The project will develop and test a toolkit to impute dense genomic information in crop breeding populations. Dense genomic information allows geneticists to unravel the genetics of traits using genome wide association studies, and breeders to speed up genetic improvement using genomic selection and genomics assisted breeding. These methods are most powerful when the density of genomic information is very high and the numbers of individuals genotyped are very large but the cost of collecting genotype information to build such datasets is prohibitive. A flexible and effective imputation toolkit will make it possible to build such datasets cheaply using imputed data. In a genetics and genomics context, imputation is the prediction of an unknown genotype in one individual from the known genotypes of other individuals (to give a trivial example, if individuals 'X' and 'Y' are known to have genotypes AA and CC respectively, then their offspring 'Z' is imputed to be AC). The value of imputation is that when combined with high-density genotype information from a few individuals, high-density information can be imputed for many individuals that have been genotyped at low-density, which vastly reduces the costs of datasets of dense genomic information. The project has three parts:- 1. We will develop heuristic imputation algorithms that exploit the information in crop pedigrees, that correct pedigree errors and that generate approximate physical maps of the genome. Existing heuristic imputation algorithms, which were designed for livestock, do not work on crops because crop pedigrees are more complex than livestock pedigrees and crop data are of many different types, whereas livestock data is fairly homogeneous in type. 2. We will develop probabilistic algorithms that integrate with the heuristic algorithms to produce a hybrid imputation algorithm for crops that combines the speed of heuristic algorithms with the flexibility and robustness of probabilistic algorithms. Existing probabilistic algorithms are too slow and require too much memory to work well with crop data. 3. We will package the software apply it to a number of specific case datasets and breeding programs in KWS, which is one of the worlds four leading crop-breeding companies.

The foundation of global food security is built on the three cereals wheat, rice and maize, where wheat is the leading source of vegetable protein in human food. In the UK this cereal is the most important crop grown with an annual value of about £1.2 billion. The average yield of wheat in the field in the UK is currently 8.4 tonnes/ha, but this yield is dependent on high levels of mineral fertilizer (especially Nitrogen, Phosphorus and Potassium) and pesticide usage. Nitrogen (N) fertiliser use is of concern because it is associated both with high levels of energy use and greenhouse gas emissions (e.g. CO2, N2O) that cause climate change, in addition to eutrophication of fresh water and marine ecosystems. However, nitrogen fertilisation is required for achieving high yield in wheat, and increasing sustainability through decrease in nitrogen input is not commercially feasible due to the resulting fall in yield. Given that high-nitrogen nutrient regimes are reality in the field, decreasing pesticide usage is a target for enhancing sustainability of wheat production. An undesirable side-effect of nitrogen fertilisation is that it increases susceptibility to pathogens. There is increasing evidence that high soil nitrogen enhances the development of fungal pathogens such as Septoria that causes wheat leaf blotch disease (Simón et al 2003; Loyce et al 2008). The mechanisms leading to these nutrient induced changes in disease development are not known. Septoria leaf blotch (STB) is currently the most important disease of wheat in Europe and is among the top three most economically damaging diseases of this crop in the United States. Despite the importance of STB, there is very little information available on the defence mechanisms or immune responses that allow wheat to counter Septoria infection. Fungicides provide the only control measure for this devastating disease, but extensive applications of fungicides increase the worldwide economic costs attributed to STB. In addition, STB outbreaks are becoming more prevalent as currently available fungicides are becoming less effective against new resistant strains of Septoria. Therefore there is an urgent need to develop new strategies to combat STB in the field. The industrial partners (KWS) in the proposal recognise that exploiting endogenous defence mechanisms that do not rely on fungicides may provide an alternative method to control this disease, and that an understanding of why Nitrogen nutrient level and disease resistance are inversely correlated is likely to lead to strategies which will enable exploitation of endogenous defence. Our preliminary data have suggested that a family of transcription factors (Tfs), the WRKY genes that have been shown to be central to plant defence in model systems, form a link between nitrogen input and Septoria disease resistance in the field. We propose to investigate the roles of these WRKY gene family TFs to reveal the identity of the specific WRKYs which are critical for Septoria resistance in the field under varying nitrogen levels and mechanisms which can be exploited to boost Septoria resistance under the high input growth conditions necessary for maintaining yield. The overall objective of this project is to gain an understanding of how the nutrient regime under which cereals are grown affects their susceptibility to STB disease, with the ultimate aim of manipulating this relationship to allow enhanced disease resistance to be retained under high or optimum nitrogen input growth conditions.

