• Accuracy of predicting milk yield from alternative milk recording schemes

      Berry, Donagh P.; Olori, V. E.; Cromie, A. R.; Veerkamp, Roel F.; Rath, Myles V; Dillon, Pat; Teagasc Walsh Fellowship Programme (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.
    • Adding value to cull cow beef

      O'Donovan, Michael; Minchin, William; Buckley, Frank; Kenny, David; Shalloo, Laurence (Teagasc, 01/08/2009)
      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, 01/08/2008)
      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.
    • Additive genetic, non-additive genetic and permanent environmental effects for female reproductive performance in seasonal calving dairy females

      Kelleher, Margaret M.; Buckley, Frank; Evans, R. D.; Berry, Donagh P.; Department of Agriculture, Food and the Marine, Ireland (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; et al. (Cambridge University Press: Published for the Institute of Food Research and the Hannah Research Institute, 18/05/2009)
      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.
    • Alterations in hepatic miRNA expression during negative energy balance in postpartum dairy cattle

      Fatima, Attia; Waters, Sinead M.; O'Boyle, Padraig; Seoighe, Cathal; Morris, Dermot G.; Teagasc Walsh Fellowship Programme (Biomed Central, 2014-01-15)
      Background Negative energy balance (NEB), an altered metabolic state, occurs in early postpartum dairy cattle when energy demands to support lactation exceed energy intake. During NEB the liver undergoes oxidative stress and increased breakdown of fatty acids accompanied by changes in gene expression. It is now known that micro RNAs (miRNA) can have a role in mediating such alterations in gene expression through repression or degradation of target mRNAs. miRNA expression is known to be altered by metabolism and environmental factors and miRNAs are implicated in expression modulation of metabolism related genes. Results miRNA expression was profiled in the liver of moderate yielding dairy cattle under severe NEB (SNEB) and mild NEB (MNEB) using the Affymetrix Gene Chip miRNA_2.0 array with 679 probe sets for Bos-taurus miRNAs. Ten miRNAs were found to be differentially expressed using the ‘samr’ statistical package (delta = 0.6) at a q-value FDR of < 12%. Five miRNAs including miR-17-5p, miR-31, miR-140, miR-1281 and miR-2885 were validated using RT-qPCR, to be up-regulated under SNEB. Liver diseases associated with these miRNAs include non-alcoholic fatty liver (NAFLD) and hepatocellular carcinoma (HCC). miR-140 and miR-17-5p are known to show differential expression under oxidative stress. A total of 32 down-regulated putative target genes were also identified among 418 differentially expressed hepatic genes previously reported for the same animal model. Among these, GPR37 (G protein-coupled receptor 37), HEYL (hairy/enhancer-of-split related with YRPW motif-like), DNJA1, CD14 (Cluster of differentiation 14) and GNS (glucosamine (N-acetyl)-6-sulfatase) are known to be associated with hepatic metabolic disorders. In addition miR-140 and miR-2885 have binding sites on the most down-regulated of these genes, FADS2 (Fatty acid desaturase 2) which encodes an enzyme critical in lipid biosynthesis. Furthermore, HNF3-gamma (Hepatocyte nuclear factor 3-gamma), a hepatic transcription factor (TF) that is involved in IGF-1 expression regulation and maintenance of glucose homeostasis is a putative target of miR-31. Conclusions This study shows that SNEB affects liver miRNA expression and these miRNAs have putative targets in hepatic genes down-regulated under this condition. This study highlights the potential role of miRNAs in transcription regulation of hepatic gene expression during SNEB in dairy cattle. Background Negative energy balance (NEB), an altered metabolic state, occurs in early postpartum dairy cattle when energy demands to support lactation exceed energy intake. During NEB the liver undergoes oxidative stress and increased breakdown of fatty acids accompanied by changes in gene expression. It is now known that micro RNAs (miRNA) can have a role in mediating such alterations in gene expression through repression or degradation of target mRNAs. miRNA expression is known to be altered by metabolism and environmental factors and miRNAs are implicated in expression modulation of metabolism related genes. Results miRNA expression was profiled in the liver of moderate yielding dairy cattle under severe NEB (SNEB) and mild NEB (MNEB) using the Affymetrix Gene Chip miRNA_2.0 array with 679 probe sets for Bos-taurus miRNAs. Ten miRNAs were found to be differentially expressed using the ‘samr’ statistical package (delta = 0.6) at a q-value FDR of < 12%. Five miRNAs including miR-17-5p, miR-31, miR-140, miR-1281 and miR-2885 were validated using RT-qPCR, to be up-regulated under SNEB. Liver diseases associated with these miRNAs include non-alcoholic fatty liver (NAFLD) and hepatocellular carcinoma (HCC). miR-140 and miR-17-5p are known to show differential expression under oxidative stress. A total of 32 down-regulated putative target genes were also identified among 418 differentially expressed hepatic genes previously reported for the same animal model. Among these, GPR37 (G protein-coupled receptor 37), HEYL (hairy/enhancer-of-split related with YRPW motif-like), DNJA1, CD14 (Cluster of differentiation 14) and GNS (glucosamine (N-acetyl)-6-sulfatase) are known to be associated with hepatic metabolic disorders. In addition miR-140 and miR-2885 have binding sites on the most down-regulated of these genes, FADS2 (Fatty acid desaturase 2) which encodes an enzyme critical in lipid biosynthesis. Furthermore, HNF3-gamma (Hepatocyte nuclear factor 3-gamma), a hepatic transcription factor (TF) that is involved in IGF-1 expression regulation and maintenance of glucose homeostasis is a putative target of miR-31. Conclusions This study shows that SNEB affects liver miRNA expression and these miRNAs have putative targets in hepatic genes down-regulated under this condition. This study highlights the potential role of miRNAs in transcription regulation of hepatic gene expression during SNEB in dairy cattle.
    • Alternatives to formic acid as a grass silage additive under two contrasting ensilability conditions

