Winter wheat (Triticum aestivum L.) is the major arable crop worldwide, with a total annual global production of about 716 million tonnes and annual UK production of about 16 million tonnes from about 1.8 million hectares of land. Currently in the UK, approximately 15-20% of annual wheat yield production is lost to drought (Foulkes et al., 2002). In the present study two field experiments in 2012-13 and 2013-14 were conducted characterising a doubled-haploid (DH) population of 94 lines derived from a cross between winter wheat Rialto and Savannah. Two glasshouse experiments were conducted using four DH lines from the Rialto x Savannah DH population and the two parents, three accessions of each of three parental wheat ancestral species (T. bessarabicum, T. uratu and A. speltoides), and seven amphidiploid lines derived from crosses between durum wheat cultivars and T. bessarabicum. Two irrigation treatments were applied in both field (fully irrigated and rain-fed) and glasshouse (well-watered and water-stressed) experiments at the University of Nottingham, School of Biosciences, Sutton Bonington Campus, UK (52o 50' N, 1o 15' W). In each experiment, grain yield and above-ground dry matter partitioning were assessed at harvest, as well as a range of physiological traits at sequential assessments through the season. In the glasshouse experiments, water uptake and water-use efficiency (above-ground dry matter to total water uptake ratio) were also measured from the date of transplantation to harvest. Quantitative trait loci (QTL) analysis was carried out for the traits measured in the Rialto x Savannah DH population in the field experiments. In the field experiments, drought reduced grain yield by 22% in 2013 and by 2% in 2014. In 2013, amongst the sub-set of six DH lines and the two parents, variation for grain ∆13C, leaf photosynthetic rate, stomatal conductance and transpiration efficiency was observed (P<0.05), and flag-leaf Amax, gs and grain ∆13C were positively associated with grain yield (R2=0.55, P<0.05; R2=0.57, P<0.05, and R2=0.47, P=0.06, respectively). However, a negative relationship was found between TE and each of grain yield (R2=0.70, P<0.01) and ∆13C (R2=0.61, P<0.05) for the cross-year mean, indicating that lower TE was based on high stomatal conductance. Amongst the 94 R x S DH lines under drought, post-anthesis NDVI was positively correlated with grain yield, above-ground dry matter and TGW, and canopy temperature was negatively associated with grain yield and TGW post-anthesis (P<0.05). Late onset and end of flag-leaf senescence were associated with greater grain yield, above-ground biomass and TGW under both irrigated and drought conditions in 2013. Therefore, overall present results suggested that genetic variation in maintaining grain yield was more related to water uptake rather than WUE under mild UK water stress. In the glasshouse, the T. bessarabicum accessions had the highest flag-leaf photosynthetic rate, transpiration efficiency and SPAD associated with smaller leaf size and higher flag-leaf specific weight under drought compared with the amphidiploid lines and Rialto x Savannah DH lines. Individual amphidiploid lines had higher flag-leaf photosynthetic rate, leaf SPAD and later onset and end of flag-leaf senescence compared with the Rialto x Savannah DH lines associated with early flowering under droughted treatments. For the QTL analysis in the Rialto x Savannah DH population, a number of QTLs clusters were identified for grain yield, yield components and physiological traits under irrigated and drought conditions. Co-located QTLs were identified on chr 3A for grain yield, above-ground dry matter, thousand grain weight, plant height, anthesis date and flag-leaf senescence duration, and for stay-green traits, thousand grain weight and grains per m2. QTLs were also identified on chr 7D and 4A co-located with stay-green traits and anthesis date under irrigated and drought conditions.

