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

  • Removal of sialic acid from bull sperm decreases motility and mucus penetration ability but increases zona pellucida binding and polyspermic penetration in vitro

    Fernandez-Fuertes, B; Blanco-Fernandez, A; Reid, C J; Meade, K G; Fair, S; Lonergan, P; Irish Department of Agriculture, Food and the Marine; 11/S/104 (Bioscientifica, 2018-06)
    This study tested the hypothesis that sperm sialic acid (Sia) is required to reach the site of fertilization, and that successful fertilization requires recognition of Sia from both the sperm and oocyte to occur. In addition, it has recently been reported that Siglecs (Sia-binding-immunoglobulin-like lectins) are present on the sperm surface. Thus, the possibility that the recognition of oocyte Sia was sperm-Siglec-mediated was also addressed. Sperm exposed to neuraminidase (NMase) exhibited lower overall and progressive motility, which translated to a decreased ability to swim through cervical mucus from cows in oestrus. In addition, when either sperm or cumulus-oocyte complexes (COCs) were treated with NMase, a decrease in cleavage and blastocyst rate was observed. However, incubation of sperm with increasing concentrations of anti-Siglec-2, -5, -6 and -10 antibodies prior to fertilization had no effect on their fertilizing ability. Interestingly, treatment with NMase increased the number of sperm bound to the ZP but also the rate of polyspermic fertilization. Flow cytometry analysis revealed no differences in the percentage of capacitated or acrosome-reacted sperm. These results suggest that Sia are required to reach the site of fertilization but need to be removed for sperm-oocyte interaction. However, fine regulation is needed to avoid abnormal fertilization which can lead to impaired embryo development.
  • Effect of passive transfer status on response to a glycoprotein E (gE)-negative bovine herpesvirus type 1 (BoHV-1) and bovine respiratory syncytial virus (BRSV) vaccine and weaning stress in pre-weaned dairy calves

    Dunn, Amanda; Welsh, Michael; Gordon, Alan; Arguello, Anastasio; Morrison, Steven J.; Earley, Bernadette; Department of Agriculture, Food and the Marine; Department of Agriculture and Rural Development in Northern Ireland; AgriSearch (farmer levy (Informa UK Limited, 2018-01-09)
    The study objectives were to: 1) examine how calves of divergent immune status respond to BRSV vaccination at 3 weeks of age; 2) trace glycoprotein E negative BoHV-1 antibodies from vaccinated dams to calf sera and to investigate how passive transfer affects response to live BoHV-1 vaccine at 6 weeks of age; 3) explore the impact of passive transfer status on blood metabolites around weaning. Thirty seven Holstein cows and their calves were included in the study. All cows were immunised with a commercial marker vaccine against BoHV-1(gE-) administered intra-muscularly at 4 month prior to the start of calving. Calves were assigned to 1 of 2 colostrum treatment groups: 1) 5% of BW in colostrum fed at birth, or 2) 10% of BW in colostrum fed at birth. Calves were also immunised at 3 weeks of age with a respiratory commercial vaccine, and a booster administered 4 weeks later. Calves were also immunised against BoHV-1 at 6 weeks of age, using one dose of a live commercial vaccine. The results demonstrated that level of passive immunity had no effect on immune response to vaccination and the importance of feeding colostrum from vaccinated BoHV-1 gE- dams to provide calves with passive protection against IBRV.
  • Comparison of single radial immunodiffusion and ELISA for the quantification of immunoglobulin G in bovine colostrum, milk and calf sera

    Dunn, Amanda; Duffy, Catherine; Gordon, Alan; Morrison, Steven; Argűello, Anastasio; Welsh, Michael; Earley, Bernadette; Department of Agriculture and Rural Development in Northern Ireland; AgriSearch (farmer levy); Department of Agriculture, Food and Marine, Ireland; et al. (Informa UK Limited, 2017-11-02)
    The overall objective was to compare immunoglobulin G (IgG) concentrations measured by single radial immunodiffusion (sRID) and ELISA-based methods in samples of bovine colostrum and transition milk from contrasting breed types (Limousin × Friesian (n = 10) and Holstein (n = 10)). Jugular blood samples were collected at 48 h post-birth from beef (n = 10) and dairy (n = 10) calves and sera harvested subsequent to colostrum consumption. Absolute colostrum IgG values determined by ELISA showed poor agreement with mean (SD) IgG values measured using sRID, fixed bias (sRID – ELISA) was 31.89 (±9.84) mg/mL; having wide limits of agreement (12.61–51.17) and a low concordance coefficient (0.26). The agreement between ELISA and sRID when measuring serum IgG was greater than that of colostrum, fixed bias (sRID – ELISA) was 12.36 (±6.60) mg/mL; having narrower limits of agreement (−0.58 to 25.30) and serum IgG concentrations had a greater concordance coefficient (0.44) between samples. Calf sera IgG measured using the indirect zinc sulphate turbidity test showed a strong correlation with the sRID and ELISA methods (P < .001), R2 = 0.78 and R2 = 0.77 respectively. Overall, the ELISA and sRID methodologies had a strong positive association with almost a twofold (1.8) difference between values; therefore, they provide diverse absolute values of IgG concentration.
  • Editorial, International Bull Fertility Conference – Theory to Practice, Westport, Ireland, 2018

    Diskin, MichaelG; Lonergan, Pat; Kenny, David A.; Fair, Sean (Elsevier, 2018)
    This supplement to Animal contains the papers associated with the keynote lectures delivered at the International Bull Fertility Conference – Theory to Practice held in Westport, Ireland from May 27th to 30th 2018. The conference was organised under the auspices of the British Society of Animal Science (BSAS) in close collaboration with Teagasc, University College Dublin, University of Limerick, the Cattle Association of Veterinary Ireland (CAVI), XL Vets, the British Cattle Veterinary Association (BCVA) and the Department of Agriculture Food and the Marine.
  • Complete Genome Sequences of Sequence Type 71 (ST71) and ST97 Staphylococcus aureus Isolates from Bovine Milk