      Lorenzo, B. Fernandez; O'Kiely, Padraig (Teagasc, Oak Park, Carlow, Ireland, 2008)
      The effects of formic acid and four alternative additives on silage fermentation, in-silo DM losses and aerobic stability were compared in an experiment using both difficultto- ensile (DIFF) and easier-to-ensile (EASI) herbages. Both were ensiled in laboratory silos with either no additive or following the application of formic acid (FA; 850 g/kg) at 3 mL/kg herbage, Add-SaFeR® (ATF1) and GrasAAT® (ATF2), both based on ammonium tetraformate, at 4 mL/kg herbage, an antimicrobial mixture (MIX; potassium formate, sodium disulfite and sodium benzoate) at 3 g/kg herbage, or Ecosyl (LAB; Lactobacillus plantarum) at 3 mL/kg herbage. There were four replicates per treatment and the silos were stored for 132 days. DIFF silage made without additive was poorly fermented. All additives increased the extent and improved the direction of DIFF silage fermentation, and reduced in-silo losses. However, MIX did not reduce butyric acid concentration and increased the extent of aerobic deterioration. LAB had a smaller effect on fermentation and in-silo losses than FA. With EASI silages, all additives restricted the extent of fermentation and improved fermentation quality, with the latter effect being smaller than for DIFF silages. LAB promoted a particularly homolactic fermentation but subsequently increased aerobic deterioration. In both DIFF and EASI silages additive treatment improved in vitro digestibility. It is concluded that only ATF1, ATF2 and MIX were as effective as FA at improving silage preservation and reducing in-silo losses with both DIFF and EASI herbages. However, ATF1 and ATF2 were superior in reducing the apparent extent of proteolysis and MIX was slightly less effective at reducing the activity of saccharolytic Clostridia.
    • Alum Activates the Bovine NLRP3 Inflammasome

