• Accuracy of predicting milk yield from alternative milk recording schemes

      Berry, Donagh; 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 A.; 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.
    • 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; 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; 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.
    • 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.
    • 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.
    • 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; 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 the TruCulture® whole blood stimulation system for immune response profiling in cattle

      O’Brien, Megan B.; McLoughlin, Rachel M.; Meade, Kieran G.; Teagasc Walsh Fellowship Programme; 0005GE (Elsevier BV, 2020-03)
      Capturing the phenotypic variation in immune responses holds enormous promise for the development of targeted treatments for disease as well as tailored vaccination schedules. However, accurate detection of true biological variation can be obscured by the lack of standardised immune assays. The TruCulture® whole blood stimulation system has now been extensively used to detect basal and induced immune responses to a range of pathogen-associated molecular patterns (PAMPs) in human peripheral blood. This study demonstrates the optimisation of this commercially available assay for systemic immune phenotyping in cattle. The early immune response in Holstein-Friesian bull calves (n = 10) was assessed by haematology, flow cytometry and cytokine expression profiling after 24 h ex-vivo PAMP (LPS, poly (I:C) and zymosan) stimulation in TruCulture® tubes. A comparative analysis was also performed with a traditional whole blood stimulation assay and cell viability using both systems was also evaluated. Results: Supernatant collected from TruCulture® tubes showed a significant increase in IL-1β and IL-8 expression compared to null stimulated tubes in response to both LPS and zymosan. In contrast, a detectable immune response was not apparent at the standard concentration of poly (I:C). Conventional whole blood cultures yielded similar response profiles, although the magnitude of the response was higher to both LPS and zymosan, which may be attributed to prokaryotic strain-specificity or batch of the stimulant used. Despite being a closed system, HIF1A expression – used as a measure of hypoxia was not increased, suggesting the TruCulture® assay did not negatively affect cell viability. This represents the first reported use of this novel standardised assay in cattle, and indicates that the concentration of poly (I:C) immunogenic in humans is insufficient to induce cytokine responses in cattle. We conclude that the low blood volume and minimally invasive TruCulture® assay system offers a practical and informative technique to assess basal and induced systemic immune responses in cattle.
    • The application of transcriptomic data in the authentication of beef derived from contrasting production systems

      Sweeney, Torres; Lejeune, Alexandre; Moloney, Aidan; 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.
    • Associating cow characteristics with mobility scores in pasture-based dairy cows

      O'Connor, Aisling; Bokkers, Eddie A.M.; de Boer, Imke J. M.; Hogeveen, Henk; Sayers, Riona; Byrne, Nicky; Ruelle, Elodie; Shalloo, Laurence; Department of Agriculture, Food and the Marine; Teagasc Walsh Fellowship Programme; et al. (Elsevier, 2019-07-10)
      The quality of dairy cow mobility can have significant welfare, economic, and environmental consequences that have yet to be extensively quantified for pasture-based systems. The objective of this study was to characterize mobility quality by examining associations between specific mobility scores, claw disorders (both the type and severity), body condition score (BCS), and cow parity. Data were collected for 6,927 cows from 52 pasture-based dairy herds, including mobility score (0 = optimal mobility; 1, 2, or 3 = increasing severities of suboptimal mobility), claw disorder type and severity, BCS, and cow parity. Multinomial logistic regression was used for analysis. The outcome variable was mobility score, and the predictor variables were BCS, type and severity of claw disorders, and cow parity. Three models were run, each with 1 reference category (mobility score 0, 1, or 2). Each model also included claw disorders (overgrown claw, sole hemorrhage, white line disease, sole ulcer, and digital dermatitis), BCS, and cow parity as predictor variables. The presence of most types of claw disorders had odds ratios >1, indicating an increased likelihood of a cow having suboptimal mobility. Low BCS (BCS <3.00) was associated with an increased risk of a cow having suboptimal mobility, and relatively higher parity was also associated with an increased risk of suboptimal mobility. These results confirm an association between claw disorders, BCS, cow parity, and dairy cow mobility score. Therefore, mobility score should be routinely practiced to identify cows with slight deviations from the optimal mobility pattern and to take preventive measures to keep the problem from worsening.
    • Association between body condition score and live weight in pasture-based Holstein-Friesian dairy cows

