• Scientific appraisal of the Irish grass-based milk production system as a sustainable source of premium quality milk and dairy products

      O'Brien, Bernadette; Hennessy, Deirdre (Teagasc (Agriculture and Food Development Authority), Ireland, 2017-12-29)
      The Irish dairy industry is critically important to the economy and general well-being of a large section of the Irish population. Its quality, sustainability and maintenance are the key for a vibrant rural society in the future. Two important elements for the future of this industry include (a) the quality, marketing and sale of dairy products on the export market and (b) sustainability from the perspectives of people, planet and profit. This paper provides a short review of current scientific evidence in relation to a number of topics, each of which is important in maintaining and developing dairy product quality and the sustainability of the Irish dairy industry. The topics addressed in the paper are as follows: the parameters of milk composition; milk processing; hygiene quality and safety; farm management practices and the regulations that govern such practices; animal health and welfare; environmental impacts; economic implications for farm families and rural communities; and the overall future sustainability of the family-based dairy farm structure.
    • Screening commercial teat disinfectants against bacteria isolated from bovine milk using disk diffusion

      Fitzpatrick, Sarah Rose; Garvey, Mary; Jordan, Kieran; Flynn, Jim; O'Brien, Bernadette; Gleeson, David; Dairy Research Ireland; Teagasc Walsh Fellowship Programme; MKLS0006; 2016054 (Veterinary World, 2019-05-06)
      Background and Aim: Teat disinfection is an important tool in reducing the incidence of bovine mastitis. Identifying the potential mastitis-causing bacterial species in milk can be the first step in choosing the correct teat disinfectant product. The objective of this study was to screen commercial teat disinfectants for inhibition against mastitis-associated bacteria isolated from various types of milk samples. Materials and Methods: Twelve commercially available teat disinfectant products were tested, against 12 mastitis-associated bacteria strains isolated from bulk tank milk samples and bacterial strains isolated from clinical (n=2) and subclinical (n=3) quarter foremilk samples using the disk diffusion method. Results: There was a significant variation (7-30 mm) in bacterial inhibition between teat disinfection products, with products containing a lactic acid combination (with chlorhexidine or salicylic acid) resulting in the greatest levels of bacterial inhibition against all tested bacteria (p<0.05). Conclusion: In this study, combined ingredients in teat disinfection products had greater levels of bacterial inhibition than when the ingredients were used individually. The disk diffusion assay is a suitable screening method to effectively differentiate the bacterial inhibition of different teat disinfectant products.
    • Seasonality of nitrogen uptake, apparent recovery of fertilizer nitrogen and background nitrogen supply in two Irish grassland soils

      Murphy, Paul N. C.; O'Connell, K.; Watson, S.; Watson, C. J.; Humphreys, James; Irish National Development Plan; Irish Dairy Levy Research Trust (Teagasc (Agriculture and Food Development Authority), Ireland, 2013)
      Improving fertilizer nitrogen (N) use efficiency is central to sustainable and profitable grassland agriculture. A plot experiment with a control and fertilizer N (calcium ammonium nitrate, 25–50 kg/ha N) applied on nine occasions from February to September 2002 was conducted at two sites in southwest Ireland to assess N uptake and apparent recovery of fertilizer N (ARFN). Apparent recovery of fertilizer N after eight weeks varied from low in February (21%) and March (46%) to high from April to August (69–98%), indicating that high N use efficiency can be achieved in Irish grasslands at these times. Low recovery in spring suggested that N was applied in excess of immediate crop requirements. Note that N uptake and ARFN values from this study are likely to be somewhat conservative, particularly for spring applications. Over the 8 weeks during which growth was monitored, most (70%) of the grass yield and N uptake response to fertilizer N were in weeks 1 to 4 after application; however, a significant (30%) response occurred in weeks 5–8. This suggested that residual N availability following grazing at 4 weeks can be significant and that there may be scope to decrease N application rates in a grazing rotation. This can potentially improve N use efficiency and decrease N surpluses, with associated economic and environmental benefits. Apparent recovery of fertilizer N was closely related to soil temperature, with a 5.8% increase in ARFN with a 1 °C increase in temperature. Background (non-fertilizer) N supply contributed an average of 164 kg/ha per year (49%) taken up by the fertilized sward, highlighting the potential importance of soil N mineralisation to grassland productivity. Note that these results are for one year at two sites and that conditions may vary between years and at other sites and also that the experiment did not reproduce the cumulative effect of repeated fertilizer application over the grazing year.
    • Short communication: Effects of changing teatcup removal and vacuum settings on milking efficiency of an automatic milking system