      Harte, Ciaran; Gorman, Aoife L.; McCluskey, S.; Carty, Michael; Bowie, Andrew G.; Scott, C. J.; Meade, Kieran G; Lavelle, Ed C.; Teagasc Walsh Fellowship Programme; Science Foundation Ireland; et al. (Frontiers, 2017-11-09)
      There has been a move away from vaccines composed of whole or inactivated antigens toward subunit-based vaccines, which although safe, provide less immunological protection. As a result, the use of adjuvants to enhance and direct adaptive immune responses has become the focus of much targeted bovine vaccine research. However, the mechanisms by which adjuvants work to enhance immunological protection in many cases remains unclear, although this knowledge is critical to the rational design of effective next generation vaccines. This study aimed to investigate the mechanisms by which alum, a commonly used adjuvant in bovine vaccines, enhances IL-1β secretion in bovine peripheral blood mononuclear cells (PBMCs). Unlike the case with human PBMCs, alum promoted IL-1β secretion in a subset of bovine PBMCs without priming with a toll-like receptor agonist. This suggests that PBMCs from some cattle are primed to produce this potent inflammatory cytokine and western blotting confirmed the presence of preexisting pro-IL-1β in PBMCs from a subset of 8-month-old cattle. To address the mechanism underlying alum-induced IL-1β secretion, specific inhibitors identified that alum mediates lysosomal disruption which subsequently activates the assembly of an NLRP3, ASC, caspase-1, and potentially caspase-8 containing complex. These components form an inflammasome, which mediates alum-induced IL-1β secretion in bovine PBMCs. Given the demonstrated role of the NLRP3 inflammasome in regulating adaptive immunity in murine systems, these results will inform further targeted research into the potential of inflammasome activation for rational vaccine design in cattle.
    • Analysis of DRB1 exon 2 genotyping by STR size analysis in Suffolk and Texel sheep breeds

      Sayers, Gearoid; Mitchel, S; Ryan, Marion T; Stear, Michael J.; Hanrahan, James P; Sweeney, Torres; Department of Agriculture, Food and the Marine; Wellcome Trust; RSF16; 061354 (Teagasc (Agriculture and Food Development Authority), Ireland, 2004)
      Alleles of the DRB1 exon 2 locus of the major histocompatibility complex have recently been associated with genetic resistance to gastrointestinal nematodes in sheep. While sequence-based typing is the standard method for allele discrimination, a rapid, high throughput method for DRB1 exon 2 genotyping is required if such information is to be incorporated into national breeding programmes. Previous studies have highlighted a simple tandem repeat (STR) located within intron 2 of the DRB1 gene, which could potentially be used to accurately assess the allele present within the adjacent exon 2. The aims of this study were firstly to compare two methods of STR analysis, Genescan™ and autoradiography, and secondly to investigate if STR analysis of DRB1 intron 2 could be used to accurately assess the profile of DRB1 exon 2. Six DRB1 exon 2 alleles were identified by sequence-based typing in Suffolk (n = 31) and eight in Texel (n = 60) sheep. The results indicated that Genescan™ was a more accurate method of STR analysis than autoradiography. The expected 1:1 correspondence between STR size, analysed by Genescan™ and DRB1 exon 2 allele, determined by sequence-based typing, was not observed. However, the correspondence was found to be degenerate, whereby some alleles were associated with two STR sizes. Thus, irrespective of the STR size identified, STR analysis by Genescan™ identified the correct allele in all cases within both populations of animals studied. However, the Genescan™ method of allele identification cannot be used for Suffolk × Texel crossbred progeny or in other breeds where the relationship between STR size and DRB1 exon 2 allele is not known.
    • Analysis of Johne’s disease ELISA status and associated performance parameters in Irish dairy cows

