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

  • Genetic variability in the feeding behavior of crossbred growing cattle and associations with performance and feed efficiency

    Kelly, David N; Sleator, Roy D; Murphy, Craig P; Conroy, Stephen B; Berry, Donagh P; Department of Agriculture, Food and the Marine Ireland; 17/S/235 (GreenBreed) (Oxford University Press (OUP), 2021-10-21)
    The objectives of the present study were to estimate genetic parameters for several feeding behavior traits in growing cattle, as well as the genetic associations among and between feeding behavior and both performance and feed efficiency traits. An additional objective was to investigate the use of feeding behavior traits as predictors of genetic merit for feed intake. Feed intake and live-weight data on 6,088 growing cattle were used of which 4,672 had ultrasound data and 1,548 had feeding behavior data. Feeding behavior traits were defined based on individual feed events or meal events (where individual feed events were grouped into meals). Univariate and bivariate animal linear mixed models were used to estimate (co)variance components. Heritability estimates (± SE) for the feeding behavior traits ranged from 0.19 ± 0.08 for meals per day to 0.61 ± 0.10 for feeding time per day. The coefficient of genetic variation per trait varied from 5% for meals per day to 22% for the duration of each feed event. Genetically heavier cattle, those with a higher daily energy intake (MEI), or those that grew faster had a faster feeding rate, as well as a greater energy intake per feed event and per meal. Better daily feed efficiency (i.e., lower residual energy intake) was genetically associated with both a shorter feeding time per day and shorter meal time per day. In a validation population of 321 steers and heifers, the ability of estimated breeding values (EBV) for MEI to predict (adjusted) phenotypic MEI was demonstrated; EBVs for MEI were estimated using multi-trait models with different sets of predictor traits such as liveweight and/or feeding behaviors. The correlation (± SE) between phenotypic MEI and EBV for MEI marginally improved (P < 0.001) from 0.64 ± 0.03 to 0.68 ± 0.03 when feeding behavior phenotypes from the validation population were included in a genetic evaluation that already included phenotypic mid-test metabolic live-weight from the validation population. This is one of the largest studies demonstrating that significant exploitable genetic variation exists in the feeding behavior of young crossbred growing cattle; such feeding behavior traits are also genetically correlated with several performance and feed efficiency metrics. Nonetheless, there was only a marginal benefit to the inclusion of time-related feeding behavior phenotypes in a genetic evaluation for MEI to improve the precision of the EBVs for this trait.
  • The influence of animal species, gender and tissue on the structural, biophysical, biochemical and biological properties of collagen sponges

    Sorushanova, Anna; Skoufos, Ioannis; Tzora, Athina; Mullen, Anne Maria; Zeugolis, Dimitrios I.; Teagasc Walsh Fellowship; Teagasc/Department of Agriculture, Food and the Marine; Science Foundation Ireland; European Research Council; 2014045; et al. (Springer Science and Business Media LLC, 2021-01-21)
    Although collagen type I is extensively used in biomedicine, no study to-date has assessed how the properties of the produced scaffolds are affected as a function of species, gender and tissue from which the collagen was extracted. Herein, we extracted and characterised collagen from porcine and bovine, male and female and skin and tendon tissues and we subsequently fabricated and assessed the structural, biophysical, biochemical and biological properties of collagen sponges. All collagen preparations were of similar purity and free-amine content (p > 0.05). In general, the porcine groups yielded more collagen; had higher (p < 0.05) denaturation temperature and resistance to enzymatic degradation; and lower (p < 0.05) swelling ratio and compression stress and modulus than the bovine groups of the same gender and tissue. All collagen preparations supported growth of human dermal fibroblasts and exhibited similar biological response to human THP-1 monocytes. These results further illustrate the need for standardisation of collagen preparations for the development of reproducible collagen-based devices.
  • Sire contribution to fertilization failure and early embryo survival in cattle

