The aim of the Teagasc Animal and Grassland Research & Innovation Programme is to increase the profitability, competitiveness and sustainability of Irish livestock production through research and innovation.

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  • Effect of divergence in residual methane emissions on feed intake and efficiency, growth and carcass performance, and indices of rumen fermentation and methane emissions in finishing beef cattle

    Smith, Paul E; Waters, Sinead M; Kenny, David A; Kirwan, Stuart F; Conroy, Stephen; Kelly, Alan K; FACCE ERA-GAS; European Union; Teagasc Walsh Scholarship Programme; 16/RD/ERAGAS/1RUMENPREDICT-ROI2017; et al. (Oxford University Press, 2021-10-01)
    Residual expressions of enteric emissions favor a more equitable identification of an animal’s methanogenic potential compared with traditional measures of enteric emissions. The objective of this study was to investigate the effect of divergently ranking beef cattle for residual methane emissions (RME) on animal productivity, enteric emissions, and rumen fermentation. Dry matter intake (DMI), growth, feed efficiency, carcass output, and enteric emissions (GreenFeed emissions monitoring system) were recorded on 294 crossbred beef cattle (steers = 135 and heifers = 159; mean age 441 d (SD = 49); initial body weight (BW) of 476 kg (SD = 67)) at the Irish national beef cattle performance test center. Animals were offered a total mixed ration (77% concentrate and 23% forage; 12.6 MJ ME/kg of DM and 12% CP) ad libitum with emissions estimated for 21 d over a mean feed intake measurement period of 91 d. Animals had a mean daily methane emissions (DME) of 229.18 g/d (SD = 45.96), methane yield (MY) of 22.07 g/kg of DMI (SD = 4.06), methane intensity (MI) 0.70 g/kg of carcass weight (SD = 0.15), and RME 0.00 g/d (SD = 0.34). RME was computed as the residuals from a multiple regression model regressing DME on DMI and BW (R2 = 0.45). Animals were ranked into three groups namely high RME (>0.5 SD above the mean), medium RME (±0.5 SD above/below the mean), and low RME (>0.5 SD below the mean). Low RME animals produced 17.6% and 30.4% less (P < 0.05) DME compared with medium and high RME animals, respectively. A ~30% reduction in MY and MI was detected in low versus high RME animals. Positive correlations were apparent among all methane traits with RME most highly associated with (r = 0.86) DME. MY and MI were correlated (P < 0.05) with DMI, growth, feed efficiency, and carcass output. High RME had lower (P < 0.05) ruminal propionate compared with low RME animals and increased (P < 0.05) butyrate compared with medium and low RME animals. Propionate was negatively associated (P < 0.05) with all methane traits. Greater acetate:propionate ratio was associated with higher RME (r = 0.18; P < 0.05). Under the ad libitum feeding regime deployed here, RME was the best predictor of DME and only methane trait independent of animal productivity. Ranking animals on RME presents the opportunity to exploit interanimal variation in enteric emissions as well as providing a more equitable index of the methanogenic potential of an animal on which to investigate the underlying biological regulatory mechanisms.
  • Multiclonal human origin and global expansion of an endemic bacterial pathogen of livestock

    Yebra, Gonzalo; Harling-Lee, Joshua D.; Lycett, Samantha; Aarestrup, Frank M.; Larsen, Gunhild; Cavaco, Lina M.; Seo, Keun Seok; Abraham, Sam; Norris, Jacqueline M.; Schmidt, Tracy; et al. (Proceedings of the National Academy of Sciences, 2022-12-05)
    Most new pathogens of humans and animals arise via switching events from distinct host species. However, our understanding of the evolutionary and ecological drivers of successful host adaptation, expansion, and dissemination are limited. Staphylococcus aureus is a major bacterial pathogen of humans and a leading cause of mastitis in dairy cows worldwide. Here we trace the evolutionary history of bovine S. aureus using a global dataset of 10,254 S. aureus genomes including 1,896 bovine isolates from 32 countries in 6 continents. We identified 7 major contemporary endemic clones of S. aureus causing bovine mastitis around the world and traced them back to 4 independent host-jump events from humans that occurred up to 2,500 y ago. Individual clones emerged and underwent clonal expansion from the mid-19th to late 20th century coinciding with the commercialization and industrialization of dairy farming, and older lineages have become globally distributed via established cattle trade links. Importantly, we identified lineage-dependent differences in the frequency of host transmission events between humans and cows in both directions revealing high risk clones threatening veterinary and human health. Finally, pangenome network analysis revealed that some bovine S. aureus lineages contained distinct sets of bovine-associated genes, consistent with multiple trajectories to host adaptation via gene acquisition. Taken together, we have dissected the evolutionary history of a major endemic pathogen of livestock providing a comprehensive temporal, geographic, and gene-level perspective of its remarkable success.
  • Transcriptome characterization and differentially expressed genes under flooding and drought stress in the biomass grasses Phalaris arundinacea and Dactylis glomerata

