Research in the ABRD encompasses nutrition, fertility, breeding, health and welfare. Research activities focus on producing profitable animals and the corresponding management strategies to deliver the productivity, sustainability and product quality targets set out in Ireland’s Food Harvest 2020 vision. The ABRD uses a powerful combination of established animal science techniques, as well as cutting-edge molecular and computational biology tools, to answer relevant industry research questions. Our focus is on dairy and beef cattle and sheep. We have developed animal models that are divergent for a range of economically important traits.

Recent Submissions

  • An observational study using blood gas analysis to assess neonatal calf diarrhea and subsequent recovery with a European Commission-compliant oral electrolyte solution

    Sayers, Riona; Kennedy, Aideen E.; Krump, Lea; Sayers, Gearoid; Kennedy, Emer; Epsilion Ltd.; IV20151256 (American Dairy Science Association, 2016-04-06)
    An observational study was conducted on dairy calves (51 healthy, 31 with neonatal diarrhea) during outbreaks of diarrhea on 4 dairy farms. Clinical assessment scores (CAS) were assigned to each healthy and diarrheic calf [from 0 (healthy) to 4 (marked illness)]. Blood gas analysis [pH, base excess (BE), Na+, K+, Ca2+, Cl−, glucose, total hemoglobin, standard HCO3−, strong ion difference (SID), and anion gap (AG)] was completed for each calf. Repeated measurements were taken in healthy animals, and pre- and postintervention measurements were taken for diarrheic calves. The mean CAS of diarrheic calves was 1.7, with 51, 30, 17, and 2% of calves scoring 1, 2, 3, and 4, respectively. The mean value for blood pH, BE, AG, and SID was 7.26, −4.93 mM, 16.3 mM, and 38.59 mM, respectively. Calves were administered an oral rehydration and buffering solution (ORBS; Vitalife for Calves, Epsilion Ltd., Cork, Ireland) and reassessed. The mean CAS decreased to 0.38 (65% of calves scored 0 and 35% scored 1) at 6 to 18 h posttreatment and to 0.03 (98% of calves scored 0 and 2% scored 1) within 24 to 48 h. Significant increases in mean value for pH, BE, HCO3−, Na+, and SID, and significant decreases in AG, K+, Ca2+, and total hemoglobin were recorded posttreatment. The correlation estimates indicated that pH, HCO3−, and BE were strongly correlated with CAS, with values exceeding 0.60 in all cases. Administration of an ORBS with a high SID and bicarbonate buffer demonstrated rapid recovery from a diarrheic episode in dairy calves.
  • 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 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 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 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.
  • Symposium review: Intramammary infections—Major pathogens and strain-associated complexity

    Keane, Orla M (Elsevier, 2019-03-01)
    Intramammary infection (IMI) is one of the most costly diseases to the dairy industry. It is primarily due to bacterial infection and the major intramammary pathogens include Escherichia coli, Streptococcus uberis, and Staphylococcus aureus. The severity and outcome of IMI is dependent on several host factors including innate host resistance, energy balance, immune status, parity, and stage of lactation. Additionally, the infecting organism can influence the host immune response and progression of disease. It is increasingly recognized that not only the infecting pathogen species, but also the strain, can affect the transmission, severity, and outcome of IMI. For each of 3 major IMI-associated pathogens, S. aureus, Strep. uberis, and E. coli, specific strains have been identified that are adapted to the intramammary environment. Strain-dependent variation in the host immune response to infection has also been reported. The diversity of strains associated with IMI must be considered if vaccines effective against the full repertoire of mammary pathogenic strains are to be developed. Although important advances have been made recently in understanding the molecular mechanism underpinning strain-specific virulence, further research is required to fully elucidate the cellular and molecular pathogenesis of mammary adapted strains and the role of the strain in influencing the pathophysiology of infection. Improved understanding of molecular pathogenesis of strains associated with bovine IMI will contribute to the development of new control strategies, therapies, and vaccines. The development of enabling technologies such as pathogenomics, transcriptomics, and proteomics can facilitate system-level studies of strain-specific molecular pathogenesis and the identification of key mediators of host-pathogen interactions.
  • RNA-seq analysis of bovine adipose tissue in heifers fed diets differing in energy and protein content