      Kennedy, Aideen E.; Byrne, Nicky; Garcia, A. B; O'Mahony, James A.; Sayers, Riona; Irish Dairy Levy Research Trust (2016-03-02)
      Background Infection with Mycobacterium avium subspecies paratuberculosis (MAP) has been associated with reductions in milk production in dairy cows and sub optimal fertility. The aim of this study was to highlight the production losses associated with testing MAP ELISA positive in Irish dairy cows. Secondary objectives included investigation of risk factors associated with testing MAP ELISA positive. A survey of management practices on study farms was also conducted, with examination of associations between management practices and herd MAP status. Blood samples were collected from 4188 breeding animals on 22 farms. Samples were ELISA tested using the ID Screen Paratuberculosis Indirect Screening Test. Production parameters examined included milk yield, milk fat, milk protein, somatic cell count, and calving interval. The association between MAP ELISA status and production data was investigated using multi-level mixed models. Logistic regression was used to identify risk factors for testing JD blood ELISA positive at individual cow level and to identify associations between farm management practices and herd MAP status. Results Data were available for 3528 cows. The apparent prevalence recorded was 7.4 %. Mixed model analysis revealed no statistically significant association between testing MAP ELISA positive and dairy cow production parameters. Risk factors associated with testing positive included larger sized herds being over twice more likely to test positive than smaller herds (OR 2.4 P = <0.001). Friesians were less likely to test positive relative to other breeds. A number of study farmers were engaged in management practices that have previously been identified as high risk for MAP transmission e.g., 73.1 % pooled colostrum and 84.6 % of study farmers used the calving area to house sick animals throughout the year. No significant associations however, were identified between farm management practices and herd MAP status. Conclusion No production losses were identified; however an apparent prevalence of 7.4 % was recorded. With the abolition of EU milk quotas herd size in Ireland is expanding, as herds included in this study were larger than the national average, results may be indicative of future JD levels if no JD control programmes are implemented to minimise transmission.
    • Analysis of meat quality traits and gene expression profiling of pigs divergent in residual feed intake

      Horodyska, Justyna; Oster, Michael; Reyer, Henry; Mullen, Anne Maria; Lawlor, Peadar G; Wimmers, Klaus; Hamill, Ruth M; European Union Seventh Framework Programme; 311794 (Elsevier, 2017-11-20)
      Residual feed intake (RFI), the difference between actual feed intake and predicted feed requirements, is suggested to impact various aspects of meat quality. The objective of this study was to investigate the molecular mechanisms underpinning the relationship between RFI and meat quality. Technological, sensory and nutritional analysis as well as transcriptome profiling were carried out in Longissimus thoracis et lumborum muscle of pigs divergent in RFI (n = 20). Significant differences in sensory profile and texture suggest a minor impairment of meat quality in more efficient pigs. Low RFI animals had leaner carcasses, greater muscle content and altered fatty acid profiles compared to high RFI animals. Accordingly, differentially expressed genes were enriched in muscle growth and lipid & connective tissue metabolism. Differences in protein synthesis and degradation suggest a greater turnover of low RFI muscle, while divergence in connective tissue adhesion may impact tenderness. Fatty acid oxidation tending towards decrease could possibly contribute to reduced mitochondrial activity in low RFI muscle.
    • Animal performance and economic implications of alternative production systems for dairy bulls slaughtered at 15 months of age

      Murphy, B.M.; Crosson, Paul; Kelly, Alan K; Prendiville, Robert; Department of Agriculture, Food and the Marine, Ireland; 11/SF/322 (Teagasc (Agriculture and Food Development Authority), Ireland, 2017-10-26)
      The objectives of this experiment were to investigate (i) the influence of varying levels of concentrate supplementation during the grazing season, (ii) alternative finishing strategies for dairy bulls slaughtered at 15 mo of age and (iii) economic implications of these management strategies. Bulls were assigned to a 2 (level of concentrate supplementation during the grazing season: 1 kg [LA] and 2 kg [HA] dry matter [DM]/head daily) × 2 (finishing strategies: concentrates ad libitum group [AL] or grass silage ad libitum plus 5 kg DM of concentrates/head daily group [SC]) factorial arrangement of treatments. Average daily gain (ADG) during the grazing season was greater (P < 0.01) for HA than for LA. Consequently, HA bulls were 16 kg heavier at housing: 214 and 230 kg, respectively (P < 0.05). During the finishing period, ADG tended (P = 0.09) to be greater for LA than for HA. Carcass weight tended (P = 0.08) to be greater for HA than for LA. Fat score was greater for HA. Live weight at slaughter (P < 0.001) and carcass weight (P < 0.001) were 41 and 23 kg greater for AL than for SC, respectively. Conformation (P < 0.05) and fat score (P < 0.05) were greater for AL than for SC. The Grange Dairy Beef Systems Model simulated whole-farm system effects of the production systems. Net margin/head was greater for LA than for HA and greater for SC than for AL. Sensitivity analysis of finishing concentrate price, calf purchase price and beef price showed no re-ranking of the systems on a net margin basis. Although greater animal performance was observed from the higher plane of nutrition, overall profitability was lower.
    • Animal Transport: Developing optimum animal handling procedures and effective transport strategies in the food production chain to improve animal welfare and food quality

