The central objective of this proposal is to improve the fatty acid (FA) content of perennial ryegrass by applying state-of-the-art genomics tools and resources and high throughput phenotyping methodologies and to quantify the impact of modified FA content on animal production, supply of beneficial omega-3 FA to the animal and greenhouse gas emissions (GHG). The project addresses some of the major challenges facing UK agriculture in a world that is undergoing climate change. The UK's climate favours grassland-based livestock production which is charged with the challenging target of increasing production whilst reducing inputs at a range of levels. Such sustainable intensification is increasingly relevant to the future of livestock agriculture. This proposal addresses sustainable agricultural production at the interface of three BBSRC strategic priority areas: crop science, livestock production and healthy and safe food. It is of high strategic relevance, specifically in understanding and exploiting the genomics for enhanced nutritional composition of pasture grasses (crop science). It will also increase the efficiency and sustainability of animal production, including minimising negative environmental impacts, such as emissions of greenhouse gases (livestock production) and investigates the potential of novel nutrient supplies from plants (healthy and safe food). Fats and oils are an important component of livestock diets, contributing a significant input of energy into the productive requirements of animals that consume them. Beyond delivering basic energy requirements for meat and milk production, FAs, and more importantly the FA profile of lipids in livestock feed can influence rumen function and the quality of animal products used for human food. We have identified a significant opportunity in relation to improving total FA content, in particular the polyunsaturated FA (PUFA) fraction, which will enable the next generation of IBERS high performance ryegrass varieties to provide benefits to UK agriculture and the environment, by potentially reducing enteric methane emissions and increasing ruminant production. It will also potentially result in human health benefits with more forage-derived PUFA being present in meat and milk. The project will combine the expertise of plant geneticists and breeders with ruminant nutritionists in an integrated multidisciplinary project. It will develop the genetic tools and resources to enable efficient selection for FA content and composition. Phenotyping plant material for FA content is however time consuming and costly. This project will therefore also develop high throughput techniques that will complement the advanced genetic approaches. The effect of modified grass FA content and composition on methane emissions, omega-3 absorption and growth of ruminants will be studied in vitro and in vivo. The project will use the results in combination with genomic selection approaches now being applied to the IBERS grass breeding programme to speed up the development of new perennial ryegrass varieties and their uptake by the livestock sector. Grass breeding programmes at IBERS have a track record of innovation and of delivery in terms of quality improvements, particularly in relation to cell wall biochemistry and the development of high water soluble carbohydrate (WSC) grasses which are well adapted to the UK and have a good agronomic performance. This proposal is being submitted through the BBSRC stand-alone LINK scheme. The project will benefit from the involvement of the only UK-owned forage grass and legume seed production and wholesale company (Germinal Holdings) and HCC representing a large part of the UK ruminant livestock sector, allowing for identification and review of key targets by the industrial partners and uptake and delivery of the outcomes of this project.