    Wærp, Hilde K. L.; Waters, Sinead M.; McCabe, Matthew S.; Cormican, Paul; Salte, Ragnar; The Research Council of Norway; TINE SA Norwegian dairies; Felleskjøpet agricultural cooperative; Animalia AS; 199448 (Public Library of Science, 2018-09-20)
    Adipose tissue is no longer considered a mere energy reserve, but a metabolically and hormonally active organ strongly associated with the regulation of whole-body metabolism. Knowledge of adipose metabolic regulatory function is of great importance in cattle management, as it affects the efficiency and manner with which an animal converts feedstuff to milk, meat and fat. However, the molecular mechanisms regulating metabolism in bovine adipose tissue are still not fully elucidated. The emergence of next-generation sequencing technologies has facilitated the analysis of metabolic function and regulation at the global gene expression level. The aim of this study was to investigate the effect of diets differing in protein and energy density level on gene expression in adipose tissue of growing replacement dairy heifers using next-generation RNA sequencing (RNAseq). Norwegian Red heifers were fed either a high- or low-protein concentrate (HP/LP) and a high- or low-energy roughage (HE/LE) diet from 3 months of age until confirmed pregnancy to give four treatments (viz, HPHE, HPLE, LPHE, LPLE) with different growth profiles. Subcutaneous adipose tissue sampled at 12 months of age was analyzed for gene expression differences using RNAseq. The largest difference in gene expression was found between LPHE and LPLE heifers, for which 1092 genes were significantly differentially expressed, representing an up-regulation of mitochondrial function, lipid, carbohydrate and amino acid metabolism as well as changes in the antioxidant system in adipose tissue of LPHE heifers. Differences between HPHE and HPLE heifers were much smaller, and dominated by genes representing NAD biosynthesis, as was the significantly differentially expressed genes (DEG) common to both HE-LE contrasts. Differences between HP and LP groups within each energy treatment were minimal. This study emphasizes the importance of transcriptional regulation of adipose tissue energy metabolism, and identifies candidate genes for further studies on early-stage obesity and glucose load in dairy cattle.
  • Effects of fertiliser nitrogen rate to spring grass on apparent digestibility, nitrogen balance, ruminal fermentation and microbial nitrogen production in beef cattle and in vitro rumen fermentation and methane output

    O'Connor, Alan; Moloney, Aidan P.; O'Kiely, Padraig; Boland, T. M.; McGee, Mark; Teagasc Walsh Fellowship Programme; Department of Agriculture, Food and the Marine; 11/S/105 (Elsevier, 2019-06-06)
    The effects of two fertiliser nitrogen (N) application rates - 15 (LN) or 80 (HN) kg N/ha - to Lolium perenne dominant swards in spring, on grass dry matter (DM) intake, digestion, rumen fermentation, microbial N production and N-balance in beef cattle, and in vitro fermentation and methane production were studied. Sixteen Charolais steers with a mean live weight (s.d.) of 475 (18.4) kg, were used in a completely randomised block design experiment and offered zero-grazed grass harvested 21-d post N application. The same grass was incubated in an eight-vessel RUSITEC in a completely randomised block design experiment. The HN treatment had a 540 kg/ha higher grass DM yield, and a 20 g/kg DM higher crude protein (CP) concentration compared to LN. There was no difference (P > 0.05) in DM intake, or in vivo DM, organic matter (OM) and N digestibility between treatments. Rumen fermentation variables pH, lactic acid, ammonia (NH3) and total volatile fatty acid (VFA) concentration were similar (P > 0.05) for both treatments. Nitrogen intake was 19 g/d higher (P < 0.05) for HN compared to LN. Total and urine N loss was 16 and 14 g/d greater (P < 0.05), respectively, for HN compared to LN, but faecal N loss did not differ (P > 0.05) between treatments. The quantity of N retained and N-use efficiency did not differ (P > 0.05) between LN and HN. Plasma urea concentration was 1 mmol/L greater (P < 0.05) for HN compared to LN. Estimated microbial N production was greater (P < 0.05) for HN compared to LN. In vitro NH3 concentrations were higher (P < 0.05) for HN compared to LN, whereas in vitro rumen pH, lactic acid and VFA concentrations and molar proportions did not differ (P > 0.05) between HN and LN. In vitro methane and total gas output were not different (P > 0.05) between treatments. Reducing fertiliser N application rate to grass in spring reduced total and urinary N excretion, which has environmental benefits, with no effects on in vitro methane output.
  • How herd best linear unbiased estimates affect the progress achievable from gains in additive and nonadditive genetic merit