      Earley, Bernadette; Murray, Margaret; Prendiville, Daniel J.; European Union (Teagasc, 2007-01-01)
      A series of studies were performed to investigate the effect of transport on liveweight, physiological and haematological responses of cattle. The first study was carried out over a 6 week period in the Spring of 2004. Eighty-four continental x bulls (mean weight (s.d.) 367 (35) kg), naïve to transport, were randomly assigned to one of six journey (J) times of 0, 6, 9, 12, 18 and 24h transport at a stocking density of 1.02m2/bull. Blood samples were collected by jugular venipuncture before, immediately after and at 1, 2, 4, 6, 8, 12 and 24h and bulls were weighed before, immediately after, and at 4, 12 and 24h. Bulls travelling for 6h (280 km), 9h (435 km), 12h (582 km), 18h (902 km) and 24h (1192 km) lost 4.7, 4.5, 5.7 (P=0.05), 6.6 (P=0.05) and 7.5 (P=0.05) percentage liveweight compared with baseline. During the 24h recovery period liveweight was regained to pre-transport levels. Lymphocyte percentages were lower (P=0.001) and neutrophil percentages were higher (P=0.05) in all animals. Blood protein and creatine kinase, glucose and NEFA concentrations were higher (P=0.05) in the bulls following transport and returned to baseline within 24h. In conclusion, liveweight and some physiological and haematological responses of bulls returned to pre-transport levels within 24h having had access to feed and water. Transport of bulls from 6 – 24hours did not impact negatively on animal welfare.
    • Anthelmintic-resistant nematodes in Irish commercial sheep flocks- the state of play

      Good, Barbara; Hanrahan, James P; de Waal, Daniel Theodorus; Patten, Thomas; Kinsella, Andrew; Lynch, Ciaran Oliver (Biomed Central, 2012-12-22)
      Anthelmintic resistance has been reported in most sheep producing countries. Prior to the mid 1990s, reports of anthelmintic resistance in Ireland were sparse and focused on benzimidazole, one of the three classes of anthelmintic available during this period. This evidence for efficacy issues on Irish farms combined with awareness that anthelmintic resistance was increasingly being reported in other countries prompted the need for more comprehensive investigations on Irish farms. Faecal egg count reduction and micro-agar larval development tests were employed to investigate resistance to benzimidazole, levamisole and macrocyclic lactone. There is compelling evidence for resistance to both benzimidazole (>88% of flocks) and levamisole (>39% of flocks). Resistance of nematode populations to macrocyclic lactone was suspected on a small number of farms (11%) but needs to be confirmed. The recent introduction of two new classes of anthelmintics, after over a 25 year interval, together with the evidence that anthelmintic resistance is reported within a relatively short time following the introduction of a new anthelmintic compound means that the challenge to the industry is immediate. Actions are urgently required to manage anthelmintic resistance so as to prolong the lifespan of anthelmintics.
    • Anthelmintic-resistant nematodes in Irish commercial sheep flocks- the state of play