Contagious ovine digital dermatitis (CODD) is an extremely severe and relatively recent cause of infectious lameness in sheep in the UK, affecting approximately 35-53% of UK sheep farms and 300,000 sheep annually. The economic impact of CODD is unknown but likely similar to that of footrot, another common cause of lameness which is estimated at £24million per year. The Farm Animal Welfare Council, who report to the UK government on farm animal welfare issues, identified that research into this new disease should be a priority. Research into footrot has led to substantial improvements for the evidenced based advice available to farmers and vets on this aspect of lameness, and has been widely taken up by the sheep industry. However many farmers are struggling to control CODD infection in their flocks and substantial research support is required here. The applicants are currently the only research group studying CODD and through funding from the British Veterinary Association, HCC and EBLEX, this research group is making advances in our understanding of the epidemiology, pathology and microbiology of the disease, including the development of control strategies using antimicrobial drugs. The outputs of this work will produce practical solutions for the farming industry. Given the severe pressure on antimicrobial usage world-wide, sustainable, non-antibiotic solutions to CODD must focus on preventative approaches such as stopping the introduction of disease into naïve flocks through biosecurity and improvement in the sheep's ability to resist infection through vaccination. Both these solutions require a greater knowledge of the agent(s) causing the disease than we currently possess. We have already demonstrated evidence that specific culturable treponemes identical to those from bovine digital dermatitis have an association with CODD lesions and data from other studies has suggested a role for Dichelobacter nodosus and Fusobacterium necrophorum. This study proposes to i) carry out substantial metagenomic (entire microbial community) investigations of CODD lesions to identify the key microbes involved and ii)to characterise the host immune response to the identified microbes and determine whether specific antigens may allow a protective immune response to underpin future vaccine studies and iii) to use additional metagenomic surveys of the host farm environment and faeces to detect the relevant microbes which should allow for relevant farmer / veterinary guidelines to improve disease control. This proposal would ensure we obtain a greater understanding of the role of different bacteria in CODD development. This information will be key to future vaccine studies so that the correct microorganisms are targeted for vaccine design. Monitoring specific immunity in the naive sheep flock to be used in this study after exposure to CODD will allow assessment of the different stages of the infective process. This will not only describe stages of microbial infections but may also identify whether some animals are able to produce an effective immune response allowing for subsequent antigen discovery for effective vaccines. Identification of the considered causal microorganisms will also allow for more appropriate antimicrobial treatments thus reducing the risk of antibiotic resistance developing. Monitoring bacterial populations of CODD lesions post treatment should inform biosecurity practices i.e. whether treated animals result in bacteriological cure or become asymptomatic CODD "carriers". Monitoring faeces and environmental samples prior and post antibiotic treatment will also allow for development of best farm practices to minimise reinfection of sheep with CODD thus preventing failure / overuse of antibiotic treatment at the flock level. Investigating CODD using the various methods described above, should improve understanding of the disease and contribute towards the eradication of this painful and expensive disease.

Liver fluke is a common parasite that affects sheep and cattle in the UK. It is found throughout the world and in some countries it affects humans too, causing serious and sometimes fatal disease. Fluke infected cattle lose weight, become anaemic, lethargic and stop being productive. This has a serious effect on the welfare of the animal and serious economic consequences for the farmer. It is thought that fluke costs UK agriculture at least £300million pounds a year through direct losses, but real costs are probably much higher. Fluke has become much more common over the past 10 years, due in part to our changing weather patterns, wet summers and mild winters favour the development of the parasite and its vector - a mud snail, found commonly throughout Britain. In a recent study we found 75% of dairy herds had evidence of fluke infection. Future climate change is predicted to have a significant impact on prevalence of infection, changing the epidemiology and increasing incidence of disease. Increased cattle movements and changes to both farm management and environmental schemes are exacerbating the problem. A limited range of drugs is available to control fasciolosis. Only one drug - triclabendazole (TCBZ), is effective against early and late juvenile and adult stages of the parasite and is used extensively for prophylaxis and treatment of disease. There is growing evidence of resistance to TCBZ in fluke populations, moreover the European Medicines Agency has recently revised its advice on drugs used to treat fluke such that they are now contra-indicated in dairy animals. Targeted use of drugs, at specific times of year will slow the development of drug resistance and reduce the overall quantity of drug used, but a better understanding of the epidemiology and transmission of disease is vital if we are to develop control programmes that rely on improved on farm management practises rather than depending solely on drugs. This ultimately will be a sustainable and cost-effective way to control both clinical and sub-clinical disease in cattle and is the express desire of the livestock industry. Specifically requested by the farming industry, the purpose of this project is to produce new, sustainable, bespoke control programmes for beef and dairy farms, to reduce losses associated with fluke infection. In order to achieve this we must first develop diagnostic tests to identify infected herds. We already have good tools that we can use on milk samples to detect infected dairy herds but we need similar tests that are appropriate for beef herds. In addition we are aware of a newly emerging parasite problem, the rumen fluke. It is not clear if this parasite causes disease but it has the potential to interfere with the diagnostic tests we are developing for fluke. Therefore we will also develop a molecular test for rumen fluke. Secondly we will develop a system to categorise snail habitats that can be used to analyse satellite maps on a regional geographic scale to obviate the need to visit every farm to investigate snail habitat. We will also investigate how cow behaviour affects how the parasite gets to a snail host and from the snail host back to the cow. These are risk factors for fluke infection on a farm. Other risk factors, particularly husbandry practices, physical and environmental factors will be obtained from a study of 250 farms and these data fed into statistical and mathematical models to determine theoretically which of these factors are the most important in determining whether a farm has fluke or not. Concurrently we will assess the cost-benefit of changing these practices. Finally we will conduct a trial to evaluate if changing farm practice is effective in reducing levels of infection. We are working in partnership with the Agricultural Levy boards of the UK to implement improved control of fluke infection to benefit animal health, welfare and profitability of livestock farming in the UK.

