Approved Walsh Fellowship Projects 2007

Abstract:

The acid resistance mechanism in Salmonella is complex involving the co-ordinated expression of several key genes. Some research on Salmonella ATR has already been reported, nevertheless, there are fundamental gaps in our knowledge. This project will apply state of the art molecular methods to address these issues and provide a more complete understanding of the mechanisms of Salmonella ATR in a range of different serotypes. A strategic aim will be to understand how animal diet can be used to limit the excretion of salmonella. This approach will contribute towards an improved understanding of the regulation of ATR genes based on diet to provide the scientific basis for the design of dietary management controls in the future.

College: Prof. Seamus Fanning, UCD. Email: sfanning@ucd.ie

Teagasc: Dr. Declan Bolton, Ashtown. Email: declan.bolton@teagasc.ie

Abstract:

Escherichia coli O157:H7 and other verocytotoxigenic E. coli (VTEC) are significant food borne pathogens and cattle and derived beef and beef products are significant vectors of these organisms as evidenced by recent outbreaks across Europe (Anon. 2005, El Almin 2006, Schimmer et al, 2005). Recent quantitative risk assessments on E. coli O157 :H7 in minced beef have demonstrated that the factors having the largest impact on predicted risk of illness are the concentration (numbers) of E. coli O157:H7 on the faeces / hide of the animal presented for slaughter and the concentration of the pathogen in beef products. An intervention to reduce numbers of the pathogen at either of these key points in the beef chain would yield a significant risk reduction. Biocontrol agents including bacteriocins (anti-microbial peptides) and bacteriophage now offer huge potential as innovative, novel control agents in beef production and processing. These agents can specifically inhibit bacteria but have no impact on human or animals. Recent research has isolated bacteriophage and bacteriocins from environmental samples which in initial assays are shown to be effective against VTEC organisms (Flynn et al, 2004). This project will assess whether these agents can be applied to reduce numbers of E. coli O157:H7 at key points in the beef chain namely to reduce shedding of the pathogen in cattle or to reduce its numbers in beef products. Research to be conducted will include a full assessment of the bacteriophage / peptides identified for their activity, broadness of action and stability. A full biochemical and molecular characterisation of the peptides and bacteriophage will be carried out to establish the active components, mode of action and the safety of the agents to ensure they do not contain any genes which would be virulent or pathogenic. The effect of environmental factors on the action and stability of the agents will be assessed initially in model beef and bovine rumen systems. Finally the optimum biocontrol agent(s) will be applied to reduce shedding in cattle and to reduce VTEC in beef products.

College: Prof. Seamus Fanning, UCD. Email: sfanning@ucd.ie

Teagasc: Geraldine Duffy, Ashtown. Email: geraldine.duffy@teagasc.ie

Abstract:

Salmonella and Yersinia enterocolita are the two bacterial pathogens of human clinical importance associated with pigs and pork products. This project will, in collaboration with UCD, refine the current risk assessment model for Salmonella along the pork chain and develop equivalent models for Y. enterocolitica. The microbiological research will include a measure of the incidence of these bacteria on farms and in pork processing plants, serotyping / speciation, antibiotic resistance and plasmid profiling as well as molecular characterisation (PFGE).

College: Prof. Ian S Blair, University of Ulster. Email: is.blair@ulster.ac.uk

Teagasc: Dr. Declan Bolton, Ashtown. Email: declan.bolton@teagasc.ie

Abstract:

This project will investigate the molecular epidemiology of Salmonella spp. and Campylobacter spp. on beef farms. It will establish the ecological sources of these bacteria and investigate the mechanisms of survival used by Salmonella and Campylobacter in a range of harsh environments encountered on farms. The data and information generated will be applied to develop on-farm activities designed to reduce/eliminate their incidence and spread on beef farms.

College: Prof. Ian S Blair, University of Ulster. Email: is.blair@ulster.ac.uk

Teagasc: Dr. Declan Bolton, Ashtown. Email: declan.bolton@teagasc.ie

Abstract:

This project will investigate the molecular epidemiology of verocytotoxigenic E. coli including E. coil 0157:H7 on beef farms. It will establish the ecological sources of these bacteria and investigate the mechanisms of survival used by VTEC in a range of harsh environments encountered on farms. The data and information generated will be applied to develop on-farm activities designed to reduce/eliminate their incidence and spread on beef farms.

College: Prof. DA McDowell, University of Ulster Email: da.mcdowell@ulster.ac.uk

Teagasc: Dr. Declan, Ashtown. Email: declan.bolton@teagasc.ie

Abstract:

This project will focus on the transmission, survival and virulence of key food borne pathogens in the beef chain. Research will include an exposure assessment and molecular epidemiological investigation of selected pathogens during beef slaughter and processing. Studies will also be conducted to assess the effect of particular stresses / controls (known and novel) during beef processing on the fitness and virulence of key pathogens. This research data will be used to develop and apply quantitative risk assessment models for pathogens in beef trim and selected processed beef products. This research will result in recommendations for strategic controls to reduce the risk from microbial pathogens in beef and beef products.

College: Prof. DA McDowell, University of Ulster. Email: da.mcdowell@ulster.ac.uk

Teagasc: Dr. Geraldine Duffy, Ashtown. Email: geraldine.duffy@teagasc.ie

Abstract:

Mid term review of the Common Agricultural Policy has resulted in removal of price supports for commodity dairy products with major increases in quantities of Irish milk supply being processed into cheese. Mild/semi-hard cheese-types for continental EU, eastern European and markets in the Americas, have been identified by the “Strategic Development Plan for the Irish Dairy Processing Sector” (Prospectus report) as an area for major development. Some cheese manufacturers have diversified into the manufacture of Continental-type cheeses, notably Swiss type. However, certain technical and quality issues have arisen during this diversification.

A serious secondary fermentation defect has occurred during ripening of cheese at 2 industrial scale Irish cheese producers over the past 2 years. This defect manifests itself late in ripening with no retrospective solution and results in downgraded and inconsistent product. It is a serious technical and competitive barrier to continued expansion in cheese diversification. There is no scientific consensus on the cause of secondary fermentation and competitor countries (Switzerland, Finland, Germany, New Zealand and USA) have invested in research to maintain quality and consistency of their continental and eye-type cheeses. Research is urgently required to determine what factors are causing secondary fermentation in Irish cheese, how they can be controlled and in a manner that does not compromise sensory and texture attributes.

Initially, this project proposes to establish the levels of, and variation within, key quality attributes (biochemical, microbiological and physiochemical) of a continental cheese-type manufactured at industrial scale from a seasonal Irish milk supply. This will facilitate correlation of secondary fermentation with variations within these key quality attributes.

Secondly, the project will undertake laboratory studies and pilot scale trials to determine; the influence of physiochemical factors on cheese pliability/elasticity and its ability to withstand increased gas pressure; the impact of Lactobacillus helveticus on stimulation of gas formation by propionic acid bacteria; and the use of facultatively heterofermentative lactobacilli to control gas formation.

This project will result in a scientific and technological platform to control secondary fermentation defects and to enhance the quality and consistency of continental-type cheeses produced using a seasonal Irish milk supply.

College: Prof. Paul L.H. McSweeney, UCC. Email: p.mcsweeney@ucc.ie

Teagasc: Diarmuid Sheehan, MFRC. Email: diarmuid.sheehan@teagasc.ie

Abstract:

Glycaemia is the concentration of glucose in the blood and is controlled by several physiological processes including the rate at which glucose is absorbed in the gastrointestinal tract after a meal. Blood glucose elicits an insulin response which in turn effects satiation and fat metabolism. The glycaemic index of a carbohydrate refers to the ability of the carbohydrate to affect blood glucose levels. Carbohydrates that break down quickly during digestion are ranked as high GI as they cause blood glucose to rise quickly. Carbohydrates that break down slowly in the digestive system release glucose slowly into the blood stream and have a low GI. Low GI foods are thought to reduce the risk of developing type 11 diabetes, cardiovascular disease and obesity. Scientific studies have demonstrated that the bodys’ glycaemic response to carbohydrates when co-ingested with proteins is lower than that from ingestion of carbohydrates alone. This project proposes to explore how dairy protein and carbohydrate combinations may be formulated with a view to modulating the bodys’ glycaemic response. Gut endocrine cells respond to ingested food by releasing various gastrointestinal satiety signals. In vitro cell culture bioassays will measure response of gut signals to novel protein-carbohydrate formulations. Data collated from in-vitro studies will be used to develop novel isoglucidic beverages for evaluation in pig clinical trials to identify their effects in vivo. For this, blood samples will be biochemically analysed to measure plasma metabolites, such as glucose and insulin, and various satiety signals. The ultimate aim is to identify a protein-carbohydrate complex with a low glycaemic response, controlled release of insulin and/or increased levels of satiety signals.