      Good, Barbara; Hanrahan, James P; de Waal, Daniel Theodorus; Patten, Thomas; Kinsella, Andrew; Lynch, Ciaran Oliver (Biomed Central, 22/12/2012)
      Anthelmintic resistance has been reported in most sheep producing countries. Prior to the mid 1990s, reports of anthelmintic resistance in Ireland were sparse and focused on benzimidazole, one of the three classes of anthelmintic available during this period. This evidence for efficacy issues on Irish farms combined with awareness that anthelmintic resistance was increasingly being reported in other countries prompted the need for more comprehensive investigations on Irish farms. Faecal egg count reduction and micro-agar larval development tests were employed to investigate resistance to benzimidazole, levamisole and macrocyclic lactone. There is compelling evidence for resistance to both benzimidazole (>88% of flocks) and levamisole (>39% of flocks). Resistance of nematode populations to macrocyclic lactone was suspected on a small number of farms (11%) but needs to be confirmed. The recent introduction of two new classes of anthelmintics, after over a 25 year interval, together with the evidence that anthelmintic resistance is reported within a relatively short time following the introduction of a new anthelmintic compound means that the challenge to the industry is immediate. Actions are urgently required to manage anthelmintic resistance so as to prolong the lifespan of anthelmintics.
    • Anti-Müllerian hormone in grazing dairy cows: Identification of factors affecting plasma concentration, relationship with phenotypic fertility, and genome-wide associations

      Gobikrushanth, M.; Purfield, Deirdre C; Canadas, E. R.; Herlihy, Mary M.; Kenneally, J.; Murray, Margaret; Kearney, Francis; Colazo, M. G.; Ambrose, D. J.; Butler, Stephen T.; et al. (Elsevier, 2019-09-11)
      The objectives of this study were to (1) characterize the distribution and variability of plasma anti-Müllerian hormone (AMH) concentration; (2) evaluate factors associated with phenotypic variation in plasma AMH; (3) examine the associations between categories of plasma AMH and reproductive outcomes [pregnancy to first artificial insemination (P/AI), and pregnancy rates within 21, 42, and 84 d after the mating start date (MSD)]; (4) estimate pedigree and genomic heritability for plasma AMH; and (5) identify and validate SNP associated with phenotypic variation in plasma AMH. Plasma AMH concentration (pg/mL) was determined from a blood sample collected (mean ± standard deviation) 10 ± 2 d after first insemination at detected estrus (IDE) in 2,628 first- and second-parity Irish dairy cows. Overall, plasma AMH had a positively skewed distribution with mean (± standard deviation), median, minimum, and maximum concentrations of 326 ± 231, 268, 15, and 2,863 pg/mL, respectively. Plasma AMH was greatest for Jersey, followed by Holstein × Jersey, Holstein × Norwegian Red, and Holstein cows (410, 332, 284, and 257 pg/mL, respectively). Second-parity cows had greater plasma AMH than first-parity cows (333 vs. 301 pg/mL, respectively). Samples collected at 7 and 8 d after first IDE had lesser plasma AMH than those collected on d 9, 10, 11, 12, and 13 after first IDE (291 and 297 vs. 317, 319, 331, 337, and 320 pg/mL). Plasma AMH was not associated with either body condition score at first IDE or the interval from calving to MSD. Cows were categorized into low (≤150 pg/mL; n = 526; lowest 20%), intermediate (>150 to ≤461 pg/mL; n = 1,576; intermediate 60%), and high AMH (>461 pg/mL; n = 526; highest 20%) groups based on plasma AMH, and associations with reproductive outcomes were tested. Cows with high and intermediate plasma AMH had 1.42- and 1.51-times-greater odds of becoming pregnant within 84 d after the MSD than those with low plasma AMH (90.3 and 90.8 vs. 86.8%, respectively); however, P/AI and pregnancy rate within 21 and 42 d after the MSD did not differ among AMH categories. Plasma AMH was moderately heritable (pedigree heritability of 0.40 ± 0.06 and genomic heritability of 0.45 ± 0.05), and 68 SNP across Bos taurus autosomes 7 and 11 were associated with phenotypic variation in plasma AMH. Out of 68 SNP, 42 were located in a single quantitative trait locus on Bos taurus autosome 11 that harbored 6 previously identified candidate genes (NR5A1, HSPA5, CRB2, DENND1A, NDUFA8, and PTGS) linked to fertility-related phenotypes in dairy cows.
    • Application of data envelopment analysis to measure technical efficiency on a sample of Irish dairy farms