      Berry, Donagh; MacDonald, Kevin A.; Penno, John W.; Roche, John R. (Cambridge University Press: Published for the Institute of Food Research and the Hannah Research Institute, 2006-11)
      The objective was to quantify the strength of the relationship between body condition score (BCS) and live weight (LW) in pasture-based Holstein-Friesian dairy cattle, and to determine the kg LW per unit BCS. A total of 26021 test-day records with information on both BCS (1–10 scale, where 1 is emaciated and 10 is obese) and LW across 1110 lactations from one research farm were used in the analysis. Correlation and regression analyses were used to determine the degree of association between BCS and LW in different parities, stages of the inter-calving interval and years. Correlations between BCS and LW were relatively consistent, with the mean correlation between BCS and LW across all data of 0·55 implying that differences in BCS explain approximately 30% of the variation in LW. Significantly different regressions of LW on BCS were present within stage of inter-calving interval by parity subclasses. Excluding calving, LW per unit BCS varied from 17 kg (early to mid lactation in parity 1) to 36 kg (early lactation in parity 4 and 5). However, LW per unit BCS was greatest at calving varying from 44 kg in first parity animals to 62 kg in second parity animals. On average, 1 BCS unit equated to 31 kg LW across all data.
    • The association between herd- and cow-level factors and somatic cell count of Irish dairy cows

      McParland, Sinead; O'Brien, Bernadette; McCarthy, J.; Department of Agriculture, Food and the Marine; 10/RD/AAQUALITYMILK/TMFRC713 (Teagasc (Agriculture and Food Development Authority), Ireland, 2013)
      Somatic cell count (SCC) is an indicator of both udder health and milk quality and is measured at an animal level through national milk recording schemes. The objective of this study was to assess the animal and herd factors contributing to elevated SCC (i.e. poorer milk quality). Test day records (n = 2,658,928) from 519,456 cow lactations obtained between 2007 and 2011 were included in the analyses. Herd factors tested included the geographical region of the herd and production system operated (spring calving or mixed calving system). Animal factors tested included breed, parity and age nested within parity. Four definitions of normalised SCC (i.e. SCS) were considered: 1) average test-day SCS within a 24 hour period (TD_SCS), 2) maximum SCS (peak_SCS), 3) minimum SCS (min_SCS), and 4) average SCS (avg_SCS) recorded across cow lactation; in addition, the proportion of test day records with an SCC count >200,000 (prop_200) or >250,000 (prop_250) within cow lactation were included. Following adjustment for fixed effects, average TD_SCS was 179,308 cells per mL while avg_SCS, and average min_SCS and peak_SCS were 119,481, 50,992 and 298,813 cells per mL, respectively. All animal and herd factors had a significant effect on SCC. Older animals, animals which were younger at calving than contemporaries and Holstein animals had higher SCC than younger alternative breed animals who calved at the median age. In addition, mixed calving production systems and herds in Connaught had higher SCC than spring calving herds in the other regions of Ireland.
    • Association between somatic cell count during the first lactation and the cumulative milk yield of cows in Irish dairy herds