Background A large proportion of the C in root exudates is easily degradable and promotes enhanced microbial growth and activity in the rhizosphere. This enhanced activity can lead to improved nutrient availability through: a) increased flux of nutrients by mass flow from the bulk soil, b) 'priming' of recalcitrant organic compounds in the soil releasing bound nutrients, c) release of organic anions and phosphatases that enhance the availability of P, d) development of associations with beneficial microorganisms (e.g. free-living N fixers, AM fungi). In this project we will test the hypothesis that there are genotypic differences among wheat varieties in their ability to modify conditions in the rhizosphere environment and affect nutrient availabilities within this zone. Aims The specific objectives of the project are: 1. To determine the genotypic variation in wheat rhizosphere processes that mediate the availability of plant nutrients. 2. To determine the genotypic variation in the activity of wheat rhizosphere-based beneficial organisms. 3. To determine which phenotypic traits are linked to improved nutrient availability in the rhizosphere of wheat. 4. To link the phenotypic traits to genetic markers for nutrient use efficiency in wheat. Brief experimental plan Objective 1: Rhizosphere processes will be monitored in 2010 and 2011 in the NUE-CROPS trials at Newcastle University, and 2011 and 2012 in the Sustainable Arable LINK project (SA Root Ideotypes, awaiting final approval from BBSRC) trials at KWS UK. Measurements will include: a) soil microbial activity, b) microbial biomass size, c) enzyme activities (e.g. carbohydrases, acid phosphatase, leucine-aminopeptidase) using the microfluorometric assay. The student will rhizosphere sample at both experimental sites, with lab activities at Newcastle University. Objective 2: Previous studies have demonstrated that free-living N fixing bacteria are sensitive to management practices and that the effects of management can be detected using state-of-the-art molecular techniques (RNA-qPCR and RNA-DGGE). The structure and activity of the free-living N fixing bacterial population in the rhizosphere will be studied using these techniques. Studies of other key functional groups in the soil (e.g. ammonia oxidizers, AM fungi) will also be conducted if the enzyme studies under objective 1 indicate differential activity of these groups. The soil molecular studies will be conducted at Newcastle University. Objective 3: The field trials (NUE-CROPS and SA Root Ideotypes) will be used to estimate the nutrient use efficiency of the different wheat genotypes. A range of phenotypic assessments (e.g. root system size, whole plant N partitioning) will be linked to nutrient use efficiency. In addition, the quantity and effects of root exudation will be studied to further elucidate the mechanisms driving genotypic differences in rhizosphere soil processes. Microcosm studies will be conducted on selected varieties (those identified as exhibiting differences in rhizosphere biology under objectives 1 and 2) using stable C isotope labelling techniques. This will allow tracing of root exudates into the rhizosphere and microbial populations. Field based phenotypic assessments will be conducted at both experimental sites; microcosm studies will be conducted at Newcastle University. Objective 4: The rhizosphere parameters assessed under objectives 1, 2 and 3 will be included as phenotypic measurements that can be linked to ongoing transcriptional and proteomic studies of wheat roots and shoots in the NUE-CROPS project. The most robust rhizosphere parameter(s) showing variation between the 64 genotypes will be used with the large array of genetic markers available from the NUE-CROPS project (~800 DArT / SSR) to identify candidate locations for QTL using association mapping methods.

