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

  • 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.
  • Associating cow characteristics with mobility scores in pasture-based dairy cows

    Bokkers, E.A.M.; de Boer, I.J.M.; Hogeveen, H.; Sayers, Riona; Byrne, N.; Ruelle, Elodie; Shalloo, Laurence; Department of Agriculture, Food and the Marine; 14 S 801 (Elsevier, 2019-09-30)
    The quality of dairy cow mobility can have significant welfare, economic, and environmental consequences that have yet to be extensively quantified for pasture-based systems. The objective of this study was to characterize mobility quality by examining associations between specific mobility scores, claw disorders (both the type and severity), body condition score (BCS), and cow parity. Data were collected for 6,927 cows from 52 pasture-based dairy herds, including mobility score (0 = optimal mobility; 1, 2, or 3 = increasing severities of suboptimal mobility), claw disorder type and severity, BCS, and cow parity. Multinomial logistic regression was used for analysis. The outcome variable was mobility score, and the predictor variables were BCS, type and severity of claw disorders, and cow parity. Three models were run, each with 1 reference category (mobility score 0, 1, or 2). Each model also included claw disorders (overgrown claw, sole hemorrhage, white line disease, sole ulcer, and digital dermatitis), BCS, and cow parity as predictor variables. The presence of most types of claw disorders had odds ratios >1, indicating an increased likelihood of a cow having suboptimal mobility. Low BCS (BCS <3.00) was associated with an increased risk of a cow having suboptimal mobility, and relatively higher parity was also associated with an increased risk of suboptimal mobility. These results confirm an association between claw disorders, BCS, cow parity, and dairy cow mobility score. Therefore, mobility score should be routinely practiced to identify cows with slight deviations from the optimal mobility pattern and to take preventive measures to keep the problem from worsening.
  • An index framework founded on the future profit potential of female beef cattle to aid the identification of candidates for culling

    Dunne, Fíona L; Berry, Donagh; Kelleher, Margaret M; Evans, Ross D; Walsh, Siobhan W; Amer, Peter R; Science Foundation Ireland; Department of Agriculture, Food and the Marine; European Union; 16/RC/3835; et al. (Oxford University Press (OUP), 2020-10-13)
    Meticulous culling decisions, coupled with careful breeding decisions, are fundamental to shifting a population distribution in the favorable direction and improving profit per cow. Nevertheless, there is a paucity of easy-to-use dynamic tools to aid in culling decisions in beef cattle. The motivation for the present study was to develop a monetary-based culling tool, here referred to as the Beef Female’s Profit Potential (BFPP), to identify females for culling. The BFPP reflects the expected lifetime profitability of an individual female in a herd for the expected remainder of her lifetime; this profit included that of the beef female herself as well as her progeny. The BFPP index framework was composed of 4 subindexes reflecting the value of an animal: (1) as a nulliparae (this was voided if the cow had already calved), (2) for the remainder of her current parity, (3) summed across each of her expected remaining parities, and (4) when she is retained within the herd and not voluntarily culled. Each subindex was comprised of different components reflecting both genetic and non-genetic effects associated with each female. Transition matrices predicting the expected longevity of each female and their expected month of calving were also utilized in calculating the expected remaining lifetime profitability of each female. The BFPP index was validated on 21,102 beef cows as well as their harvested progeny from 875 herds by stratifying the cows, within herd, into 4 strata based on their BFPP. The mean of the within-herd correlation between the BFPP and the Irish national replacement (i.e., breeding) index was, on average, 0.45 indicating the shortcomings of the breeding index as a culling tool. Cows within the top BFPP stratum had a genetic expectation of accruing almost an additional €36 profit per calving, relative to cows within the worst stratum; when validated on the cow’s own calving interval and survival performance as well as their progeny’s carcass performance, the actual phenotypic value was estimated to be an additional €32 profit per calving. A proportion of this additional profit was due to the harvested progeny of the high BFPP cows having, on average, heavier, more conformed carcasses with less fat cover relative to their poor BFPP contemporaries. This BFPP framework is a useful and easy-to-use tool to aid in producer decision making on the choice of females to voluntarily cull but also on which replacement heifers to graduate into the mature herd.
  • 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; MultiRepro; et al. (Elsevier BV, 2021-02)
    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 fromthe 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 liveweight 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.
  • Mycobacterium avium subspecies paratuberculosis infection in cattle – a review in the context of seasonal pasture-based dairy herds

