• 16S rRNA gene sequencing of mock microbial populations- impact of DNA extraction method, primer choice and sequencing platform

      Fouhy, Fiona; Clooney, Adam G; Stanton, Catherine; Claesson, Marcus J; Cotter, Paul D (Biomed Central, 2016-06-24)
      Background Next-generation sequencing platforms have revolutionised our ability to investigate the microbiota composition of complex environments, frequently through 16S rRNA gene sequencing of the bacterial component of the community. Numerous factors, including DNA extraction method, primer sequences and sequencing platform employed, can affect the accuracy of the results achieved. The aim of this study was to determine the impact of these three factors on 16S rRNA gene sequencing results, using mock communities and mock community DNA. Results The use of different primer sequences (V4-V5, V1-V2 and V1-V2 degenerate primers) resulted in differences in the genera and species detected. The V4-V5 primers gave the most comparable results across platforms. The three Ion PGM primer sets detected more of the 20 mock community species than the equivalent MiSeq primer sets. Data generated from DNA extracted using the 2 extraction methods were very similar. Conclusions Microbiota compositional data differed depending on the primers and sequencing platform that were used. The results demonstrate the risks in comparing data generated using different sequencing approaches and highlight the merits of choosing a standardised approach for sequencing in situations where a comparison across multiple sequencing runs is required.
    • The 2003 CAP reform: Do decoupled payments affect agricultural production?

      Howley, Peter; Hanrahan, Kevin; Donnellan, Trevor (Teagasc, Oak Park, Carlow, Ireland, 2009)
      The move from coupled payment policy instruments to payments that are decoupled from production have made estimating future trends in agricultural output much more challenging. Using a dynamic multi product partial equilibrium model, the overall aim of this paper is to examine the potential supply inducing effect of decoupled payments. This issue is important in the context of WTO negotiations, and, in particular, in discussions surrounding the appropriateness of decoupled payments being included as a ‘green box’ policy. The results suggest that farm operators, to a large extent, do not treat these payments as fully decoupled and they do in fact maintain a strong supply inducing effect on agricultural production. Findings suggest, however, that this trade distorting effect is less than previously coupled payments.
    • A comparison of SWAT, HSPF and SHETRAN/GOPC for modelling phosphorus export from three catchments in Ireland

      Nasr, Ahmed Elssidig; Bruen, Michael; Jordan, Philip; Moles, Richard; Kiely, Gerard; Byrne, Paul (Elsevier, 2012-07-02)
      Recent extensive water quality surveys in Ireland revealed that diffuse phosphorus (P) pollution originating from agricultural land and transported by runoff and subsurface flows is the primary cause of the deterioration of surface water quality. P transport from land to water can be described by mathematical models that vary in modelling approach, complexity and scale (plot, field and catchment). Here, three mathematical models (SWAT, HSPF and SHETRAN/GOPC) of diffuse P pollution have been tested in three Irish catchments to explore their suitability in Irish conditions for future use in implementing the European Water Framework Directive. After calibrating the models, their daily flows and total phosphorus (TP) exports are compared and assessed. The HSPF model was the best at simulating the mean daily discharge while SWAT gave the best calibration results for daily TP loads. Annual TP exports for the three models and for two empirical models were compared with measured data. No single model is consistently better in estimating the annual TP export for all three catchments.
    • Abstracts of papers presented at the 33rd Foodscience and Technology Research Conference, University College, Cork

      various; Hanrahan, J. P. (Teagasc (Agriculture and Food Development Authority), Ireland, 2004)
    • Accuracy of predicting milk yield from alternative milk recording schemes

      Berry, Donagh P.; Olori, V. E.; Cromie, A.R.; Veerkamp, R. F.; Rath, M.; Dillon, Pat (Cambridge University Press, 2005-02)
      The effect of reducing the frequency of official milk recording and the number of recorded samples per test-day on the accuracy of predicting daily yield and cumulative 305-day yield was investigated. A control data set consisting of 58 210 primiparous cows with milk test-day records every 4 weeks was used to investigate the influence of reduced milk recording frequencies. The accuracy of prediction of daily yield with one milk sample per test-day was investigated using 41 874 testday records from 683 cows. Results show that five or more test-day records taken at 8-weekly intervals (A8) predicted 305-day yield with a high level of accuracy. Correlations between 305-day yield predicted from 4-weekly recording intervals (A4) and from 8-weekly intervals were 0.99, 0.98 and 0.98 for milk, fat and protein, respectively. The mean error in estimating 305-day yield from the A8 scheme was 6.8 kg (s.d. 191 kg) for milk yield, 0.3 kg (s.d. 10 kg) for fat yield, and −0.3 kg (s.d. 7 kg) for protein yield, compared with the A4 scheme. Milk yield and composition taken during either morning (AM) or evening (PM) milking predicted 24-h yield with a high degree of accuracy. Alternating between AM and PM sampling every 4 weeks predicted 305-day yield with a higher degree of accuracy than either all AM or all PM sampling. Alternate AM-PM recording every 4 weeks and AM + PM recording every 8 weeks produced very similar accuracies in predicting 305-day yield compared with the official AM + PM recording every 4 weeks.
    • Acrylamide formation in potato products