      Kelly, Eoin; Shalloo, Laurence; Geary, Una; Kinsella, Anne; Wallace, Michael (Teagasc, 2012-12)
      The aim of this study was to determine the levels of technical efficiency on a sample of Irish dairy farms utilizing Data Envelopment Analysis (DEA) and to identify key management and production factors that differ between producers indentified as efficient and inefficient. DEA was used in this study to generate technical efficiency scores under assumptions of both constant returns to scale (CRS) and variable returns to scale (VRS). The average technical efficiency score was 0.785 under CRS and 0.833 under VRS. Key production characteristics of efficient and inefficient producers were compared using an analysis of variance. More technically efficient producers used less input per unit of output, had higher production per cow and per hectare and had a longer grazing season, a higher milk quality standard, were more likely to have participated in milk recording and had greater land quality compared to the inefficient producers.
    • The Application of Next Generation Sequencing to Profile Microbe Related Cheese Quality Defects

      O'Sullivan, Daniel; Teagasc Walsh Fellowship Programme (2015)
      High throughput next generation sequencing, together with advanced molecular methods, has considerably enhanced the field of food microbiology. By overcoming biases associated with culture dependant approaches, it has become possible to achieve novel insights into the nature of food-borne microbial communities. In this thesis, several different sequencingbased approaches were applied with a view to better understanding microbe associated quality defects in cheese. Initially, a literature review provides an overview of microbeassociated cheese quality defects as well as molecular methods for profiling complex microbial communities. Following this, 16S rRNA sequencing revealed temporal and spatial differences in microbial composition due to the time during the production day that specific commercial cheeses were manufactured. A novel Ion PGM sequencing approach, focusing on decarboxylase genes rather than 16S rRNA genes, was then successfully employed to profile the biogenic amine producing cohort of a series of artisanal cheeses. Investigations into the phenomenon of cheese pinking formed the basis of a joint 16S rRNA and whole genome shotgun sequencing approach, leading to the identification of Thermus species and, more specifically, the pathway involved in production of lycopene, a red coloured carotenoid. Finally, using a more traditional approach, the effect of addition of a facultatively heterofermentative Lactobacillus (Lactobacillus casei) to a Swiss-type cheese, in which starter activity was compromised, was investigated from the perspective of its ability to promote gas defects and irregular eye formation. X-ray computed tomography was used to visualise, using a non-destructive method, the consequences of the undesirable gas formation that resulted. Ultimately this thesis has demonstrated that the application of molecular techniques, such as next generation sequencing, can provide a detailed insight into defect-causing microbial populations present and thereby may underpin approaches to optimise the quality and consistency of a wide variety of cheeses.
    • The application of transcriptomic data in the authentication of beef derived from contrasting production systems

      Sweeney, Torres; Lejeune, Alexandre; Moloney, Aidan P; Monahan, Frank J; Gettigan, Paul M; Downey, Gerard; Park, Stephen D. E.; Ryan, Marion T; Department of Agriculture, Food and the Marine (Biomed Central, 2016-09-21)
      Background Differences between cattle production systems can influence the nutritional and sensory characteristics of beef, in particular its fatty acid (FA) composition. As beef products derived from pasture-based systems can demand a higher premium from consumers, there is a need to understand the biological characteristics of pasture produced meat and subsequently to develop methods of authentication for these products. Here, we describe an approach to authentication that focuses on differences in the transcriptomic profile of muscle from animals finished in different systems of production of practical relevance to the Irish beef industry. The objectives of this study were to identify a panel of differentially expressed (DE) genes/networks in the muscle of cattle raised outdoors on pasture compared to animals raised indoors on a concentrate based diet and to subsequently identify an optimum panel which can classify the meat based on a production system. Results A comparison of the muscle transcriptome of outdoor/pasture-fed and Indoor/concentrate-fed cattle resulted in the identification of 26 DE genes. Functional analysis of these genes identified two significant networks (1: Energy Production, Lipid Metabolism, Small Molecule Biochemistry; and 2: Lipid Metabolism, Molecular Transport, Small Molecule Biochemistry), both of which are involved in FA metabolism. The expression of selected up-regulated genes in the outdoor/pasture-fed animals correlated positively with the total n-3 FA content of the muscle. The pathway and network analysis of the DE genes indicate that peroxisome proliferator-activated receptor (PPAR) and FYN/AMPK could be implicit in the regulation of these alterations to the lipid profile. In terms of authentication, the expression profile of three DE genes (ALAD, EIF4EBP1 and NPNT) could almost completely separate the samples based on production system (95 % authentication for animals on pasture-based and 100 % for animals on concentrate- based diet) in this context. Conclusions The majority of DE genes between muscle of the outdoor/pasture-fed and concentrate-fed cattle were related to lipid metabolism and in particular β-oxidation. In this experiment the combined expression profiles of ALAD, EIF4EBP1 and NPNT were optimal in classifying the muscle transcriptome based on production system. Given the overall lack of comparable studies and variable concordance with those that do exist, the use of transcriptomic data in authenticating production systems requires more exploration across a range of contexts and breeds.
    • Artificial rearing affects piglets pre-weaning behaviour, welfare and growth performance