    O'Callaghan, E.; Sánchez, J.M.; McDonald, M.; Kelly, A.K.; Hamdi, M.; Maicas, C.; Fair, S.; Kenny, D.A.; Lonergan, P.; Science Foundation Ireland; et al. (American Dairy Science Association, 2021-06)
    Despite passing routine laboratory tests of semen quality, bulls used in artificial insemination (AI) exhibit a significant range in field fertility. The objective of this study was to determine whether subfertility in AI bulls is due to issues of sperm transport to the site of fertilization, fertilization failure, or failure of early embryo or conceptus development. In experiment 1, Holstein-Friesian bulls (3 high fertility, HF, and 3 low fertility, LF) were selected from the national population of AI bulls based on adjusted fertility scores from a minimum of 500 inseminations (HF: +4.37% and LF: −12.7%; mean = 0%). Superovulated beef heifers were blocked based on estimated number of follicles at the time of AI and inseminated with semen from HF or LF bulls (n = 3–4 heifers per bull; total 19 heifers). Following slaughter 7 d later, the number of corpora lutea was counted and the uteri were flushed. Recovered structures (oocytes/embryos) were classified according to developmental stage and stained with 4′,6-diamidino-2-phenylindole to assess number of cells and accessory sperm. Overall recovery rate (total structures recovered/total corpora lutea) was 52.6% and was not different between groups. Mean (± standard error of the mean) number of embryos recovered per recipient was 8.7 ± 5.2 and 9.4 ± 5.5 for HF and LF, respectively. Overall fertilization rate of recovered structures was not different between groups. However, more embryos were at advanced stages of development (all blastocyst stages combined), reflected in a greater mean embryo cell number on d 7 for HF versus LF bulls. Number of accessory sperm was greater for embryos derived from HF than for LF bulls. The aim of experiment 2 was to evaluate the effect of sire fertility on survival of bovine embryos to d 15. Day 7 blastocysts were produced in vitro using semen from the same HF (n = 3) and LF (n = 3) bulls and transferred in groups of 5–10 to synchronized heifers (n = 7 heifers per bull; total 42 heifers). Conceptus recovery rate on d 15 was higher in HF (59.4%,) versus LF (45.0%). Mean length of recovered conceptuses for HF bulls was not affected by fertility status. In conclusion, while differences in field fertility among AI sires used in this study were not reflected in fertilization rate, differences in embryo quality were apparent as early as d 7. These differences likely contributed to the higher proportion of conceptuses surviving to d 15 in HF bulls.
  • Early life nutrition affects the molecular ontogeny of testicular development in the young bull calf

    Coen, Stephen; Keogh, Kate; Lonergan, Patrick; Fair, Sean; Kenny, David (Research Square Platform LLC, 2022-05-25)
    Enhanced early life nutrition accelerates sexual development in the bull calf through neuroendocrine-signalling mediated via the hypothalamic-pituitary-testicular axis. Our aim was to assess the impact of contrasting feeding regimes in bull calves during the first 12 weeks of life on the testes transcriptome and proteome. Holstein-Friesian bull calves were offered either a high (HI) or moderate (MOD) plane of nutrition, designed to support target growth rates of 1.0 and 0.5 kg/day, respectively. At 12 weeks of age all calves were euthanized, testicular parenchyma sampled, and global transcriptome (miRNAseq and mRNAseq) and proteome analyses undertaken. Bioinformatic analyses revealed 7 differentially expressed (DE) miRNA and 20 DE mRNA. There were no differentially abundant proteins between the two dietary groups. Integration of omics results highlighted a potential role for the cadherin gene, CDH13, in earlier reproductive development. Furthermore, co-regulatory network analysis of the proteomic data revealed CDH13 as a hub protein within a network enriched for processes related to insulin, IGF-1, androgen and Sertoli cell junction signalling pathways as well as cholesterol biosynthesis. Overall, results highlight a potential role for CDH13 in mediating earlier reproductive development as a consequence of enhanced early life nutrition in the bull calf.
  • An association analysis of sow parity, live-weight and back-fat depth as indicators of sow productivity