      Upton, John; Bolona, P. Silva; Reinemann, D. J.; Teagasc Wash Fellowship Programme; University of Wisconsin-Madison; Lely, The Netherlands (Elsevier, 2019-08-22)
      The aim of this experiment was to assess strategies to reduce milking time in a pasture-based automatic milking system (AMS). Milking time is an important factor in automatic milking because any reductions in box time can facilitate more milkings per day and hence higher production levels per AMS. This study evaluated 2 end-of-milking criteria treatments (teatcup removal at 30% and 50% of average milk flowrate at the quarter-level), 2 milking system vacuum treatments (static and dynamic, where the milking system vacuum could change during the peak milk flowrate period), and the interaction of these treatment effects on milking time in a Lely Astronaut A4 AMS (Maassluis, the Netherlands). The experiment was carried out at the research facility at Teagasc Moorepark, Cork, Ireland, and used 77 spring-calved cows, which were managed on a grass-based system. Cows were 179 DIM, with an average parity of 3. No significant differences in milk flowrate, milk yield, box time, milking time, or milking interval were found between treatments in this study on cows milked in an AMS on a pasture-based system. Average and peak milk flowrates of 2.15 kg/min and 3.48 kg/min, respectively, were observed during the experiment. Small increases in maximum milk flowrate were detected (+0.09 kg/min) due to the effect of increasing the system vacuum during the peak milk flow period. These small increases in maximum milk flowrate were not sufficient to deliver a significant reduction in milking time or box time. Furthermore, increasing the removal setting from 30% of the average milk flowrate to 50% of the average milk flowrate was not an effective means of reducing box time, because the resultant increase in removal flowrate of 0.12 kg/min was not enough to deliver practical or statistically significant decreases in milking time or box time. Hence, to make significant reductions in milking time, where cows have an average milk flow of 2 kg/min and yield per milking of 10 kg, end-of-milking criteria above 50% of average milk flowrate at the quarter level would be required.
    • Short Communication: The effect of dry period duration and dietary energy density on the rennet gelation properties of milk in early lactation

      Butler, Stephen; de Feu, M.A.; O'Brien, Bernadette; Guinee, Timothy P.; Murphy, J.J.; National Development Plan (Dublin, Ireland) (American Dairy Science Association and Elsevier Inc., 2010-02)
      This study was carried out to examine the effects of decreasing dry period duration (DP) and altering the energy density of the diet during early lactation on the rheological characteristics of milk. Forty mature Holstein-Friesian cows were used in a completely randomized design with a 2 × 2 factorial arrangement of treatments. Cows were randomly assigned to one of two dry period treatments and one of two nutritional treatments. The dry period treatments were continuous milking (CM) or an 8-week standard dry period (SDP), and the nutritional treatments were a standard energy diet (SE) or a high energy diet (HE). Actual dry period lengths were 6.3 ± 1.7 days and 62.1 ± 1.9 days for cows for the CM and SDP treatments, respectively. Milk samples were collected at 2, 6 and 10 weeks postpartum. The concentration of fat, protein and lactose was determined in each sample. The rennet gelation properties were measured at 31 ° C using dynamic low-amplitude strain oscillatory rheometry. The following parameters were obtained from the resultant elastic shear modulus (G′): gelation time (GT), maximum curd firming rate (CFRmax) and gel strength (GS). Reducing dry period duration from 62 to 6 days resulted in increases in milk protein concentration (31.8 vs. 34.7 g/kg; P < 0.001), CFRmax (2.58 vs. 3.60 Pa/min; P < 0.001) and GS (69.4 vs. 90.5 Pa; P = 0.003). Raising the dietary energy density decreased percentage milk fat (43.1 vs. 37.7 g/kg; P < 0.001) but otherwise had no effect. GS was correlated with CFRmax (r = 0.98; P < 0.001), and both variables were correlated with milk protein concentration (r = 0.71; P < 0.001, and r = 0.73; P < 0.001, respectively). The results indicate that decreasing the duration of DP increased milk protein concentration and improved the rennet gelation properties of milk, but that dietary energy density had little effect.
    • The significance of livestock as a contributor to global greenhouse gas emissions today and in the near future