College: Prof. Linda Morgan, University of Surrey. Email: l.morgan@surrey.ac.uk

Teagasc: Dr. L. Giblin, MFRC. Email:  fiona.ohalloran@teagasc.ie

Abstract:

Lameness is the second most important production disease after mastitis in dairy cattle and is such a painful condition that it has serious implications for animal welfare. Owing to the cost involved in treating lameness and the negative effect it has on milk yield the financial implications are enormous. Most lameness research comes from countries where cows calve all year round and/or are continuously housed. The factors influencing lameness are different in grass based production systems based on seasonal calving. Most of the lameness in lactating cows in such systems arises from walking to and from the milking parlour twice daily. The risk factors include distance travelled, abrasiveness of the walking surface and the weather; wet, muddy condition result in softer hooves that are more susceptible to injury. There are two reasons why lameness is set to increase in Irish dairy herds. The first is that Irish herds are increasing in size to remain profitable. This means that cows have to walk longer distances. Secondly the policy of extending the grazing season to include as much grazed grass as possible in cows diets means that they are outdoors in cold, wet weather in the early spring and late autumn. Ultimately cows are likely to start the housing period with existing injuries and thin soles. Given that the feet are at risk of a host of other problems indoors, the problem of lameness in cows at calving is likely to escalate. The first step in addressing this problem is to better understand the factors governing changes in the structural characteristics of the hooves of cows at pasture and to determine the relationship with foot health. Secondly this project will investigate ways of protecting the feet from trauma during lactation. Alternative substrates for farm roadways such as wood chips and the use of rubber flooring in the parlour collecting yards will be evaluated.

College: Dr. Alison Hanlon. Email: alison.hanlon@ucd.ie

Teagasc: Dr. Laura Boyle, Moorpark Production. Email:  laura.boyle@teagasc.ie

Abstract:

Non-point sources of agricultural pollution are difficult to identify and control, and are one of the main reason that rivers fail to reach good ecological and chemical status decreed by the European Water Framework Directive and various regulations on nitrate management. Integrated constructed wetlands (ICW) have been designed to treat farmyard wastewater and runoff following good sustainability principles such as adequate sludge dewatering, water treatment, optimal integration into the landscape, ecosystem and biodiversity enhancement, and excellent compliance with socio-economic needs.

Wetland systems for farmyard runoff treatment are currently designed based on empirical observations. There is a clear need for a decision support tool for the design and operation of ICW dewatering and treating slurry from pig farms incorporating standard engineering and microbiological variables. This can only be achieved by incorporating molecular microbiological techniques into novel engineering decision support methodologies.

Wastewaters from intensive agricultural activities contain high concentrations of nitrogen that contributes to water management problems. It has long been recognized that certain microbial groups in animal waste are responsible for breaking down various organic compounds. However, no research has been done on the functional composition of the different bacterial groups in ICW responsible for pig wastewater purification. Moreover, the retrieval and potential recycling of organic residue including detritus requires further research.

The application of molecular microbiological techniques will assist in, for example, measuring the potential oxidation of ammonia and nitrite. This project will lead to the identification of the key biochemical processes within ICW treating pig wastewater, which are important for a better understanding of spatial and temporal nitrogen and phosphorus transformation processes. A neuro-fuzzy modelling approach will be used to gain insight into the processes within ICW in space and time and how such processes affect system performance.

College: Dr. Miklas Scholz, University of Edinburgh. Email: m.scholz@ed.ac.uk

Teagasc: Dr. Noel Culleton, Johnstown Castle. Email:  noel.culleton@teagasc.ie

Abstract:

This project has two sections:

Take a representative set of soil samples of Irish tillage soils, at 40 locations in Ireland (at depths of 0 to 50 cm) and quantify the soils with regard to bulk density (BD), texture, Soil Organic Carbon (SOC) and carbon fractionation (that is, the slow, active and passive pools required for modelling). Integrate this new, more detailed data to the National Soils Database (NSD) of 1310 samples (completed at 0 to 10cm depth by Fay, Teagasc 2006). Fay (2006) has established SOC levels but because soil physical properties were not recorded, the NSD data currently cannot be used to estimate soils C stocks. In this proposal, the new data will be used to estimate SOC stocks as BD and SOC concentrations will be measured. This proposal also complements the EPA project SoilC (McGoff, Kiely) that has looked at a total 60 sites (25 grassland, 12 tillage, 9 forestry and 14 peatlands ) to a depth of 50cm. Use statistical modelling techniques to add value to the NSD project by extending its knowledge of tillage soils from its current depth of 0 to 10 cm to the greater depth of 0 to 50cm..

Test the widely used Soil Organic Matter (SOM) models, including CENTURY, RothC and PaSim to determine the most suitable model to quantify the SOC stocks in Irish tillage soils. Select the most appropriate model. Calibrate the model using the three temporal datasets on SOC (Brogan 1965, McGrath 1996 and Fay 2006) and model possible changes to the SOC stocks in tillage lands with a view to determining soil carbon sequestration potential. Conduct a range of scenario modelling to assist in evaluating sustainable management options for Irish tillage land.

The reporting from this project of both the experimental work of (1) and the modelling work of (2) will inform policy on carbon in tillage soils and how it is related to tillage agricultural activities.

College: Dr. Mike Williams, TCD. Email: g.kiely@ucc.ie

Teagasc: Prof. J. Burke, Oak Park. Email: jim.burke@teagasc.ie

Abstract:

Ash is a very important hardwood species for farm forestry in Ireland in terms of economic potential, rotation length and adaptability to a wide range of soil and climate types. The Irish government introduced substantial planting grants around 1992 for farmers to plant trees with an extra premium for planting hardwood species including ash. This led to a shortage of home-produced plants from home-collected seeds. Consequently plants and seeds of several species were imported to fill the needs (from various sources including France, Czech Rep, Poland and the Netherlands). Many of these plantings developed very bad stem-form, unusual morphology, poor vigour, and extensive canker. In others the morphological characters were less obvious. However, it was clear that the problem was due to the source of the plants/ seeds and that the imported material was probably hybrid ash derived from F. excelsior × F. angustifolia. In a few known cases it was determined that the material came from France. Today, there are at least 100 afforested sites in which suspected hybrid ash was planted.

There is a lack of understanding of hybrid ash in general, its occurrence in Ireland, and potential of it to interbreed with native ash. It is important to study these hybrid ash plantations to assess the scale of the problem and to gather essential biological/genetic data. This proposal therefore aims to carry out a set of morphological, physiological and molecular tests to characterise material from suspected sites and to assess the potential of these plantations to interbreed with indigenous ash (at 50-100 suspected sites).

Funding to cover research costs of this project (but not staffing costs) have been secured (see previous table for detail) from the COFORD Forest Research Programme 2006/7, by Douglas and Hodkinson, in collaboration with colleagues at Univ Paris XI and INRA. We are seeking funding for a postgraduate PhD researcher to undertake the part of the work in this larger project.

College: Trevor Roland Hodkinson, TCD. Email: trevor.hodkinson@tcd.ie

Teagasc: Dr. Gerry Douglas, Kinsealy. Email: gerry.douglas@teagasc.ie

Abstract:

The principal aim of this project is to evaluate the economic potential of open-air outdoor recreation associated with improved public access to farm land for walking using stated preference techniques. Unlike other EU countries formal public access provision is limited and dependence on by-product access is high. Farmers frequently face external costs and nuisance effects due to access provision. Consequently, detailed on-farm surveys (Teagasc National Farm Survey) will be carried out with landowners in order to establish the financial, institutional and cultural conditions necessary to ensure that farmers provide improved recreational access and carry out the required improvements and maintenance to support this activity. The project will also identify landowner preferences for different types of payment vehicle and different institutional mechanisms involved in providing this public good. A detailed socio-economic analysis of these measures will be carried out identifying economic, social, cultural and political factors that may restrict subsequent provision of this public good. Outcomes will be disseminated through statutory agencies and non-governmental organizations involved in recreational access provision.

College: Dr. Tom van Rensburg, NUI Galway. Email: thomas.vanrensburg@nuigalway.ie

Teagasc: Dr. Stephen Hynes, RERC. Email: stephen.hynes@teagasc.ie

Abstract:

Energy security is now a big concern in many countries as a result of instability in complex international energy markets and the strong upward trend in energy prices driven partly by growing demand from the emerging economies. High energy prices increase production and marketing costs throughout the economy and squeeze profit margins particularly in industries heavily reliant on energy. In the agri-food sector costs are increased throughout the food supply chain, ultimately increasing food costs and causing a number of significant knock-on effects, for example the growing of energy crops and biofuel production. All of this can have far reaching consequences for long-run resource reallocation in the food supply chain and the rest of economy. It is vital for policy analysis purposes that economic research has the capacity to capture the full impacts of these complex interactions, in the short, medium and longer term, throughout the food supply chain and in the wider economy. Due to its superiority in capturing technical, environmental and economic linkages and constraints between different sectors in the economic system, this project will develop and use a computable general equilibrium (CGE) modelling approach to analyse economic and environmental impacts of changing energy prices in the food supply chain and wider economy. Economic impact here refers for example to redistribution of resources (land, labour and capital) changes in producer and consumer surplus, quantification of multiplier effects and supply/demand elasticities. Environmental impact will be more focused on quantification of CO2 emissions and nitrate balances.

