• 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.
    • 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.
    • 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.
    • 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.
    • 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.
    • Are some teat disinfectant formulations more effective against specific bacteria isolated on teat skin than others?

      Fitzpatrick, Sarah R; Garvey, Mary; Flynn, Jim; Jordan, Kieran; Gleeson, David E; Dairy Research Ireland; Teagasc Walsh Fellowship Programme; 2016054 (Biomed Central, 2019-04-25)
      The use of pre- and post-milking teat disinfectants can reduce teat bacterial load and aid in the collection of high-quality milk. The objective of this study was to compare the reduction in bacteria populations on teat skin after the application of different commercial teat disinfectant products. Ten teat disinfectant products were applied to the teats of 10 Holstein–Friesian cows. One cow received one teat disinfectant product at each sampling point before cluster application for milking. A composite swab sample was taken of the 4 teats of each cow before and after teat disinfectant application. Swab samples were placed on three different selective agars to enumerate bacterial counts of staphylococcal, streptococcal and coliforms isolates on teat skin. Staphylococcal isolates were the most prominent bacterial group recovered on teat swabs (49%), followed by streptococcal (36%) and coliform (15%) isolates before the application of disinfectant. The average bacterial reductions on teat skin were shown to be 76%, 73% and 60% for staphylococcal, streptococcal and coliform isolates, respectively. All of the teat disinfectant products tested reduced teat bacterial load for all three bacterial groups. Product 4 containing 0.6% w/w diamine was the most effective against bacterial populations of staphylococcal and streptococcal isolates on teat skin with a reduction of 90% and 94%, respectively. Whereas product 10, which contained 0.5% w/w iodine, resulted in the highest reduction in coliforms on teat skin with a reduction of 91%. Results from this study suggest that specific bacterial population loads on teats can be reduced using different teat disinfectant formulations.
    • 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.
    • Associating cow characteristics with mobility scores in pasture-based dairy cows

      O'Connor, Aisling; Bokkers, E.A.M.; de Boer, I.J.M.; Hogeveen, H.; Sayers, Riona; Byrne, Nicky; Ruelle, Elodie; Shalloo, Laurence; Irish Department of Agriculture, Food and the Marine; Teagasc Walsh Fellowship Programme (Elsevier for American Dairy Science Association, 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 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.
    • Association of bovine leptin polymorphisms with energy output and energy storage traits in progeny tested Holstein-Friesian dairy cattle sires

      Giblin, Linda; Butler, Stephen T.; Kearney, Breda M.; Waters, Sinead M.; Callanan, Michael J.; Berry, Donagh; Department of Agriculture, Food and the Marine, Ireland; Irish Dairy Levy Research Trust; Teagasc Walsh Fellowship Programme; RSF-06-0353; et al. (Biomed Central, 29/07/2010)
      Background: Leptin modulates appetite, energy expenditure and the reproductive axis by signalling via its receptor the status of body energy stores to the brain. The present study aimed to quantify the associations between 10 novel and known single nucleotide polymorphisms in genes coding for leptin and leptin receptor with performance traits in 848 Holstein-Friesian sires, estimated from performance of up to 43,117 daughter-parity records per sire. Results: All single nucleotide polymorphisms were segregating in this sample population and none deviated (P > 0.05) from Hardy-Weinberg equilibrium. Complete linkage disequilibrium existed between the novel polymorphism LEP-1609, and the previously identified polymorphisms LEP-1457 and LEP-580. LEP-2470 associated (P < 0.05) with milk protein concentration and calf perinatal mortality. It had a tendency to associate with milk yield (P < 0.1). The G allele of LEP-1238 was associated (P < 0.05) with reduced milk fat concentration, reduced milk protein concentration, longer gestation length and tended to associate (P < 0.1) with an increase in calving difficulty, calf perinatal mortality and somatic cells in the milk. LEP-963 exhibited an association (P < 0.05) with milk fat concentration, milk protein concentration, calving difficulty and gestation length. It also tended to associate with milk yield (P < 0.1). The R25C SNP associated (P < 0.05) with milk fat concentration, milk protein concentration, calving difficulty and length of gestation. The T allele of the Y7F SNP significantly associated with reduced angularity (P < 0.01) and reduced milk protein yield (P < 0.05). There was also a tendency (P < 0.1) for Y7F to associate with increased body condition score, reduced milk yield and shorter gestation (P < 0.1). A80V associated with reduced survival in the herd (P < 0.05). Conclusions Several leptin polymorphisms (LEP-2470, LEP-1238, LEP-963, Y7F and R25C) associated with the energetically expensive process of lactogenesis. Only SNP Y7F associated with energy storage. Associations were also observed between leptin polymorphisms and calving difficulty, gestation length and calf perinatal mortality. The lack of an association between the leptin variants investigated with calving interval in this large data set would question the potential importance of these leptin variants, or indeed leptin, in selection for improved fertility in the Holstein-Friesian dairy cow.
    • Association of genetic polymorphisms related to Johne’s disease with estimated breeding values of Holstein sires for milk ELISA test scores