    Dunne, F. L.; McParland, Sinead; Kelleher, Margaret M.; Walsh, S.W.; Berry, Donagh P.; Science Foundation Ireland; Department of Agriculture, Food and the Marine; 16/RC/3835 (Elsevier, 2019-04-10)
    Sustainable dairy cow performance relies on coevolution in the development of breeding and management strategies. Tailoring breeding programs to herd performance metrics facilitates improved responses to breeding decisions. Although herd-level raw metrics on performance are useful, implicitly included within such statistics is the mean herd genetic merit. The objective of the present study was to quantify the expected response from selection decisions on additive and nonadditive merit by herd performance metrics independent of herd mean genetic merit. Performance traits considered in the present study were age at first calving, milk yield, calving to first service, number of services, calving interval, and survival. Herd-level best linear unbiased estimates (BLUE) for each performance trait were available on a maximum of 1,059 herds, stratified as best, average, and worst for each performance trait separately. The analyses performed included (1) the estimation of (co)variance for each trait in the 3 BLUE environments and (2) the regression of cow-level phenotypic performance on either the respective estimated breeding value (EBV) or the heterosis coefficient of the cow. A fundamental assumption of genetic evaluations is that 1 unit change in EBV equates to a 1 unit change in the respective phenotype; results from the present study, however, suggest that the realization of the change in phenotypic performance is largely dependent on the herd BLUE for that trait. Herds achieving more yield, on average, than expected from their mean genetic merit, had a 20% greater response to changes in EBV as well as 43% greater genetic standard deviation relative to herds within the worst BLUE for milk yield. Conversely, phenotypic performance in fertility traits (with the exception of calving to first service) tended to have a greater response to selection as well as a greater additive genetic standard deviation within the respective worst herd BLUE environments; this is suggested to be due to animals performing under more challenging environments leading to larger achievable gains. The attempts to exploit nonadditive genetic effects such as heterosis are often the basis of promoting cross-breeding, yet the results from the present study suggest that improvements in phenotypic performance is largely dependent on the environment. The largest gains due to heterotic effects tended to be within the most stressful (i.e., worst) BLUE environment for all traits, thus suggesting the heterosis effects can be beneficial in mitigating against poorer environments.
  • The genetic architecture of milk ELISA scores as an indicator of Johne's disease (paratuberculosis) in dairy cattle

    Brito, Luiz F.; Mallikarjunappa, Sanjay; Sargolzaei, Mehdi; Koeck, Astrid; Chesnais, Jacques; Schenkel, Flavio S.; Meade, Kieran G; Miglior, Filippo; Karrow, Niel A.; The Semex Alliance; et al. (Elsevier, 2018-09-13)
    Johne's disease (or paratuberculosis), caused by Mycobacterium avium ssp. paratuberculosis (MAP) infection, is a globally prevalent disease with severe economic and welfare implications. With no effective treatment available, understanding the role of genetics influencing host infection status is essential to develop selection strategies to breed for increased resistance to MAP infection. The main objectives of this study were to estimate genetic parameters for the MAP-specific antibody response using milk ELISA scores in Canadian Holstein cattle as an indicator of resistance to Johne's disease, and to unravel genomic regions and candidate genes significantly associated with MAP infection. After data editing, 168,987 milk ELISA records from 2,306 herds, obtained from CanWest Dairy Herd Improvement, were used for further analyses. Variance and heritability estimates for MAP infection status were determined using univariate linear animal models under 3 scenarios: (a) SCEN1: the complete data set (all herds); (b) SCEN2: herds with at least one suspect or test-positive animal (ELISA optical density ≥0.07); and (c) SCEN3: herds with at least one test-positive animal (ELISA optical density ≥0.11). Heritability estimates were calculated as 0.066, 0.064, and 0.063 for SCEN1, SCEN2, and SCEN3, respectively. The correlations between estimated breeding values for resistance to MAP infection and other economically important traits, when significant, were favorable and of low magnitude. Genome-wide association analyses identified important genomic regions on Bos taurus autosome (BTA)1, BTA7, BTA9, BTA14, BTA15, BTA17, BTA19, and BTA25 showing significant association with MAP infection status. These regions included 2 single nucleotide polymorphisms located 2 kb upstream of positional candidate genes CD86 and WNT9B, which play key roles in host immune response and tissue homeostasis. This study revealed the genetic architecture of MAP infection in Canadian Holstein cattle as measured by milk ELISA scores by estimating genetic parameters along with the identification of genomic regions potentially influencing MAP infection status. These findings will be of significant value toward implementing genetic and genomic evaluations for resistance to MAP infection in Holstein cattle.
  • Genetic selection for hoof health traits and cow mobility scores can accelerate the rate of genetic gain in producer-scored lameness in dairy cows