      Brunton, Nigel; Gormley, Ronan T.; Butler, Francis; Cummins, Enda; Danaher, Martin; O'Keeffe, Michael (Teagasc, 2006-08)
      Acrylamide, a substance classified as a potential carcinogen, occurs in heated starchy foods at concentrations many times in excess of levels permitted in drinking water. Early surveys indicated that levels of acrylamide in potato products such as French fries and potato crisps were the highest of the foodstuffs investigated. The present project addressed this issue by determining levels of acrylamide precursors (asparagine and reducing sugars) in raw potatoes and levels of acrylamide in (i) potato products from different storage regimes, (ii) spot-sampled potatoes purchased from a local supermarket, (iii) samples that received pre-treatments and were fried at different temperatures and (iv) French fries reheated in different ovens.A risk assessment of the estimated acrylamide intake from potato products for various cohorts of the Irish population was also conducted.
    • Adding value to beef forequarter muscles

      Kenny, Tony; Lennon, Ann; Ward, Patrick; Sullivan, Paul; McDonald, Karl; Downey, Gerard; O'Neill, Eileen (Teagasc, 2008-11)
      The forequarter constitutes 50% of the weight of a beef carcase but only about 25% of its value. To fulfill the objectives of this project, the work was organised into 4 parts as follows: 1.Characterisation of the available raw material, in terms of properties of individual muscles seamed out from carcasses of representative types of animals produced in Ireland. 2.Comparison of yields and operator time for seaming and conventional boning. 3.Utilisation of separated muscles in added-value products using appropriate tenderising, bonding and forming technology. 4.Transfer of the knowledge and technology to the industry.
    • Adding value to Beef Forequarter Muscles

      Kenny, Tony; Lennon, Ann; Ward, Patrick; Sullivan, Paul; McDonald, Karl; O’Neill, Eileen; Downey, Gerard (Teagasc, 2008-11-01)
      The forequarter constitutes 50% of the weight of a beef carcase but only about 25% of its value.To fulfill the objectives of this project, the work was organised into 4 parts as follows: 1.Characterisation of the available raw material, in terms of properties of individual muscles seamed out from carcasses of representative types of animals produced in Ireland. 2.Comparison of yields and operator time for seaming and conventional boning. 3.Utilisation of separated muscles in added-value products using appropriate tenderising, bonding and forming technology. 4.Transfer of the knowledge and technology to the industry.
    • Adding value to cull cow beef

      O'Donovan, Michael; Minchin, William; Buckley, Frank; Kenny, David; Shalloo, Laurence (Teagasc, 2009-08-01)
      This project addressed the prospects of increasing the value of cull cow beef and examined the potential of a number of different management and dietary strategies. In Ireland, the national cow herd contributes 350,000 animals to total beef production annually, which represents 22% of all cattle slaughtered (DAF, 2007). A dominant feature of beef production in Ireland is the disposal of cows from the dairy and beef industries, the time of year at which culling occurs influences the number of cows available for slaughter. Suitability of a cow for slaughter is generally not a consideration for dairy or beef farmers.
    • Adding value to milk by increasing its protein and CLA contents

      Murphy, J.J.; Stanton, Catherine; O'Donovan, Michael; Kavanagh, S.; Maher, J.; Patton, Joe; Mohammed, Riaz (Teagasc, 2008-08-01)
      The mid-summer milk protein study was undertaken on 34 commercial dairy farms in 2005 to evaluate the influence of dietary and management variables on milk protein content in mid-season. Data on grass composition, genetic merit of the herds and milk protein content were collected and analysed by multiple regression. Both calving date and genetic merit for milk protein content were significantly associated with milk protein content and were used as adjustment factors when evaluating the association between measures of grass quality and milk protein content. Milk protein content was associated with grass OMD (P = 0.04) and NDF content (P = 0.02) but not with CP content (P = 0.80). It is concluded that herds calving earlier, with a greater genetic merit for milk protein content and consuming better quality pasture would have greater milk protein contents in mid-season.
    • Adding value to milk by increasing its protein and CLA contents.