    Klaas, Manfred; Haiminen, Niina; Grant, Jim; Cormican, Paul; Finnan, John; Arojju, Sai Krishna; Utro, Filippo; Vellani, Tia; Parida, Laxmi; Barth, Susanne; et al. (Oxford University Press (OUP), 2019-06-26)
    Background and Aims Perennial grasses are a global resource as forage, and for alternative uses in bioenergy and as raw materials for the processing industry. Marginal lands can be valuable for perennial biomass grass production, if perennial biomass grasses can cope with adverse abiotic environmental stresses such as drought and waterlogging. Methods In this study, two perennial grass species, reed canary grass (Phalaris arundinacea) and cocksfoot (Dactylis glomerata) were subjected to drought and waterlogging stress to study their responses for insights to improving environmental stress tolerance. Physiological responses were recorded, reference transcriptomes established and differential gene expression investigated between control and stress conditions. We applied a robust non-parametric method, RoDEO, based on rank ordering of transcripts to investigate differential gene expression. Furthermore, we extended and validated vRoDEO for comparing samples with varying sequencing depths. Key Results This allowed us to identify expressed genes under drought and waterlogging whilst using only a limited number of RNA sequencing experiments. Validating the methodology, several differentially expressed candidate genes involved in the stage 3 step-wise scheme in detoxification and degradation of xenobiotics were recovered, while several novel stress-related genes classified as of unknown function were discovered. Conclusions Reed canary grass is a species coping particularly well with flooding conditions, but this study adds novel information on how its transcriptome reacts under drought stress. We built extensive transcriptomes for the two investigated C3 species cocksfoot and reed canary grass under both extremes of water stress to provide a clear comparison amongst the two species to broaden our horizon for comparative studies, but further confirmation of the data would be ideal to obtain a more detailed picture.
  • Pathogens, patterns of pneumonia, and epidemiologic risk factors associated with respiratory disease in recently weaned cattle in Ireland

    Murray, Gerard M.; More, Simon J.; Sammin, Dónal; Casey, Mìcheàl J.; McElroy, Máire C.; O’Neill, Rónan G.; Byrne, William J.; Earley, Bernadette; Clegg, Tracy A.; Ball, Hywel; et al. (SAGE, 2017-01-11)
    We examined the pathogens, morphologic patterns, and risk factors associated with bovine respiratory disease (BRD) in 136 recently weaned cattle (“weanlings”), 6–12 mo of age, that were submitted for postmortem examination to regional veterinary laboratories in Ireland. A standardized sampling protocol included routine microbiologic investigations as well as polymerase chain reaction and immunohistochemistry. Lungs with histologic lesions were categorized into 1 of 5 morphologic patterns of pneumonia. Fibrinosuppurative bronchopneumonia (49%) and interstitial pneumonia (48%) were the morphologic patterns recorded most frequently. The various morphologic patterns of pulmonary lesions suggest the involvement of variable combinations of initiating and compounding infectious agents that hindered any simple classification of the etiopathogenesis of the pneumonias. Dual infections were detected in 58% of lungs, with Mannheimia haemolytica and Histophilus somni most frequently recorded in concert. M. haemolytica (43%) was the most frequently detected respiratory pathogen; H. somni was also shown to be frequently implicated in pneumonia in this age group of cattle. Bovine parainfluenza virus 3 (BPIV-3) and Bovine respiratory syncytial virus (16% each) were the viral agents detected most frequently. Potential respiratory pathogens (particularly Pasteurella multocida, BPIV-3, and H. somni) were frequently detected (64%) in lungs that had neither gross nor histologic pulmonary lesions, raising questions regarding their role in the pathogenesis of BRD. The breadth of respiratory pathogens detected in bovine lungs by various detection methods highlights the diagnostic value of parallel analyses in respiratory disease postmortem investigation.
  • Surgical castration with pain relief affects the health and productive performance of pigs in the suckling period