    Ring, Siobhan C.; Twomey, Alan J.; Byrne, Nicky; Kelleher, Margaret M.; Pabiou, Thierry; Doherty, Michael L.; Berry, Donagh P.; Department of Agriculture, Food and the Marine (American Dairy Science Association, 2018-09-13)
    Cattle breeding programs that strive to reduce the animal-level incidence of lameness are often hindered by the availability of informative phenotypes. As a result, indicator traits of lameness (i.e., hoof health and morphological conformation scores) can be used to improve the accuracy of selection and subsequent genetic gain. Therefore, the objectives of the present study were to estimate the variance components for hoof health traits using various phenotypes collected from a representative sample of Irish dairy cows. Also of interest to the present study was the genetic relationship between both hoof health traits and conformation traits with producer-scored lameness. Producer-recorded lameness events and linear conformation scores from 307,657 and 117,859 Irish dairy cows, respectively, were used. Data on hoof health (i.e., overgrown sole, white line disease, and sole hemorrhage), mobility scores, and body condition scores were also available from a research study on up to 11,282 Irish commercial dairy cows. Linear mixed models were used to quantify variance components for each trait and to estimate genetic correlations among traits. The estimated genetic parameters for hoof health traits in the present study were greater (i.e., heritability range: 0.005 to 0.27) than previously reported in dairy cows. With the exception of analyses that considered hoof health traits in repeatability models, little difference in estimated variance components existed among the various hoof-health phenotypes. Results also suggest that producer-recorded lameness is correlated with both hoof health (i.e., genetic correlation up to 0.48) and cow mobility (i.e., genetic correlation = 0.64). Moreover, cows that genetically tend to have rear feet that appear more parallel when viewed from the rear are also genetically more predisposed to lameness (genetic correlation = 0.39); genetic correlations between lameness and other feet and leg type traits, as well as between lameness and frame type traits, were not different from zero. Results suggest that if the population breeding goal was to reduce lameness incidence, improve hoof health, or improve cow mobility, genetic selection for either of these traits should indirectly benefit the other traits. Results were used to quantify the genetic gains achievable for lameness when alternative phenotypes are available.
  • Effect of finishing diet and duration on the sensory quality and volatile profile of lamb meat

    Gkarane, Vasiliki; Brunton, Nigel; Allen, Paul; Gravador, Rufielyn S.; Claffey, Noel A.; Diskin, Michael G.; Fahey, Alan G.; Farmer, Linda J.; Moloney, Aidan P; Alcalde, Maria J.; et al. (Elsevier, 2018-08-02)
    Animal production factors can affect the sensory quality of lamb meat. The study investigated the effect of diet composition and duration of consumption on the proximate analysis, volatile profile and sensory quality of lamb meat. Ninety-nine male Texel × Scottish Blackface lambs were raised at pasture for 10 months before being assigned in groups of 11 to one of the following treatments: 100% Silage (S) for 36 (S36), 54 (S54) or 72 (S72) days; 50% Silage - 50% Concentrate (SC) for 36 (SC36), 54 (SC54) or 72 (SC72) days; 100% Concentrate (C) for 36 (C36) or 54 (C54) or 72 (C72) days. A trained sensory panel found Intensity of Lamb Aroma, Dry Aftertaste and Astringent Aftertaste to be higher in meat from lambs on the concentrate diet. Discriminant analysis showed that the volatile profile enabled discrimination of lamb based on dietary treatment but the volatile differences were insufficient to impact highly on sensory quality. Muscle from animals in the S54 group had higher Manure/Faecal Aroma and Woolly Aroma than the SC54 and C54 groups, possibly related to higher levels of indole and skatole. Further research is required to establish if these small differences would influence consumer acceptability.
  • Effect of suckler cow vaccination against glycoprotein E (gE)-negative bovine herpesvirus type 1 (BoHV-1) on passive immunity and physiological response to subsequent bovine respiratory disease vaccination of their progeny