      Mallikarjunappa, Sanjay; Schenkel, Flavio S; Brito, Luiz F; Bissonnette, Nathalie; Miglior, Filippo; Chesnais, Jacques; Lohuis, Michael; Meade, Kieran G; Karrow, Niel A; Semex Alliance; et al. (Biomed Central, 2020-05-27)
      Background Johne’s disease (JD) is a chronic intestinal inflammatory disease caused by Mycobacterium avium subsp. paratuberculosis (MAP) infection in ruminants. Since there are currently no effective vaccine or treatment options available to control JD, genetic selection may be an alternative strategy to enhance JD resistance. Numerous Single Nucleotide Polymorphisms (SNPs) have been reported to be associated with MAP infection status based on published genome-wide association and candidate gene studies. The main objective of this study was to validate these SNPs that were previously identified to be associated with JD by testing their effect on Holstein bulls’ estimated breeding values (EBVs) for milk ELISA test scores, an indirect indicator of MAP infection status in cattle. Results Three SNPs, rs41810662, rs41617133 and rs110225854, located on Bos taurus autosomes (BTA) 16, 23 and 26, respectively, were confirmed as significantly associated with Holstein bulls’ EBVs for milk ELISA test score (FDR < 0.01) based on General Quasi Likelihood Scoring analysis (GQLS) analysis. Single-SNP regression analysis identified four SNPs that were associated with sire EBVs (FDR < 0.05). This includes two SNPs that were common with GQLS (rs41810662 and rs41617133), with the other two SNPs being rs110494981 and rs136182707, located on BTA9 and BTA16, respectively. Conclusions The findings of this study validate the association of SNPs with JD MAP infection status and highlight the need to further investigate the genomic regions harboring these SNPs.
    • Association of genetic polymorphisms related to Johne’s disease with estimated breeding values of Holstein sires for milk ELISA test scores

      Mallikarjunappa, Sanjay; Schenkel, Flavio S.; Brito, Luiz F.; Bissonnette, Nathalie; Miglior, Filippo; Chesnais, Jacques; Lohuis, Michae; Meade, Kieran G.; Karrow, Niel A; The Semex Alliance; et al. (Springer Open, 2020-05-27)
      Background: Johne’s disease (JD) is a chronic intestinal inflammatory disease caused by Mycobacterium avium subsp. paratuberculosis (MAP) infection in ruminants. Since there are currently no effective vaccine or treatment options available to control JD, genetic selection may be an alternative strategy to enhance JD resistance. Numerous Single Nucleotide Polymorphisms (SNPs) have been reported to be associated with MAP infection status based on published genome-wide association and candidate gene studies. The main objective of this study was to validate these SNPs that were previously identified to be associated with JD by testing their effect on Holstein bulls’ estimated breeding values (EBVs) for milk ELISA test scores, an indirect indicator of MAP infection status in cattle. Results: Three SNPs, rs41810662, rs41617133 and rs110225854, located on Bos taurus autosomes (BTA) 16, 23 and 26, respectively, were confirmed as significantly associated with Holstein bulls’ EBVs for milk ELISA test score (FDR < 0.01) based on General Quasi Likelihood Scoring analysis (GQLS) analysis. Single-SNP regression analysis identified four SNPs that were associated with sire EBVs (FDR < 0.05). This includes two SNPs that were common with GQLS (rs41810662 and rs41617133), with the other two SNPs being rs110494981 and rs136182707, located on BTA9 and BTA16, respectively. Conclusions: The findings of this study validate the association of SNPs with JD MAP infection status and highlight the need to further investigate the genomic regions harboring these SNPs.
    • Association of season and herd size with somatic cell count for cows in Irish, English, and Welsh dairy herds