    Field, Niamh L.; McAloon, Conor G.; Gavey, Lawrence; Mee, John F; Teagasc (Biomed Central, 2022-05-20)
    Johne’s disease is an infectious disease affecting cattle, other ruminants and non-ruminant wildlife worldwide, caused by Mycobacterium avium subspecies paratuberculosis (MAP). This review provides an up-to-date concise overview of the pathogenesis of MAP, the significance of Johne’s disease in cattle and the use of diagnostic testing at both animal and herd level in the context of seasonal pasture-based herds. While MAP can only replicate intracellularly, the bacterium is sufficiently robust to survive for months in the environment. Transmission of MAP is mostly via the faecal-oral route, however in-utero transmission in also possible. The bacteria evade the immune system by persisting in macrophages in the small intestine submucosa, with this latent stage of infection lasting, in most cases, for at least two years before bacterial shedding and clinical signs begin. The slowly progressive nature of MAP infection, poor performance of diagnostic tests and management systems that expose susceptible calves to infection make control of Johne’s disease challenging, particularly in seasonal calving herds. Testing of individual animals provides little assurance for farmers and vets due to the poor sensitivity and, in the case of ELISA, imperfect specificity of the available tests. Repeated herd-level testing is utilised by the IJCP to detect infected herds, identify high risk animals, and provide increasing confidence that test-negative herds are free of infection. The IJCP aims to control the spread of Johne’s disease in cattle in Ireland, in order to protect non-infected herds, limit the economic and animal health impact of the disease, improve calf health and reassure markets of Johne’s disease control in Ireland.
  • 28. The effect of phenotypically ranking beef cattle for residual methane output on daily methane emissions, intensity and animal productivity

    Smith, Paul E.; Waters, Sinéad M.; Kenny, David A.; Kirwan, Stuart F.; Conroy, Stephen; Kelly, Alan K.; European Union; 16/RD/ERAGAS/1RUMENPREDICT-ROI2017; 818368 (Elsevier BV, 2021-04)
    Beef cattle ranked as having low residual methane output had lower emissions intensity and similar overall productive performance as their high emissions ranking contemporaries. The concept of residual methane output is proposed as an appropriate trait to more equitably identify animals on the basis of low emissions beef production
  • Irish research response to dairy quality in an era of change

    O'Brien, Bernadette J.; Beresford, Tom; Cotter, Paul D.; Gleeson, D.; Kelly, A.; Kilcawley, Kieran; Magan, J.; McParland, Sinead; Murphy, E.; O’Callaghan, Tom; et al. (Teagasc, 2022-02-26)
    The Irish dairy sector is recognised for its very significant contribution to the national economic status; it is now worth ∼€5 billion annually and represents the largest food and drink export category, which, in turn, represents one of the four largest manufacturing industries in the country. Given anticipated further growth in global demand for dairy products and the positive attributes and capabilities that Ireland has to meet that demand, in terms of pasture-based production and cost competitiveness, it is incumbent for the sector to attain the highest quality milk and dairy products. The combined collaborative approach between research and industry has ensured significant progress and enabled Ireland to remain at the forefront globally in terms of production of quality milk and dairy products. This paper highlights some specific scientific platforms and technologies currently shaping the industry in this regard and discusses current research activity as well as anticipating key requirements for future progress. While research, and farm and processing plant management have accomplished very significant advances in milk and dairy product quality, some overarching emerging challenges include product substitution and sustainability. Some key pillars for the future have been identified on which a strong, efficient dairy sector can be maintained and progressed. Specifically, the use of evidence-based information and real-time measures in prediction and decision-making will be a crucial pillar for the dairy sector of the future. This can promote an approach of proactive maintenance and optimisation of production through improved predictability and control of manufacturing processes.
  • Animal welfare research – progress to date and future prospects

    Boyle, Laura A; Conneely, M.; Kennedy, Emer; O’Connell, N.; O'Driscoll, Keelin; Earley, Bernadette (Teagasc, 2022-02-26)
    RECORDABSTRACTARTICLE Animal welfare research – progress to date and future prospects OTHER Author(s): L. Boyle 1 , M. Conneely 1 , E. Kennedy 1 , N. O’Connell 2 , K. O’Driscoll 1 , B. Earley 3 , Publication date (Electronic): 26 February 2022 Journal: Irish Journal of Agricultural and Food Research Publisher: Compuscript Keywords: Animal welfare, beef, dairy, pig, poultry, welfare assessment Abstract The welfare status of an animal is dependent on its ability to cope and exist in harmony with its environment, such that good physical and psychological health is maintained. Improving animal welfare is an increasingly important aspect of livestock production systems due, in a large extent, to increased consumer concerns about animal production practices. Animal welfare is an integrated part of quality assurance programmes for sustainable animal production, considering that welfare, health, management, economy, consumer acceptance and environmental impact are interdependent. The major welfare concerns in the livestock industry in recent years relate to the rearing and management of dairy calves, the welfare of the dairy cow, effect of husbandry management procedures on the welfare of beef cattle, rearing of sows in gestation and farrowing crates, and the broiler (meat) chicken sector. The paper will focus on scientific research underpinning these welfare concerns, with a particular focus on research conducted on the island of Ireland.
  • The development of effective ruminant breeding programmes in Ireland from science to practice