A CGE model for Northern Ireland will be developed based on the current version of Northern Ireland input/output table. This version of the table includes 22 economic sectors of which 18 are agri-food. For the purpose of this analysis an expansion of the energy sector block in the table will be necessary via primary research. Quantification of emissions will involve close collaboration with environmental scientists.

The techniques to develop and use a CGE model are now rather mature and standard. However, major quality assurance issues arise in the generation of appropriate data to construct a regional I/O table, encompassing the range of economic and environmental variables, and then to construct and run the model in order to produce outputs that provide valuable decision support to the policy, NGO and private sectors. We will combine existing data estimation techniques with business surveys to update and expand the current database and social accounting matrix.

College: Dr. Ziping Wu, Queens University. Email: z.wu@qub.ac.uk

Teagasc: Mr. Trevor Donnellan, RERC. Email:  trevor.donnellan@teagasc.ie

Abstract:

The RERC project - Audit of Policy in Rural Areas (RMIS 5577) - is currently examining various aspects of the impact of housing policy in rural areas. It is envisaged that the research that is the subject of this application – Rural Perspectives on Public Service Provision – will feed into RMIS 5577 by providing an analysis of housing benefit in a rural context.

Research is already being carried out within the Rural Economy Research Centre by a PhD student on Housing Benefits in Europe and the Impact of Housing Benefit Policy Reform in Ireland. This research is funded by the Combat Poverty Agency. It is envisaged that the same researcher could extend their analysis to focus explicitly on the rural dimensions of housing benefit, thereby contributing a vital component to RMIS 5577, and also generating complementarities in research effort.

The aim of this research is to assess the impact of various critical policy instruments on rural residents. To do this, the research will utilise a variety of data sources such as the European Survey of Income and Living Conditions (EU-SILC), the Living in Ireland Survey, the European Community Household Panel (ECHP) and a survey of housing benefit recipients.

More generally it is clear that the impact of policies such as housing, health, education, transport and enterprise on rural areas, critically influences the living conditions of rural residents and the broader human, social and industrial capital environment faced by rural enterprises. As such, the output from this research application will enhance understanding of a critical policy area – housing support mechanism - that should be used to underpin the competitiveness, sustainability and viability of rural Ireland, all of which are key elements of the Teagasc Statement of Strategy 2005-2007.

College: Prof. Michael Cuddy, NUI Galway. Email: michael.cuddy@nuigalway.ie

Teagasc: Dr. Cathal O'Donoghue, RERC. Email: cathal.odonoghue@teagasc.ie

Abstract:

In today’s dynamic environment supporting healthy eating needs to be based on a thorough analysis of consumer attitudes and behaviour. The determinants of healthy eating are many and varied and include both lifestyle (in particular diet and exercise) and psychosocial factors. In the context of this study, the focus is on lifestyles, as unhealthy diets are very much linked to lifestyle decisions, which in turn are driven by the values of the individual. In the context of food lifestyles, Peters et al.(2002:70) note that “high in fat and energy density, easily available, relatively inexpensive, good tasting and served in large portions” have been conducive to an ‘obesogenic’ environment. These factors therefore influence the health status of a diet. Clearly research that can go some way to better understanding population cohorts’ perspectives on food should aid industry in their endeavours to create new products that ensure the healthy choice is the easy choice for consumers.

This research proposes the application of the Food Related Lifestyle (FRL) segmentation tool to investigate the impact of such lifestyles on healthy eating patterns. Both qualitative and quantitative research will be conducted. Focus group discussions will inform the design of the research instrument, in particular on the barriers that impact on the healthy dietary choice across potential lifestyle segments. The focus group discussions will also be used to expand the FRL tool to integrate the food lifestyles of the non-meal preparers in the household. This research will contribute to a greater understanding of food consumer’s motivations and choices and should enable food companies to optimise their marketing parameters based on characteristics of chosen segments.

College: Dr. Mary McCarthy, UCC. Email: m.mccarthy@ucc.ie

Teagasc: Dr. Maeve Henchion, Ashtown. Email: maeve.henchion@teagasc.ie

Abstract:

The competitive advantage of the Irish dairy industry has been based on low costs of production through the maximum utilisation of grazed grass. While some farmers have made substantial productivity gains through improved pasture utilisation and effective use of supplements, others have combined these feeds less efficiently. Consequently there is a role for robust decision support tools to assist farmers in making both strategic and tactical decisions to feed their herds as efficiently as possible. These decision tools will be created in conjunction with grazing research aimed at improving the overall profitability and sustainability of grazing enterprises, largely through proactive management and decision making.

College: Dr. A.M. Butler, UCD. Email: annemarie.butler@ucd.ie

Teagasc: Drs. B. Horan, Moorepark Production. Email: laurence.shalloo@teagasc.ie

Abstract:

Irish Agriculture is under increasing pressure both environmentally and economically. Increasing environmental regulations such as the recently legislated nitrates directive and the impending Water Framework Directive require minimum loss of nutrients from farm production systems. Economically, agricultural production costs are increasing while receipts are declining. Grazed grass is the cheapest form of feed available for milk and meat production in Ireland (Dillon, 2007; O'Kiely, 1994). A biophysical model offers the opportunity to model both herbage production and nitrogen (N) flows and losses from different soil types and climatic regions. In this project an existing biophysical model – EcoMod/DairyMod – will be calibrated and validated for use under Irish conditions (soil type and climate). This would provide a very valuable research tool to simulate exploratory scenarios which would otherwise be very costly to undertake both in terms of resources and time. In addition, pre-experimental modelling of treatments would result in the selection of scenarios most likely to be of importance to Irish agriculture. Post experimental modelling will also be possible, allowing research results from one site with one set of conditions to be modelled and compared against other locations and conditions. The model will be used in conjunction with the Moorepark Dairy Systems Model (MDSM) to determine optimum production systems within existing and futuristic restrictions. Various dairy production systems scenarios, e.g. production versus environmental targets for a range of soil and rainfall zones, will be modelled and output used in the MDSM. Furthermore, EcoMod/DairyMod has a very strong grass growth element. These modelling principles will be used to develop a grass growth predictor which can be used as a decision support tool. Such a decision support tool can be used to predict grass growth from time of year and simple meteorological forecasts (rainfall, temperature). This would prove to be a very effective tool for Irish grassland farmers, as it would allow for better management of feed budgets, thereby maximising animal production.

College: Dr. A.M. Butler, UCD. Email: annemarie.butler@ucd.ie

Teagasc: Dr. D. Hennessy, Moorepark Production. Email:  deirdre.hennessy@teagasc.ie

Abstract:

Benchmarking can enable farmers to gain critical insights into how they can improve overall efficiency by comparing their performance across a number of dimensions with standards of best practice in those areas. However, despite its clear potential benefits as a management tool, benchmarking has remained underutilised by the farming population generally. Building on the existing benchmarking system, Dairy Profit Monitor, this study will develop and apply state-of-the-art methodologies for benchmarking and performance evaluation by drawing on international experiences such as the Danish Focus-Finder system. Similar to Focus-Finder, it is suggested that a Data Envelopment Analysis method is used to estimate the best-practice frontier across the multiple dimensions of input usage in dairy systems. The technique will estimate technical and profit efficiency scores and will be used to define peer groups that permit more meaningful comparisons for individual farms. The study will also examine the mechanisms for reporting benchmarking data to farmers with a view to encouraging greater use of such data for improving managerial performance.

College: Dr. Michael Wallace, UCD. Email: michael.wallace@ucd.ie

Teagasc: Dr. Laurence Shalloo, Moorepark Production. Email: laurence.shalloo@teagasc.ie

Abstract:

In this study, sustainable technologies to treat soiled water for reuse as yard washing water will be examined at laboratory and pilot plant scale. The objective of the study is to develop on-farm sustainable technologies that will: (i) substantially reduce the usage of pristine water on dairy farms and (ii) significantly decrease problems associated with the spreading of soiled water. The soiled water will be collected in holding tanks –existing on most farms - where settlement of solids will take place. After passing through the holding tanks, the clarified wastewater will be pumped onto a filter bed of wood chips for the further removal of solids along with the biological reduction of organic carbon. A large proportion of the nitrogen and phosphorus in the washwaters will be utilised in the growth of biomass in the woodchips. Further reduction of the remaining soluble nitrogen in the effluent will be carried out using a low technology biofilm reactor technology developed at NUI Galway. The treated water will be collected in a storage tank and used as yard wash water. The woodchips, including the biomass, will be spread on the land once or twice a year and will be composted there, ensuring that there is a recycle of nitrogen and phosphorus to the soil. Laboratory scale reactors will be developed to establish (i) suitable depths, types and sizes of the wood chips to ensure that no clogging of the filters occur and (ii) organic carbon and hydraulic loading rates on the filters. The wood chip filter technology along with the NUI Galway developed nutrient removal technology will then be examined at pilot plant scale on a dairy farm site .