      O'Mara, Frank P. (Elsevier Inc., 23/06/2011)
      Animal agriculture is responsible for 8–10.8% of global greenhouse gas (GHG) emissions as assessed by IPCC accounting and, on the basis of lifecycle analysis, the contribution of livestock is up to 18% of global emissions. Asia is the source of the most enteric CH4 emissions with Latin America, Africa, Western Europe and North America being significant sources. These emissions are dominated by emissions from cattle. When GHG emissions are related to food production, the four most efficient regions are Eastern and Western Europe, North America, and the non-EU former Soviet Union which produced 46.3% of ruminant meat and milk energy and only 25.5% of enteric CH4 emissions in 2005. In comparison, the three least efficient producers (Asia, Africa, Latin America) produced an equivalent amount (47.1%) of ruminant meat and milk energy, and almost 69% of enteric CH4 emissions in 2005. Livestock related emissions will increase as world population and food demand increases; enteric CH4 emissions are projected to grow by over 30% from 2000 to 2020. There are mitigations available now, but it is imperative to develop new mitigations and ways to implement existing technologies more cost effectively.
    • SNP variation in the promoter of the PRKAG3 gene and association with meat quality traits in pig

      Ryan, Marion T; Hamill, Ruth M; O'Halloran, Aisling M; Davey, Grace C; McBryan, Jean; Mullen, Anne Maria; McGee, Chris; Gispert, Marina; Southwood, Olwen I; Sweeney, Torres; et al. (Biomed Central, 25/07/2012)
      Background: The PRKAG3 gene encodes the γ3 subunit of adenosine monophosphate activated protein kinase (AMPK), a protein that plays a key role in energy metabolism in skeletal muscle. Non-synonymous single nucleotide polymorphisms (SNPs) in this gene such as I199V are associated with important pork quality traits. The objective of this study was to investigate the relationship between gene expression of the PRKAG3 gene, SNP variation in the PRKAG3 promoter and meat quality phenotypes in pork. Results: PRKAG3 gene expression was found to correlate with a number of traits relating to glycolytic potential (GP) and intramuscular fat (IMF) in three phenotypically diverse F1 crosses comprising of 31 Large White, 23 Duroc and 32 Pietrain sire breeds. The majority of associations were observed in the Large White cross. There was a significant association between genotype at the g.-311A>G locus and PRKAG3 gene expression in the Large White cross. In the same population, ten novel SNPs were identified within a 1.3 kb region spanning the promoter and from this three major haplotypes were inferred. Two tagging SNPs (g.-995A>G and g.-311A>G) characterised the haplotypes within the promoter region being studied. These two SNPs were subsequently genotyped in larger populations consisting of Large White (n = 98), Duroc (n = 99) and Pietrain (n = 98) purebreds. Four major haplotypes including promoter SNP’s g.-995A>G and g.-311A>G and I199V were inferred. In the Large White breed, HAP1 was associated with IMF% in the M. longissmus thoracis et lumborum (LTL) and driploss%. HAP2 was associated with IMFL% GP-influenced traits pH at 24 hr in LTL (pHULT), pH at 45 min in LTL (pH45LT) and pH at 45 min in the M. semimembranosus muscle (pH45SM). HAP3 was associated with driploss%, pHULT pH45LT and b* Minolta. In the Duroc breed, associations were observed between HAP1 and driploss% and pHUSM. No associations were observed with the remaining haplotypes (HAP2, HAP3 and HAP4) in the Duroc breed. The Pietrain breed was monomorphic in the promoter region. The I199V locus was associated with several GP-influenced traits across all three breeds and IMF% in the Large White and Pietrain breed. No significant difference in promoter function was observed for the three main promoter haplotypes when tested in vitro. Conclusion: Gene expression levels of the porcine PRKAG3 are associated with meat quality phenotypes relating to glycolytic potential and IMF% in the Large White breed, while SNP variation in the promoter region of the gene is associated with PRKAG3 gene expression and meat quality phenotypes.
    • Stakeholder involvement in establishing a milk quality sub-index in dairy cow breeding goals: a Delphi approach