Increased demand for food, climate change and greater dependence on food imports in less developed countries represent a challenge to achieve global food security. Wheat (Triticum aestivum L.) is the most widely grown crop and an essential component in ensuring global food security. Therefore, breeders need to develop new cultivars with higher grain yield potential. One physiological avenue to raise yield potential is by improving the allocation of assimilate to the spike during stem elongation to enhance grains m-2 and harvest index (proportion of above-ground dry matter at harvest in grain; HI). Partitioning to spikes could be increased to enhance floret survival by reducing competition from alternative sinks, including roots, leaves, stems and infertile tillers (Foulkes et al., 2011). However, attention must also be paid to maintaining post-anthesis source (photosynthetic capacity) to ensure grain growth of new cultivars is not source-limited. Although yield grains in wheat have historically been associated with traits influencing the capacity of the grains to store assimilate (sink), rather than influencing potential assimilate production (source), there is some evidence that modern cultivars are moving closer towards source limitation of grain growth (Acreche and Slafer 2009). So it is important to quantify the source and sink balance in CIMMYT elite germplasm and its physiological determinants to guide further strategies for yield potential improvement. The objectives of this study were to: i) Identify physiological traits determining enhanced above-ground biomass per unit area and radiation-use-efficiency (above-ground biomass per unit photosynthetically active radiation (PAR) interception; RUEPAR), spike fertility and HI in modern high biomass CIMMYT spring wheat germplasm, ii) quantify post-anthesis source: sink balance according to responses to a degraining to source-sink manipulation treatment, and iii) identify marker-trait associations for grain weight response to degraining (as an indication of source-sink balance) and senescence-related traits. In this study, a panel of twenty six elite CIMMYT spring wheat cultivars and a wheat association mapping (WAMI) panel of 294 genotypes comprising advanced lines and cultivars were evaluated in replicated field experiments under full irrigation in NW Mexico. The 26 cultivar panel was grown in in three seasons (2010-11, 2011-12 and 2012-13) and the WAMI panel in two seasons (2012-13 and 2013-14). In the 26 cultivar panel, growth analysis was carried at key development stages to assess above-ground dry matter (AGDM), DM partitioning and green canopy area. Assessment of fractional PAR interception by the canopy was carried out during the stem-elongation phase (GS31-GS65+7d) and RUEPAR was calculated over this phase in 2011-12 and 2012-13. Flag-leaf stomatal conductance was measured at around anthesis and senescence parameters were assessed at the canopy level and at leaf level. In both the 26 cultivar panel and the WAMI panel experiments, a degraining treatment was carried out at anthesis (GS65) +7-14 days by removing half of the spikelets to assess grain weight responses compared to control spikes as an indicator of source-sink balance and leaf and canopy senescence parameters were quantified in the control treatment. In the 26 cultivar panel, grain yield variation was associated more strongly with AGDM at harvest than HI; and biomass was positively associated with year of release. Radiation-use efficiency during stem elongation (GS61 – GS65+7d) showed genetic variation in one year out of two in which this trait was measured and a positive association with crop growth rate (AGDM g m-2 d-1) and with flag-leaf nitrogen (N) content. Furthermore, both flag-leaf stomatal conductance at anthesis and RUEPAR showed a positive association with grain yield among the 26 cultivars. There was genetic variation in each of spike partitioning index (proportion of AGDM as spike at GS65+7d) and fruiting efficiency (grain per g spike DM at GS61+7d) positively associated with grains m-2 amongst the 26 genotypes, and there was no trade-off between SPI and FE. Fruiting efficiency was associated with a greater proportion of lemma DM within the spike morphological components (glume, rachis, lemma, palea and awn). Results showed there is scope to increase biomass through RUEPAR and RUEPAR could be enhanced by selecting for increased stomatal conductance and/or flag-leaf N content. Grain weight responses to the degraining treatment in both the 26 cultivar panel and the WAMI panel showed that grain growth was either sink limited or co-limited by sink and source in the genotypes. In both panels, genotypes with higher grain yield showed higher grain weight responses to degraining (indicating a greater extent of source limitation); and greater grain weight responses were associated with faster senescence rate, supporting a co-limitation of source and sink in modern high yielding CIMMYT spring wheat cultivars. The genetic association mapping analysis identified a marker-trait association for grain weight response to degraining (an indicator of source-sink balance) on chromosome 7A in the WAMI panel. Grain m-2 was not associated with grain yield indicating that grain weight at some extent is driving gains to grain yield due to its positive association with year of release. Grain yield positively correlated with response to degraining over years, grain weight response to degraining was negatively associated with Flag leaf senescence in the WAMI population. Genetic variation in radiation interception by the canopy during stem elongation from GS31 to GS65+7d positively associated with accumulated above-ground dry matter amongst the CIMCOG genotypes. There was genetic variation in radiation-use efficiency (in 2013) during stem elongation and RUE was positively related with above-ground biomass at anthesis amongst the CIMCOG genotypes. Therefore, in order to increase grain yield is necessary to increase simultaneously source and sink traits.