College: Dr. Michael Rodgers, NUI Galway. Email: michael.rodgers@nuigalway.ie

Teagasc: Dr. P. French, Moorpark Production. Email: padraig.french@teagasc.ie

Abstract:

Accurate identification of cattle infected with M. avium subsp. paratuberculosis (MAP, Johne’s Disease; ParaTB) is vitally important in controlling and eradicating Johne’s disease. Diagnosis of the disease has proven exceptionally difficult due to the nature of the micro-organism, which infects animals at an early age via ingestion, but does not result in readily apparent clinical signs for several years. Current identification of infected individuals ‘on-farm’ involves recognition of clinical signs. Diagnostic tests such as faecal culture for confirmation of infection are highly impractical primarily due to the fact that results are not conclusive until sixteen weeks post-culture. The Department of Agriculture and Food has described Johne’s Disease as an ‘emerging problem in Ireland’s cattle herds’ and while a link to Crohn’s Disease remains to be proven, Johne’s Disease may have zoonotic implications which could seriously impact the Irish dairy industry. Thus in the interest of food safety, it has now become very apparent that identification of preclinical infected animals is paramount, in both preventing the entry of infected milk into the food chain and, in preventing further dissemination of the disease.

This project aims to address the lack of reliable and rapid tests for the early diagnosis of Johne’s infection. A number of new techniques, which have been applied to the identification of cattle infected with MAP, including immunological, flow cytometry and molecular based techniques will be evaluated. Newly developed techniques will be used to detect novel disease biomarkers. Application of these techniques will be examined for disease surveillance suitability. The assays will also be used to track the disease in calves in order to establish how early in the disease cycle that infection can be detected. These diagnostic tests will be linked to the epidemiology of the disease in problem herds.

College: Dr. Torres Sweeney, UCD. Email: torres.sweeney@ucd.ie

Teagasc: Dr. John Mee, Moorepark Production. Email:  john.mee@teagasc.ie

Abstract:

The use of artificial insemination (AI) in dairy cattle has recently declined. The rate of genetic improvement, measured by the Economic Breeding Index (EBI), is currently unacceptably low at approximately €5 per year. It is estimated that under optimal selection conditions, the rate of genetic improvement could be 5 times higher than that currently achieved. A recent Teagasc survey highlighted inconvenience of heat detection and labour availability as the principal barriers to increased AI usage (Shalloo et al., 2006). It is currently estimated that less than one third of replacements coming into the national dairy herd are from AI sires. The primary objectives of this project are to identify the factors that affect oestrous expression, and to increase the use of AI in the dairy industry. To address these objectives, we propose carrying out research projects that will (i) evaluate different heat detection aids and determine the extent of suboestrus in Irish dairy herds; (ii) increase our understanding of the control of oestrous expression; and (iii) develop practical methods for synchronisation of oestrus in seasonal calving systems of production; It is anticipated that the proposed research will stimulate increased use of AI, in addition to increasing our understanding of the control of oestrous expression.

College: Prof. Mark Crowe, UCD. Email: michael.doherty@ucd.ie

Teagasc: Dr. Stephen Butler, Moorepark. Email: stephen.butler@teagasc.ie

Abstract:

Until the start of this decade, genetic selection in dairy cattle was based exclusively on milk production. Remarkable advances in milk yield per cow were achieved under this strategy, but was accompanied by undesirable negative effects on health and fertility. In recent years, the Economic Breeding Index has been developed, and genetic improvement in Ireland now involves selection for milk yield, health and fertility. This is called a balanced breeding objective. The traits included in the breeding objective are summarised into sub-indices: production, fertility, calving performance, beef performance and health. Within the national herd, it is now possible to identify cows with similar EBI production sub-indices, but with extremes of high and low EBI fertility sub-indices. It is anticipated that the predicted differences in fertility would result in phenotypic differences in conception and pregnancy rates, but differences in milk yield would be negligible. This would allow a rigorous examination of the genetic causes of subfertility, and would have the benefit of removing the confounding effects of differences in milk yield that are typically associated with studies examining differences between strains of dairy cows with phenotypic differences in fertility. This project proposes to examine differences in productive efficiency, hormone and metabolite profiles, expression of key developmental genes in oocytes and embryos, and to look at differences in the expression of key genes in liver, muscle and adipose tissue.

College: Prof. Pat Lonergan, UCD. Email: pat.lonergan@ucd.ie

Teagasc: Dr. Stephen Butler, Moorepark Production. Email: stephen.butler@teagasc.ie

Abstract:

A seasonal grass based system of milk production gives Irish milk producers competitive advantage over their European counterparts who use higher concentrate input systems. However, grass based diets may not provide adequate nutrients for the current high producing cows in Irish herds and there has been an increasing interest from producers in higher input total mixed ration (TMR) systems. Specifically, the uptake of the partial TMR (pTMR) approach to pasture supplementation in advance of independent research, and its effect on dairy farming competitiveness and sustainability when compared with traditional feeding strategies, warrants investigation. Moreover, the efficacy of employing a high-fibre/low energy TMR feeding strategy during the dry period in the context of a pasture-based system requires clarification. The objective of this project is to evaluate the conventional grass based dietary strategy in comparison to TMR diets, in the Irish system of milk production. The impact on milk production and composition, metabolic status and hepatic function will be assessed. The dietary strategies will be evaluated in the dry and early lactation periods especially. The results from this project will facilitate more informed decision making in relation to the most appropriate feeding strategy for the current high producing Irish dairy cow. The results will also provide valuable data for analysis of the impact of feeding system on animal health and overall farm profitability.

College: Dr. Finbar Mulligan, UCD. Email: finbar.mulligan@ucd.ie

Teagasc: Dr. John Murphy, Moorepark Production. Email: johnpaul.murphy@teagasc.ie

Abstract:

Agriculture is an important source of nitrate in surface and ground waters in Ireland and across Europe. Farmers are now legally required to comply with measures to protect water from loss of nitrogen and phosphorus based on EU and National policies. The project will study the effect of winter milk production with 1) intensive (3 livestock units (LU)/ha with 300kg N/ha) and 2) extensive (2 LU/ha with 200 kg/ha N) treatments on groundwater nitrate and other nutrient levels, on a low vulnerability site at Teagasc, Johnstown Castle. Groundwater monitoring wells (GMW, 5 per plot) will be installed in 8 plots (four replicates per treatment). In addition, nutrient levels in water samples collected from the GMWs will be compared with nutrients in the top metre of soil using a) Teflon suction cups, b) soil wicks and c) soil samples in each plot. The spatial variation in nitrogen from GMWs and nitrogen balances using a suitable model will also be studied.

The justification for this study is to provide information on nitrogen losses to water from grassland under an intensive and extensive winter milk production system. The project will complement a stimulus funded study at a highly vulnerable site for nitrate leaching, currently located at Moorepark. Results will be written up in scientific papers, a thesis and reports.

College: Dr. Catherine Watson, QUB. Email: catherine.watson@dardni.gov.uk

Teagasc: Dr. Hubert Tunney, Johnstown Castle. Email: hubert.tunney@teagasc.ie

Abstract:

This project has two sections:

Take a representative set of soil samples of Irish tillage soils, at 40 locations in Ireland (at depths of 0 to 50 cm) and quantify the soils with regard to bulk density (BD), texture, Soil Organic Carbon (SOC) and carbon fractionation (that is, the slow, active and passive pools required for modelling). Integrate this new, more detailed data to the National Soils Database (NSD) of 1310 samples (completed at 0 to 10cm depth by Fay, Teagasc 2006). Fay (2006) has established SOC levels but because soil physical properties were not recorded, the NSD data currently cannot be used to estimate soils C stocks. In this proposal, the new data will be used to estimate SOC stocks as BD and SOC concentrations will be measured. This proposal also complements the EPA project SoilC (McGoff, Kiely) that has looked at a total 60 sites (25 grassland, 12 tillage, 9 forestry and 14 peatlands ) to a depth of 50cm. Use statistical modelling techniques to add value to the NSD project by extending its knowledge of tillage soils from its current depth of 0 to 10 cm to the greater depth of 0 to 50cm..

• Test the widely used Soil Organic Matter (SOM) models, including CENTURY, RothC and PaSim to determine the most suitable model to quantify the SOC stocks in Irish tillage soils. Select the most appropriate model. Calibrate the model using the three temporal datasets on SOC (Brogan 1965, McGrath 1996 and Fay 2006) and model possible changes to the SOC stocks in tillage lands with a view to determining soil carbon sequestration potential. Conduct a range of scenario modelling to assist in evaluating sustainable management options for Irish tillage land.
• The reporting from this project of both the experimental work of (1) and the modelling work of (2) will inform policy on carbon in tillage soils and how it is related to tillage agricultural activities.