    Earley, Bernadette; Tiernan, Katie; Duffy, Catherine; Dunn, Amanda; Waters, Sinead M.; Morrison, Steven; McGee, Mark; Department of Agriculture, Food and the Marine; 11/S/131 (Elsevier, 2018-01-10)
    The study objectives were: 1) to characterise the development of immunocompetence in beef suckler calves from birth to three months of age, and 2) to trace glycoprotein E (gE)-negative bovine herpesvirus type 1 (BoHV-1) antibodies from dam to calf and subsequent vaccination against pneumonia. Thirty multiparous beef suckler, spring-calving cows, consisting of two genotypes were involved; Limousin × Friesian (LF) and Charolais × Limousin (CL). Cows were immunised against the inactivated antigen strain of BoHV-1 (gE- (IBR marker vaccine) at day − 84 and received a booster at day − 56 relative to the expected calving date (d 0). Calves were immunised at 14 and 42 days of age against PI-3 virus, BRSV and Mannheimia (Pasteurella) haemolytica serotype A1 using a commercial vaccine administered subcutaneously. Additionally, calves were immunised against BoHV-1 at 42 days of age, using 1 dose of a live commercial vaccine administered intranasally. Blood samples were collected from all calves (n = 30) via jugular venipuncture at birth, prior to colostrum feeding (0 h), at 12 h (h), 24 h, 72 h and 168 h after the initial feeding of colostrum, and at d 7, 14, 28, 42, 56 and 84 post birth. The mean ratio of gE negative antibodies circulating in the blood of LF and CL dams pre-partum scored negative to gE ab (S/N ≥ 0.70). Antibody levels of BoHV-1 (wild type (wt)) peaked at 12 h post-birth in calves and declined thereafter, as the maternal antibodies decayed. There was no difference in BoHV-1 and BRSV antibody levels in calves post vaccination.
  • Sharpea and Kandleria are lactic acid producing rumen bacteria that do not change their fermentation products when co-cultured with a methanogen

    Kumar, Sandeep; Treloar, Bryan P.; Teh, Koon Hoong; McKenzie, Catherine M.; Henderson, Gemma; Attwood, Graeme T.; Waters, Sinead M.; Patchett, Mark L.; Janssen, Peter H.; Teagasc Walsh Fellowship Programme; et al. (Elsevier, 2018-07-25)
    Sharpea and Kandleria are associated with rumen samples from low-methane-emitting sheep. Four strains of each genus were studied in culture, and the genomes of nine strains were analysed, to understand the physiology of these bacteria. All eight cultures grew equally well with d-glucose, d-fructose, d-galactose, cellobiose, and sucrose supplementation. d-Lactate was the major end product, with small amounts of the mixed acid fermentation products formate, acetate and ethanol. Genes encoding the enzymes necessary for this fermentation pattern were found in the genomes of four strains of Sharpea and five of Kandleria. Strains of Sharpea produced traces of hydrogen gas in pure culture, but strains of Kandleria did not. This was consistent with finding that Sharpea, but not Kandleria, genomes contained genes coding for hydrogenases. It was speculated that, in co-culture with a methanogen, Sharpea and Kandleria might change their fermentation pattern from a predominately homolactic to a predominately mixed acid fermentation, which would result in a decrease in lactate production and an increase in formation of acetate and perhaps ethanol. However, Sharpea and Kandleria did not change their fermentation products when co-cultured with Methanobrevibacter olleyae, a methanogen that can use both hydrogen and formate, and lactate remained the major end product. The results of this study therefore support a hypothesis that explains the link between lower methane yields and larger populations of Sharpea and Kandleria in the rumens of sheep.
  • Blood immune transcriptome analysis of artificially fed dairy calves and naturally suckled beef calves from birth to 7 days of age