    Lavery, A.; Lawlor, P.G.; Magowan, E.; Miller, H.M.; O’Driscoll, K.; Berry, D.P.; Department of Agriculture, Food and the Marine, Ireland; University of Leeds (Elsevier BV, 2019)
    Understanding how critical sow live-weight and back-fat depth during gestation are in ensuring optimum sow productivity is important. The objective of this study was to quantify the association between sow parity, live-weight and back-fat depth during gestation with subsequent sow reproductive performance. Records of 1058 sows and 13 827 piglets from 10 trials on two research farms between the years 2005 and 2015 were analysed. Sows ranged from parity 1 to 6 with the number of sows per parity distributed as follows: 232, 277, 180, 131, 132 and 106, respectively. Variables that were analysed included total born (TB), born alive (BA), piglet birth weight (BtWT), pre-weaning mortality (PWM), piglet wean weight (WnWT), number of piglets weaned (Wn), wean to service interval (WSI), piglets born alive in subsequent farrowing and sow lactation feed intake. Calculated variables included the within-litter CV in birth weight (LtV), pre-weaning growth rate per litter (PWG), total litter gain (TLG), lactation efficiency and litter size reared after cross-fostering. Data were analysed using linear mixed models accounting for covariance among records. Third and fourth parity sows had more (P<0.05) TB, BA and heavier BtWT compared with gilts and parity 6 sow contemporaries. Parities 2 and 3 sows weaned more (P<0.05) piglets than older sows. These piglets had heavier (P<0.05) birth weights than those from gilt litters. LtV and PWM were greater (P<0.01) in litters born to parity 5 sows than those born to younger sows. Sow live-weight and back-fat depth at service, days 25 and 50 of gestation were not associated with TB, BA, BtWT, LtV, PWG, WnWT or lactation efficiency (P>0.05). Heavier sow live-weight throughout gestation was associated with an increase in PWM (P<0.01) and reduced Wn and lactation feed intake (P<0.05). Deeper back-fat in late gestation was associated with fewer (P<0.05) BA but heavier (P<0.05) BtWT, whereas deeper back-fat depth throughout gestation was associated with reduced (P<0.01) lactation feed intake. Sow back-fat depth was not associated with LtV, PWG, TLG, WSI or piglets born alive in subsequent farrowing (P>0.05). In conclusion, this study showed that sow parity, live-weight and back-fat depth can be used as indicators of reproductive performance. In addition, this study also provides validation for future development of a benchmarking tool to monitor and improve the productivity of modern sow herd.
  • Hoof lesions in partly housed pasture-based dairy cows

    Browne, N.; Hudson, C.D.; Crossley, R.E.; Sugrue, K.; Huxley, J.N.; Conneely, M.; Dairy Research Ireland; Teagasc Walsh Scholarship (Elsevier, 2022-09-27)
    Lameness is a symptom of a painful disorder affecting the limbs, which impacts dairy cow welfare and productivity. Lameness is primarily caused by hoof lesions. The prevalence of different lesion types can differ depending on environmental conditions and farm management practices. The aims of this observational study were to establish the cow-level and herd-level lesion prevalence during both housing and grazing periods in a partly housed, pasture-based system, establish the prevalence of lesions always associated with pain (“alarm” lesion), identify the lesions associated with a higher lameness score, determine relationships between lesions, and identify risk factors for digital dermatitis. On 98 farms during the grazing period and on 74 of the same farms during the housing period, every cow was lameness scored (0–3 lameness scoring scale), and the hind hooves of lame cows (score 2 and 3) were examined (maximum 20 cows per visit) and the prevalence of each lesion type recorded. To gather data on potential predictors for the risk factor analysis, a questionnaire with the farmer was conducted on lameness management practices and infrastructure measurements were taken at each visit. Cow-level data were also collected (e.g., parity, breed, milk yield, and so on). Noninfectious lesions were found to be more prevalent than infectious lesions in this system type. The most prevalent lesion types during both grazing and housing periods were white line separation, sole hemorrhages and overgrown claws; all remaining lesions had a cow-level prevalence of less than 15%. The cow-level prevalence of alarm lesions was 19% during the grazing period and 25% during the housing period; the most prevalent alarm lesion was sole ulcers during both periods. We found significantly more foreign bodies within the hoof sole (grazing = 14%, housing = 7%) and overgrown claws (grazing = 71%, housing = 55%) during the grazing period compared with the housing period. Cows with foul of the foot, sole ulcer, white line abscess, toe necrosis or an amputated claw had higher odds of being more severely lame, compared with mildly lame. The strongest correlation between lesions were between toe necrosis and digital dermatitis (r = 0.40), overgrown claws and corkscrew claws (r = 0.33), and interdigital hyperplasia and digital dermatitis (r = 0.31) at herd level. At the cow level, the strongest correlation was between overgrown claws and corkscrew claws (r = 0.27), and digital dermatitis and heel erosion (r = 0.22). The farmers' perception of the presence of digital dermatitis (and lameness) was significantly correlated with the actual presence of digital dermatitis recorded. Additional risk factors for the presence of digital dermatitis were cow track and verge width near the collecting yard, and stone presence on the cow tracks. Results from this study help further our understanding of the causes of lameness in partly housed, pasture-based dairy cows, and can be used to guide prevention and treatment protocols.
  • Detection of Genomic Imprinting for Carcass Traits in Cattle Using Imputed High-Density Genotype Data.