College: Prof. Gerald Kiely, UCC. Email: g.kiely@ucc.ie

Teagasc: Dr. Owen Carton, Johnstown Castle. Email:  owen.carton@teagasc.ie

Abstract:

Early embryo loss is one of the greatest factors affecting fertility in the dairy and beef herds. Uterine function and the need to maintain an adequate supply of growth factors, binding and transport proteins to support adequate embryo growth and development until implantation has potentially the greatest influence on this loss. From previous studies we now know that uterine function can be affected by changes in nutrition and that uterine gene expression is sensitive to small changes in the steroidal environment. It is the translation and expression of these genes as proteins within the cell, however, that ultimately defines its function. With a potential order of magnitude increase in the number of proteins expressed as a result of alternate splicing and post translational modification, it is the study of these proteins in the post genomic era that hold the key to associating protein form with function. This projects sets out to use state of the art proteomic and bioinformatic techniques to characterise for the first time the low molecular proteome of the bovine uterus, how this is affected by changes in systemic progesterone and by stage of cycle. This project also aims to identify uterine specific or uterine predominant proteins and functional pathways implicated in embryo growth and survival.

This projects is a collaborative one between Athenry and the Proteomic Research Centre of the UCD Conway Institute of Biomolecular & Biomedical Research, UCD.

College: Prof. Michael John Dunn, UCD. Email: michael.dunn@ucd.ie

Teagasc: Dermot Morris, Athenry. Email: dermot.morris@teagasc.ie

Abstract:

Farmers currently produce a wide variety of feedstuffs for cattle subject to each farms’ unique set of circumstances. Due to improved agronomic practices, new varieties and the increased availability of purchased feeds the options available to Irish farmers are continually increasing. Climate change may increase further the number of crops which are viable in Ireland and will also have yield and quality implications for crops that are currently grown here. The components of the cost of home produced feedstuffs are diverse and involve many interconnected elements. These components include farm and soil properties, input costs and weather variables in addition to a range of opportunity and risk costs.

A computerised management information system will be developed to facilitate the rapid, repeatable and consistent calculation of the cost of a range of home produced feedstuffs for cattle. The program will be developed on an appropriate framework and will provide a decision support resource for Irish farmers. A user interface will be constructed to permit the friendly operation of the system.

The output of this research will be published in appropriate scientific journals. The program will be used to calculate the cost of producing feedstuffs on Irish farms under a range of scenarios. Areas where research data is lacking will also be identified and, if feasible, appropriate data will be produced.

College: Dr. Michael Wallace, UCD. Email: michael.wallace@ucd.ie

Teagasc: Dr. P Crosson, Grange. Email:  paul.crosson@teagasc.ie

Abstract:

Microarrays are now widely used for gene expression profiling in many animal science based experiments. Raw data emanating from microarray experiments, however, are very noisy and there are many sources of variation and bias. The raw data needs to be quality assessed and interactively "pre- processed" to minimise or remove this variation before statistical analysis in order to achieve any meaningful result. This requires a combination of visualisation and statistical tools which vary depending on what microarray platform or experimental design was used. A number of stand alone tools based on the statistical software R and Bioconductor routines are readily available for these types of analyses. However, the analysis pipeline is not always clear to the user, and the desired tools are not always vailable from the one source, without resorting to a command line interface, unfamiliar to most users. A serfriendly interface is required to facilitate the pre-processing and analysis of microarray experiments in Teagasc addressing the most common microarray platforms and array formats and following all progression through an analysis pipeline that is extensible and capable of addressing current as well as future needs.

College: Prof. John Hinde, NUI Galway. Email: john.hinde@nuigalway.ie

Teagasc: Dermot Morris, Athenry. Email:  dermot.morris@teagasc.ie

Abstract:

Beef genetic evaluations in Ireland have recently moved to an across breed evaluation incorporating data from crossbred animals and thereby replacing the previous within-breed genetic evaluations. Furthermore, traits associated with profitability in Irish beef herds have been identified and weighted based on relative economic importance into an overall breeding objective and subindexes. Two of the pre-requisites for inclusion of a trait in a breeding objective, other than its economic importance, are that it is easily measurable (or genetically linked to easily measurable traits) and exhibits genetic variation. Individual carcase cut yields (e.g., yield of loin cuts) are not routinely measured although they are linked to conformation as scored at slaughter. However, digital images of each carcase are now routinely recorded and stored which may provide greater detail on individual cut yields. The objective of most beef farmers should be to cost-effectively increase the yield of high value carcase cuts, further reinforcing the necessity to include actual carcase cut data in beef breeding objectives. Furthermore, sires proven outside of Ireland are treated similar to young test sires (regarding their published accuracy of their estimated breeding values) in Ireland. A large consortium of countries, led by Interbull, are undertaking research into applying animal model across country evaluation assuming across country interaction (AMACI) in beef cattle which accounts for non-unity genetic correlations between the “same trait” in different countries. This project will form part of the large international consortium and will address issues pertinent to Irish beef farmers. The main objectives of this study is to investigate the potential of digital images from mechanical grading of carcases in Ireland to predict meat yields, and subsequently to estimate genetic parameters for these newly derived traits in Ireland and their genetic correlation with routinely recorded traits in other countries. Large national and international databases will be used in the study

College: Dr. Freddy Fikse, SLU. Email: Freddy.Fikse@hgen.slu.se

Teagasc: Dr. Donagh Berry,Grange. Email: donagh.berry@teagasc.ie

Abstract:

The biological efficiency of producing beef from the suckler herd is low with a very large maternal cost to production. In calf-to-beef and calf to weanling systems, about half and two-thirds, respectively of the total energy consumed goes towards maintenance of the cow herd. As feed costs represent the largest single variable cost in beef production in Ireland consequently, feed efficiency is an important trait to consider when developing programs to identify cattle that are more economically and environmentally sustainable to produce. However, beef breeding selection strategies need to focus on improving feed efficiency without negatively altering cow performance or the performance (and carcass traits) of the progeny. Traditionally, feed efficiency was expressed as the ratio of weight gain to feed intake (FCR) but selection for this measure can lead to an increase in mature size and thus maintenance requirements. An alternative measure of feed efficiency proposed is residual feed intake (RFI), defined as the difference between an animal’s actual feed intake and its predicted intake and is largely independent of growth and body size. However, there is a paucity of substantive information on the impact of selection for RFI on the productivity of breeding females and their progeny particularly in the context of whole systems. The objectives of this proposal are to ascertain the biological basis for and quantify the productivity of, divergent selection for RFI in beef suckler cows and their progeny. Selecting herd replacements from low RFI animals should permit the production of energy efficient cows and progeny with lower maintenance requirements (i.e. consume less for a given bodyweight and growth rate) and consequently with environmental and economical benefits for producers.

College: Dr. David Kenny, UCD. Email: david.kenny@ucd.ie

Teagasc: Dr. Mark McGee, Grange. Email: mark.mcGee@teagasc.ie

Abstract:

Recent changes under CAP reform will require a greater focus on biological as well as economical efficiency within beef production systems. Feed can account for over 80% of the variable costs in beef production and is therefore a major factor determining competitiveness. Furthermore, up to 75% of total dietary energy consumed is for maintenance energy requirements. An increase in feed efficiency can have up to 7 to 8 times the economic impact as a similar increase in weight gain of cattle and is therefore, an important trait for inclusion in selection programs for beef cattle. Although considerable genetic variation is known to exist in feed efficiency, the expense of measuring individual feed intake has precluded its effective incorporation into selection programs. A newer concept of measuring feed efficiency known as net feed efficiency (NFE) or residual feed intake (RFI) has recently found favour in the breeding programs of a number of major beef exporting countries including Australia and Canada due to its value identifying genetically feed efficient animals with minimal effects on mature size. However there is a general lack of knowledge on the genetic control of net feed efficiency, and its relationship with other economically important traits. This project proposes to use a dataset comprising of detailed feed intake, performance and pedigree information collected over twenty years at the ICBF National Beef Bull Performance test station to elucidate genetic parameters for NFE and other economically relevant traits in Irish beef cattle. The project is a desktop studyand will compliment and bolster existing projects in this area at both UCD and Teagasc. The project will ultimately provide detailed genetic information that can be used to enhance the recently developed beef Economic Breeding Index

College: Drs. David Kenny, UCD. Email: david.kenny@ucd.ie

Teagasc: Dr. Mark McGee, Grange. Email: mark.mcgee@teagasc.ie

Abstract:

Cow conception rate is a major component of reproductive and production efficiency in beef and dairy herds. There is evidence of repeatable differences and of genetic variability between cows in conception rate and cow sustainability. Furthermore, it has been shown that conception rate or embryo survival rate is critically dependent on an optimum uterine environment prior to implantation. The critical period is the first two weeks after fertilisation when the embryo is totally dependent on the uterine fluid for its nutrition. Embryo loss is associated with the concentration of systemic progesterone and recently it has been shown that the concentration of systemic progesterone also affects uterine gene expression. There is evidence to suggest that progesterone-responsive changes in gene expression in the uterus are thus likely to affect embryo survival. However, while the uterine environment is critical to embryo survival, there is no published information on the direct association between conception rate or embryo survival rate and uterine gene expression. The objective of this proposal is to use a 23,000 bovine gene master array, the Affymetrix Bovine GeneChip®, to identify uterine gene expression profiles in animals of high and low conception rates and to relate changes in gene expression with key biochemical pathways and to interpret how this may influence uterine function and embryo survival. Furthermore, this project will (i) establish the uterine gene expression basis for difference in embryo survival rate, and (ii) produce data that may help identify genetic markers for embryo survival rate/conception rate in cattle which may be exploitable at industry level. The new knowledge generated by this proposal will enhance our understanding of cow fertility and will quantify the extent of gene expression differences existing for an important trait like uterine function.