      Schmitt, Océane; O'Driscoll, Keelin; Boyle, Laura; Baxter, Emma M.; Department of Agriculture, Food and the Marine; 13S428 (Elsevier, 2018-11-02)
      One strategy adopted on farms to deal with managing large litters involves removing piglets from their mothers at seven days old to be reared in specialised accommodation with milk replacer. Effects on piglet behaviour, growth and some aspects of welfare were evaluated in this study by comparing 10 pairs of two litters (one sow-reared: SR, one artificially-reared: AR) selected at seven days-old at a similar weight. Piglet behaviour was recorded for 20 min following transfer of AR piglets to the artificial-rearing enclosure (D0) and for 20 min hourly between 09:00 h and 17:00 h (8 h) on D5 and D12. Hourly 5 min live observations were also undertaken. Qualitative Behavioural Assessment (QBA) was conducted on D14 to evaluate piglets’ emotional state. Survival and illness events were recorded until weaning. On D0, D1, D8 and D15 piglets were weighed and scored for tear staining, dirtiness of the face and severity of lesions on the snout, limbs, ear and tail. Survival and illness rates, as well as the rates of behaviours/min were analysed using GLMMs. Weights and QBA scores were analysed using GLM. Lesions, tear staining and dirtiness scores were averaged per litter and analysed using GLM. When AR piglets were transferred to the artificial-rearing enclosure, their behaviour was not different to SR piglets. Over the two observation days, AR piglets performed more belly-nosing (F1,76.53 = 42.25; P < 0.001), nursing-related displacements (F1,79 = 19.32, P < 0.001), visits to the milk cup (compared to nursing bouts; F1,73.8 = 38.42, P < 0.001), and oral manipulation of littermates’ ears (F1,91.95 = 12.79, P < 0.001) and tails (F1,58.54 = 15.63, P < 0.001) than SR piglets. However, SR piglets played alone (F1,88.99 = 8.29, P < 0.005) and explored their environment (F1,99.42 = 4.52, P < 0.05) more frequently than AR piglets. The QBA scores indicated a lower emotional state in AR piglets (t25.1=-3.25, P < 0.05). Survival rate and overall illness rate of piglets were similar between the treatments. AR piglets experienced a growth check following their transfer to the artificial-rearing enclosure and remained lighter than SR piglets through to weaning (6.53 ± 0.139 kg vs. 7.97 ± 0.168 kg, t256 = 9.79, P < 0.001). Overall, snout lesion scores were not different between the treatments, but AR piglets had lower limb (F1,10.1 = 5.89, P < 0.05) and ear (F1,14.5 = 24.89, P < 0.001) lesion scores and higher tail lesion scores (F1,34.5 = 15.54, P < 0.001). AR piglets were dirtier (F1,17.4 = 23.38, P < 0.001) but had lower tear staining scores (F1,19.1 = 68.40, P < 0.001) than SR piglets. In conclusion, artificial rearing impaired piglets’ behaviour, welfare and growth.