      Henchion, Maeve; McCarthy, Mary; Resconi, Virginia C.; Berry, Donagh; McParland, Sinead; Department of Agriculture, Food and the Marine, Ireland; 11/SF/311 (Cambridge University Press, 17/11/2015)
      The relative weighting on traits within breeding goals are generally determined by bio-economic models or profit functions. While such methods have generally delivered profitability gains to producers, and are being expanded to consider non-market values, current approaches generally do not consider the numerous and diverse stakeholders that affect, or are affected, by such tools. Based on principles of respondent anonymity, iteration, controlled feedback and statistical aggregation of feedback, a Delphi study was undertaken to gauge stakeholder opinion of the importance of detailed milk quality traits within an overall dairy breeding goal for profit, with the aim of assessing its suitability as a complementary, participatory approach to defining breeding goals. The questionnaires used over two survey rounds asked stakeholders: (a) their opinion on incorporating an explicit sub-index for milk quality into a national breeding goal; (b) the importance they would assign to a pre-determined list of milk quality traits and (c) the (relative) weighting they would give such a milk quality sub-index. Results from the survey highlighted a good degree of consensus among stakeholders on the issues raised. Similarly, revelation of the underlying assumptions and knowledge used by stakeholders to make their judgements illustrated their ability to consider a range of perspectives when evaluating traits, and to reconsider their answers based on the responses and rationales given by others, which demonstrated social learning. Finally, while the relative importance assigned by stakeholders in the Delphi survey (4% to 10%) and the results of calculations based on selection index theory of the relative emphasis that should be placed on milk quality to halt any deterioration (16%) are broadly in line, the difference indicates the benefit of considering more than one approach to determining breeding goals. This study thus illustrates the role of the Delphi technique, as a complementary approach to traditional approaches, to defining breeding goals. This has implications for how breeding goals will be defined and in determining who should be involved in the decision-making process.
    • Stress and immunological response of heifers divergently ranked for residual feed intake following an adrenocorticotropic hormone challenge

      Kelly, Alan K; Lawrence, P.; Earley, Bernadette; Kenny, David A.; McGee, Mark (Biomed Central, 2017-08-08)
      Background When an animal is exposed to a stressor, metabolic rate, energy consumption and utilisation increase primarily through activation of the hypothalamic-pituitary-adrenal (HPA) axis. Changes to partitioning of energy by an animal are likely to influence the efficiency with which it is utilised. Therefore, this study aimed to determine the physiological stress response to an exogenous adrenocorticotropic hormone (ACTH) challenge in beef heifers divergently ranked on phenotypic residual feed intake (RFI). Results Data were collected on 34 Simmental weaning beef heifers the progeny of a well characterized and divergently bred RFI suckler beef herd. Residual feed intake was determined on each animal during the post-weaning stage over a 91-day feed intake measurement period during which they were individually offered adlibitum grass silage and 2 kg of concentrate per head once daily. The 12 highest [0.34 kg DM/d] and 12 lowest [−0.48 kg DM/d] ranking animals on RFI were selected for use in this study. For the physiological stress challenge heifers (mean age 605 ± 13 d; mean BW 518 ± 31.4 kg) were fitted aseptically with indwelling jugular catheters to facilitate intensive blood collection. The response of the adrenal cortex to a standardised dose of ACTH (1.98 IU/kg metabolic BW0.75) was examined. Serial blood samples were analysed for plasma cortisol, ACTH and haematology variables. Heifers differing in RFI did not differ (P = 0.59) in ACTH concentrations. Concentration of ACTH peaked (P < 0.001) in both RFI groups at 20 min post-ACTH administration, following which concentration declined to baseline levels by 150 min. Similarly, cortisol systemic profile peaked at 60 min and concentrations remained continuously elevated for 150 min. A RFI × time interaction was detected for cortisol concentrations (P = 0.06) with high RFI heifers had a greater cortisol response than Low RFI from 40 min to 150 min relative to ACTH administration. Cortisol response was positively associated with RFI status (r = 0.32; P < 0.01). No effect of RFI was evident for neutrophil, lymphocytes, monocyte, eosinophils and basophil count. Plasma red blood cell number (6.07 vs. 6.23; P = 0.02) and hematocrit percentage (23.2 vs. 24.5; P = 0.02) were greater for low than high RFI animals. Conclusions Evidence is provided that feed efficiency is associated with HPA axis function and susceptibility to stress, and responsiveness of the HPA axis is likely to contribute to appreciable variation in the efficiency feed utilisation of cattle.
    • A study of the somatic cell count (SCC) of Irish milk from herd management and environmental perspectives