College: Dr. David Kenny, UCD. Email: david.kenny@ucd.ie

Teagasc: Dr. Sinead Waters, Athenry. Email:  sinead.waters@teagasc.ie

Abstract:

Reproductive efficiency is a key factor governing economic performance of both beef and dairy herds and is of particular importance to seasonal calving systems. Nutrition is widely accepted to play a fundamental role in the modulation of reproductive events in all species including cattle. Even short term energy restriction can have major effect on ovarian function and embryo survival. The underlying biological mechanisms by which nutrition affects reproductive efficiency in dairy and beef cattle are poorly delineated. Because of the difficulty in studying both dairy and beef cows in the post partum period (access, cost, complexity of variables) we have developed a repeatable short-term dietary restricted heifer model to characterise the short term effects of NEB on endocrine, physiological and metabolic variables. We now propose to use the same well-defined model to establish the effects of short-term NEB on gene expression profiling in a number of key organs involved in the nutrition-reproduction axis (anterior pituitary, hypothalamic, preoptic and the ventromedial hypothalamus)as well as metabolomics fingerprinting of follicle fluid and blood to describe and establish biomarkers for animal nutritional status, sensitivity to dietary restriction or negative energy balance and or predictive of reproductive status or success. This project proposes to use a combination of global and targeted molecular techniques in associated with emdocrinological and physiological measurements to elucidate the complex interplay between nutrient, hormone and gene expression on the reproductive process. Specifically the obejectives of the project are to screen tissues of the hypothalamic-pituitary-ovarian axis to determine the effect of nutrient restriction on gene expression within these critical organs. Furthermore, metabolic profiling of follicular fluid and blood will provide information on the concentrations of important metabolites and hormones known to influence reproductive events. This project will build on existing basic and applied expertise in both participating institutions

College: Dr. David Kenny, UCD. Email: david.kenny@ucd.ie

Teagasc: Dr. Michael Diskin, Athenry. Email: sinead.waters@teagasc.ie

Abstract

The efficiency of nutrient utilization influences the profitability and the environmental footprint of livestock farming. Feed is the largest variable cost in beef production. In recent years, research has focussed towards understanding the feed intake and feed conversion efficiency of beef cattle. Understanding the genetic factors influencing feed intake characteristics of animals could enhance feed efficiency and provide marker assisted selection strategies towards more efficient utilization of feed nutrients.

Europeptide Y (NPY), a peptide produced by the hypothalamic region of the mammalian brain, is a major determinant of feed intake and appetite control in animals. Experiments involving laboratory animals clearly suggest that the NPY gene could be a potential target for understanding the feed intake and feed utilization behaviour in animals. In this regard, a project involving the sequencing of the bovine NPY gene in the applicant's laboratory has highlighted a number of single nucleotide polymorphisms (SNPs) in the putative promoter, exonic and intronic regions of the gene, which could play a vital role in determining feed intake characteristics.

To further our understanding of the nucleotide polymorphisms in the NPY gene in the Irish beef cattle herd, our objective is to determine the frequency of the SNPs of the neuropeptide gene in the major breeds of beef cattle and to determine the level of association of the NPY-SNPs with the feed intake characteristics of beef cattle.

College: Dr. Torres Sweeney, UCD. Email: torres.sweeney@ucd.ie

Teagasc: Dr. Sinead Waters. Email: sinead.waters@teagasc.ie

Abstract:

Miscanthus species are perennial, C4 grasses capable of tremendous biomass growth under a wide range of climatic conditions. Attention has focussed on biomass crops because of the need for alternative energy sources for sustainable living. Very few Miscanthus genotypes have been assessed for their biomass potential but work is underway to develop new genotypes. The overall aim of this project is to gather essential genomic information required for plant breeding in this poorly understood genus. The focus will be on the characterization of the nuclear and cytoplasmic gene pools. The entire chloroplast genome sequence will be sequenced, partial sequences of the mitochondrial genome will be generated and chromosome number and ploidy variation recorded for the nuclear genome.

Little is known about the cytoplasmic genomes (chloroplast and mitochondrial) of Miscanthus or of their variation. To address this, we will sequence its entire plastid genome (and sections of the mitochondrial genome) and study their features via annotated genome diagrams and via comparisons to other grasses especially sugarcane, sorghum and maize (same grass tribe). Structural rearrangements will be recorded and assessments made of the molecular evolution of their genes. We will assess the cytoplasmic gene pools available for breeding by developing and applying molecular markers (including but not exclusively SSR variants) suitable for rapid screening of diversity. We will quantify diversity, group haplotypes and study infra-generic variation. We will also assess if cpDNA and mtDNA are maternally inherited in Miscanthus.

Miscanthus species form a polyploid complex including several other genera (including Saccharum). For polyploid complex assessment we will use chromosome counts in conjunction with flow cytometry. The aim is to study nuclear DNA content and ploidy variation in the breeding genepools and to compare these to the assessments of plastid genome variation. We will determine crossability groups and gather essential information for future ploidy manipulation.

College: Trevor Roland Hodkinson, TCD. Email: trevor.hodkinson@tcd.ie

Teagasc: Dr. Susanne Barth, Oak Park. Email: susanne.barth@teagasc.ie

Abstract:

We propose a PhD fellowship for fine mapping quantitative trait loci in Lolium (ryegrass), identifying genes or genomic regions related to biomass heterosis, exploiting a large, well-characterized mapping population and a genome-scan from a Walsh fellowship ending in 2007.

The project fits well into the priority areas for the Walsh Fellowship call 2007: “Ryegrass and clover (breeding)” since it will generate markers for biomass yield, to date still the most important trait in the Oak Park breeding program, and the proposal fits as well in the category “Non-food uses of crops; Plant genomics for sustainable farming systems” since ryegrass will be a valuable biomass and bioenergy crop for Ireland in the future.

Methods used will be further fine mapping of selected chromosomal regions of three ryegrass chromosomes using SSR and RFLP markers. Synteny relationships among the grasses for these regions will be established using the Triticeae RFLP marker anchor set. From flow sorted BAC libraries clones will be picked using anchored RFLP markers as probes and chromosomal breakpoints identified using fluorescent in situ hybridization (FISH) with these probes. This will link the physical and genetic maps for these regions.

Practical outcomes of the research of this project will be the identification of molecular markers linked to dry weight biomass to aid the breeding selection process in early cycles. Scientifically the outcomes of the research will give more insights in syntenic relationships among the grasses and will give ideas how chromosomal rearrangements contribute to the expression of strong phenotypes like heterosis for biomass yield. A young researcher will be trained on genetics and bioinformatics techniques, and will develop biotechnological approaches to plant breeding. A number of peer refereed scientific publications are targeted and a PhD thesis will be the outcome of the project.

College: Pat Heslop-Harrison, University of Leicester Email: phh4@le.ac.uk

Teagasc: Dr. Susanne Barth, Oak Park. Email: susanne.barth@teagasc.ie

Abstract:

Self incompatibility (SI) is the primary mechanism by which outbreeding plants prevent self-pollination, which can lead to inbreeding depression in outbreeding species. Many agriculturally important plant species, including white clover exhibit SI. However, there are several breeding scenarios in which the ability to reliably self clover plants would be advantageous. Foremost amongst these is the ability to develop inbred germplasm, offering the possibilities of fixing key traits and producing F1 hybrid clover lines. Little is known about the genetic control of SI in clover, although some self-fertile lines have been observed in breeding programmes. This project is focused on developing a better understanding of the molecular mechanisms underlying SI in white clover. Specifically, a combined structural and functional genomics approach will be used in conjunction with classical genetics studies to identify the genes comprising, and the genetic location of the S-locus in white clover. Identifying clover S-locus genes will allow us to differentiate between different self-incompatibility alleles and also identify alleles of these genes which confer the rare self-fertility phenotype. The ability to identify these self-fertility (SF) alleles at the DNA level may enable the development of molecular markers to transfer the self-fertility phenotype to a genetically diverse range of genotypes, opening the possibility of hybrid line production in white clover.

College: Dr. Glyn Jenkins, University of Wales. Email: gmj@aber.ac.uk

Teagasc: Dr. Susanne Barth, Oak Park. Email: susanne.Barth@teagasc.ie

Abstract:

This project is concerned with understanding and modelling the main drivers for greenhouse gas emissions from a key European grassland site where at least three years of data are available. The main experiment involves a field manipulation study where grazing and fertilizer application are the key variables. Measurements of both nitrous oxide and CO2 flux from the soil will be taken over two years along side measurements of aboveground biomass, soil nitrate, soil ammonia, soil temperature and water filled pore space. A secondary experiment concerns the determination of both respiratory and denitrification capacity of soil cores sampled from a pre-existing ‘transect’ of European grasslands, each having a different C/N ratio. Data obtained from both experiments will be combined with previous data sets from the grassland site allowing a full field testing and uncertainty analysis of the widely used process based model, DNDC (Denitrification Decomposition). Combining data from this study with ongoing measurements of CO2 and N flux using eddy covariance and denuder columns will allow construction of a near complete carbon and N budget for the grassland site. Empirical models of both N2O and CO2 flux (gross) from the soil will also be constructed to allow a far less ‘data-hungry’ means of predicting greenhouse gas fluxes from European soils.