    Morales, Joaquin; Dereu, Andre; Manso, Alberto; de Frutos, Laura; Piñeiro, Carlos; Manzanilla, Edgar G.; Wuyts, Niels; Zoetis Inc. (Springer Science and Business Media LLC, 2017-09-06)
    Background Surgical castration is still practiced in many EU countries to avoid undesirable aggressive behavior and boar taint in male pigs. However, evidence shows that castration is painful and has a detrimental influence on pig health. This study investigated the clinical and productive effects of surgical castration in the suckling period. A total of 3696 male pigs, 3 to 6 days old, comprising of 721 litters from two different farms were included in the study. Within each litter, half of the males were kept as intact males (IM) and half were surgically castrated (CM). Surgical castration was conducted by a trained farmer. Average daily gain (ADG), body weight at weaning (BWW), percentage of pre-weaning mortality (PWM) and antibiotic usage were measured. Pig major acute phase protein (PigMAP) serum concentrations were analyzed prior to castration, and on days 1 and 10 after castration. Productive performance data were analyzed using a linear mixed model. Mortality and percentage of pigs treated with antibiotics were analyzed using the Fisher’s exact test. Results No overall differences in BWW and ADG were observed between the two groups. However, differences were observed when the same effects were analyzed in the 25% lightest, 50% medium and 25% heaviest pigs at birth. PWM was higher in CM than in IM groups (6.3% vs 3.6%; p < 0.001), especially in the light (12.2% vs 6.2%; p = 0.02) and in the medium (5.5% vs 2.7%; p = 0.04) weight groups. In the heaviest pigs group PWM was not affected by castration, but IM tended to show higher ADG (p = 0.06) and showed higher BWW (8.0 kg vs 7.8 kg; p = 0.05) than CM. There were no differences in percentage of pigs treated with antibiotics between the two groups (5.8% vs 5.8%; p = 0.98) in this study. Furthermore, PigMAP was increased in CM the day after castration (0.944 mg/ml vs 0.847 mg/ml; p = 0.025), but there was no difference between CM and IM groups at day 10. Conclusions Surgical castration has a negative impact on production in the suckling period because it causes an increase in PWM, especially in pigs in the three lower quartiles for body weight, and negatively affects the BWW in pigs born in the highest quartile for body weight.
  • The transcriptome of the endometrium and placenta is associated with pregnancy development but not lactation status in dairy cows

    Moore, Stephen G.; McCabe, Matthew S.; Green, Jacob C.; Newsom, Emily M.; Lucy, Matthew C. (Oxford University Press (OUP), 2017-06-19)
    Infertility in lactating dairy cows is explained partially by the metabolic state associated with high milk production. The hypothesis was that lactating and nonlactating cows would differ in endometrial and placental transcriptomes during early pregnancy (day 28 to 42) and this difference would explain the predisposition for lactating cows to have embryonic loss at that time. Cows were either milked or not milked after calving. Reproductive [endometrium (caruncular and intercaruncular) and placenta] and liver tissues were collected on day 28, 35, and 42 of pregnancy. The hypothesis was rejected because no effect of lactation on mRNA abundance within reproductive tissues was found. Large differences within liver demonstrated the utility of the model to test an effect of lactation on tissue gene expression. Major changes in gene expression in reproductive tissues across time were found. Greater activation of the transcriptome for the recruitment and activation of macrophages was found in the endometrium and placenta. Changes in glucose metabolism between day 28 and 42 included greater mRNA abundance of rate-limiting genes for gluconeogenesis in intercaruncular endometrium and evidence for the establishment of aerobic glycolysis (Warburg effect) in the placenta. Temporal changes were predicted to be controlled by CSF1, PDGFB, TGFB1, and JUN. Production of nitric oxide and reactive oxygen species by macrophages was identified as a mechanism to promote angiogenesis in the endometrium. Reported differences in pregnancy development for lactating vs. nonlactating cows could be explained by systemic glucose availability to the conceptus and appeared to be independent of the endometrial and placental transcriptomes.
  • Association between the prion protein genotype and animal performance traits in a large multibreed sheep population

    McHugh, Noirin; O'Brien, A.C.; Pabiou, T.; McDermott, K.; Berry, Donagh; Department of Agriculture, Food and the Marine; 14/S/849 (Elsevier, 2022-07-31)
    Genetic susceptibility to scrapie, a fatal disease of sheep and goats, is modulated by polymorphisms in the prion protein (PrP). Neither the frequency of the PrP genotypes nor their association with animal performance has been investigated in a large multibreed Irish sheep population. Scrapie genotypes were available on 16 416 animals; the breeds represented included purebred Belclare (733), Charollais (333), Suffolk (739), Texel (1 857), Vendeen (191), and crossbreds (12 563). Performance data on lambing, lamb and ewe performance as well as health traits were available. The association between alternative approaches of describing the PrP genotype (i.e. 15 individually called PrP genotypes, five genotype classes representing susceptibility to scrapie, or number of ARR haplotypes) and animal performance were quantified using animal linear mixed models. All 15 of the possible scrapie genotypes were detected, although the frequency differed by breed. The frequency of the five PrP haplotypes in the entire population were 0.70 (ARR), 0.15 (ARQ), 0.11 (ARH), 0.02 (AHQ) and 0.01 (VRQ); the most susceptible haplotype (VRQ) was only detected in purebred Texels and crossbreds. No association was detected between the PrP genotype of either the animal or dam and any of the lambing traits (i.e. lambing difficulty score, perinatal mortality and birth weight). With the exception of ultrasound muscle depth, no association between the PrP genotype and any of the lamb performance traits (i.e. lamb BW and carcass) was observed. Lambs carrying the category four PrP genotype (i.e. ARR/VRQ) had 1.20 (SE = 0.45) mm, 1.38 (SE = 0.12) mm, 1.47 (S = 0.25) mm shallower ultrasound muscle depth relative to lambs of the less susceptible scrapie categories of 1, 2, 3, respectively (P < 0.05). Nonetheless, no association between PrP genotype and lamb carcass conformation, the ultimate end goal of producers, was detected. Ewe litter size, body condition score or lameness did not differ by PrP genotype of the ewe (P > 0.05). For ewe mature BW, ARH/VRQ ewes differed from most other ewe PrP genotypes and were, on average, 3.79 (SE = 1.66) kg heavier than ARR/ARR genotype ewes. Lamb dag score differed by dam PrP genotype (P < 0.05), although the differences were small. Results from this study show that scrapie is segregating within the Irish sheep population, but the PrP genotype was not associated with most traits investigated and, where associations were detected, the biological significance was minimal. This suggests minimal impact of selection on PrP genotype on performance, at least for the traits investigated in the present study.
  • A novel hybrid coagulation-constructed wetland system for the treatment of dairy wastewater