Wheat is the UK's primary arable crop and provides a large proportion of the global calorie, protein and micro-nutrient requirements for both humans and livestock. Current predictions indicate that a 1C increase in global temperature would lead to a 4.1-6.3% decrease in wheat yield, yet yield needs to be increased by an estimated 60% by 2050 to meet the demands of a growing population. To address this challenge and improve the reliability of the wheat yield to changing climates we must understand how plants respond to temperature. I will utilise the naturally existing genetic diversity in wheat and combine this with recently curated mutant populations and the newly annotated wheat genome sequence to identify genes and biological processes involved in temperature adaptation in wheat. Currently, we do not understand the genetic or molecular basis of how wheat responds to temperatures under standard growing conditions, ~6-24C. My recent research focuses on this temperature range and has challenged the assumption that the response to overwintering (vernalization) only occurs at < 6C. This was identified after I observed heat activation of the same genes that function in low temperature vernalization. This raises the possibility that many of the genes involved in the vernalization response can also be employed to regulate and increase crop robustness and yield at higher ambient temperatures. I plan to build on this discovery by identifying other genes involved in regulating the key developmental transition from vegetative to reproductive growth under field conditions, and then explore how these genes function (Objective 1). To date the majority of research on temperature responses has been limited to constant controlled temperature conditions, yet my research indicates that the mechanisms by which plants respond to variable temperatures, such as those experienced by crop plants growing in the field, are actually quite different. I will also investigate the molecular function of genes which have been shown to be important in vernalization and identify the proteins they interact with and how they function under different temperature conditions (Objectives 2 and 3). Finally, I will investigate methods to accelerate vernalization under experimental conditions to increase research and wheat breeding capabilities with wheat that requires vernalization (Objective 4). This Fellowship is timely as it combines my recent advances in understanding the molecular basis of temperature responses in wheat with the newly (2018) released wheat genome sequence, curated mutant populations and high-throughput genome sequencing capabilities. The Fellowship will be conducted at the University of Bristol as this will facilitate interdisciplinary collaborations as well as collaborations within the renowned School of Biological Sciences. In addition, Bristol has established field trial sites and world-leading sequencing resources, both of which are important for this research. The Fellowship will also support collaboration between the Fellow and industry to enable knowledge exchange from this research to influence the performance of wheat under diverse environmental conditions. This research will advance our knowledge of temperature adaptation in wheat and enable the formation of an integrated understanding of how plants use temperature to regulate key developmental decisions. This will have societal benefit by providing information and resources that can be exploited in the wheat breeding industry, for example, to reduce the duration of breeding cycles and provide methods to increase the robustness of wheat yield to the erratic temperature patterns associated with climate change.

In bread wheat, important agronomical traits are distributed along chromosomes. Traditionally, plant breeders cross high yielding parental lines and then select for progeny in subsequent generations that carry desirable attributes whist removing undesirable traits. However, the process of 'gene-shuffling' (meiotic recombination) is non-random and skewed towards the ends of the chromosomes. Therefore, desirable traits are often transmitted as a block together with undesirable traits. This is analogous to dealing a deck of cards where a significant proportion of the cards are tethered by an elastic band. In this case a desirable hand cannot be achieved until the elastic band is severed and the cards are able to segregate freely. In this proposal we aim to understand why desirable and undesirable traits in bread wheat are often tethered together, so that we can break this bond, and release the full potential of available natural variation. Then, we aim to modulate this process so that the plant breeder can decide which traits can be 'dealt' together in the same variety. This unlocking of wheat's natural variation will lead to the production, via classical plant breeding, of superior varieties with favourable agronomic traits such as increased yield and improved nutrient acquisition. To provide direct evidence that our research has application we will work with two of the UK's largest wheat breeders KWS and RAGT to target chromosomal regions, which are known to be transmitted as blocks. We will show that by using novel procedures, we can increase the amount of recombination in these blocks. Increasing the amount of recombination in any of these regions will enable breeders to generate new gene combinations which will lead to new varieties with, for instance, increased protein content or pathogen resistance. Further down the breeder's pipeline our research will directly translate to new varieties with superior characteristics that will help maintain farm incomes and improve sustainability of the UK arable and milling industries. In addition high yielding varieties will reduce dependence on imported grain and associated transport and environmental costs and improved pipelines for the generation of new UK varieties that will enhance reliability and competitiveness in overseas markets.