    Surlis, Carla; Earley, Bernadette; McGee, Mark; Keogh, Kate; Cormican, Paul; Blackshields, Gordon; Tiernan, Katie; Dunn, Amanda; Morrison, Steven; Arguello, A.; et al. (Nature Publishing Group, 2018-10-18)
    Neonatal calves possess a very immature and naïve immune system and are reliant on the intake of maternal colostrum for passive transfer of immunoglobulins. Variation in colostrum management of beef and dairy calves is thought to affect early immune development. Therefore, the objective of this study was to examine changes in gene expression and investigate molecular pathways involved in the immune-competence development of neonatal Holstein dairy calves and naturally suckled beef calves using next generation RNA-sequencing during the first week of life. Jugular whole blood samples were collected from Holstein (H) dairy calves (n = 8) artificially fed 5% B.W. colostrum, and from beef calves which were the progenies of Charolais-Limousin (CL; n = 7) and Limousin-Friesian beef suckler cows (LF; n = 7), for subsequent RNA isolation. In dairy calves, there was a surge in pro-inflammatory cytokine gene expression possibly due to the stress of separation from the dam. LF calves exhibited early signs of humoral immune development with observed increases in the expression genes coding for Ig receptors, which was not evident in the other breeds by 7 days of age. Immune and health related DEGs identified as upregulated in beef calves are prospective contender genes for the classification of biomarkers for immune-competence development, and will contribute towards a greater understanding of the development of an immune response in neonatal calves.
  • RNA-seq analysis of bovine adipose tissue in heifers fed diets differing in energy and protein content

    Waerp, Hilde K. L.; Waters, Sinead M.; McCabe, Matthew; Cormican, Paul; Salte, Ragnar; Research Council of Norway; TINE SA Norwegian dairies; Felleskjøpet agricultural cooperative; Animalia AS; 199448 (PLOS, 2018-09-20)
    Adipose tissue is no longer considered a mere energy reserve, but a metabolically and hormonally active organ strongly associated with the regulation of whole-body metabolism. Knowledge of adipose metabolic regulatory function is of great importance in cattle management, as it affects the efficiency and manner with which an animal converts feedstuff to milk, meat and fat. However, the molecular mechanisms regulating metabolism in bovine adipose tissue are still not fully elucidated. The emergence of next-generation sequencing technologies has facilitated the analysis of metabolic function and regulation at the global gene expression level. The aim of this study was to investigate the effect of diets differing in protein and energy density level on gene expression in adipose tissue of growing replacement dairy heifers using next-generation RNA sequencing (RNAseq). Norwegian Red heifers were fed either a high- or low-protein concentrate (HP/LP) and a high- or low-energy roughage (HE/LE) diet from 3 months of age until confirmed pregnancy to give four treatments (viz, HPHE, HPLE, LPHE, LPLE) with different growth profiles. Subcutaneous adipose tissue sampled at 12 months of age was analyzed for gene expression differences using RNAseq. The largest difference in gene expression was found between LPHE and LPLE heifers, for which 1092 genes were significantly differentially expressed, representing an up-regulation of mitochondrial function, lipid, carbohydrate and amino acid metabolism as well as changes in the antioxidant system in adipose tissue of LPHE heifers. Differences between HPHE and HPLE heifers were much smaller, and dominated by genes representing NAD biosynthesis, as was the significantly differentially expressed genes (DEG) common to both HE-LE contrasts. Differences between HP and LP groups within each energy treatment were minimal. This study emphasizes the importance of transcriptional regulation of adipose tissue energy metabolism, and identifies candidate genes for further studies on early-stage obesity and glucose load in dairy cattle.
  • Effect of equine chorionic gonadotropin treatment during a progesterone-based timed artificial insemination program on reproductive performance in seasonal-calving lactating dairy cows