      O'Brien, Bernadette; Berry, Donagh; Kelly, Philip; Meaney, William J; O'Callaghan, Edmond J (Teagasc, 2009-12-01)
      The objective of this study was to investigate the herd management practices associated with somatic cell count (SCC) and total bacteria count (TBC), to geographically analyse SCC on a national basis, to investigate cow factors associated with SCC and to estimate the milk loss associated with high SCC across parities. From the 400 farms surveyed during farm visits throughout spring and winter, a profile of herd management was developed and the associations between management practices and milk SCC and TBC were established. Management practices associated with low SCC included the use of dry cow therapy, participation in a milk recording scheme, the use of teat disinfection post-milking, a higher frequency of cleaning and increased farm hygiene. Management practices associated with low TBC included the use of heated water in the milking parlour, participation in a milk recording scheme, tail clipping of cows at a frequency greater than once per year and increased farm hygiene. The spatial analysis showed that the south of the country had the greatest density of milk-recording herds. Approximately 60% of all herds in the study were from four counties (Cork, Kerry, Limerick and Tipperary). Average bulk tank SCC increased from 110,264 cells/mL in 2003 to 118,782 cells/mL in 2005, followed by a decrease to 108,454 cells/mL in 2007. Spatial clustering of high SCC scores was not observed (i.e., SCC on one farm was not related to SCC on other farms), which is consistent with mastitis being a herd problem as opposed to an area-based problem. SCC increased with parity from 97,000 cells/mL in parity 1 to 199,000 cell/mL in parity 6. SCC decreased between the period 5 to 35 days in milk (DIM) and 36 to 65 DIM, and increased thereafter. Cows calving in the months of January and September were associated with lower average 305 day SCC. The rate of increase in SCC from mid to late lactation was greatest in older parity animals. There was a test day milk loss of 1.43, 2.08, 2.59, 2.56 and 2.62 litres (parities 1 to 5, respectively) associated with an increase of SCC category from <51,000 to >400,000 cells/mL. When SCC was adjusted (test day SCC/dilution estimate, and test day SCC + (-ß)(test day milk yield)) to account for milk yield, similar trends in milk loss were observed. Alternatively, adjusting SCC (SCC*test day milk yield/mean test day milk yield) to account for milk yield showed an increase in test day milk with increasing SCC category. The results from this study highlight that adherence to best milking/farming practice will help reduce SCC and TBC on farms. The results contribute to the knowledge relating to SCC through increasing the accuracy of milk loss due to SCC and management practices associated with SCC. The results in the study can also be used in the development of strategies to reduce SCC on farms.
    • Suckler Bulls Slaughtered at 15 Months of Age: Effect of Different Production Systems on the Fatty Acid Profile and Selected Quality Characteristics of Longissimus Thoracis

      Moran, Lara; Wilson, Shannon S.; McElhinney, Cormac K.; Monahan, Frank J.; McGee, Mark; O'Sullivan, Maurice G.; O'Riordan, Edward G.; Kerry, Joseph P.; Molomey, Aidan P.; Department of Agriculture, Food and the Marine; et al. (MDPI AG, 2019-07-18)
      The objective was to compare the quality of beef from bulls reared in typical Irish indoor systems or in novel grass-based systems. Bulls were assigned to one of the following systems: (a) grass silage plus barley-based concentrate ad libitum (CON); (b) grass silage ad libitum plus 5 kg of concentrate (SC); (c) grazed grass without supplementation (G0); (d) grazed grass plus 0.5 kg of the dietary dry matter intake as concentrate (GC) for (100 days) until slaughter (14.99 months). Carcass characteristics and pH decline were recorded. Longissimus thoracis was collected for analytical and sensory analysis. Lower carcass weight, conformation and fatness scores were found for grazing compared to CON and SC groups. CON bulls had highest intramuscular fat and lighter meat colour compared with grazing bulls. The SC meat (14 days aged) was rated higher for tenderness, texture, flavour and acceptability compared with grazing groups. CON saturated and monounsaturated fatty acid (FA) concentration was highest, conversely, omega-3 FA concentration was higher for GC compared with CON, while no differences were found in polyunsaturated FA. In conclusion, while market fatness specification was not reached by grazed grass treatments, beef eating quality was not detrimentally affected and nutritional quality was improved.
    • Teagasc Hill Sheep Conference 2017 Programme