    Kenny, David; Sleator, Roy D; Murphy, Craig P; Evans, Ross D; Berry, Donagh P; Department of Agriculture, Food and the Marine; Science Foundation Ireland; RSF 17/S/235; 16/RC/3835; VistaMilk (Frontiers, 2022-07-15)
    Genomic imprinting is an epigenetic phenomenon defined as the silencing of an allele, at least partially, at a given locus based on the sex of the transmitting parent. The objective of the present study was to detect the presence of SNP-phenotype imprinting associations for carcass weight (CW), carcass conformation (CC) and carcass fat (CF) in cattle. The data used comprised carcass data, along with imputed, high-density genotype data on 618,837 single nucleotide polymorphisms (SNPs) from 23,687 cattle; all animal genotypes were phased with respect to parent of origin. Based on the phased genotypes and a series of single-locus linear models, 24, 339, and 316 SNPs demonstrated imprinting associations with CW, CC, and CF, respectively. Regardless of the trait in question, no known imprinted gene was located within 0.5 Mb of the SNPs demonstrating imprinting associations in the present study. Since all imprinting associations detected herein were at novel loci, further investigation of these regions may be warranted. Nonetheless, knowledge of these associations might be useful for improving the accuracy of genomic evaluations for these traits, as well as mate allocations systems to exploit the effects of genomic imprinting.
  • Validation of maternal and terminal sheep breeding objectives using Irish field data

    McHugh, Noirin; McDermott, Kevin; Bohan, Alan; Farrell, Lydia J; Herron, Jonathan; Pabiou, Thierry; Irish Department of Agriculture, Food and Marine; GREENBREED (17/S/235); ERA-GAS (2019EN202; GrassToGas) (Oxford University Press (OUP), 2022-07-23)
    Genetic evaluations provide producers with a tool to aid in breeding decisions and highlight the increase in performance achievable at the farm level through genetic gain. Despite this, large-scale validation of sheep breeding objectives using field data is lacking in the scientific literature. The objective of the present study was to evaluate the phenotypic differences for a range of economically important traits for animals divergent in genetic merit for the Irish national maternal and terminal sheep breeding objectives. A dataset of 17,356 crossbred ewes and 54,322 progeny differing in their maternal and terminal breeding index recorded in 139 commercial flocks was available. The association of the maternal index of the ewe or terminal index of the ram and a range of phenotypic performance traits, including lambing, lamb performance, ewe performance, and health traits, were undertaken. Ewes excelling on the maternal index had higher litter sizes and produced progeny with greater perinatal lamb survival, heavier live weights from birth to postweaning and reduced days to slaughter (P < 0.05). Ewe maternal index had no quantifiable impact on lambing ease, carcass conformation, or fat, the health status of the ewe or lamb, ewe barren rate, or ewe live weight. Lambs born to rams of superior terminal index produced heavier lambs from preweaning onwards, with a reduced day to slaughter (P < 0.05). Lambing traits, lamb health, and carcass characteristics of the progeny did not differ between sires stratified as low or high on the terminal index (P > 0.05). Results from this study highlight that selecting either ewes or rams of superior maternal or terminal attributes will result in an improvement on pertinent performance traits of the national sheep flock, resulting in greater flock productivity and profitability.
  • Bio-economic modelling of sheep meat production systems with varying flock litter size using field data