      Murphy, J.J.; Stanton, Catherine; O'Donovan, Michael; Kavanagh, S.; Maher, J.; Patton, J.; Mohammed, R. (Teagasc, 2008-08-01)
      Five experiments were undertaken in this project; one on mid-summer milk protein and four on milk CLA content. Thus the two main objectives of this project were to determine the factors associated with milk protein concentration in mid-summer and to investigate potential further strategies to increase the CLA content of pasture produced milk.
    • Adding Value To Under utilised Fish Species

      Fagan, John; Gormley, Ronan T.; Mitchell, Michelle; Downey, Gerard (Teagasc, 2006-02-01)
      Tightening fish quotas and supply shortages for conventional species are causing major difficulties for both fishermen and seafood processors. There is a need, therefore, to explore the potential of underutilised fish species both as fillets or portions and as added-value products. The current project at Ashtown Food Research Centre (AFRC) addressed this issue for a number of underutilised species via (a) sous vide processing (with savoury sauces),(b)marinating (salt- and sugar-based marinades) and (c) via a combination of freeze-chilling and modified atmosphere packaging (MAP).A range of physico-chemical and sensory tests was conducted on the products and their shelf-life status was also determined.
    • Adding value to under-utilised fish species

      Fagan, John; Gormley, Ronan T.; Mitchell, Michelle; Downey, Gerard (Teagasc, 2006-02)
      Tightening fish quotas and supply shortages for conventional species are causing major difficulties for both fishermen and seafood processors. There is a need, therefore, to explore the potential of underutilised fish species both as fillets or portions and as added-value products. The current project at Ashtown Food Research Centre (AFRC) addressed this issue for a number of underutilised species via (a) sous vide processing (with savoury sauces),(b)marinating (salt- and sugar-based marinades) and (c) via a combination of freeze-chilling and modified atmosphere packaging (MAP).A range of physico-chemical and sensory tests was conducted on the products and their shelf-life status was also determined.
    • Additive genetic, non-additive genetic and permanent environmental effects for female reproductive performance in seasonal calving dairy females

      Kelleher, M.M.; Buckley, Frank; Evans, R.D.; Berry, Donagh P. (Teagasc (Agriculture and Food Development Authority), Ireland, 2016-09-08)
      Excellent reproductive performance (i.e. 365-day calving interval) is paramount to herd profit in seasonal-calving dairy systems. Reproductive targets are currently not being achieved in Irish dairy herds. Furthermore, most research on the genetics of reproductive performance in dairy cattle has focused primarily on lactating cows and relatively few studies have attempted to quantify the genetic contribution to differences in reproductive performance in nulliparae. The objective of the present study was to estimate the contribution of both the additive and non-additive genetic components, as well as the permanent environmental component, to phenotypic variation in the reproductive traits in nulliparous, primiparous and multiparous seasonal-calving dairy females. Reproductive phenotypes were available on up to 202,525 dairy females. Variance components were estimated using (repeatability where appropriate) linear animal mixed models; fixed effects included in the mixed models were contemporary group, parity (where appropriate), breed proportion, inter-breed specific heterosis coefficients and inter-breed specific recombination loss coefficients. Heritability of the reproductive traits ranged from 0.004 (pregnancy rate to first service) to 0.17 (age at first service in nulliparae), while repeatability estimates for the reproductive traits in cows ranged from 0.01 (calving interval) to 0.11 (pregnant in the first 42 days of the breeding season). Breed-specific heterosis regression coefficients suggest that, relative to the parental mean, a first-cross Holstein–Jersey crossbred was almost 7 days younger at first calving, had a 9-day shorter calving interval, a 6 percentage unit greater pregnancy rate in the first 42 days of the breeding season and a 3 percentage unit greater survival rate to next lactation. Heifer calving rate traits were strongly genetically correlated with age at first calving (–0.97 to –0.66) and calving rate in the first 42 days of the calving season for first parity cows (0.77 to 0.56), but genetic correlations with other cow reproductive traits were weak and inconsistent. Calving interval was strongly genetically correlated with the majority of the cow traits; 56%, 40%, and 92% of the genetic variation in calving interval was explained by calving to the first service interval, number of services and pregnant in the first 42 days of the breeding season, respectively. Permanent environmental correlations between the reproductive performance traits were generally moderate to strong. The existence of contributions from non-additive genetic and permanent environmental effects to phenotypic differences among cows suggests the usefulness of such information to rank cows on future expected performance; this was evidenced by a stronger correlation with future reproductive performance for an individual cow index that combined additive genetic, non-additive genetic and permanent environmental effects compared to an index based solely on additive genetic effects (i.e. estimated breeding values).
    • Administration of a live culture of Lactococcus lactis DPC 3147 into the bovine mammary gland stimulates the local host immune response, particularly IL-1β and IL-8 gene expression