      Boyle, Gerry; Kirby, Tim; O'Sullivan, Kevin; Byrne, Declan; Keena, Catherine; Maguire, Fergal; Sheridan, Helen; Gorman, Monica; McLaren, Ann; Lambe, Nicola; et al. (Teagasc, 2017-02-08)
      Proceedings of the Teagasc Hill Sheep Conference 2017 which took place on the 8th of February 2017 in the The Malton Hotel, Killarney, Co. Kerry.
    • Teagasc Profit Monitor Analysis - Dairy Farms 2016

      Teagasc Specialist Service (Teagasc, 2017-05-10)
      The analyses in this publication are based on data provided by Teagasc dairy farmer clients relating to the production year 2016 and entered onto the PM system prior to 27th February 2017. In all, 1,505 farms are represented; 1,352 of these are engaged in spring milk production with the balance (153) engaged in winter/ liquid milk production. In addition, a matched sample analysis of 276 farmers who have completed PM analysis for each year in the period 2008 to 2016 is included. A summary of the key figures are included in the main tables and a more detailed breakdown of costs contained in the later tables. Where ‘Top 25%’ results are presented, the dataset was initially ranked on the basis of net profit per hectare. For the first time in the Dairy PM publication, the author has included an own labour charge (for the farmer’s own and unpaid family labour). This is a welcome development as it recognises that farmer’s labour input (and that of other unpaid family members) is required and rewarded for the milk produced. The labour adjustment is made following the calculation of the enterprise net profit and the adjusted net profit is an estimated return to management, owned land and owned capital.
    • Teagasc submission made in response to the Consultation Paper on Interim Review of Ireland’s Nitrates Derogation 2019

      Spink, John; Buckley, Cathal; Burgess, Edward; Daly, Karen M.; Dillon, Pat; Fenton, Owen; Horan, Brendan; Humphreys, James; Hyde, Tim; McCarthy, Brian; et al. (Teagasc, 2019-06-04)
      This submission was made in response to the consultation process run jointly by the Department of Housing, Planning, Community and Local Government (DHPCLG) and the Department of Agriculture, Food and the Marine (DAFM) inviting views and comments on proposals for the Interim Review of Ireland’s Nitrates Derogation Programme in 2019. It has been prepared by Teagasc’s Water Quality Working Group in consultation with the Gaseous Emissions Working Group. These working groups have members drawn from both the Knowledge Transfer and Research Directorates of Teagasc. It was prepared following consultation with colleagues across Teagasc using their collective knowledge and expertise in agri-environmental science and practice and the implementation of the Good Agricultural Practice (GAP) and Nitrates Derogation Regulations.
    • Transcriptomic analysis of the stress response to weaning at housing in bovine leukocytes using RNA-seq technology

      O'Loughlin, Aran; Lynn, David J; McGee, Mark; Doyle, Sean; McCabe, Matthew; Earley, Bernadette; Teagasc Walsh Fellowship Programme (Biomed Central, 2012-06-18)
      Background: Weaning of beef calves is a necessary husbandry practice and involves separating the calf from its mother, resulting in numerous stressful events including dietary change, social reorganisation and the cessation of the maternal-offspring bond and is often accompanied by housing. While much recent research has focused on the physiological response of the bovine immune system to stress in recent years, little is known about the molecular mechanisms modulating the immune response. Therefore, the objective of this study was to provide new insights into the molecular mechanisms underlying the physiological response to weaning at housing in beef calves using Illumina RNA-seq.Results: The leukocyte transcriptome was significantly altered for at least 7 days following either housing or weaning at housing. Analysis of differentially expressed genes revealed that four main pathways, cytokine signalling, transmembrane transport, haemostasis and G-protein-coupled receptor (GPRC) signalling were differentially regulated between control and weaned calves and underwent significant transcriptomic alterations in response to weaning stress on day 1, 2 and 7. Of particular note, chemokines, cytokines and integrins were consistently found to be up-regulated on each day following weaning. Evidence for alternative splicing of genes was also detected, indicating a number of genes involved in the innate and adaptive immune response may be alternatively transcribed, including those responsible for toll receptor cascades and T cell receptor signalling.Conclusions: This study represents the first application of RNA-Seq technology for genomic studies in bovine leukocytes in response to weaning stress. Weaning stress induces the activation of a number of cytokine, chemokine and integrin transcripts and may alter the immune system whereby the ability of a number of cells of the innate and adaptive immune system to locate and destroy pathogens is transcriptionally enhanced. Stress alters the homeostasis of the transcriptomic environment of leukocytes for at least 7 days following weaning, indicating long term effects of stress exposure in the bovine. The identification of gene signature networks that are stress activated provides a mechanistic framework to characterise the multifaceted nature of weaning stress adaptation in beef calves. Thus, capturing subtle transcriptomic changes provides insight into the molecular mechanisms that underlie the physiological response to weaning stress.
    • Using models to establish the financially optimum strategy for Irish dairy farms