    Farrell, L.; Creighton, P.; Bohan, A.; McGovern, F.; McHugh, N.; Irish Department of Agriculture, Food and Marine; European Union ERA-GAS; 16/S/696 Multipro; 2019EN202; GrassToGas (Elsevier, 2022-10-31)
    Sheep meat producers derive the majority of income from sales of weaned lambs, determined by flock conception rates, litter size, and lamb survival. Field data from commercial flocks can inform sensitivity analyses of the effect of litter size on flock productivity, feed demand, and gross margin. This study adapted an established bio-economic model of a flock of breeding ewes informed by statistical relationships (from linear models) between flock litter size (lambs born per ewe lambing) and production factors (such as flock barren rate, litter birth type and lamb birth weight) identified using 156 145 animal records from the Irish national sheep breeding database. Sensitivity analyses were undertaken to investigate the effects of flock litter size on flock production, feed demand, and gross margin. Results showed that as flock litter size increased, the proportion of lambs born as multiples increased, with 14 % of lambs born as singles when flock litter size was 2.2 lambs born per ewe lambing. Flock gross margin increased from €2 205 to €7 730 as litter size increased from 1.0 to 2.0 lambs born per ewe lambing. As litter size increased from 1.0 to 2.2 lambs born per ewe lambing, flock gross margin increased linearly by, on average, €52 per 0.01 increase in litter size. At a litter size of > 2.2 lambs born per ewe lambing, flock gross margin increased on average €12 per 0.01 increase in litter size. At a litter size of 2.2 lambs born per ewe lambing, flock efficiency (at 65.0 kg of lamb weaned per ewe presented for breeding), weaning rate (at 1.5 lambs weaned per ewe presented for breeding; not including excess lambs from large litters sold within a week after birth and thus not weaned on-farm), and gross margin (at €8 500) began to plateau. The results indicate lower marginal returns in gross margin at very high flock litter size, due to the lower value of additional lambs born as triplets and quadruplets compared with single- and twin-born lambs. However, the diminishing economic returns occurred at higher flock litter size than are currently biologically achieved in most flocks. Quantification from this analysis demonstrates how the value of increasing the number of lambs born changes at very high flock litter size, which can inform the priorities and performance benchmarking for international sheep meat production industries.
  • Phenotypic factors associated with lamb live weight and carcass composition measurements in an Irish multi-breed sheep population

    McGovern, Fiona Mary; McHugh, Noirin; Fitzmaurice, Shauna; Pabiou, Thierry; McDermott, Kevin; Wall, Eamon; Fetherstone, Nicola; Irish Department of Agriculture, Food and the Marine; MULTIREPRO (16/S/696); GREENBREED (17/S/235) (Oxford University Press (OUP), 2020-11-14)
    Understanding the phenotypic factors that affect lamb live weight and carcass composition is imperative to generating accurate genetic evaluations and further enables implementation of functional management strategies. This study investigated phenotypic factors affecting live weight across the growing season and traits associated with carcass composition in lambs from a multibreed sheep population. Four live weight traits and two carcass composition traits were considered for analysis namely; birth, preweaning, weaning, and postweaning weight, and ultrasound muscle depth and fat depth. A total of 427,927 records from 159,492 lambs collected from 775 flocks between the years 2016 and 2019, inclusive were available from the Irish national sheep database. Factors associated with live weight and carcass composition were determined using linear mixed models. The heaviest birth, preweaning, and weaning weights were associated with single born lambs (P < 0.001), however by postweaning, there was no difference observed in the weights of single and twin born lambs (P > 0.01). Breed class affected lamb live weight and carcass composition with terminal lambs weighing heaviest and having greater muscle depth than all other breed classes investigated (P < 0.001). Lambs born to first parity dams were consistently lighter, regardless of time of weighing (P < 0.001), while dams lambing for the first time as ewe lambs produced lighter lambs than those lambing for the first time as hoggets (P < 0.001). Greater heterosis coefficients (i.e., >90% and ≤100%) resulted in heavier lambs at weaning compared with lambs with lower levels of heterosis coefficients (P < 0.001). A heterosis coefficient class <10% resulted in lambs with greater muscle depth while recombination loss of <10% increased ultrasound fat depth (P < 0.001). Results from this study highlight the impact of multiple animal level factors on lamb live weight and carcass composition which will enable more accurate bio-economic models and genetic evaluations going forward.
  • Commercial beef farms excelling in terminal and maternal genetic merit generate more gross profit