      McCoy, Finola; Archer, Simon; Wapenaar, Wendela; Green, Martin J.; Teagasc Walsh Fellowship Programme (Elsevier, 2014-01-30)
      Reduced potential milk yield is an important component of mastitis costs in dairy cows. The first aim of this study was to assess associations between somatic cell count (SCC) during the first lactation, and cumulative milk yield over the first lactation and subsequent lifetime of cows in Irish dairy herds. The second aim was to assess the association between SCC at 5 to 30 d in milk during parity 1 (SCC1), and SCC over the entire first lactation for cows in Irish dairy herds. The data set studied included records from 51,483 cows in 5,900 herds. Somatic cell count throughout the first lactation was summarized using the geometric mean and variance of SCC. Data were analyzed using linear models that included random effects to account for the lack of independence between observations, and herd-level variation in coefficients. Models were developed in a Bayesian framework and parameters were estimated from 10,000 Markov chain Monte Carlo simulations. The final models were a good fit to the data. A 1-unit increase in mean natural logarithm SCC over the first lactation was associated with a median decrease in first lactation and lifetime milk yield of 135 and 1,663 kg, respectively. A 1-unit increase in the variance of natural logarithm SCC over the first lactation was associated with a median decrease in lifetime milk yield of 719 kg. To demonstrate the context of lifetime milk yield results, microsimulation was used to model the trajectory of individual cows and evaluate the expected outcomes for particular changes in herd-level geometric mean SCC over the first lactation. A 75% certainty of savings of at least €199/heifer in the herd was detected if herd-level geometric mean SCC over the first lactation was reduced from ≥120,000 to ≤72,000 cells/mL. The association between SCC1 and SCC over the remainder of the first lactation was highly herd dependent, indicating that control measures for heifer mastitis should be preferentially targeted on an individual-herd basis toward either the pre- and peripartum period, or the lactating period, to optimize the lifetime milk yield of dairy cows.
    • Association between somatic cell count early in the first lactation and the lifetime milk yield of cows in Irish dairy herds

      Archer, Simon; McCoy, Finola; Wapenaar, Wendela; Green, Martin J.; Teagasc Walsh Fellowship Programme (Elsevier, 2013-03-14)
      Change in lifetime milk yield is an important component of the cost of diseases in dairy cows. Knowledge of the likelihood and scale of potential savings through disease prevention measures is important to evaluate how much expenditure on control measures is rational. The aim of this study was to assess the association between somatic cell count (SCC) at 5 to 30 d in milk during parity 1 (SCC1), and lifetime milk yield for cows in Irish dairy herds. The data set studied included records from 53,652 cows in 5,922 Irish herds. This was split into 2 samples of 2,500 and 3,422 herds at random. Linear models with lifetime milk yield and first-lactation milk yield as the outcomes and random effects to account for variation between herds were fitted to the data for the first sample of herds; data for the second sample were used for cross-validation. The models were developed in a Bayesian framework to include all uncertainty in posterior predictions and parameters were estimated from 10,000 Markov chain Monte Carlo simulations. The final model was a good fit to the data and appeared generalizable to other Irish herds. A unit increase in the natural logarithm of SCC1 was associated with a median decrease in lifetime milk yield of 864 kg, and a median decrease in first-lactation milk yield of 105 kg. To clarify the meaning of the results in context, microsimulation was used to model the trajectory of individual cows, and evaluate the expected outcomes for particular changes in the herd-level prevalence of cows with SCC1 ≥400,000 cells/mL. Differences in mean lifetime milk yield associated with these changes were multiplied by an estimated gross margin for each cow to give the potential difference in milk revenue. Results were presented as probabilities of savings; for example, a 75% probability of savings of at least €97 or €115/heifer calved into the herd existed if the prevalence of cows with SCC1 ≥400,000 cells/mL was reduced from ≥20 to <10 or <5%, respectively, and at least €71/heifer calved into the herd if the prevalence of cows with SCC1 ≥400,000 cells/mL was reduced from ≥10 to <5%. The results indicate large differences in lifetime milk yield, depending on SCC early in the first lactation and the findings can be used to assess where specific interventions to control heifer mastitis prepartum are likely to be cost effective.
    • Association between somatic cell count early in the first lactation and the lifetime milk yield of cows in Irish dairy herds