      Ruelle, Elodie; Delaby, Luc; Wallace, Michael; Shalloo, Laurence; European Union; Department of Agriculture, Food and the Marine; 11/S/132 (Elsevier, 2017-11-02)
      Determining the effect of a change in management on farm with differing characteristics is a significant challenge in the evaluation of dairy systems due to the interacting components of complex biological systems. In Ireland, milk production is increasing substantially following the abolition of the European Union milk quota regime in 2015. There are 2 main ways to increase the milk production on farm (within a fixed land base): either increase the number of animals (thus increasing the stocking rate) or increase the milk production per animal through increased feeding or increased lactation length. In this study, the effect of increased concentrate feeding or an increase in grazing intensity was simulated to determine the effect on the farm system and its economic performance. Four stocking rates (2.3, 2.6, 2.9, and 3.2 cow/ha) and 5 different concentrate supplementation strategies (0, 180, 360, 600, and 900 kg of dry matter/lactation) resulting in 20 different scenarios were evaluated across different milk, concentrate, and silage purchase prices. Each simulation was run across 10 yr of meteorological data, which had been recorded over the period 2004 to 2013. Three models—the Moorepark and St Gilles grass growth model, the pasture-based herd dynamic milk model, and the Moorepark dairy systems model—were integrated and applied to simulate the different scenarios. Overall, this study has demonstrated that the most profitable scenario was a stocking rate of 2.6 cow/ha with a concentrate supplementation of 600 kg of dry matter/cow. The factor that had the greatest influence on profitability was variability of milk price.
    • Validation and Improvement of the Beef Production Sub-index in Ireland for Beef Cattle

      Drennan, Michael J; McGee, Mark; Clarke, Anne Marie; Kenny, David A.; Evans, R. D.; Berry, Donagh (Teagasc, 2009-12-01)
      The objectives of the following study were to: a. Quantify the effect of sire genetic merit for BCI on: 1. feed intake, growth and carcass traits of progeny managed under bull or steer beef production systems. 2. live animal scores, carcass composition and plasma hormone and metabolite concentrations in their progeny. b. Compare the progeny of : 1. Late-maturing beef with dairy breeds and 2. Charolais (CH), Limousin (LM), Simmental (SM) and Belgian Blue (BB) sires bred to beef suckler dams, for feed intake, blood hormones and metabolites, live animal measurements, carcass traits and carcass value in bull and steer production systems.
    • Variance components for bovine tuberculosis infection and multi-breed genome-wide association analysis using imputed whole genome sequence data

      Ring, S. C.; Purfield, D. C.; Good, M.; Breslin, P.; Ryan, E.; Blom, A.; Evans, R. D.; Doherty, M. L.; Bradley, D. G.; Berry, Donagh; et al. (Public Library of Science (PLoS), 2019-02-14)
      Bovine tuberculosis (bTB) is an infectious disease of cattle generally caused by Mycobacterium bovis, a bacterium that can elicit disease humans. Since the 1950s, the objective of the national bTB eradication program in Republic of Ireland was the biological extinction of bTB; that purpose has yet to be achieved. Objectives of the present study were to develop the statistical methodology and variance components to undertake routine genetic evaluations for resistance to bTB; also of interest was the detection of regions of the bovine genome putatively associated with bTB infection in dairy and beef breeds. The novelty of the present study, in terms of research on bTB infection, was the use of beef breeds in the genome-wide association and the utilization of imputed whole genome sequence data. Phenotypic bTB data on 781,270 animals together with imputed whole genome sequence data on 7,346 of these animals’ sires were available. Linear mixed models were used to quantify variance components for bTB and EBVs were validated. Within-breed and multi-breed genome-wide associations were undertaken using a single-SNP regression approach. The estimated genetic standard deviation (0.09), heritability (0.12), and repeatability (0.30) substantiate that genetic selection help to eradicate bTB. The multi-breed genome-wide association analysis identified 38 SNPs and 64 QTL regions associated with bTB infection; two QTL regions (both on BTA23) identified in the multi-breed analysis overlapped with the within-breed analyses of Charolais, Limousin, and Holstein-Friesian. Results from the association analysis, coupled with previous studies, suggest bTB is controlled by an infinitely large number of loci, each having a small effect. The methodology and results from the present study will be used to develop national genetic evaluations for bTB in the Republic of Ireland. In addition, results can also be used to help uncover the biological architecture underlying resistance to bTB infection in cattle.
    • The variation in morphology of perennial ryegrass cultivars throughout the grazing season and effects on organic matter digestibility