    Mohamed, A.Y.A.; Siggins, A.; Healy, M.G.; Ó hUallacháin, Daire; Fenton, Owen; Tuohy, P.; Teagasc Walsh Fellowship; RMIS-0386 (Elsevier, 2022-07-29)
    Constructed wetlands (CWs) are a cost-effective and sustainable treatment technology that may be used on farms to treat dairy wastewater (DWW). However, CWs require a large area for optimal treatment and have poor long-term phosphorus removal. To overcome these limitations, this study uses a novel, pilot-scale coagulation-sedimentation process prior to loading CWs with DWW. This hybrid system, which was operated on an Irish farm over an entire milking season, performed well at higher hydraulic loading rates than conventional CWs, and obtained removal efficiencies ≥99 % for all measured water quality parameters (chemical oxygen demand, total nitrogen and phosphorus, total suspended solids and turbidity), which complied with EU directives concerning urban wastewater treatment. Overall, the hybrid coagulation-CW is a promising technology that requires a smaller area than conventional CWs and minimal operator input, and produces high effluent quality.
  • An evaluation of four private animal health and welfare standards and associated quality assurance programmes for dairy cow production

    More, S.J.; Marchewka, J.; Hanlon, A.; Balzani, A.; Boyle, Laura Ann; Department of Agriculture, Food and the Marine; RSF 17/S/230 (Elsevier, 2021-12-31)
    Private standards in animal health and welfare (AHW) and associated quality assurance (QA) programmes are an important instrument for food policy with the potential to substantially improve AHW. However, there are concerns that they do not necessarily do so. In this study, we evaluated four private AHW standards and associated QA programmes for dairy cow production, from Denmark, Ireland, the Netherlands and the United Kingdom, using an existing (but adapted) conceptual framework. The framework considers criteria relating to programme goals including relevance to AHW, programme beneficiaries, effectiveness, efficiency and transparency. The current study focused on information that was publicly available online. We found limited objective information to support programme claims, although there were considerable differences between programmes. Across all programmes, problems were identified with respect to transparency, and attempts to scrutinise claims would not be a straightforward process for most consumers. Among the programmes, there were notable examples of best-practice in AHW, relating to science-based evidence, separation of risk assessment and risk management, animal-based measures, farm benchmarking, ongoing programme-level metrics and measurement, and ongoing programme review. There is a need for careful scrutiny of private standards and QA programmes, to provide consumers with assurance with respect to programme effectiveness and transparency. Further, it is important that programme efficiencies are maximised. There is a strong case for regulatory oversight of private standards in AHW and associated QA programmes. This could be within existing or defined policy instruments, both to facilitate the positive impact of these programmes and to build confidence among consumers of the validity of programme claims.
  • Application of machine-learning methods to milk mid-infrared spectra for discrimination of cow milk from pasture or total mixed ration diets

    Frizzarin, Maria; O'Callaghan, Tom; Murphy, T.B.; Hennessey, Deirdre; Casa, A.; Science Foundation Ireland; Department of Agriculture, Food and the Marine; 16/RC/3835; 18/SIRG/5562 (Elsevier, 2021-12-31)
    The prevalence of “grass-fed” labeled food products on the market has increased in recent years, often commanding a premium price. To date, the majority of methods used for the authentication of grass-fed source products are driven by auditing and inspection of farm records. As such, the ability to verify grass-fed source claims to ensure consumer confidence will be important in the future. Mid-infrared (MIR) spectroscopy is widely used in the dairy industry as a rapid method for the routine monitoring of individual herd milk composition and quality. Further harnessing the data from individual spectra offers a promising and readily implementable strategy to authenticate the milk source at both farm and processor levels. Herein, a comprehensive comparison of the robustness, specificity, and accuracy of 11 machine-learning statistical analysis methods were tested for the discrimination of grass-fed versus non-grass-fed milks based on the MIR spectra of 4,320 milk samples collected from cows on pasture or indoor total mixed ration–based feeding systems over a 3-yr period. Linear discriminant analysis and partial least squares discriminant analysis (PLS-DA) were demonstrated to offer the greatest level of accuracy for the prediction of cow diet from MIR spectra. Parsimonious strategies for the selection of the most discriminating wavelengths within the spectra are also highlighted.
  • A survey of biosecurity and health management practices on Irish dairy farms engaged in contract-rearing