Although wheat demand is expected to increase along with a projected growing population, the global rate of wheat yield increase appears to be declining. Genetic progress in yield potential in the past has been achieved mainly through increases in grains m-2 and harvest index with no major changes in above-ground biomass; however, HI has not increased since about 1990 indicating that further increases in yield potential will rely on increases in biomass while optimizing grain DM partitioning. A panel of 26 high biomass CIMMYT elite spring wheat cultivars (CIMMYT Mexico Core Germplasm; CIMCOG) was evaluated for grain yield, above-ground dry-matter (AGDM), DM partitioning and spike fertility in three field experiments (2011, 2012 and 2013) in NW Mexico. An additional field experiment was carried out in 2014 on a subset of four cultivars to examine source-sink related traits by imposing source manipulation treatments (leaf-lamina removal and leaf-sheath shading) on the crop. The main objective was to identify the physiological determinants of grains m-2 and HI in relation to DM partitioning among organs and to prioritise traits for application in breeding to increase HI in high biomass genotypes. Genetic variation in grain yield among genotypes was explained mainly by differences in AGDM. Fruiting efficiency (grains per unit spike DM at anthesis) was affected by high rachis specific weight and appeared to be important in grains m-2 determination. Trends for positive associations were observed between HI and spike partitioning index (Spike DM / AGDM - at anthesis; SPI). Stem DM proportion (mainly structural DM in internodes 2 and 3) was negatively associated with SPI; peduncle length and peduncle DM as a proportion of the stem DM on the other hand were more strongly associated to spike DM per unit area. In 2014, reductions in final grain weight in response to source reduction treatments were relatively low compared to the estimated reductions in light interception. No up-regulation of photosynthesis rate was observed by the flag-leaf or the spike in response to source reductions, suggesting that grain growth was overall sink limited but close to a co-limitation by source and sink. These results indicated scope for designing a plant ideotype to raise HI in high biomass spring wheat cultivars with reductions in stem structural DM (in upper internodes) without major effects on water soluble carbohydrate accumulation (in lower internodes). Finally, results from the source-sink manipulation treatments indicated limited scope for reductions in leaf-sheath and lamina DM partitioning during stem elongation to favour spike growth.

Wheat (Triticum aestivum L.) grain yield potential is generally sink-limited under favourable conditions with grain growth limited mainly by the number of grains formed per unit area. In the CIMMYT program in NW Mexico, novel large-ear phenotype traits (e.g. high assimilate partitioning to ear, high fertile florets ear-1) have been developed and may offer scope for increasing grain number per unit area (Gaju et al., 2009). In this study, ear fertility traits and their genetic regulation were investigated in backcross lines derived from novel large-ear doubled-haploid lines (UK Rialto x novel large-ear CIMMYT L14 line cross) backcrossed into either UK spring wheat Ashby or UK winter wheat Humber. Forty four BC3 near isogenic lines (NILs) (7 spring and 37 winter wheat NILs, currently BC3S5 and BC3S6) and 34 BC1S7 lines (18 spring and 16 winter wheat NILs, currently BC1S7) and their recurrent parents (Ashby or Humber, respectively) were chosen for physiological analysis in field experiments at University of Nottingham, UK and KWS, Thriplow, Hertfordshire, UK for evaluating novel variation for ear fertility traits and grain yield and specific introgressed target QTL on ear fertility traits and grain yield in 2012/13 and 2013/14. In highest/lowest performing BC3 spring NILs, above ground dry matter (AGDM) per main shoot increased by 97%, grain dry weight (GDW) ear-1 by 95% and grain number (GN) ear-1 by 68%, but grain yield was decreased by 71% associated with fewer ears m-2 (-87%) compared to the Ashby recurrent parent. For BC3 winter NILs, results showed that there was variation above Humber, for grain yield 100% DM (+22%), grains m-2 (+16%), harvest index (HI) (+6%), spikelets ear-1 (+14%), fertile spikelets ear-1 (+15%), rachis length (cm) (+24%) and thousand grain weight (TGW) (g) (+21%) (P<0.10). In the experiment at KWS Thriplow, the effects of the Tin1A gene in pairs of BC1S7 NILs contrasting in tiller number were investigated in the Ashby and Humber backgrounds. Amongst five pairs of spring NILs contrasting for the tiller inhibition Tin1A locus, the Tin1A lines were reduced in tillers m-2 (-16%), grain yield (-9%) and ears m-2 (-19%) but increased in spikelets ear-1 (+12%). In two pairs of winter NILs contrasting for the Tin1A locus, the Tin1A lines reduced tillers m-2 (-18%), grain yield (-6%), ears m-2 (-16%) but increased GN ear-1 (+20%), spikelets ear-1 (+11%) and GN spikelets-1 (+6%). The extent of tiller reduction was overall too severe in the spring NILs with Ashby background to lead to increased yield in the lines carrying the L14 allele. In winter NILs, grain yield and biomass were increased with high canopy green area and better maintenance of green area during grain filling. This suggested grain growth may have been partly limited by source supply of assimilate during grain filling possibly during the latter stages of grain filling. A strong relationship between individual grain weight and rate of grain filling was consistent in BC3 spring NILs. Grain weight was increased in BC3 winter NILs with increasing rate of grain filling but duration of grain filling was decreased. DNA samples from each BC3S5 line were screened using 8 SSR markers for the introgressed ear fertility QTLs identified in the Rialto x CIMMYT L14 DH population. The genotyping results showed the CIMMYT L14 allele for a novel QTL on chromosome 3A was associated with increases in ear fertility traits (grain number ear-1, spikelets ear-1, and grain DM shoot-1) amongst the BC3S5-6 lines when compared to the Humber recurrent parent and confirmed the presence of Tin1A gene in the Ashby background determining ear fertility and grain yield effects.

Lodging is a persistent phenomenon that reduces grain quality and grain yield of wheat. It is defined as the permanent displacement of the plant/shoots from their vertical position. During the Green revolution, wheat plant height was reduced to avoid lodging and allowed growers to increase nitrogen fertilization. This resulted in a considerable increase of grain yield. After the Green Revolution, plant growth regulators were used to further reduce plant height which continued increasing lodging resistance and grain yield. However, lodging susceptibility has not disappeared completely and as yields increase, there is evidence that growers cannot continue to rely on these strategies, raising the question of how to further improve lodging resistance of wheat. Collaborative studies by physiologists, biologists and engineers generated a deeper understanding of lodging (through stem and anchorage failure mechanisms) and the development of models of the lodging process, together with better crop husbandry or agronomic management strategies. Most of these studies were made on winter wheat under a reduced range of environmental conditions. This thesis attempted to further develop lodging mechanisms and models using spring wheat and a wider range of environmental and agronomic conditions and to investigate the genetic control of lodging-proof traits. Field experiments on spring wheat cultivars were carried out in irrigated conditions in NW Mexico and on a winter wheat Avalon x Cadenza doubled-haploid population in rainfed conditions in the UK. A lodging-proof crop was designed for spring wheat growing in NW Mexico that suggests the need for both increased structural stem biomass and a wider root plate spread (anchorage strength). The model also infers that trade-offs with grain yield will occur, mainly because of overlapping of the development of lodging traits with grain yield formation processes. Rapid selection tools for lodging resistance will play a primary role if lodging resistance is to be improved concurrently with grain yield. Fine mapping and validation of QTLs related to lodging traits identified in this study can be used to develop reliable genetic markers that can accelerate selection for lodging resistance concurrently with improvement of genetic yield potential.