    Randi, Federico; Sánchez, José Maria; Herlihy, Mary M.; Valenza, Alessio; Kenny, David A.; Butler, Stephen T.; Lonergan, P.; Department of Agriculture, Food and the Marine; 13S515; 13S528 (Elsevier, 2018-08-23)
    The aim of this study was to investigate the effect of progesterone (P4)-based timed artificial insemination (TAI) programs on fertility in seasonal-calving, pasture-based dairy herds. A total of 1,421 lactating dairy cows on 4 spring-calving farms were stratified based on days in milk (DIM) and parity and randomly allocated to 1 of 3 treatments: (1) control: no hormonal treatment; cows inseminated at detected estrus; (2) P4-Ovsynch: cows received a 7-d P4-releasing intravaginal device (PRID Delta; CEVA Santé Animale, Libourne, France) with 100 μg of a gonadotropin-releasing hormone (GnRH) analog (Ovarelin; CEVA Santé Animale) at PRID insertion, a 25-mg injection of PGF2α (Enzaprost; CEVA Santé Animale) at PRID removal, GnRH at 56 h after device removal and TAI 16 h later; (3) P4-Ovsynch+eCG: the same as P4-Ovsynch, but cows received 500 IU of equine chorionic gonadotropin (eCG; Syncrostim; CEVA Santé Animale) at PRID removal. At 10 d before mating start date (MSD), all cows that were ≥35 DIM were examined by transrectal ultrasound to assess presence or absence of a corpus luteum; body condition score (BCS) was also recorded. Pregnancy diagnosis was performed by transrectal ultrasonography 30 to 35 d after insemination. Overall pregnancy/AI (P/AI) was not different between groups (50.9, 49.8, and 46.3% for control, P4-Ovsynch, and P4-Ovsynch+eCG, respectively) but the 21-d pregnancy rate was increased by the use of synchronization (35.0, 51.7, and 47.2%, respectively). Compared with the control group, synchronization significantly reduced the interval from MSD to conception (34.6, 23.0, and 26.5 d, respectively) and consequently reduced the average days open (98.0, 86.0, and 89.0 d). Across all treatment groups, DIM at the start of synchronization affected P/AI (42.3, 49.5, and 53.9% for <60, 60–80, and >80 DIM, respectively), but neither parity (46.5, 50.4, and 48.4% for parity 1, 2, and ≥3, respectively) nor BCS (44.0, 49.4, and 58.6% for ≤2.50, 2.75–3.25, and ≥3.50, respectively) affected the likelihood of P/AI. Two-way interactions between treatment and DIM, parity, or BCS were not detected. In conclusion, the use of TAI accelerated pregnancy establishment in cows in a pasture-based system by reducing days open, but eCG administration at PRID removal did not affect P/AI.
  • The relationship between serum insulin-like growth factor-1 (IGF-1) concentration and reproductive performance, and genome-wide associations for serum IGF-1 in Holstein cows

    Gobikrushanth, M.; Purfield, Deirdre C; Colazo, M. G.; Wang, Z.; Butler, Stephen T.; Ambrose, D. J.; Growing Forward 2; Alberta Livestock and Meat Agency; Alberta Milk; Teagasc Walsh Fellowship Programme; et al. (Elsevier, 2019-07-19)
    The objectives of this study were to determine (1) factors associated with serum concentration of insulin-like growth factor-1 (IGF-1); (2) the relationship between serum IGF-1 concentration during the first week postpartum and ovarian cyclicity status by 35 d postpartum (DPP); (3) an optimum serum IGF-1 concentration threshold predictive of pregnancy to first artificial insemination (P/AI), including its diagnostic values; (4) the associations among categories of serum IGF-1 concentration and reproductive outcomes (P/AI and pregnancy risk up to 150 and 250 DPP); and (5) single nucleotide polymorphisms (SNP) associated with phenotypic variation in serum IGF-1 concentration in dairy cows. Serum IGF-1 concentration was determined at 7 (±2.4; ±standard error of the mean) DPP in 647 lactating Holstein cows (213 primiparous, 434 multiparous) from 7 herds in Alberta, Canada. The overall mean, median, minimum, and maximum serum IGF-1 concentrations during the first week postpartum were 37.8 (±1.23), 31.0, 20.0, and 225.0 ng/mL, respectively. Herd, age, parity, precalving body condition score, and season of blood sampling were all identified as factors associated with serum IGF-1 concentrations. Although serum IGF-1 concentration during the first week postpartum had no association with ovarian cyclicity status by 35 DPP in primiparous cows, it was greater in cyclic than in acyclic multiparous cows (32.2 vs. 27.4 ng/mL, respectively). The optimum serum IGF-1 thresholds predictive of P/AI were 85.0 ng/mL (sensitivity = 31.9%; specificity = 89.1%) and 31.0 ng/mL (sensitivity = 45.5%; specificity = 66.9%) for primiparous and multiparous cows, respectively. When cows were grouped into either high or low IGF-1 categories (greater or less than or equal to 85.0 ng/mL for primiparous cows and greater or less than or equal to 31.0 ng/mL for multiparous cows, respectively), primiparous cows with high IGF-1 had 4.43 times greater odds of P/AI and a tendency for higher pregnancy risk up to 150 DPP than those with low IGF-1, but not up to 250 DPP. Likewise, multiparous cows with high IGF-1 had 1.61 times greater odds of P/AI than those with low IGF-1. Pregnancy risk up to 150 and 250 DPP, however, did not differ between IGF-1 categories in multiparous cows. Moreover, 37 SNP across 10 Bos taurus autosomes were associated with variation in serum IGF-1 concentration, and 4 previously identified candidate genes related to fertility that were in linkage disequilibrium with some of these SNP were also identified.
  • Characterization of best linear unbiased estimates generated from national genetic evaluations of reproductive performance, survival, and milk yield in dairy cows