    McCarthy, M.C.; O'Grady, L.; McAloon, C.G.; Mee, John F.; Teagasc Walsh Scholarship (Elsevier, 2021-12-31)
    A survey was conducted to investigate potential differences in biosecurity and health management practices on Irish dairy farms that sent their heifers for contract-rearing (source dairy farms, SDF; n = 62) and those rearing their own heifers (control farms, CF; n = 50). Participating farmers were surveyed by postal questionnaire between September and November 2018. The overall response rate was 93%. Results show that structurally, SDF were larger, less fragmented, and more specialized than CF. Outsourcing of labor-intensive activities to external contractors was more common among SDF than CF, exposing them to potentially increased biosecurity risks associated with animal movements, use of shared equipment, and increased frequency of farm visitors. The majority of SDF sent heifers to a single-origin rearing facility (70%), with heifers most commonly arriving at the rearing unit between 2 and 4 mo (53%) and returning to the dairy farm between 18 and 21 mo of age (56%). Despite the increased biosecurity risk associated with contract-rearing, implementation of disease prevention measures was not superior on SDF compared with CF. For both farm types, there was scope for improvement to visitor biosecurity protocols, quarantine procedures, colostrum feeding practices, and hygiene of calving areas. This research provides an overview of the demographics and farm management practices implemented by dairy farmers engaged in contract-rearing of replacement heifers, and will serve to inform farmers, veterinary advisors, and policy makers.
  • The effect of natural and induced calving of beef heifers on stress-related gene expression and maternal health and immunity

    Beltman, M.E.; Lewis, J.; McCabe, M.; Keogh, Kate; Kenny, David A.; UCD Seed Funding Scheme; SF827 (Elsevier, 2022-06-30)
    The peri-partum processes can exert stress on a cow on many levels. There is little evidence about acute stress around the calving event and subsequent potential effects for the cows’ immunological status or subsequent reproductive health. To investigate this, 55 crossbred recipient beef heifers carrying purebred Simmental embryos were assigned to one of three groups on day 285 of gestation: (i) control (no parturition induction treatment; n = 19); (ii) induction of parturition with corticosteroid (n = 20) and (iii) induction of parturition with corticosteroid plus prostaglandin (n = 16). Interval from induction of parturition to calving and calving ease was recorded. Reproductive tract examinations were conducted on Day 21 (D21) and Day 42, and a sample was obtained for the determination of uterine cytology on D21. Blood samples were taken from the dams two weeks before parturition, one day after parturition (D1) and two weeks after parturition (D14) for gene expression and cortisol and calcium concentration determination. Calves were weighed at birth and subsequently every week until they were 10 weeks of age. A colostrum sample was taken immediately after calving and stored for subsequent Immunoglobin G (IgG) concentration analysis. Data were analysed using ANOVA with posthoc Tukey, Spearman correlation and stepwise backwards linear regression using SAS. Quantitative reverse transcription PCR was performed on the following immune genes: Interleukins IL1a and b, IL2, IL4, IL8, Tumour Necrosis Factor Alpha, Interferon-gamma, Lymphotoxin, Toll-Like Receptor, Nuclear factor of kappa light polypeptide gene enhancer in B cells 1 and 2, glucocorticoid receptor alpha, as well as the neutrophil genes that regulate inflammation: Fas, L-selectin, MMP-9 and BPI. The results show that compared with non-induced contemporaries, induction has no negative effect on dystocia or subsequent calf weight gain but can have a positive effect on colostral IgG concentration. Blood calcium concentrations on both D1 and D14 postcalving are associated with subsequent uterine health. Parturition events were reflected in temporal changes in the expression of the cytokines IFNγ, TNFα, IL1b, IL4, IL8 and Haptoglobin in the dams’ blood, all of which are associated with the immune competence of the cow during this period. The conclusion is that induction of calving can have a positive effect on colostral IgG concentration. Calcium concentrations postcalving are associated with subsequent reproductive tract health. Events associated with the peri- and postpartum period are all reflected in temporal changes in immune function-related cytokines.
  • Internal teat sealants alone or in combination with antibiotics at dry-off – the effect on udder health in dairy cows in five commercial herds