    Kelly, David N; Connolly, K; Kelly, P; Cromie, A R; Murphy, C P; Sleator, R D; Berry, D P; Department of Agriculture, Food and the Marine Ireland; 17/s/235 (GreenBreed) (Oxford University Press (OUP), 2021-06-09)
    Validation of beef total merit breeding indexes for improving performance and profitability has previously been undertaken at the individual animal level; however, no herd-level validation of beef genetic merit and profit has been previously investigated. The objective of the present study was to quantify the relationship between herd profitability and both herd-average terminal and maternal genetic merit across 1,311 commercial Irish beef herds. Herd-level physical and financial performance data were available from a financial benchmarking tool used by Irish farmers and their extension advisors. Animal genetic merit data originated from the Irish Cattle Breeding Federation who undertake the national beef and dairy genetic evaluations. Herd-average genetic merit variables included the terminal index of young animals, the maternal index of dams, and the terminal index of service sires. The herds represented three production systems: 1) cow-calf to beef, 2) cow-calf to weanling/yearling, and 3) weanling/yearling to beef. Associations between herd financial performance metrics and herd average genetic merit variables were quantified using a series of linear mixed models with year, production system, herd size, stocking rate, concentrate input, and the two-way interactions between production system and herd size, stocking rate, and concentrate input included as nuisance factors. Herd nested within the county of Ireland (n = 26) was included as a repeated effect. Herds with young cattle excelling in terminal index enjoyed greater gross and net profit per hectare (ha), per livestock unit (LU), and per kg net live-weight output. The change in gross profit per LU per unit change in the terminal index of young animals was €1.41 (SE = 0.23), while the respective regression coefficient for net profit per LU was €1.37 (SE = 0.30); the standard deviation of the terminal index is €37. Herd-average dam maternal index and sire terminal index were both independently positively associated with gross profit per ha and gross profit per LU. Each one unit increase in dam maternal index (standard deviation of €38) was associated with a €1.40 (SE = 0.48) and €0.76 (SE = 0.29) greater gross profit per ha and per LU, respectively. Results from the present study at the herd-level concur with previous validation studies at the individual animal level thus instilling further confidence among stakeholders as to the expected improvement in herd profitability with improving genetic merit.
  • Evaluation of partial body weight for predicting body weight and average daily gain in growing beef cattle

    MacNeil, Michael D; Berry, Donagh P; Clark, Sam A; Crowley, John J; Scholtz, Michiel M; Vytelle LLC, a Wheatsheaf Group company (Oxford University Press (OUP), 2021-07-22)
    Information on body weight and average daily gain (ADG) of growing animals is key not only to monitoring performance, but also for use in genetic evaluations in the pursuit of achieving sustainable genetic gain. Accurate calculation of ADG, however, requires serial measures of body weight over at least 70 days. This can be resource intensive and thus alternative approaches to predicting individual animal ADG warrant investigation. One such approach is the use of continuously collected individual animal partial body weights. The objective of the present study was to determine the utility of partial body weights in predicting both body weight and ADG; a secondary objective was to deduce the appropriate length of test to determine ADG from partial body weight records. The dataset used consisted of partial body weights, predicted body weights and recorded body weights recorded for 8,972 growing cattle from a range of different breed types in 35 contemporary groups. The relationships among partial body weight, predicted body weight and recorded body weight at the beginning and end of the performance test were determined and calculated ADG per animal from each body weight measure were also compared. On average, partial body weight explained 90.7 ± 2.0% of the variation in recorded body weight at the beginning of the postweaning gain test and 87.9 ± 2.9% of the variation in recorded body weight at its end. The GrowSafe proprietary algorithm to predict body weight from the partial body weight strengthened these coefficients of determination to 95.1 ± 0.9% and 94.9 ± 0.8%, respectively. The ADG calculated from the partial body weight or from the predicted body weight were very strongly correlated (r = 0.95); correlations between these ADG values with those calculated from the recorded body weights were weaker at 0.81 and 0.78, respectively. For some applications, ADG may be measured with sufficient accuracy with a test period of 50 days using partial body weights. The intended inference space is to individual trials which have been represented in this study by contemporary groups of growing cattle from different genotypes.
  • Development of a syndromic surveillance system for Irish dairy cattle using milk recording data

    Douglass, Alexander P.; O'Grady, Luke; McGrath, Guy; Tratalos, Jamie; Mee, John F.; Barrett, Damien; Sánchez-Miguel, Cosme; More, Simon J.; Madouasse, Aurélien; Green, Martin; et al. (Elsevier, 2022-07-31)
    In the last decade and a half, emerging vector-borne diseases have become a substantial threat to cattle across Europe. To mitigate the impact of the emergence of new diseases, outbreaks must be detected early. However, the clinical signs associated with many diseases may be nonspecific. Furthermore, there is often a delay in the development of new diagnostic tests for novel pathogens which limits the ability to detect emerging disease in the initial stages. Syndromic Surveillance has been proposed as an additional surveillance method that could augment traditional methods by detecting aberrations in non-specific disease indicators. The aim of this study was to develop a syndromic surveillance system for Irish dairy herds based on routinely collected milk recording and meteorological data. We sought to determine whether the system would have detected the 2012 Schmallenberg virus (SBV) incursion into Ireland earlier than conventional surveillance methods. Using 7,743,138 milk recordings from 730,724 cows in 7037 herds between 2007 and 2012, linear mixed-effects models were developed to predict milk yield and alarms generated with temporally clustered deviations from predicted values. Additionally, hotspot spatial analyses were conducted at corresponding time points. Using a range of thresholds, our model generated alarms throughout September 2012, between 4 and 6 weeks prior to the first laboratory confirmation of SBV in Ireland. This system for monitoring milk yield represents both a potentially useful tool for early detection of disease, and a valuable foundation for developing similar tools using other metrics.
  • Localization of urea transporter B in the developing bovine rumen