      Beecher, Marion; Hennessy, Deirdre; Boland, T. M.; McEvoy, Mary; O'Donovan, Michael; Lewis, Eva (Wiley, 2013-09-19)
      The grass plant comprises leaf, pseudostem, true stem (including inflorescence) and dead material. These components differ in digestibility, and variations in their relative proportions can affect sward quality. The objective of this study was to determine the change in the proportion and organic matter digestibility (OMD) of leaf, pseudostem, true stem and dead components of four perennial ryegrass cultivars (two tetraploids: Astonenergy and Bealey and two diploids: Abermagic and Spelga) throughout a grazing season. The DM proportions and in vitro OMD of leaf, pseudostem, true stem and dead in all cultivars were determined during ten grazing rotations between May 2011 and March 2012. There was an interaction between rotation and cultivar for leaf, pseudostem, true stem and dead proportions. In May and June, Astonenergy had the highest leaf and lowest true stem proportion (P < 0·05). From July onwards, there was no difference in leaf or true stem proportion between cultivars. Bealey had the highest annual mean OMD (752 g kg−1) and Spelga the lowest (696 g kg−1; P < 0·05). The OMD followed the order leaf > pseudostem > true stem > dead. Bealey had the highest combined leaf and pseudostem proportion 0·92, which explains why it had the highest OMD. In this study, the tetraploid cultivars had the highest leaf and pseudostem proportion and OMD. For accurate descriptions of a sward in grazing studies and to accurately determine sward morphological composition, pseudostem should be separated from true stem, particularly during the reproductive stage when true stem is present.
    • Variations in travel time for N loading to groundwaters in four case studies in Ireland:Implications for policy makers and regulators

      Fenton, Owen; Coxon, Catherine E.; Haria, Atul H.; Horan, Brendan; Humphreys, James; Johnston, Paul; Murphy, Paul N. C.; Necpalova, Magdalena; Premrov, Alina; Richards, Karl G. (School of Agriculture, Food Science and Veterinary Medicine, University College Dublin in association with Teagasc, 2009)
      Mitigation measures to protect waterbodies must be implemented by 2012 to meet the requirements of the EU Water Framework Directive. The efficacy of these measures will be assessed in 2015. Whilst diffuse N pathways between source and receptor are generally long and complex, EU legislation does not account for differences in hydrological travel time distributions that may result in different water quality response times. The “lag time” between introducing mitigation measures and first improvements in water quality is likely to be different in different catchments; a process that should be considered by policy makers and catchment managers. Many examples of travel time variations have been quoted in the literature but no Irish specific examples are available. Lag times based on initial nutrient breakthrough at four contrasting sites were estimated to a receptor 500 m away from a source. Vertical travel times were estimated using a combination of depth of infiltration calculations based on effective rainfall and subsoil physical parameters and existing hydrological tracer data. Horizontal travel times were estimated using a combination of Darcian linear velocity calculations and existing tracer migration data. Total travel times, assuming no biogeochemical processes, ranged from months to decades between the contrasting sites; the shortest times occurred under thin soil/subsoil on karst limestone and the longest times through thick low permeability soils/subsoils over poorly productive aquifers. Policy makers should consider hydrological lag times when assessing the efficacy of mitigation measures introduced under the Water Framework Directive. This lag time reflects complete flushing of a particular nutrient from source to receptor. Further research is required to assess the potential mitigation of nitrate through denitrification along the pathway from source to receptor.