    Clabby, C.; McParland, Sinead; Dillon, Pat; Arkins, S.; Flynn, J.; Murphy, J.; Silva Boloña, P.; Dairy Research Ireland; Teagasc Walsh Scholarship (Elsevier, 2022)
    In the dairy industry, the dry period has been identified as an area for potential reduction in antibiotic use, as part of a one health approach to preserve antibiotic medicines for human health. The objective of this study was to assess the impact of dry cow treatment on somatic cell count (SCC), intramammary infection (IMI) and milk yield on five commercial Irish dairy herds. A total of 842 cows across five spring calving dairy herds with a monthly bulk tank SCC of < 200 000 cells/mL were recruited for this study. At dry-off, cows which had not exceeded 200 000 cells/mL in the previous lactation were assigned one of two dry-off treatments: internal teat seal (ITS) alone (Lo_TS) or antibiotic plus ITS (Lo_AB + TS). Cows which exceeded 200 000 cells/mL in the previous lactation were treated with antibiotic plus ITS and included in the analysis as a separate group (Hi_AB + TS). Test-day SCC and lactation milk yield records were provided by the herd owners. Quarter milk samples were collected at dry-off, after calving and at mid-lactation for bacteriological culture and quarter SCC analysis. Cow level SCC was available for 789 cows and was log-transformed for the purpose of analysis. Overall, the log SCC of the cows in the Lo_TS group was significantly higher than the cows in Lo_AB + TS group and not statistically different to the cows in the Hi_AB + TS group in the subsequent lactation. However, the response to treatment differed according to the herd studied; the log SCC of the cows in the Lo_TS group in Herds 3, 4 and 5 was not statistically different to the cows in Lo_AB + TS group, whereas in the other two herds, the log SCC was significantly higher in the Lo_TS when compared to the Lo_AB + TS group. There was a significant interaction between dry-off group and herds on SCC and odds of infection in the subsequent lactation. The results of this study suggest that the herd prevalence of IMI may be useful in decision-making regarding the treatment of cows with ITS alone at dry-off to mitigate its impact on udder health.
  • Modelling the production, profit, and greenhouse gas emissions of Irish sheep flocks divergent in genetic merit

    Farrell, L.; Herron, J.; Pabiou, T.; McHugh, Noirin; McDermott, K.; Shalloo, Laurence; O'Brien, D.; Bohan, A.; Department of Agriculture, Food and the Marine; 17/S/235; et al. (Elsevier, 2022-08-31)
    CONTEXTSheep production industries face the challenge of increasing farm production and profit while reducing environmental impacts. OBJECTIVESGenetic selection using multi-trait breeding indices can be used to improve flock productivity, profitability, and greenhouse gas (GHG) emissions intensities (kg CO2-eq /kg of product), however validation of the improved performance of animals ranked higher on breeding indices at a flock level is required. METHODSPhenotypic data from 387,580 production records of animals born between 2018 and 2020 of known genetic merit in commercial flocks were inputted to an established bio-economic model. Two contrasting flocks were compared, a flock of ewes ranked High (top 20%) on the Irish replacement Index bred with rams ranked High on the replacement and terminal indices, and a flock of ewes ranked Low (bottom 20%) on the Irish replacement Index bred with rams ranked Low on the replacement and terminal indices. The two flocks were then simulated using life cycle assessment to estimate the GHG emissions profile for both systems. RESULTS AND CONCLUSIONFlock weaning rates were 1.70 and 1.53 lambs weaned per ewe presented for breeding for the High and Low genetic merit flocks, respectively. The flock of High genetic merit ewes sold 0.17 more lambs per ewe, equating to 3.29 kg more lamb carcass per ewe, than the flock of Low genetic merit ewes; lambs from the High genetic merit flock were also sold at an earlier age. The greater production of the High genetic merit flocks resulted in an additional €18/ewe net profit than the Low genetic merit flock. Although total flock GHG emissions were higher for the High genetic merit flock, GHG emissions intensities were lower at 21.7 and 23.3 kg CO2-eq /kg lamb carcass sold for the High and Low genetic merit flocks, respectively. The lower emissions intensity of the High genetic merit flock was due to the dilution effect of higher lamb production and lambs being drafted for slaughter ealier. SIGNIFICANCEThe results suggest Irish sheep producers can make substantial profit gains through selection according to the national breeding indices while also reducing their environmental impact, and farmers should consider genetic merit when purchasing their rams, particularly sires of replacement ewe lambs.
  • Quantification of cow milk yield and pre-weaning calf growth response in temperate pasture-based beef suckler systems: A meta-analysis

    Sapkota, D.; Kelly, A. K.; Crosson, Paul; White, R.R.; McGee, Mark; Teagasc Walsh Scholarship Programme (Elsevier, 2020-11-30)
    The objectives of this study were to quantitatively summarize factors associated with cow milk yield (MY) and calf growth response in pasture-based beef cow-calf suckler systems and to discern how cow genotype and parity influenced these responses. A dataset of 344 treatment mean observations was compiled from 69 studies that reported data on cow MY, and calf pre-weaning average daily live weight gain (ADG) and/or weaning weight (WW). Data were analysed using linear mixed effects models with study and region included as random effects. Models were developed for cow MY, calf ADG and WW response and each model was evaluated based on different model fit statistics. The final cow MY model included cow origin (Dairybeef or Beef), cow maturity (early-maturing (EM) or late-maturing (LM) genotypes) and parity. Dairybeef produced 35.4% more milk (8.64 vs. 6.38 kg/day) than Beef cows, and LM produced 20.9% more milk (8.20 vs. 6.78 kg/day) than EM genotypes (P < 0.001). Multiparous cows had a 14.8% higher MY (8.11 vs. 7.06 kg/day) compared to primiparous cows (P < 0.001). Lactation curve persistency was better (P < 0.05) for Beef and EM compared to Dairybeef and LM genotype cows, respectively. The final models of calf ADG and WW included cow origin, cow maturity and parity. Calves from Dairybeef and LM cows were 14 and 20 kg heavier (P < 0.001) at weaning (210-day adjusted) compared to those from Beef and EM genotype cows, respectively. Calves from multiparous cows were 13 kg heavier at weaning than those from primiparous cows (P < 0.001). The response in calf ADG associated with a 1 kg increase in cow daily MY was 47 and 53 g for Dairybeef and Beef cows, respectively (P < 0.001). Corresponding responses for EM and LM cows were 51 and 55 g (P < 0.001). In conclusion, the relationships between cow MY and calf pre-weaning growth, as well as the quantitative impact of cow genotype and parity were determined for pasture-based beef suckler systems; the coefficients generated can be used for improving beef cow-calf management strategies, beef cattle breeding programmes and bio-economic modelling purposes.
  • Cow- and herd-level risk factors for lameness in partly housed pasture-based dairy cows