Willow short rotation coppice (SRC) is seen as an important renewable energy source within temperate regions including the UK and its deployment within the agri-environment is supported by a number of goverment policies. Willow SRC represents a significant land use change and its deployment has raised questions regarding the possible impacts on biodiversity and the delivery of ecosystem services. This work assessed the impact of three commercial willow SRC plantations on ecosystem processes through the use of herbivory, decomposition and predation bioassays. Comparisons were also made between the willow SRC plantations and the abundance and diversity of: summer ground flora and winged invertebrates in the alternative land use options of set-aside and cereal crops; predatory ground invertebrates and small mammals in winter wheat and barely. In comparison to cereal crops the willow SRC plantations contained a higher abundance and species richness of ground flora and small mammals, and a higher abundance and family richness of predatory ground invertebrates. Ground flora richness was higher in the set-aside land than within the willow SRC. The ground flora community within the willow SRC was markedly different to both set aside and arable land with a shift from an annual and ruderal to competitive and perennial dominated community. The composition of winged invertebrate Orders also varied between the land uses with higher numbers of Hymenoptera and Hemiptera trapped within the willow SRC plantations than within the arable and set-aside land. No differences were detected on rates of predation on invertebrate prey, seedling herbivory and decomposition between willow SRC and set-aside land. In comparison to cereal crops higher rates of decomposition and higher rates of predation by small mammals in the autumn were recorded in willow SRC. Overall the results suggest that, willow SRC plantations may benefit farm-scale biodiversity by providing a habitat where plants and animals that are uncommon on alternative land use can persist. Moreover positive effects on the species richness of small mammals and the abundance and richness of predatory invertebrates may have positive implication for natural pest control both within willow SRC plantations and possibly on surrounding landscape. Comparisons to set-aside did, however, highlight that willow SRC is not a panacea for all species and care must be taken in the location and fraction of the landscape that is devoted to this crop

Roots are key organs for the uptake of nutrients in plants. Leguminous plants form nodules, providing a niche for symbiotic nitrogen-fixing bacteria, enabling plants to colonize nitrogen depleted soils. Lateral root formation shares genetic regulation, as well as developmental features, with nodulation. This led us to investigate whether shared genetic control can be revealed in lateral root development responses of Arabidopsis thaliana to rhizobia. The phenotypic response of Arabidopsis to Sinorhizobium meliloti was analyzed. Arabidopsis lateral root length was found to be shorter, indicating a potential link between bacterial perception and lateral root development, even in a non symbiotic host plant. To gain more insight, a transcriptome time series was carried out. The response of Arabidopsis to Sinorhizobium inoculation compared to the response of nitrogen treatment were analyzed. In order to identify highly localized, yet important minimal regulatory cues and maximize the spatial specificity of the data, this analysis was carried out in isolated cortical and pericycle cells. Combined, in response to the two treatments approximately a 20% of the Arabidopsis genome is differentially expressed during the first 48 hours. Bioinformatic tools (clustering and network inference) were used to obtain a chronology of different responses, highlighting which metabolic processes change over time and identify potential gene regulatory mechanisms. The data and approach presented here present a unique analysis of the response to Sinorhizobium and nitrogen treatment and open the way to further tissue specific analysis of transcriptional regulation in plants. The similarities and differences between the response to Sinorhizobium (a potentially neutral bacteria) and Ralstonia (a pathogen of Arabidopsis roots) were evaluated using an analysis of gene expression at two early time points after inoculation. There was significant overlap in transcriptional response to both treatments, as well as striking differences: we find pathogen defense genes in the response to Sinorhizobium, rather than Ralstonia. We also find a core of 11 auxin responsive genes that have similar differential expression between treatments. Our results show that Rhizobium has a distinct transcriptional and phenotypic effect on Arabidopsis roots that is distinct from a pathogenic interaction. Several network hub genes are proposed as potential targets for further studying this effect.