    Cormican, Paul; Keane, Orla M.; Department of Agriculture Food and the Marine; 14/S/802 (American Society for Microbiology, 2018-08-09)
    This is the announcement of draft genome sequences for Staphylococcus aureus strains belonging to sequence type 97 (ST97) and ST71. These sequence types are commonly associated with bovine mastitis, and the strains were isolated in Ireland in 2010 from the milk of cows with clinical mastitis.
  • Use of clinic refractometer at farm as a tool to estimate the IgG content in goat colostrum

    Castro, Noemí; Gómez-González, Lenny Andrea; Earley, Bernadette; Argüello, Anastasio (Informa UK Limited, 2018-11-22)
    Refractometry has been proposed as a farm technique to estimate the IgG concentration in colostrum. In order to validate the method in goat colostrum using a clinical refractometer, 216 colostrum and milk samples were obtained from 54 dairy goats. Samples were evaluated for protein concentration using a clinical refractometer and IgG concentration was measured using a commercial ELISA. The r2 for the linear regression between refractometry value and IgG concentration measured by ELISA was 0.79, and the area under the receiver operating characteristics curve was 0.99. The proposed cut-off value using the clinical refractometer was 10 mg/mL. At this point, the sensitivity, specificity, negative predictive value, positive predictive value, Youden’s index and accuracy were 100%, 95.19%, 100%, 76.32%, 0.95% and 95.83%, respectively.
  • C7 vertebra homeotic transformation in domestic dogs – are Pug dogs breaking mammalian evolutionary constraints?

    Brocal, J.; De Decker, S.; José‐López, R.; Garcia Manzanilla, Edgar; Penderis, J.; Stalin, C.; Bertram, S.; Schoenebeck, J. J.; Rusbridge, C.; Fitzpatrick, N.; et al. (Wiley, 2018-05-14)
    The number of cervical vertebrae in mammals is almost constant at seven, regardless of their neck length, implying that there is selection against variation in this number. Homebox (Hox) genes are involved in this evolutionary mammalian conservation, and homeotic transformation of cervical into thoracic vertebrae (cervical ribs) is a common phenotypic abnormality when Hox gene expression is altered. This relatively benign phenotypic change can be associated with fatal traits in humans. Mutations in genes upstream of Hox, inbreeding and stressors during organogenesis can also cause cervical ribs. The aim of this study was to describe the prevalence of cervical ribs in a large group of domestic dogs of different breeds, and explore a possible relation with other congenital vertebral malformations (CVMs) in the breed with the highest prevalence of cervical ribs. By phenotyping we hoped to give clues as to the underlying genetic causes. Twenty computed tomography studies from at least two breeds belonging to each of the nine groups recognized by the Federation Cynologique Internationale, including all the brachycephalic 'screw-tailed' breeds that are known to be overrepresented for CVMs, were reviewed. The Pug dog was more affected by cervical ribs than any other breed (46%; P < 0.001), and was selected for further analysis. No association was found between the presence of cervical ribs and vertebral body formation defect, bifid spinous process, caudal articular process hypoplasia/aplasia and an abnormal sacrum, which may infer they have a different aetiopathogenesis. However, Pug dogs with cervical ribs were more likely to have a transitional thoraco-lumbar vertebra (P = 0.041) and a pre-sacral vertebral count of 26 (P < 0.001). Higher C7/T1 dorsal spinous processes ratios were associated with the presence of cervical ribs (P < 0.001), supporting this is a true homeotic transformation. Relaxation of the stabilizing selection has likely occurred, and the Pug dog appears to be a good naturally occurring model to further investigate the aetiology of cervical ribs, other congenital vertebral anomalies and numerical alterations.
  • Divergent functional isoforms drive niche specialisation for nutrient acquisition and use in rumen microbiome

    Rubino, Francesco; Carberry, Ciara; Waters, Sinéad M.; Kenny, David; McCabe, Matthew S; Creevey, Christopher J; European Community's Seventh Framework Programme; Teagasc and the Walsh Fellowships scheme; Science Foundation Ireland (SFI) Stokes lecturer scheme; Biotechnology and Biological Sciences Research Council (BBSRC); et al. (Springer Science and Business Media LLC, 2017-01-13)
    Many microbes in complex competitive environments share genes for acquiring and utilising nutrients, questioning whether niche specialisation exists and if so, how it is maintained. We investigated the genomic signatures of niche specialisation in the rumen microbiome, a highly competitive, anaerobic environment, with limited nutrient availability determined by the biomass consumed by the host. We generated individual metagenomic libraries from 14 cows fed an ad libitum diet of grass silage and calculated functional isoform diversity for each microbial gene identified. The animal replicates were used to calculate confidence intervals to test for differences in diversity of functional isoforms between microbes that may drive niche specialisation. We identified 153 genes with significant differences in functional isoform diversity between the two most abundant bacterial genera in the rumen (Prevotella and Clostridium). We found Prevotella possesses a more diverse range of isoforms capable of degrading hemicellulose, whereas Clostridium for cellulose. Furthermore, significant differences were observed in key metabolic processes indicating that isoform diversity plays an important role in maintaining their niche specialisation. The methods presented represent a novel approach for untangling complex interactions between microorganisms in natural environments and have resulted in an expanded catalogue of gene targets central to rumen cellulosic biomass degradation.
  • 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.
  • 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.
  • 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.
  • 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.
  • 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.
  • 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.

View more