College: Dr. Charles Spillane, UCC. Email: willimsm@tcd.ie

Teagasc: Dr. Ewen Mullins, Oak Park. Email: ewen.mullins@teagasc.ie

Abstract:

The overall objective of this project is to develop a method of evaluating the on-farm persistence and wear tolerance of perennial ryegrass (Lolium perenne L) varieties from variety plot trials. Persistency is the ability of grasses to replace dying tillers ending reproductive growth and wear tolerance is the ability of a swards tiller structure to resist physical damage (animal/machinery). The interaction of these factors determines the extent a ryegrass variety can deliver its yield potential over-years on-farm. Through a review of literature three methods of evaluating sward persistency/wear tolerance will be chosen and implemented throughout the grazing season. The method will be refined and on-farm validated throughout the year to deliver a time efficient yet highly repeatable method of measuring longevity potential. This will be carried out using simulated and actual grazing plots to determine if a correlation exists. In addition, the effects of animal treading and trafficability on sward entirety/endurance will also be investigated both in simulated wear and actual grazing plots.

In conjunction with the establishment of in-field methods of measuring sward persistency, NIRS (Near Infra-Red Spectroscopy) will be used to assess sward purity. Different ratios of ryegrass and weed grasses (Agrostis/Holcus/Poa) will be used to create a robust NIRS calibration. This will be validated from existing plots within this study, with known compositions. The end point will be a NIRS calibration that accurately quantifies the ryegrass content of contaminated swards.

The final component of the project is to generate an economic value for sward longevity on-farm, which will be incorporated into a grass selection index model to convert variety trial results into an economic index specific to individual management systems. This project will have important economic implications for the grassland industry by identifying robust varieties that retain optimum grazing productivity but lower the frequency of costly reseeding.

College: Dr. Trevor Gilliland, QUB. Email: trevor.gilliland@afbini.gov.uk

Teagasc: Dr. Michael O'Donovan, Moorepark. Email: michael.odonovan@teagasc.ie

Abstract:

In commercial nursery stock production there can be a build up of disease causing organisms in ornamental shrub varieties such as Hebe, Weigela, Lavatera, and Choisya. This results in significant plant losses and increased production costs at producer level. In many cases the organisms can be systemic and are propagated together with the plant.  This project aims to improve the health status of selected lines through meristem culture and micropropagation. 

Many different varieties of popular species such as Euonymous, Escallonia, Viburnum and Photinia exist. Varieties can become mixed up during repeated propagations and also new mutations can arise.  The existence of several clones within varieties of the ornamental shrubs leads to production inefficiencies because of different physiological properties of each clone in relation to growth rate, plant form and disease tolerance. Similarly, disputes between producers and buyers in relation to conformity to the registered variety often occur.  It is proposed to collect clonal varieties of the specified ornamentals and to compare them to registered varieties in National Collections. Variety identification of each line will be based on morphology, growth performance and disease tolerance. Once sorted, the best performing clonal lines of each variety will be returned to the growers.

Public and private gardens contain ornamental forms adapted to Irish conditions. In some cases just a single plant of these rare selections exists. This proposal aims to make collections of such stocks of plants and also to apply the most appropriate propagation methods to produce small stocks of plants of each type for further evaluation including their potential for commercialisation.

Increasing the supply of well characterised clonal material, the provision of healthy stock plants and making available of rare or scarce Irish selections will improve the capacity of innovative nurseries to increase their product range and their production efficiency.

College: Dr. Alan Hunter, UCD. Email: katarina.hedlund@ekol.lu.se

Teagasc: Dr. Gerry Douglas, Kinsealy. Email: gerry.douglas@teagasc.ie

Abstract:

Dry Bubble disease, caused by Verticillium fungicola, is a major pathogen of the cultivated mushroom and can cause significant economic losses each year. Outbreaks can occur from as early as the pre-cropping stage, and in such cases losses can be in the region of about 10-15% or higher. The presence of mushroom flies on a farm will facilitate disease spread and hinder control. Currently only one fungicide, prochloraz, is approved to control dry bubble disease, to which a level of tolerance has been reported; there are no knock-down insecticides permitted during the crop production phase to reduce fly numbers at critical times; therefore prevention, good hygiene and early detection and treatment are the best approaches to minimise the damage this disease can inflict. We propose to evaluate molecular diagnostic tools to detect this pathogen in mushroom farm debris samples taken in and around mushroom farms in order to provide information on the potential disease pressure levels on a farm at a given time. We will conduct bioassays using mushroom farm debris samples to determine the potential for infected debris to cause disease. We will correlate the results of molecular diagnostics on debris samples with disease expression in bioassays to provide data on the efficacy of molecular diagnostic tools to correctly predict disease pressure. We will quantify levels of disease expression following infection of experimental crops at known levels of disease inoculum and crop management and we will obtain information to explain different patterns of disease expression in crops. We will evaluate the role of mushroom flies and eggs in the spread of dry bubble disease. We will produce a disease forecasting tool that will predict likely disease outcomes based on measurements of specific disease parameters.

College: Dr. Kevin Kavanagh, NUI Maynooth. Email: kevin.kavanagh@nuim.ie

Teagasc: Dr. Helen Grogan, Kinsealy. Email:  helen.grogan@teagasc.ie

Abstract

Hydrogen sulphide gas (H2S) is produced as a result of anaerobic activity within a heap of stored spent mushroom compost (SMC), which dissipates quickly when disturbed and spread on land. However, during the initial disturbance and handling, H2S levels can be momentarily very high and life threatening.

We propose to establish the dynamics of H2S release and dissipation from SMC during its storage and handling. We will conduct pilot studies indoors and outside to determine if there is a greater risk associated with handling stored SMC in an enclosed space compared with an open space, in terms of the dissipation pattern of H2S. We will determine the influence of key parameters such as SMC composition, steam pre-treatment and length of storage on H2S emissions, using a bench top flask incubation method. We will determine the sulphur content of SMC from different sources and with different gypsum (CaSO4.2H2O) content to determine if composts with a high content of sulphur–containing gypsum produce higher H2S gas emissions. We will characterise the microbial population in stored SMC to determine the relative importance of microbes involved in (a) the mineralization of organic sulphur compounds (e.g. microbial biomass and humus) and (b) the reduction of inorganic sulphates (e.g. CaSO4.2H2O) in terms of H2S production.

We will monitor H2S gas emissions during the removal of stored SMC heaps around the country at times when they are being removed for spreading on land. We will focus measurements on the Human Occupied Zone (HOZ) where people are most likely to be at risk (at the face of the heap, in trailers, tractor cabs). We will develop guidelines for the safe handling of stored SMC with respect to health and safety of the operators. Results will be published in a PhD thesis, peer reviewed papers and presented at conferences.

College: Dr. Tom Curran, UCD. Email: tom.curran@ucd.ie

Teagasc: Dr. Helen Grogan, Kinsealy. Email: helen.grogan@teagasc.ie

Abstract:

Artificial insemination (AI) when used in conjunction with accurate progeny testing can substantially increase the rate of genetic improvement. However, cervical AI using frozen-thawed semen is not cost effective in Ireland due to unacceptably low pregnancy rates. We have shown that that ewe breed is a critical determinant of the success of cervical AI using frozen-thawed semen (Donovan et al., 2004, 2006) and that this breed effect is due to the failure of sperm to penetrate the cervical barrier (Fair et al., 2005).

The objectives of the project are to:

• Determine the physicochemical properties (composition, concentration of mucinases and glysosidases) of cervical mucus and the structure of the cervical tissue (collagen content and state) at critical time points prior and up to the time of AI in relation to ewe breed and progestagen treatment.
• Define the pattern of expression of genes coding for mucin and the allele frequency profile of these genes in different breeds.
• Examine for evidence of breed-by-synchronisation treatment interactions and thus identify breed specific synchronisation treatments that could maximise pregnancy rate in practice.

College: Dr. John Fry, UCD. Email: alex.evans@ucd.ie

Teagasc: Stuart Green, Rural Economy - Kinsealy. Email: stuart.green@teagasc.ie

Abstract

Monitor farms are a central part of the Teagasc advisory services extension effort. Monitor farmers have agreed to implement a farm management and recording system aimed at achieving the goals set out in the Teagasc advisory programme. The farms are established as part of dairy, drystock and tillage advisory programmes and many are run as part of a joint programme with an industry partner. The performance of monitor farms relative to the general population of farms has been extensively examined.

Little, however, is known about the impact of monitor farms as part of the extension effort and how they are rated by various stakeholders in the agricultural industry. In particular, there is scant understanding of the types of technology and knowledge that are diffused through monitor farms to the wider farming community, the mechanisms through which such technology and knowledge are diffused and the obstacles and barriers to the adoption of this technology and knowledge on the part of farmers and other stakeholders.