Wheat (Triticum aestivum L) is the most widely grown crop in the world and accounts for approximately 31% of global cereal consumption every year (FAO, 2012). Furthermore, wheat is the most traded product worldwide (Dixon et al. 2009). In UK, wheat is the largest arable crop, it is grown on about 1.8 M ha p.a. For wheat productivity and grain quality, nitrogen (N) is the most important fertilizer applied, and modern wheat culitvars are generally selected under high N supply. However, N fertilizer represents a significant cost of production and may have negative environmental impacts. N-use efficiency (grain DM yield / soil and fertilizer N available; NUE) can be divided into two main components: N-uptake efficiency (N uptake / soil and fertilizer N available; NUPE) and N-utilization. efficiency (grain DM yield / NUP; NUTE). The current study aims to identify novel variation for grain yield, above-ground dry matter (AGDM). NUE and NUE components in a panel of AE Watkins landraces compared to UK check cultivars in the glasshouse and field trials and in two Single Seed Descent (SSD) populations derived from the crosses between UK spring wheat Paragon and Watkins landrace line 481 (PxW481) and between Paragon and Watkins landrace line 141 (PxW141) in field experiments and to investigate the physiological and genetic bases of this variation. Two glasshouse experiments (2011/12 and 2012/13) examining 17 genotypes (comprising five UK check cultivars and 12 Watkins landraces), and one field experiment (2011/12) examining a panel of 10 genotypes (comprising three UK cultivars and seven of the 12 Watkins landraces examined in the field) were carried out. In addition, three field experiments examining two SSD populations PxW481 (79 lines) (in 2011/12 and 2012/13) and PxW141 (97 lines) (in 2012/13) under two N treatments (HN=200 kg N/ha and LN=0 kg N/ha) were carried out. The glasshouse experiments were located at the University of Nottingham, School of Biosciences, Sutton Bonington Campus, UK and field experiments were located at the University of Nottingham experimental station at Bunny Park, Nottinghamshire, UK. The genetic maps were presently constructed using 201 and 491 markers, including single nucleotide polymorphism (SNPs) and microsatellites (SSR) for PxW481 and PxW141, respectively. Grain yield (GY), yield components, AGDM, NUPE, NUTE, and physiological traits including leaf light-saturated photosynthesis rate (Amax), flag leaf chlorophyll content (SPAD) and the spectral reflectance index, Normalized Difference Vegetation Index (NDVI, indicative of canopy size, field experiments only) were measured in the experiments. Genetic variation in grain yield was more closely associated with AGDM than with harvest index (HI) in the glasshouse and in the field under both HN and LN. For biomass production, the results showed that Paragon, Rialto, Xi19 and landrace W141 had higher AGDM than all other genotypes. In summary, UK check cultivars generally had higher grain yield (GY) compared to Watkins landraces and higher AGDM in the glasshouse under HN conditions. Similar results were found in the field under HN; however, under LN, the majority of Watkins lines maintained GY and AGDM than the UK cultivars compared to HN conditions. With regard to N uptake at harvest, the Watkins landraces W040, W141 and W579 had similar NUP to Paragon and higher than Oakley in the glasshouse. In the field, in general, Watkins lines maintained relatively better NUPE under LN than the UK check cultivars. A negative association amongst genotypes was found between NUTE and grain N concentration (%) in the glasshouse and in the field under HN and LN treatments, with the strongest association observed under LN conditions. Variation for light-saturated leaf photosynthesis rate (Amax) was also observed amongst Watkins lines. In the glasshouse experiments, the UK cultivars, and landraces W141 and W352, generally had higher pre-anthesis Amax than other Watkins landrace lines. In the field experiment, landrace lines W352 and W141 had higher pre-anthesis Amax than Paragon under LN, whereas lines, W223 and W034 had higher values under HN. Genetic variation in GY and AGDM were overall better associated with post-athesis flag-leaf Amax than with pre-anthesis flag-leaf Amax in the field, and the associations with post-anthesis Amax tended to be stronger under HN rather than under LN conditions. With regard to the two SSD mapping populations, both N and genotype had a significant effect on GY, AGDM, NUPE and NUTE for PxW481 in all three experiments. For the PxW481 population, no SSD line had either higher GY or AGDM than Paragon under HN, while under LN, 13 lines had higher GY and two lines had higher AGDM than Paragon (P < 0.05). For the PxW141 population, three lines had higher grain yield under HN and three lines had higher GY under LN than Paragon. Five and 10 SSD lines under HN and LN, respectively, had higher AGDM than Paragon. The transgressive segregation for GY was due to either