Bread wheat is of fundamental importance to UK, European and world agriculture, with an estimated 2007 world harvest of ~ 550 m tonnes. In the UK, ~1.8 m hectares are planted with wheat, yielding ~7.2 tonnes per hectare, with a farm-gate value of £2.6 billion. The UK has ideal growth conditions for wheat and has a world-class crop improvement programme. Despite its importance, wheat production world-wide has not kept pace with increased demand, and productivity is threatened by disease, increased fertiliser costs, competition for high quality agricultural land, resource limitations, and adverse environmental conditions that dramatically reduce optimal yields. It has been estimated that in Europe productivity has to be doubled to keep pace with demand and to maintain stable prices. Therefore by narrowing the gap between maximal yields and actual yields, and increasing maximal potential yields, sustainable and adequate production of one of the world's most importance crops could be secured. The large increases in wheat yield have been primarily due to genetic improvements brought about by selective breeding of elite lines. The power of breeding can be increased by enabling the incorporation of wider genetic diversity and accelerating the identification of best-performing genotypes. This can be achieved using DNA sequence markers to identify genetic diversity underlying key traits. We aim to use next generation sequencing and a novel computational and comparative genomics strategy to identify sequence differences in the genomes of 5 key varieties that can be used to define different versions of a single gene in different varieties. Finding this type of marker in wheat has been problematic in the past because wheat is a hexaploid, with potentially 3 copies of each gene, and most of the sequence differences in wheat lines are between these three copies of a gene in a variety, rather than between genes in different varieties. With this information and a set of markers, breeding companies and academic scientists will be able to identify and select specific regions of the genomes of different varieties, and use this information to isolate genes and select lines with that region of DNA in it from crosses. This capability will fundamentally alter wheat research by enabling the use of more diverse lines in breeding, including wild species that have a wealth of under-exploited traits, including stress tolerance. Finally this genotyping study will facilitate a far greater level of academic research in a key UK crop. The sequencing and informatics strategies we aim to develop will also establish ways to sequence the complete genome of wheat. Currently the large size of the genome, its hexaploid composition and predominant repeat composition, is a large barrier to progress. However, the high throughput and low cost of next generation sequencing provides a solution to the scale of the wheat genome. Our proposed work will enable sequencing to focus on gene-rich regions and increase the potential for assembling gene-rich genome sequences. Furthermore, using a novel bioinformatics strategy that uses the complete genome sequence of a closely-related species as a 'template' for identifying both gene structures such as introns and an approximate order of genes, our work will define new ways of assembling gene sequences and the order of genes in wheat chromosomes. This will lower the barriers for future work aimed at larger-scale genome sequencing and analysis. Finally this project is closely linked to the UK breeding community through WGIN, to academic laboratories studying wheat in the UK through the Monogram Network, and to the international wheat genomics community through the International Wheat Genome Sequencing Consortium. This will ensure the rapid transfer of information to key stakeholders.

Abstracts are not currently available in GtR for all funded research. This is normally because the abstract was not required at the time of proposal submission, but may be because it included sensitive information such as personal details.

The majority of countries around the world maintain a disinfectant residual to control planktonic microbial contamination and/or regrowth within Drinking Water Distribution Systems (DWDS). Conversely, some European countries prohibit this practice because the residuals react to create disinfection by-products, which are regulated toxins with carcinogenic effects. Critically, the impact of disinfectant residuals on biofilms is unknown, including their role in creating a preferential environment for pathogens. Biofilms grow on all surfaces; they are a matrix of microbial cells embedded in extracellular polymeric substances. With biofilms massively dominating the organic content of DWDS, there is a need for a definitive investigation of the processes and impacts underlying DWDS disinfection and biofilm interactions such that all the risks and benefits of disinfection residual strategies can be understood and balanced. This balance is essential for the continued supply of safe drinking water, but with minimal use of energy and chemicals. The central provocative proposition is that disinfectant residuals promote a resistant biofilm that serves as a beneficial habitat for pathogens, allowing pathogens to proliferate and be sporadically mobilised into the water column where they then pose a risk to public health. This project will, for the first time, study and model the impact of disinfectant residual strategies on biofilms including pathogen sheltering, proliferation, and mobilisation to fill this important gap in DWDS knowledge. The potential sources of pathogens in our DWDS are increasing due to the ageing nature of this infrastructure, for example, via ingress at leaks during depressurisation events. Volumes of ingress and hence direct exposure risks are small but could seed pathogens into biofilm, with potential for proliferation and subsequent release. An integrated, iterative continuum of physical experiments and modelling is essential to deliver the ambition of the proposed research. We will make use of the latest developments in microbiology, internationally unique pilot scale experimental facilities, population biology and microbial risk assessment modelling to understand the interactions between the disinfection residuals, biofilms, pathogens and hydraulics of drinking water distribution systems. This research will combine globally renowned expertise in mathematical modelling, drinking water engineering, quantitative microbial risk assessment, and molecular microbial ecology to deliver this ambitious and transformative project. If the central proposition is proven, then current practice in the UK and the majority of the developed world could be increasing health risks through the use of disinfectant residuals. The evidence generated from this research will be central to comprehensive risk assessment. A likely outcome is that by testing the hypothesis, we will prove under what conditions the selective pressures on biofilms are unacceptable, and in so doing understand and enable optimisation of disinfection residuals types and concentrations for different treated water characteristics. Although focused on the impacts of disinfectant residuals and pathogens, the research will also generate wider knowledge of biofilm behaviour, interactions and impacts between biofilms and water quality within drinking water distribution systems in general and relevant to other domains. The impact of this research will be to deliver a step change in protecting public health whilst minimising chemical and energy use through well informed trade-offs between acute drinking water pathogen (currently unknown) and chronic disinfectant by-product (known and increasing) exposure. The ultimate beneficiaries will be the public, society and economy due to the intrinsic link between water quality and public health.