Using qualitative research methods such as case studies, social network analysis and ethnographic or participant observation approaches to identify technology and knowledge transfer and absorption from monitor farms to the wider farming community, this project will complement data from existing Teagasc sources on farmers’ interaction with monitor farms.

Therefore, this project aims to examine the diffusion of technology and knowledge from Teagasc’s monitor farms to the wider farming community. The methodology developed for assessing such transfers from monitor farms can be used in future evaluations of the impact of monitor farms, and may be transferable to the evaluation of other extension activities.

College: Dr. Rachael Hilliard, NUI Galway. Email: rachel.hilliard@nuigalway.ie

Teagasc: Kevin Heanue, Rural Economy. Email: kevin.heanue@teagasc.ie

Abstract

This project would maintain, improve and extend an existing computable general equilibrium policy model of the Irish economy with a detailed representation of the Irish agri-food sector previously developed under a Walsh Fellowship. Improvement would arise from model updating, taking account of the publication of the 2000 CSO input-output tables, as well as more validity checking of key parameter values. The innovative part of the project would be its extension to include a microsimulation model to capture the behaviour of individual households represented in the Household Budget Survey. This would allow tracking of the impact of policy changes at national and international levels affecting the agricultural, food and rural sectors to the welfare impacts on individual farm and rural households. Potential model uses would be to identify the impacts of policy changes on different types of households, e.g. part-time vs. full time farmers, rural vs. urban households, small vs. large farmers as well as on farmers in different systems. The project output would complement existing work being undertaken in the RERC on the impact of European agri-food policy in Ireland and spatial microsimulation modelling.

College: Prof. Alan Matthews, TCD. Email: alan.matthews@tcd.ie

Teagasc: Prof. Cathal O'Donoghue, Rural Economy. Email: cathal.odonoghue@teagasc.ie

Abstract

An increase in global temperatures of the magnitude projected by Global Climate Models (GCMs), in the order of between 2 to 4oC, is likely to present significant new challenges and opportunities for a mid-latitude country like Ireland. Any increase in temperature will result in an increased potential for phenological development. As temperature is one of the primary factors affecting growth, life cycle and production patterns of plant and insect development, any changes in temperature as a consequence of climate change will likely result in changes in yield productivity and incidence of pest infestations. While the influence of climate on the distribution of agricultural pests and diseases is well established in the literature, much of this research has focused on forecasting in the short to medium term (days to weeks to months). An assessment of the long term effects of climate change on the prevalence of both native and non-native pests and diseases, temporally and spatially, will be a crucial factor in determining the potential productivity of existing and introduced crop varieties over the course of the present century.

It is important that we are adequately prepared for such challenges due to the long lead in time required for adjustment in these sectors. Future planning for locating new or introduced crop types and varieties more suited to a changed climate and planning and planting of new forest stands, need to take cognisance of changes that are ongoing in the Irish climate and its resultant impacts on the distribution of pests and diseases.

College: Dr. Rowan Fealy, NUI Maynooth. Email: rowan.fealy@nuim.ie

Teagasc: Reamonn Fealy, Kinsealy. Email: reamonn.fealy@teagasc.ie

Abstract

Ireland’s landscape and the effective long-term management of it, is becoming increasingly more relevant at the present time. The process of landscape characterisation through Landscape Character Assessment (LCA) focuses on what makes one landscape different from the next. Particular combinations of geology, landform, soils, vegetation, land use, field patterns and human settlement create character. Character makes each part of the landscape distinct and gives each its particular sense of place. The Rural Environment Protection Scheme (REPS) has been in operation since 1994 and besides its obvious benefits to farmers and ecological management- the scheme provides a valuable opportunity for improved landscape quality. The Forestry Environment Protection Scheme (FEPS) will provide an opportunity to create woodlands that can contribute more to landscape character. This project looks at the impacts of REPS/FEPS on the landscape. For the purpose of this study, the assessment will take place in a county. Geographic Information Systems (GIS) will be used to produce a Landscape Character Assessment. The final output would be moving in the direction of a National LCA scheme. This project fits in well with an existing programme in RERC looking at non-direct economic value of landscape.

College: Dr. John Fry, UCD. Email: john.fry@ucd.ie

Teagasc: Dr. JP Hanrahan, Athenry. Email: seamus.hanrahan@teagasc.ie

Abstract

Artificial insemination, when used in conjunction with accurate progeny testing schemes can substantially increase the rate of genetic progress. In sheep, while cervical AI with fresh semen yields acceptable pregnancy rates, the short shelf life of fresh semen (10 to 14 hours) coupled with a very restricted breeding season, the natural limitation on the number of semen doses achievable per unit time plus small flock size seriously restrict the widespread use of individual sires. The use of frozen semen is hampered by major ewe breed effects on conception rate coupled with the fact that the process of freezing and thawing irreversibly affects a significant proportion of sperm with typical estimates of 50% survival post thawing. The advantages of using fresh semen include the ability to use low sperm numbers per insemination, thus maximizing inseminations per ejaculate, inexpensive storage and ease of use in the field. The major disadvantage currently is the limited shelf life. The experiments in this proposal aim to establish the optimal conditions for the storage of fresh semen in sheep in to increase the number of effective doses per ejaculate and to facilitate genetic progress.

College: Dr. Pat Lonergan, UCD. Email: pat.lonergan@ucd.ie

Teagasc: Dr. JP Hanrahan, Athenry. Email: seamus.hanrahan@teagasc.ie

Abstract

Grazed grass is an essential component of the horse’s diet and the cheapest and most readily available source of forage. In the bloodstock industry Ireland is renowned for its limestone rich pastures. Grazed grass will supply varying amounts of energy, crude protein, minerals and vitamins depending on geographical location, time of year and the level of management imposed. Horses are often described as trickle feeders i.e. consuming small quantities over long periods of time. Studies have reported that horses kept outdoors will spend up to 16 hours per day grazing (Goodwin 2002, Cooper et al 2004). Horses are non-ruminant herbivores and when stabled their natural foraging behaviour is restricted. In confined environments horses will engage in stereotypic behaviour e.g. crib-biting, weaving and wind sucking and these can be problematic for owners. Despite the importance of grazed grass in the nutrition of horses little information is available on intake and metabolism of nutrients when horses graze. In addition the impact of different grazing systems on the productivity of the grazing sward for horses has not been exploited. This study will investigate these aspects. The study will be conducted during the peak grazing period. Horses of similar breed, age and workload will be divided into two groups and randomly allocated to one of the following grazing systems (1) a rotational grazing system or (2) a continuous grazing system. Intakes of energy, dry matter, protein, ADF, NDF, ADL, minerals and vitamins will be measured on both systems. These intake measurements will help stud owners allocate appropriate quantities of concentrate to working horses and establish the need, if any, for supplementation. Measurements of pre and post herbage mass, sward and tiller density, grazing heights and identification of grass species will also be made. Managing the grazing area is essential for the long-term demand of horses during the grazing period. The methods used to profile the grass sward in this study will not only set guidelines for stud owners on grazing management but also introduce methods that they can apply on farm to help estimate the forage intake of their horses.

College: Dr Bridget Younge, University of Limerick. Email: bridget.younge@ul.ie

Teagasc: Dr Siobhan Kavanagh, Kildalton. Email: siobhan.kavanagh@teagasc.ie.

Abstract

This study will examine, from a sociological perspective, the suicidal experiences of young, rural, men – who have been identified as a significant ‘at risk’ group (Reach Out Strategy 2005). The research will investigate the motivation for their suicidal attempt and examine in particular aspects of the rural environment that may have contributed to their distress. This will be explored through the experiences of men in the West of Ireland who have attempted suicide. Using a qualitative methodology involving in-depth, unstructured, interviews this study will explore their economic, social and emotional environments and how they respond to psychological difficulties. The interviews will be audio-taped, transcribed and analysed using manual and computer methods. Permission to carry out this study has already been granted (see attached). Overall, the study aims to construct the issue of suicide from the perspective of the respondents and this will be reflected in the research instrument and particularly in the interview themes which emerge.

This study will address a significant gap in knowledge relating to rural men and suicide. Despite their known vulnerability to suicide relatively little is known of how rural men experience social, economic and psychological difficulties, how they perceive these difficulties and their attitudes to help-seeking. Generalised, usually unsubstantiated accounts, of the causes of male psychological difficulties abound but they do little to explain the underlying causes of this public health problem. Existing research tends to be survey-based which under-emphasizes individual motivation as well as the socio-economic and cultural landscape. Moreover, the gendered nature of help-seeking is rarely explored although evidence suggests men’s reluctance to identify and seek help for psychological problems (Cleary 2005, Russell et al 2004). This research project will be supervised by Dr. Anne Cleary (UCD) who has carried out a similar study of young men in an urban setting (Cleary 2005). (300/300)

College: Dr. Anne Cleary, UCD. Email: anne.cleary@ucd.ie

Teagasc: Mr. Frank Laffey, Athenry. Email:  frank.laffey@teagasc.ie

• Back to Walsh Fellowship Programme.