AGDM or HI, depending on the line. In both populations under both N treatments, genetic variation in NUE was more strongly associated with NUPE than with NUTE under HN and LN; however, the response of NUE to N availability was better associated with NUTE. Averaging years for the PxW481 population under HN, no SSD line had higher NUPE than Paragon, while under LN L481-76 had higher NUPE than Paragon. For PxW141, no SSD line had higher NUPE than Paragon either under HN or under LN conditions. Seventeen SSD lines of the PxW481 population had significantly higher NUTE than Paragon under HN and 10 lines higher under LN conditions. For PxW141 under HN, L141-95 and L141-94 had higher NUTE than Paragon under HN, while under LN 12 SSD lines had higher values. In both the PxW481 and PxW141 populations, genotype and N treatment had an effect on NDVI (canopy size) for all measurements pre and post-anthesis. Genetic variation in yield, biomass and NUPE were more closely associated with NDVI measured at around anthesis than at other measurement dates. In addition, the correlation amongst genotypes was stronger under LN than under HN conditions. Genetic variation for flag-leaf senescence parameters was also found in both mapping populations, and association with grain yield amongst genotypes was stronger under LN conditions than under HN conditions in both populations. QTL analysis identified two major QTLs for grain yield on 6AL and 5A under HN and one major QTL on 2B under LN conditions in the PxW481 population. The QTL on 6AL co-located with a QTL for NUPE, while the one on 5A co-located with a putative QTL for AGDM. Simonds et al. (2014) reported a major stable QTL in the same region of 6AL in the Spark x Rialto DH population across several environments. Under LN conditions, the QTL on 2B co-located with a QTL for plant height. For AGDM, a major QTL under both HN and LN was identified on chr 4B in the PxW481 population. This QTL co-located with a QTL for NUPE under both HN and LN conditions. In addition, a major QTL under HN for NUPE on 3BL (PxW481) co-located with QTLs for GY and AGDM. Another major QTL on 2A (PxW141), co-located with flag-leaf stay-green traits. This is consistent with the findings of Bogard et al. (2011) who reported two QTLs for NUPE under LN on 2A, associated with a delay in onset of flag-leaf senescence. With regard to NUTE, two major QTLs on 3B, co-locating with QTL for GY and HI, and on 1B, co-locating with a QTL for N grain concentration, were found for the PxW481 population under LN. In addition, three QTLs on 3A, co-locating with a QTL for TGW, and on 6D and on 7B, co-locating with QTLs for TGW, were identified.

Rhizoctonia solani is a species complex comprising 13 anastomosis groups (AG) that cause disease in a broad range of crops. Various AGs of R. solani are pathogenic to winter wheat causing damping-off and root rots. Rhizoctonia cerealis, the fungal agent of sharp eyespot, is known to commonly occur on the stems of wheat as part of stem base disease complex (SBD) consisting also of eyespot and brown foot rot (BFR). Eyespot is caused by Oculimacula acuformis or O. yallundae and BFR is principally caused by Microdochium nivale or M. majus. The population dynamics of SBD pathogens are continually changing due to environmental and agronomic pressures. Therefore, information on the current population dynamics and factors that influence population changes can guide the implementation of effective control measures. Furthermore the presence and dynamics of Rhizoctonia spp. in English wheat crops has not been previously investigated and there is also limited knowledge on the yield losses associated with root and stem base rhizoctonia diseases in wheat. This work aimed to elucidate crop losses and control of R. solani and R. cerealis in English wheat crops. An investigation was conducted into the incidence and severity of root and stem base diseases and population dynamics of their associated pathogens in 102 English winter wheat crops. Crop losses and control of the main Rhizoctonia spp. identified in English wheat crops were further investigated in artificially inoculated field experiments. Additional characterisation of Rhizoctonia spp. was investigated using ITS sequencing, isolate pathogenicity and in vitro fungicide sensitivity experiments. The predominant AG of R. solani in English winter wheat crops identified in 63% of soil samples was AG 2-1 with the highest DNA concentrations found in soil where the previous crop was oilseed rape. This suggests that OSR in the rotation is selecting for AG 2-1. Field experiments showed that wheat was not a major host of AG 2-1 since the pathogen failed to cause significant effects on wheat growth and yield. Sharp eyespot co-occurred with eyespot and BFR in English wheat crops. In 2011/12 at GS 65-75 sharp eyespot symptoms and R. cerealis DNA were detected in 90 and 94% of crops, respectively. The population structure of R. cerealis in English wheat crops revealed all isolates