      Beecher, Christine; Daly, Mairead; Berry, Donagh P.; Klostermann, Katja; Flynn, James; Meaney, William J; Hill, Colin; McCarthy, Tommie V.; Ross, R Paul; Giblin, Linda (Cambridge University Press: Published for the Institute of Food Research and the Hannah Research Institute, 2009-05-18)
      Mastitis is one of the most costly diseases to the dairy farming industry. Conventional antibiotic therapy is often unsatisfactory for successful treatment of mastitis and alternative treatments are continually under investigation. We have previously demonstrated, in two separate field trials, that a probiotic culture, Lactococcus lactis DPC 3147, was comparable to antibiotic therapy to treat bovine mastitis. To understand the mode of action of this therapeutic, we looked at the detailed immune response of the host to delivery of this live strain directly into the mammary gland of six healthy dairy cows. All animals elicited signs of udder inflammation 7 h post infusion. At this time, clots were visible in the milk of all animals in the investigation. The most pronounced increase in immune gene expression was observed in Interleukin (IL)-1b and IL-8, with highest expression corresponding to peaks in somatic cell count. Infusion with a live culture of a Lc. lactis leads to a rapid and considerable innate immune response.
    • Advanced and conventional methods for vegetative propagation of selected lines of oak and cherry.

      Douglas, Gerry C. (Teagasc, 1999-04-01)
      Oak and wild cherry (Prunus avium) are important broadleaved species. We have identified superior trees and conserved them by grafting. Methods for the large scale propagation of selected trees was evaluated using the technology of micropropagation. For oak we could establish shoot cultures from mature oaks but their propagation rate was too low and difficult for practical application. With wild cherry micropropagation is a feasible option for large scale production of selected material. Genetic fingerprinting technology was developed and applied to oaks. We showed that all material propagated vegetatively from oak was genetically similar to the original donor tree. Furthermore we used genetic fingerprinting to analyse a unique stand of elite oaks in Co. Westmeath and determined that the selected trees were not closely related to each other. The analysis of genetic fingerprints of 16 elite oaks also showed that five of them had an unusual pattern of DNA and one tree was identified as a rare triploid tree.
    • Agricultural nutrient surpluses as potential input sources to grow third generation biomass (microalgae): A review

      Fenton, Owen; O hUallachain, Daire (Elsevier, 2012-05)
      Biofuel consumption is increasing and in order to meet EU targets, alternatives to first and second generation biofuels are being examined. The use of micro-algal biomass in the production of biofuel is an area of research which has received attention in recent years. Traditionally, microalgae are commercially grown using synthetic fertilisers, the price of which is linked with rising oil prices. An alternative to the use of inorganic fertiliser is to use surplus agricultural manures in their raw state, bi-products of anaerobic digestion, or runoff and artificial drainage waters, all of which have variable nutrient contents within and across source types. Many studies showed that manures containing a high nutrient content e.g. pig and poultry manures, or bi-products from anaerobic digestion, are potentially viable sources of nutrients to grow algae. Feasibility issues prevail such as variable nutrient contents amongst and across source types, transparency issues and early and sustained nutrient losses during the storage phase. Agitation and efficient nutrient testing before use are important. In Ireland, pig and poultry manures, dairy dirty water, artificial drainage or runoff waters where coupled with agitation during storage to prevent P precipitation and a CO2 source, all have potential to be used in the future.
    • Agriculture, meteorology and water quality in Ireland: a regional evaluation of pressures and pathways of nutrient loss to water