      Archer, Simon; McCoy, Finola; Wapenaar, Wendela; Green, Martin J.; Teagasc Walsh Fellowship Programme (Elsevier, 2013-01-12)
      The aims of this study were to describe associations of time of year, and herd size with cow somatic cell count (SCC) for Irish, English, and Welsh dairy herds. Random samples of 497 and 493 Irish herds, and two samples of 200 English and Welsh (UK) herds were selected. Random effects models for the natural logarithm of individual cow test day SCC were developed using data from herds in one sub-dataset from each country. Data from the second sub-datasets were used for cross validation. Baseline model results showed that geometric mean cow SCC (GSCC) in Irish herds was highest from February to August, and ranged from 111,000 cells/mL in May to 61,000 cells/mL in October. For cows in UK herds, GSCC ranged from 84,000 cells/mL in February and June, to 66,000 cells/mL in October. The results highlight the importance of monitoring cow SCC during spring and summer despite low bulk milk SCC at this time for Irish herds. GSCC was lowest in Irish herds of up to 130 cows (63,000 cells/mL), and increased for larger herds, reaching 68,000 cells/mL in herds of up to 300 cows. GSCC in UK herds was lowest for herds of 130–180 cows (60,000 cells/mL) and increased to 63,000 cells/mL in herds of 30 cows, and 68,000 cells/mL in herds of 300 cows. Importantly, these results suggest expansion may be associated with increased cow SCC, highlighting the importance of appropriate management, to benefit from potential economies of scale, in terms of udder health.
    • Association of season and herd size with somatic cell count for cows in Irish, English, and Welsh dairy herds

      Archer, Simon C.; Mc Coy, Finola; Wapenaar, Wendela; Green, Martin J.; Teagasc Walsh Fellowship Programme (Elsevier BV, 2013-06-03)
      The aims of this study were to describe associations of time of year, and herd size with cow somatic cell count (SCC) for Irish, English, and Welsh dairy herds. Random samples of 497 and 493 Irish herds, and two samples of 200 English and Welsh (UK) herds were selected. Random effects models for the natural logarithm of individual cow test day SCC were developed using data from herds in one sub-dataset from each country. Data from the second sub-datasets were used for cross validation. Baseline model results showed that geometric mean cow SCC (GSCC) in Irish herds was highest from February to August, and ranged from 111,000 cells/mL in May to 61,000 cells/mL in October. For cows in UK herds, GSCC ranged from 84,000 cells/mL in February and June, to 66,000 cells/mL in October. The results highlight the importance of monitoring cow SCC during spring and summer despite low bulk milk SCC at this time for Irish herds. GSCC was lowest in Irish herds of up to 130 cows (63,000 cells/mL), and increased for larger herds, reaching 68,000 cells/mL in herds of up to 300 cows. GSCC in UK herds was lowest for herds of 130–180 cows (60,000 cells/mL) and increased to 63,000 cells/mL in herds of 30 cows, and 68,000 cells/mL in herds of 300 cows. Importantly, these results suggest expansion may be associated with increased cow SCC, highlighting the importance of appropriate management, to benefit from potential economies of scale, in terms of udder health.
    • Associations between colostrum management, passive immunity, calf-related hygiene practices, and rates of mortality in preweaning dairy calves

      Barry, John; Bokkers, Eddie A.M.; Berry, Donagh; de Boer, Imke J.M.; McClure, J. Trenton; Kennedy, Emer; Teagasc Walsh Fellowship Programme (Elsevier, 2019-09-11)
      Calves are particularly vulnerable to health issues before weaning and experience high rates of mortality. Poor colostrum quality or substandard colostrum management, combined with poor hygiene, can increase disease susceptibility, contributing to elevated mortality rates. This study aimed to assess colostrum and calf management together with subsequent mortality rates in preweaning calves. Forty-seven Irish spring-calving, pasture-based dairy herds were enrolled in the study. To investigate whether colostrum and hygiene practices change as the calving season progresses, each farm was visited in both the first and last 6 wk of the calving season. The concentration of IgG in 250 colostrum samples and 580 calf serum samples was determined by radial immunodiffusion assay. Mean colostrum IgG concentration was 85 mg/mL, and mean calf serum IgG concentration was 30.9 and 27.1 mg/mL, respectively, in the first and last 6 wk of the calving season. Smaller herd size and younger age at sampling were associated with higher calf serum IgG concentration. Dairy breed calves were associated with higher serum IgG concentrations compared with beef breed calves; no association was detected based on sex. For feeding equipment hygiene, we assessed the presence of protein residues and found that hygiene levels tended to worsen from the first to the final 6 wk of the calving season. We found no association between feeding equipment hygiene and herd size or 28-d calf mortality rate. Colostrum and calf management practices were not associated with either calf serum IgG concentration or 28-d calf mortality rate. We found that IgG concentration in colostrum produced in Irish dairy herds was generally good, although large variation existed, emphasizing the need for assessment of colostrum before feeding. Results also suggested that hygiene practices associated with calf rearing can be improved, particularly in the latter half of the calving season.