    Browne, N.; Hudson, C.D.; Crossley, R.E.; Sugrue, K; Kennedy, E.; Huxley, J.N.; Conneely, Muireann; Teagasc Walsh Scholarship (Elsevier, 2021-10-02)
    Lameness in dairy cows is a major animal welfare concern and has substantial economic impact through reduced production and fertility. Previous risk factor analyses have focused on housed systems, rather than those where cows were grazed for the majority of the year and housed only for the winter period. Therefore, the aim of this observational study was to identify a robust set of cow-level and herd-level risk factors for lameness in a pasture-based system, based on predictors from the housing and grazing periods. Ninety-nine farms were visited during the grazing period (April 2019–September 2019), and 85 farms were revisited during the housing period (October 2019–February 2020). At each visit, all lactating cows were scored for lameness (0 = good mobility, 1 = imperfect mobility, 2 = impaired mobility, 3 = severely impaired mobility), and potential herd-level risk factors were recorded through questionnaires and infrastructure measurements. Routine cow-level management data were also collected. Important risk factors for lameness were derived though triangulation of results from elastic net regression, and from logistic regression model selection using modified Bayesian information criterion. Both selection methods were implemented using bootstrapping. This novel approach has not previously been used in a cow-level or herd-level risk factor analysis in dairy cows, to the authors' knowledge. The binary outcome variable was lameness status, whereby cows with a lameness score of 0 or 1 were classed as non-lame and cows with a score of 2 or 3 were classed as lame. Cow-level risk factors for increased lameness prevalence were age and genetic predicted transmitting ability for lameness. Herd-level risk factors included farm and herd size, stones in paddock gateways, slats on cow tracks near the collecting yard, a sharper turn at the parlor exit, presence of digital dermatitis on the farm, and the farmers' perception of whether lameness was a problem on the farm. This large-scale study identified the most important associations between risk factors and lameness, based on the entire year (grazing and housing periods), providing a focus for future randomized clinical trials.
  • Effect of feeding single-dam or pooled colostrum on maternally derived immunity in dairy calves

    Barry, J.; Bokkers, E.A.M.; Sayers, Riona; Murphy, J.P.; de Boer, I.J.M.; Kennedy, E.; Teagasc Walsh Fellowship (Elsevier, 2021-08-26)
    The role of colostrum management in providing adequate immunological protection to neonatal calves has been widely investigated, and thresholds for colostrum quality, as well as optimum volume and timing for colostrum feeding have been established. However, limited information is available on the effect of colostrum source (single dam or pooled) on passive immunity, as well as subsequent antibody survival in the calf. This study aimed to assess the effect of feeding single-dam colostrum (own and other dam) or pooled colostrum on transfer of passive immunity, and also investigate the rate of depletion of disease-specific antibodies among dairy calves. In total, 320 cows and 119 dairy heifer calves were enrolled in the study. Calves were blood-sampled immediately after birth and received either own-dam, other-dam, or pooled colostrum. Calves were blood-sampled at 24 h to assess serum IgG concentrations and at monthly intervals thereafter to document disease-specific antibody survival. Mean colostrum IgG concentration was higher for other-dam treatment group, whereas own-dam and pooled treatments were similar. For all treatment groups, the mean IgG concentration was >80 mg/mL, exceeding the quality threshold of 50 mg/mL. Mean calf serum IgG concentration was lower for calves fed pooled colostrum compared with those that received colostrum from a single cow. There was a negative association with 24-h serum IgG and calf birth bodyweight; calves <30 kg at birth had the highest 24-h serum IgG concentration. Survival of antibodies to bovine viral diarrhea, Salmonella infection, leptospirosis, bovine parainfluenza 3 virus, bovine respiratory syncytical virus, rotavirus, and coronavirus was not associated with colostrum source; however, antibodies to infectious bovine rhinotracheitis had a greater period of survival among calves fed own-dam colostrum. We found that feeding single-dam colostrum can thus improve calf immunity through increased serum IgG levels and antibody survival rates. Furthermore, we hypothesize that immune exclusion may occur with pooled colostrum; therefore, providing pooled colostrum may still be a good practice as long as it can be ensured that enough antibodies are absorbed into the blood stream to deal with pathogens calves may encounter because different dams may have antibodies against different strains of viruses and bacteria, yielding cross protection.
  • Identification of functional candidate variants and genes for feed efficiency in Holstein and Jersey cattle breeds using RNA-sequencing

