems after harvest. The different ‘ratoon’ methods did not significantly affect the incidence of covered kernel smut or level of stem borers. On-farm trials in Mwingi District (2000-2) showed that short duration sorghum ratooned outperformed direct sown sorghum. The timing of the cutting back of the stems had an effect on plant survival and yield; cutting back stems at harvest produced higher yields than cutting the stems at the on-set of rains, however cutting the stems at the onset of rains increased plant survival when the stems were dry at harvest. A decision tree was produced outlining the decisions a farmer needs to make when deciding whether or not to practice ratooning. Four factors were identified as important for varieties to perform well under the practice of ratooning: drought tolerance, stem strength, non-senescence and the ability to produce tillers during growth stage 3.

Fusarium head blight (FHB) is a devastating fungal disease of wheat and other small grain cereals worldwide caused by a complex of toxigenic Fusarium spp. and non-toxigenic Microdochium spp. Infection leads to a reduction of grain yield, loss of grain quality and the production of harmful mycotoxins. Control methods for FHB include both cultural and chemical strategies, however the development of cultivars with improved FHB resistance is considered as the most sustainable method for controlling the impact of this disease. Resistance to FHB is a polygenic trait and can be improved by stacking multiple resistance genes together, however there are currently no highly FHB resistant genotypes with acceptable agronomic characteristics available, therefore passive disease resistance can potentially make significant contributions to improved FHB resistance. The aim of this study was to identify novel physiological traits in wheat conferring passive resistance to FHB using ground inoculated field experiments to enable disease escape mechanisms to be expressed, and spray inoculated glasshouse experiments to test if the identified traits were associated with genetic resistance. The most consistent traits relating to FHB were flag leaf length, plant height and awn length. Since these relationships were present in both field and glasshouse experiments, they are likely caused by a genetic linkage or pleiotropy, with genes conferring FHB resistance or susceptibility. Remaining leaf area was less consistently related to FHB, however, since canopy leaf area showed a positive relationship with the development of FHB in ground inoculated field experiments, there is a basis to support the role of reduced canopy leaf area as conferring passive resistance to FHB. In general, relationships were poor between visual FHB symptoms and both pathogen DNA and grain mycotoxin contamination. This was theorised to be due to the use of a mixed species inoculation which introduced antagonism between FHB species and which included more than one producer of several mycotoxins quantified. Therefore the use of visual FHB assessments under mixed species inoculation is concluded to be a poor indicator of both pathogen infection and mycotoxin contamination.

A substantial increase in wheat yield is needed for global food security. This requires a comprehensive understanding of the physiological and genetic basis of yield determination. The present study aimed to dissect yield physiologically and genetically in a recombinant inbred line mapping population derived from bread wheat × spelt. A total of 201 traits were investigated in the field and glasshouse across three years, and these traits formed five themes: genetic variation in yield and yield components, and the usefulness of spelt as a genetic resource; tillering dynamics; biomass accumulation; flowering time and subsequent leaf senescence; and grain filling processes. Large genetic variation in all traits was found, and spelt showed many desirable traits and alleles independent of low threshability, so it can be used to broaden genetic diversity for yield improvement in bread wheat, while maintaining the free-threshing habit. Quantitative trait loci for tiller production and survival were identified, which were also affected by light environment under the canopy: low red:far red ratio (R:FR) led to early tillering cessation, few total shoots, high infertile shoot number and shoot abortion, probably resulting from an assimilate shortage due to early and enhanced stem growth induced by low R:FR. More fertile tillers normally contributed to plant yield and grain number, but reduced individual grain weight, partly because of smaller carpels and fewer stem water soluble carbohydrates at anthesis. In addition, preanthesis biomass accumulation increased yield and yield components. For grain weight, slightly early anthesis and delayed but fast leaf senescence were associated with larger grains. Carpel size at anthesis, grain dry matter and water accumulation, as well as grain morphological expansion, determined final grain weight, because of pleiotropy or tight gene linkages. These findings provide deeper insight into yield determination in wheat, and facilitate trait-based physiological and molecular breeding.

Modern bread wheat (Triticum aestivum) initially derived from wild progenitors which underwent hybridisation and domestication events. It is hypothesised that modern plant breeding has reduced the genetic variation among modern cultivars (Sparkes, 2010). Ancient wheat species form a conduit between wild ancient wheat and cultivated Triticum species, and may harbour the genetic variation required to supplement the modern bread wheat gene pool. The current work investigated a range of morphological and physiological aspects of several ancient species including several representatives of spelt, emmer and einkorn. These were compared to modern bread wheat in two field and three glasshouse experiments with the aim to investigate their resource use efficiency, where radiation use and water use formed the crux. The main components of the current work relate to 1) canopy interception characteristics 2) leaf photosynthetic capabilities and 3) water use. Spelt genotypes demonstrated increased WUE and green area longevity compared with modern bread wheat. Emmer displayed increased WUE, assessed on three scales using instantaneous transpiration efficiency (ITE), biomass to water uptake ratios, and carbon isotope discrimination (Δ13C). In addition, the mechanisms whereby emmer, einkorn and spelt maintained ITE appeared to differ. Emmer was observed to increase photosynthetic rates, whereas spelt maintained low transpiration as a result of low stomatal conductance. Einkorn however, maintained ITE through an intermediate of both of these mechanisms. This was further supported by species differences for maximum photosynthetic rates (Asat) which, for emmer and einkorn, were comparable with modern bread wheat. Investigation of WUE through Δ13C and biomass production to water uptake ratios ranked species similarly, showing emmer and spelt to have superior WUE during grain filling. Additionally, spelt was observed to produce biomass comparable to modern bread wheat, thought to be due to enhanced RUE (observed in one field trial) or increased green area longevity rather than increased assimilation capability. In field experiments, biomass production and light interception was relatively high for einkorn species, however this was believed to derive from excessive tiller production due to poor emergence. Overall, ancient species did partition a larger proportion of assimilates toward tillers. Modern bread wheat produced fewer tillers, but directed more biomass towards the ear, and therefore had greater harvest indices (HI) compared to all ancient species. Despite this broad analysis, further investigation of the mechanisms responsible for these traits is required. This research therefore indicates that there is sufficient variation for traits, which could be used to improve radiation and water use efficiency, and therefore warrants further exploration. With further investigation, resource capture and utilisation efficiency, and the morphological traits that confer these advantages in these genotypes, genetic markers could be identified with the aim to introduce valuable traits for the production of novel modern bread wheat varieties. The differences observed between these ancient wheat species and modern bread wheat provide an opportunity through which modern wheat gene pools may be improved to stabilise yields, particularly in sub-optimal environmental conditions, thus increasing biomass production per unit resource, thereby enhancing the productivity and the efficiency of crop systems.