    Berry, Donagh; Dunne, F.L.; McHugh, Noirin; McParland, Sinead; O’Brien, A.C.; Twomey, A.J. (Teagasc, 2022-02-25)
    A genetic improvement programme is a sustainable, cumulative and permanent approach to achieving year-on-year performance gains. Its success is predicated not only on an efficient and effective breeding programme but also on a vision of the traits of importance in the future. A single, industry-owned, centralised database for cattle and sheep has been the foundation for genetic improvement programmes in Ireland. While DNA information has been heralded as a breakthrough for accelerating genetic gain, the basic principles of a successful animal breeding programme still remain the same: (1) a pertinent breeding goal, (2) the appropriate breeding objective to deliver on the breeding goal, (3) an accurate genetic evaluation system, (4) an efficient and effective breeding scheme, and (5) a system to disseminate the elite germplasm to the end user; also of importance is a system for validating the underlying procedures and principles. The constituent traits and their relative emphasis within breeding objectives will continue to be contentious. Traits that will need to be considered more in future ruminant breeding objectives include environmental impact, product quality and animal well-being, including health; while not always explicitly included in Irish breeding objectives for cattle and sheep, indirect improvements for many are expected via the genetic improvement in traits like reproductive performance and survival as well as macro measures of quality such as milk fat and protein concentration and carcass merit. Crucial for the future sustainability of ruminant production systems is the co-evolution of management systems and breeding programmes so that the animal of the future is suited to the most sustainably efficient production system.
  • Dietary supplementation with fish oil and safflower oil, during the finishing period, alters brisket muscle fatty acid profile and n-6/n-3 ratio but not carcass traits of dairy beef bulls

    Byrne, C. J.; Fair, S.; Dick, J. R.; Lonergan, P.; Kenny, David A.; Department of Agriculture, Food and the Marine; 11/S/116 (American Registry of Professional Animal Scientists, 2021-08)
    Objective: With increases in the global population, there is a need to identify strategies that increase beef output while maintaining or improving health benefits of beef products. Studies have demonstrated that there are many benefits to human health in response to reducing the dietary n-6 to n-3 ratio. The aim of this study was to characterize the carcass characteristics and brisket muscle fatty acid profile of young dairy bred bulls following dietary supplementation with n-6 or n-3 polyunsaturated fatty acids (PUFA). Material and Methods: Holstein-Friesian (n = 43) and Jersey (n = 7) bulls with a mean ± s.e.m. age and bodyweight of 420.1 ± 5.86 days and 382.0 ± 8.94 kg, respectively, were offered a cereal based concentrate diet on an ad libitum basis, fortified with one of three lipid supplements: control (CTL; no supplementary lipid), n-6 PUFA safflower (SO), or n-3 PUFA enriched fish oil (FO). Bulls were individually offered their respective diet for 12 weeks prior to slaughter. Carcass weight, conformation and fat score were recorded at slaughter for all animals, while brisket muscle was collected from 26 randomly selected bulls and lipid profile analysed using GC. Results and Discussion: Total n-3 PUFA concentration was greater for FO than either SO or CTL diets (P < 0.05). Although there was no difference in the muscle total n-6 concentration between diets (P = 0.52), n-6 to n-3 ratio was 3.2 and 3.9 times lower for FO (P < 0.001) than either CTL or SO diets, respectively. Total intake of n-3 PUFA accounted for 72% of the variation in the n-6 to n-3 ratio. Despite the differences in fatty acid profiles, there was no effect of dietary lipid supplementation on carcass weight (P = 0.63), conformation (P = 0.79), or fat score (P = 0.84. Implications and Applications: Beef producers can feed n-6 and/or n-3 PUFA enriched diets that would result in beef having potential health benefits and greater branding potential.
  • Performance of lactating suckler cows of diverse genetic merit and genotype under a seasonal pasture-based system

    McCabe, S.; McHugh, Noirin; O'Connell, N. E.; Prendiville, Robert (Teagasc, 2021-12-21)
    The objective of this study was to investigate the effect of genetic merit of the national Irish maternal index and genotype (i.e. beef vs. beef × dairy [BDX]) of beef cows and subsequent performance of their progeny. With the exception that high genetic merit cows produced 0.57 kg more milk and tended to have 0.04 of a lower body condition score (BCS), no significant differences were observed between cows of diverse genetic merit. Differences between contrasting cow genotype were apparent. Beef cows were 50 kg heavier and had a BCS 0.27 greater than BDX cows. The BDX cows produced 1.67 kg more milk and had a greater 24-d submission rate than beef cows. Calves generated from BDX cows were 19 kg heavier at weaning and were worth €51 more than progeny generated from beef cows. Beef cow progeny, however, had 0.77 of a greater conformation score at slaughter than BDX. While differences were observed across cows of different replacement strategies, results from the current study showed that genetic selection for national maternal index had no effect on the overall performance of suckler cows in a pasture-based spring-calving system.

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