    Dunne, F. L.; Kelleher, Margaret M.; Walsh, S.W.; Berry, Donagh P.; MultiRepro project; Department of Agriculture, Food and the Marine (Elsevier, 2018-05-16)
    Genetic evaluations decompose an observed phenotype into its genetic and nongenetic components; the former are termed BLUP with the solutions for the systematic environmental effects in the statistical model termed best linear unbiased estimates (BLUE). Geneticists predominantly focus on the BLUP and rarely consider the BLUE. The objective of this study, however, was to define and quantify the association between 8 herd-level characteristics and BLUE for 6 traits in dairy herds, namely (1) age at first calving, (2) calving to first service interval (CFS), (3) number of services, (4) calving interval (CIV), (5) survival, and (6) milk yield. Phenotypic data along with the fixed and random effects solutions were generated from the Irish national multi-breed dairy cow fertility genetic evaluations on 3,445,557 cows; BLUE for individual contemporary groups were collapsed into mean herd-year estimates. Data from 5,707 spring-calving herds between the years 2007 and 2016 inclusive were retained; association analyses were undertaken using linear mixed multiple regression models. Pearson coefficient correlations were used to quantify the relationships among individual trait herd-year BLUE, and transition matrices were used to understand the dynamics of mean herd BLUE estimates over years. Based on the mean annual trends in raw, BLUP, and BLUE, it was estimated that BLUE were associated with at least two-thirds of the improvement in CIV and milk production over the past 10 yr. Milk recording herds calved heifers for the first time on average 15 d younger, had an almost 2 d longer CFS but 2.3 d shorter CIV than non-milk-recording herds. Larger herd sizes were associated with worse BLUE for both CFS and CIV. Expanding herds and herds that had the highest proportion of cows born on the farm itself, on average, calved heifers younger and had shorter CIV. By separating the raw performance of a selection of herds into their respective BLUE and BLUP, it was possible to identify herds with inferior management practices that were being compensated by superior genetics; similarly, herds were identified with superior BLUE, but because of their inferior genetic merit, were not reaching their full potential. This suggests that BLUE could have a pivotal role in a tailored decision support tool that would enable producers to focus on the most limiting factor hindering them from achieving their maximum performance.
  • GWAS and eQTL analysis identifies a SNP associated with both residual feed intake and GFRA2 expression in beef cattle

    Higgins, Marc G.; Fitzsimons, Clare; McClure, Matthew C.; McKenna, Clare; Conroy, S.B.; Kenny, David A.; McGee, Mark; Waters, Sinead M.; Morris, Derek W.; Department of Agriculture, Food and the Marine; et al. (Nature Publishing Group, 2018-09-24)
    Residual feed intake (RFI), a measure of feed efficiency, is an important economic and environmental trait in beef production. Selection of low RFI (feed efficient) cattle could maintain levels of production, while decreasing feed costs and methane emissions. However, RFI is a difficult and expensive trait to measure. Identification of single nucleotide polymorphisms (SNPs) associated with RFI may enable rapid, cost effective genomic selection of feed efficient cattle. Genome-wide association studies (GWAS) were conducted in multiple breeds followed by meta-analysis to identify genetic variants associated with RFI and component traits (average daily gain (ADG) and feed intake (FI)) in Irish beef cattle (n = 1492). Expression quantitative trait loci (eQTL) analysis was conducted to identify functional effects of GWAS-identified variants. Twenty-four SNPs were associated (P < 5 × 10−5) with RFI, ADG or FI. The variant rs43555985 exhibited strongest association for RFI (P = 8.28E-06). An eQTL was identified between this variant and GFRA2 (P = 0.0038) where the allele negatively correlated with RFI was associated with increased GFRA2 expression in liver. GFRA2 influences basal metabolic rates, suggesting a mechanism by which genetic variation may contribute to RFI. This study identified SNPs that may be useful both for genomic selection of RFI and for understanding the biology of feed efficiency.

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