      Archer, S.C.; Mc Coy, F.; Wapenaar, W.; Green, M.J.; Teagasc Walsh Fellowship Programme (Elsevier for American Dairy Science Association, 2013-05-18)
      Change in lifetime milk yield is an important component of the cost of diseases in dairy cows. Knowledge of the likelihood and scale of potential savings through disease prevention measures is important to evaluate how much expenditure on control measures is rational. The aim of this study was to assess the association between somatic cell count (SCC) at 5 to 30 d in milk during parity 1 (SCC1), and lifetime milk yield for cows in Irish dairy herds. The data set studied included records from 53,652 cows in 5,922 Irish herds. This was split into 2 samples of 2,500 and 3,422 herds at random. Linear models with lifetime milk yield and first-lactation milk yield as the outcomes and random effects to account for variation between herds were fitted to the data for the first sample of herds; data for the second sample were used for cross-validation. The models were developed in a Bayesian framework to include all uncertainty in posterior predictions and parameters were estimated from 10,000 Markov chain Monte Carlo simulations. The final model was a good fit to the data and appeared generalizable to other Irish herds. A unit increase in the natural logarithm of SCC1 was associated with a median decrease in lifetime milk yield of 864 kg, and a median decrease in first-lactation milk yield of 105 kg. To clarify the meaning of the results in context, microsimulation was used to model the trajectory of individual cows, and evaluate the expected outcomes for particular changes in the herdlevel prevalence of cows with SCC1 ≥400,000 cells/mL. Differences in mean lifetime milk yield associated with these changes were multiplied by an estimated gross margin for each cow to give the potential difference in milk revenue. Results were presented as probabilities of savings; for example, a 75% probability of savings of at least €97 or €115/heifer calved into the herd existed if the prevalence of cows with SCC1 ≥400,000 cells/ mL was reduced from ≥20 to <10 or <5%, respectively, and at least €71/heifer calved into the herd if the prevalence of cows with SCC1 ≥400,000 cells/mL was reduced from ≥10 to <5%. The results indicate large differences in lifetime milk yield, depending on SCC early in the first lactation and the findings can be used to assess where specific interventions to control heifer mastitis prepartum are likely to be cost effective.
    • Association between somatic cell count early in the first lactation and the longevity of Irish dairy cows

      Archer, Simon; McCoy, Finola; Wapenaar, Wendela; Green, Martin J.; Teagasc Walsh Fellowship Programme (Elsevier, 2013-03-21)
      Reduced longevity of cows is an important component of mastitis costs, and increased somatic cell count (SCC) early in the first lactation has been reported to increase culling risk throughout the first lactation. Generally, cows must survive beyond the first lactation to break even on their rearing costs. The aim of this research was to assess the association between SCC of primiparous cows at 5 to 30 days in milk (SCC1), and survival over a 5-y period for cows in Irish dairy herds. The data set used for model development was based on 147,458 test day records from 7,537 cows in 812 herds. Cows were censored at their last recording if identified at a later date in other herds or if recorded at the last available test date for their herd, otherwise, date of disposal was taken to be at the last test date for each cow. Survival time was calculated as the number of days between the dates of first calving and the last recording, which was split into 50-d intervals. Data were analyzed in discrete time logistic survival models that accounted for clustering of 50-d intervals within cows, and cows within herds. Models were fitted in a Bayesian framework using Markov chain Monte Carlo simulations. Model fit was assessed by comparison of posterior predictions to the observed disposal risk for cows aggregated by parameters in the model. Model usefulness was assessed by cross validation in a separate data set, which contained 144,113 records from 7,353 cows in 808 herds, and posterior predictions were compared with the observed disposal risk for cows aggregated by parameters of biological importance. Disposal odds increased by a factor of 5% per unit increase in ln SCC1. Despite this, posterior predictive distributions revealed that the probability of reducing replacement costs by >€10 per heifer calved, through decreasing the herd level prevalence of cows with SCC1 ≥400,000 cells/mL (from an initial prevalence of ≥20 to <10%) only exceeded 50% for less than 1 in 5 Irish herds. These results indicate that the effect of a reduction in the prevalence of cows with SCC1 ≥400,000 cells/mL on replacement costs alone for most Irish dairy herds is small, and future research should investigate other potential losses, such as the effect of SCC1 on lifetime milk yield.