Studies were undertaken to investigate the potential for using sorghum bran from a traditional wet-milling process as a raw material for the fermentative production of value-added products, namely ethanol and itaconic acid. This was deemed of importance because renewable ethanol sources are required to replace environmentally unfriendly fossil-based fuels, while renewable itaconic acid could replace fossil-based industrial monomers if an economically viable source can be found. Emphasis was placed on optimising both yields (g/l) and substrate conversion, as a function of the theoretical maximum possible, for both compounds. The compositions of sorghum white bran (WB) and red bran (RB) were first elucidated to determine their suitability for downstream fermentation uses. Results revealed that the brans appeared to contain adequate components for biomass growth, with approximate carbohydrate, protein, lipid and ash contents of 69 %, 16 %, 3 %, 2 % and 70 %, 17 %, 4 %, 1 % found in WB and RB, respectively. Second, methods to obtain glucose-rich hydrolysates (for later use in fermentations) from the sorghum bran were investigated. It was found that amylolytic enzymes could produce enzyme hydrolysates (WBEH and RBEH) with glucose contents ranging from 48 g/l to 61 g/l. Alternatively, the brans could be digested to simple sugars using 3 % H2SO4 which converted up to 70.5 % of the bran into glucose, with dilute acid hydrolysates (WBDAH and RBDAH) having glucose contents ranging from 48 g/l - 57 g/l. Levels of the common fermentation inhibitors hydroxymethylfurfural, furaldehyde and vanillin were relatively low in all sorghum bran hydrolysates. Spot plate tests and phenotypic microarrays revealed that several yeast species metabolised and thrived on the hydrolysates. Ethanol mini-fermentations were successful with Kluyveromyces marxianus attaining the highest 88.9 % of theoretical maximum ethanol on RBEH, with other yeast strains also producing high yields. Production of itaconic acid by fermentation with 46 isolates of Aspergillus terreus was then attempted. Screening experiments on a defined glucose medium revealed that IA production levels were not normally distributed in nature. The highest producers were employed in 25 ml fermentation using the sorghum hydrolysates as a feedstock but the yields were found to be low compared to use of the defined glucose medium, with the highest yield (by isolate 49-22) being 5.5 g/l which corresponds to just 32.4 % conversion efficiency. Several approaches were therefore investigated to attempt to improve IA yields from A. terreus fermentations. Firstly, several hydrolysate purification techniques were attempted. The use of activated charcoal improved RBDAH yields very slightly, although most treatments resulted in lower IA yield. Secondly, ultraviolet mutagenesis was attempted using two high IA producing isolates, 49-22 and 49-5. Several promising mutants were obtained including one showing a 3.5-fold increase over the parent. However, these high yields could not be replicated in subsequent experiments. Thirdly, attempts were made to induce the sexual cycle of A. terreus in order to generate genetically diverse offspring that might include progeny with improved IA production. A molecular diagnostic was used to determine mating type and several isolates of opposite MAT were crossed in all possible combinations on three media under various temperature and gaseous exchange conditions. Hyphal masses containing cleistothecia, asci and ascospores were produced from two weeks onwards, which varied in number according to conditions and crossing partners. Most isolates were of low fertility, but 49-40, 49-43 and 49-44 were identified as “super-maters”. Sorghum flour agar (SFA) produced approximately seven times more structures than other agar media assayed, the effect of temperature varied according to media, whilst allowing gas exchange resulted in more hyphal masses than sealing the plates. Although asci containing 4-8 ascospores were identified, difficulties were encountered in obtaining viable ascospore offspring. Only one putative recombinant offspring was obtained, as evidenced by molecular verification using RAPD-PCR and MAT markers. This isolate exhibited low IA yields in fermentations. Finally, fermentation optimisations were performed using the response surface methodology approach. A half-factorial screening experiment was used to select three fermentation factors then a central composite design (CCD) performed to obtain the optimum conditions. Optimum conditions for IA fermentation using RBDAH as a feedstock were found to be 30 oC, pH 4.0 and an A. terreus inoculum of 1.0 x106 spores/ml, resulting in 13.5 g/l IA and 28.3 % of theoretical maximum possible conversion, representing a 2.45-fold increase over non-optimised values obtained in initial time-point experiments. Higher pH and inoculum sizes, with lower temperatures favoured IA formation. Scale up to fermentation volumes of 200 ml and 500 ml was performed and these also generated even higher yields of 13.9 g/l and 16.3 g/l IA, corresponding to 49.6 % and 46.1 % of theoretical maximum respectively. Overall, it was concluded that hydrolysates obtained from the wet-milling of sorghum bran can be used in the fermentative production of value-added chemicals with promising yields and efficiency, which warrants further research attention.