      Schulte, Rogier P.; Richards, Karl G.; Daly, Karen M.; Kurz, I.; McDonald, E.J.; Holden, N.M. (Royal Irish Academy, 2006-07-31)
      The main environmental impact of Irish agriculture on surface and ground water quality is the potential transfer of nutrients to water. Soil water dynamics mediate the transport of nutrients to water, and these dynamics in turn depend on agro-meteorological conditions, which show large variations between regions, seasons and years. In this paper we quantify and map the spatio-temporal variability of agro-meteorological factors that control nutrient pressures and pathways of nutrient loss. Subsequently, we evaluate their impact on the water quality of Irish rivers. For nitrogen, pressure and pathways factors coincide in eastern and southern areas, which is reflected in higher nitrate levels of the rivers in these regions. For phosphorus, pathway factors are most pronounced in north-western parts of the country. In south-eastern parts, high pressure factors result in reduced biological water quality. These regional differences require that farm practices be customised to reflect the local risk of nutrient loss to water. Where pathways for phosphorus loss are present almost year-round—as is the case in most of the north-western part of the country—build-up of pressures should be prevented, or ameliorated where already high. In south-eastern areas, spatio-temporal coincidence of nutrient pressures and pathways should be prevented, which poses challenges to grassland management.
    • Agriculture, Rural Development and Potential for a ‘Middle Agriculture’ in Ireland

      Macken-Walsh, Aine (Teagasc, Oak Park, Carlow, Ireland, 2010-03)
      This paper gives a brief overview of current farm viability in Ireland and summarises some of the main ‘barriers’ to farm families’ engagement in contemporary rural development programmes. Against this backdrop, the paper discusses the potential of a middle agriculture model for rural development. The capacity of such a model to address some of the economic, social and cultural predicaments of Irish family farms is outlined. The potential of the model is also discussed in terms of how it may respond to contemporary EC rural development policy priority objectives.
    • The Agrodiversity Experiment: three years of data from a multisite study in intensively managed grasslands

      Kirwan, Laura; Connolly, John; Brophy, Caroline; Baadshaug, Ole; Belanger, Gilles; Black, Alistair D; Camus, Tim; Collins, Rosemary; Cop, Jure; Delgado, Ignacio; De Vliegher, Alex; Elgersma, Anjo; Frankow-Lindberg, Bodil; Golinski, Piotr; Grieu, Philippe; Gustavsson, Anne-Maj; Helgadottir, Aslaug; Hoglind, Mats; Huguenin-Elie, Olivier; Jorgensen, Marit; Kadziuliene, Zydre; Lunnan, Tor; Luscher, Andreas; Kurki, Paivi; Porqueddu, Claudio; Sebastia, M.-Teresa; Thumm, Ulrich; Walmsley, David; Finn, John A.; European Co-Operation in Science and Technology; Irish Research Council for Science, Engineering and Technology; Science Foundation Ireland; 852; 09/RFP/EOB2546 (Ecological Society of America, 2014-06-11)
      Intensively managed grasslands are globally prominent ecosystems. We investigated whether experimental increases in plant diversity in intensively managed grassland communities can increase their resource use efficiency. This work consisted of a coordinated, continental-scale 33-site experiment. The core design was 30 plots, representing 15 grassland communities at two seeding densities. The 15 communities were comprised of four monocultures (two grasses and two legumes) and 11 four-species mixtures that varied in the relative abundance of the four species at sowing. There were 1028 plots in the core experiment, with another 572 plots sown for additional treatments. Sites agreed a protocol and employed the same experimental methods with certain plot management factors, such as seeding rates and number of cuts, determined by local practice. The four species used at a site depended on geographical location, but the species were chosen according to four functional traits: a fast-establishing grass, a slow-establishing persistent grass, a fast-establishing legume, and a slow-establishing persistent legume. As the objective was to maximize yield for intensive grassland production, the species chosen were all high-yielding agronomic species. The data set contains species-specific biomass measurements (yield per species and of weeds) for all harvests for up to four years at 33 sites. Samples of harvested vegetation were also analyzed for forage quality at 26 sites. Analyses showed that the yield of the mixtures exceeded that of the average monoculture in >97% of comparisons. Mixture biomass also exceeded that of the best monoculture (transgressive overyielding) at about 60% of sites. There was also a positive relationship between the diversity of the communities and aboveground biomass that was consistent across sites and persisted for three years. Weed invasion in mixtures was very much less than that in monocultures. These data should be of interest to ecologists studying relationships between diversity and ecosystem function and to agronomists interested in sustainable intensification. The large spatial scale of the sites provides opportunity for analyses across spatial (and temporal) scales. The database can also complement existing databases and meta-analyses on biodiversity–ecosystem function relationships in natural communities by focusing on those same relationships within intensively managed agricultural grasslands.