    Lam, S.; Miglior, F.; Fonseca, P.A.S.; Gómez-Redondo, I.; Zeidan, J.; Suárez-Vega, A.; Schenkel, F.; Guan, L.L.; Waters, Sinéad M; Stothard, P.; et al. (Elsevier, 2021-02-28)
    The identification of functional genetic variants and associated candidate genes linked to feed efficiency may help improve selection for feed efficiency in dairy cattle, providing economic and environmental benefits for the dairy industry. This study used RNA-sequencing data obtained from liver tissue from 9 Holstein cows [n = 5 low residual feed intake (RFI), n = 4 high RFI] and 10 Jersey cows (n = 5 low RFI, n = 5 high RFI), which were selected from a single population of 200 animals. Using RNA-sequencing, 3 analyses were performed to identify: (1) variants within low or high RFI Holstein cattle; (2) variants within low or high RFI Jersey cattle; and (3) variants within low or high RFI groups, which are common across both Holstein and Jersey cattle breeds. From each analysis, all variants were filtered for moderate, modifier, or high functional effect, and co-localized quantitative trait loci (QTL) classes, enriched biological processes, and co-localized genes related to these variants, were identified. The overlapping of the resulting genes co-localized with functional SNP from each analysis in both breeds for low or high RFI groups were compared. For the first two analyses, the total number of candidate genes associated with moderate, modifier, or high functional effect variants fixed within low or high RFI groups were 2,810 and 3,390 for Holstein and Jersey breeds, respectively. The major QTL classes co-localized with these variants included milk and reproduction QTL for the Holstein breed, and milk, production, and reproduction QTL for the Jersey breed. For the third analysis, the common variants across both Holstein and Jersey breeds, uniquely fixed within low or high RFI groups were identified, revealing a total of 86,209 and 111,126 functional variants in low and high RFI groups, respectively. Across all 3 analyses for low and high RFI cattle, 12 and 31 co-localized genes were overlapping, respectively. Among the overlapping genes across breeds, 9 were commonly detected in both the low and high RFI groups (INSRR, CSK, DYNC1H1, GAB1, KAT2B, RXRA, SHC1, TRRAP, PIK3CB), which are known to play a key role in the regulation of biological processes that have high metabolic demand and are related to cell growth and regeneration, metabolism, and immune function. The genes identified and their associated functional variants may serve as candidate genetic markers and can be implemented into breeding programs to help improve the selection for feed efficiency in dairy cattle.
  • Formulation of a decision support tool incorporating both genetic and non-genetic effects to rank young growing cattle on expected market value

    Dunne, F. L.; Evans, R. D.; Kelleher, M.M.; Walsh, S. W.; Berry, Donagh; Science Foundation Ireland; Department of Agriculture, Food and Marine; European Union; 16/RC/3835; 679GenTORE (727213) (Elsevier, 2021-02-28)
    While breeding indexes exist globally to identify candidate parents of the next generation, fewer tools exist that provide guidance on the expected monetary value of young animals. The objective of the present study was therefore to develop the framework for a cattle decision-support tool which incorporates both the genetic and non-genetic information of an animal and, in doing so, better predict the potential market value of an animal, whatever the age. Two novel monetary indexes were constructed and their predictive ability of carcass value was compared to that of the Irish national Terminal breeding index, typical of other terminal indexes used globally. A constructed Harvest index was composed of three carcass-related traits [i.e., 1) carcass weight, 2) carcass conformation and 3) carcass fat, each weighted by their respective economic value] and aimed at purchasers of animals close to harvest; the second index, termed the Calf index, also included docility and feed intake (weighted by their respective economic value), thus targeting purchasers of younger calves for growing (and eventually harvesting). Genetic and non-genetic fixed and random effect model solutions from the Irish national genetic evaluations underpinned all indexes. The two novel indexes were formulated using three alternative estimates of an animal's total merit for comparative purposes: 1) an index based solely on the animal's breed solutions, 2) an index which also included within-breed animal differences, and 3) an index which, as well as considering additive and non-additive genetic effects, also included non-genetic effects (referred to as production values [PVs]). As more information (i.e., within breed effects and subsequently non-genetic effects) was included in the total merit estimate, the correlations strengthened between the two proposed indexes and the animal's calculated carcass market value; the correlation coefficients almost doubled in strength when total merit was based on PV-based estimates as compared to the breed solutions alone. Including phenotypic live-weight data, collected during the animal's life, strengthened the predictive ability of the indexes further. Based on the results presented, the proposed indexes may fill the void in decision support when purchasing or selling cattle. In addition, given the dynamic nature of indexes, they have the potential to be updated in real-time as information becomes available.

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