belonged to the subgroup AG D-I. Sharp eyespot incidence and severity showed considerable season to season variation primarily due to environmental conditions with cool, wet and humid summer conditions favouring the disease. However, agronomy practices did not have a major influence on sharp eyespot and R. cerealis DNA in soil or in planta. In field experiments R. cerealis caused significant plant establishment losses, stem browning and reduction in grain yield of 8.5% in winter wheat. The pathogenicity of R. cerealis isolates to wheat was confirmed in controlled environment experiments where significant damping-off and stem browning on 10 day old wheat seedlings occurred. In this study root rot was not correlated with any pathogen and was likely caused by a complex of species. Root rot incidence and severity in English wheat fields and in field experiments showed a decreasing trend in both seasons. BFR was the predominant SBD in English wheat crops occurring in 100% of crops by GS 37 in both seasons. Eyespot showed season to season variation and was favoured by warm, wet and humid conditions in the spring. The causal agents of eyespot the Oculimacula spp. were the most common occurring species in the soil and in planta of English wheat crops. DNA of Oculimacula spp. and Microdochium spp. was detected in ≥90% of stem bases in both seasons, showing these species are ubiquitous in English wheat crops. Results indicated a shift in the Oculimacula spp. population in English wheat crops with both species occurring together although O. yallundae was clearly the predominant species in terms of biomass. Protecting plants in the establishment phase of development from Rhizoctonia spp. is critical as early infections can lead to seedling death. Seed treatments are considered the most effective way to target and deliver fungicides to control infections by Rhizoctonia spp. In field experiments sedaxane + fludioxonil provided more consistent control of damping-off and stem browning than fludioxonil alone. In addition, fungicide EC50 values to inhibit mycelial growth of R. solani and R. cerealis isolates were lower for sedaxane than fludioxonil or prothioconazole. Sedaxane + fludioxonil also significantly reduced BFR up to GS 39, but showed inconsistent control of sharp eyespot beyond GS 13. To conclude, this study has found that AG 2-1 is widespread in English wheats crops and this may have implications for the growth and development of OSR. Rhizoctonia cerealis was shown to significantly reduced emergence and grain yield of winter wheat. This suggests control of this pathogen should receive greater attention especially at the establishment phase of development and that seed treatments (i.e. sedaxane) are the most effective control option to protect seedlings.

Wheat is a staple food for 35% of the world’s population providing roughly 20% of its calorific and 25% of its protein intake. Puccinia triticina, Zymoseptoria tritici and Fusarium graminearum are some of the most economically damaging fungi causing huge wheat yield losses. Problems that arise when trying to manage fungal pathogens include: the ability of fungal species to quickly adapt and overcome resistant cultivars of wheat, the overuse of fungicides leading to a high selection pressure for pathogen resistance and early detection often being dependent upon the experience and skill of the observer. This thesis focuses on developing detection methods which highlight the need for an integrated approach to disease management. In this study a specific monoclonal antibody, 29.G7.A9, was developed for early detection of Fusarium graminearum macroconidia spores. Immunofluorescence demonstrated the ability of this antibody to bind to the native protein in F. graminearum spores. The 29.G7.A9 antibody was incorporated into a portable amperometric immunosensor system for spore detection using screen printed electrodes. A Z. tritici population from three farms was analysed for the prevalence and distribution of amino acid alterations in the CYP51 protein, as well as the presence of inserts in the putative CYP51 promoter region, resulting in two general potential targets for detecting azole resistance being proposed. A clustering effect was observed with certain variant types showing association to certain geographical locations i.e. farm, field, and areas within a field. For this reason a future sampling plan was suggested with different sampling options in order to optimise the detection of certain variant types that may occur within a population in a specific location. A method was established to quantitatively characterize the development of Z. tritici on wheat plants throughout a complete infection cycle as well as observe differences in disease progression when different doses of a fungicide (epoxiconazole) were applied. This thesis provides techniques and information for generating further research and contributing new ideas for a more integrated approach for fungal crop pathogen detection research.