The increasing frequency of extreme climate events in the UK suggests the approach of the 'Perfect Storm' described by Beddington (2009). In 2012 an early season drought followed by extreme rainfall and flooding over extensive areas of the UK drove the need for the 'climate smart' agriculture that will be used here to address the dual challenges of climate change and food security. Over an 80h period in November 2012, more than 46 x 106L of rain fell on the North Wyke Farm Platform (NWFP), 90% of which was immediately lost as overland flow or in drainage. Droughts also challenge the sustainability of UK grasslands and occur increasingly in winter where the warmer temperatures now encountered encourage continued winter growth placing drought susceptible varieties at risk. UK grasslands occupy 65% of all available agricultural land and unlike most other crops comprise perennial species that provide crop yields over many years. The combination of their extensive land-cover and persistency provides grasslands opportunities for environmental service in addition to their traditional roles as high quality forage for livestock agriculture. This is achieved through selection of the appropriate varieties and when necessary their modification, and improved grassland management, with benefits likely to persist over years. Grasslands provide catchments for many UK rivers and act as regulators of water capture, its release, and quality dependent on their composition. IBERS is widely recognised for innovative approaches to breeding grass and clover varieties. However, variety development has untill now neglected programmes to improve root design or the opportunities for improved root-soil interactions that will deliver improved soil structure, hydrology, nutrient use and reduce the compaction that compromises crop yields. A recent BBSRC study published in Nature Scientific Reports (involving the PI of this proposal) demonstrated the potential for a novel grass species hybrid to initiate significant root-soil interactions that would if reproduced at the field-scale generate significant benefits in terms of flood control (DOI:10.1038/srep01683). Equivalent results have been recorded in white clover. In the current project, the potential of both for flood control will be assessed at the field scale, independently and as mixtures. The project will use two new BBSRC-supported National Capabilities: the National Plant Phenomics Centre (NPPC) and the North Wyke Farm Platform (NWFP). The project will investigate at different scales from the individual plant genotype, to the plot, through to the crop the potential for environmental service that may be achieved through a modified root design or growth pattern. The results achieved from the NPCC and NWFP facilities will be validated by testing selected varieties on commercial farms in diverse locations and under alternative livestock management systems. The proposal will use the latest BBSRC high-throughput phenomic and genomic technologies, with a suite of well characterised and relevant experimental populations together with molecular markers to engage in marker-assisted breeding for improved root designs in elite forage grass and clover varieties. Plant materials suitable for entry into National List trials will be developed within the time-course of the project. This proposal is being submitted through the BBSRC stand-alone LINK scheme. The project will benefit from the involvement of industrial partners that represent the various sectors of the UK grassland and livestock industry allowing for identification and review of key targets, and evaluation of the impact of the research, dissemination of the results within the grassland sector, and uptake and delivery of project outcomes.