    Zhong, Chongliang; Lyons, Tamsin; Heussaff, Orla; Doyle, Evelyn; O'Hara, Eoin; Waters, Sinead M.; Kenny, David; Stewart, Gavin S.; The China Scholarship Council; University College Dublin (Elsevier, 2022-09-30)
    Urea nitrogen secreted from blood to rumen is a crucial factor shaping the symbiotic relationship between host ruminants and their microbial populations. Passage of urea across rumen epithelia is facilitated by urea transporter B (UT-B), but the long-term regulation of these proteins remains unclear. As ruminal function develops over a period of months, the developing rumen is an excellent model with which to investigate this regulation. Using rumen epithelium samples of calves from birth to 96 d of age, this study performed immunolocalization studies to localize and semi-quantify UT-B protein development. As expected, preliminary experiments confirmed that ruminal monocarboxylate transporter 1 (MCT1) short chain fatty acid transporter protein abundance increased with age (P < 0.01, n = 4). Further investigation revealed that ruminal UT-B was present in the first few weeks of life and initially detected in the basolateral membrane of stratum basale cells. Over the next 2 months, UT-B staining spread to other epithelial layers and semi-quantification indicated that UT-B abundance significantly increased with age (P < 0.01, n = 4 or 6). These changes were in line with the development of rumen function after the advent of solid feed intake and weaning, exhibiting a similar pattern to both MCT1 transporters and papillae growth. This study therefore confirmed age-dependent changes of in situ ruminal UT-B protein, adding to our understanding of the long-term regulation of ruminal urea transporters.
  • Low-cost do-it-yourself (DIY) mannequin for blood collection: A comprehensive evaluation about its use in teaching

    Tvarijonaviciute, Asta; Carrillo-Sanchez, Juana D.; Rubio, Camila P.; Contreras-Aguilar, María D.; Muñoz-Prieto, Alberto; Pardo-Marin, Luis; Cerón, José J.; Franco-Martínez, Lorena; Martínez-Subiela, Silvia (Elsevier, 2022-11)
    The use of mannequins to practice different clinical procedures in undergraduate students complies with the 3R principle (Replacement, Reduction, Refinement) without affecting professional competencies. However, commercial solutions are often expensive and therefore, not available for many schools. The main aim of this study was to describe the development and validation of an economical Do-It-Yourself mannequin for jugular blood collection from dogs. The use of the mannequin was evaluated by (1) assessment of the opinion of students and experts and (2) by conducting a pilot study where salivary biomarkers of stress were determined in students and dogs. The costs of the materials needed for the mannequin confection were less than 60 Euros and it was easily built in less than 1 h. The mannequin was very well accepted and scored by both, students and experts, being mostly liked a lot and considered it to be very useful for the practices (Scored 8, 9 or 10/10). Students that could first practice with the mannequin reported a self-perceived higher level of confidence and had lower levels of alpha-amylase in saliva after the procedure. Overall, the mannequin enables the initiation of blood sampling skills in agreement with 3R principles and is easy to perform, economically affordable and sustainable. This model could be adapted to other vein simulations and animal species, and has the potential to help students deal with stressful situations such as taking blood samples from a live animal.
  • Gene co-expression networks contributing to reproductive development in Holstein-Friesian bull calves

    Keogh, K.; Kenny, D.A.; Irish Department of Agriculture, Food and the Marine; Irish Research Council; 11/S/116; Goipg/2013/1391 (Elsevier, 2022-05-31)
    Enhanced early life nutrition stimulates the functionality of the hypothalamic-pituitary–testicular (HPT) biochemical signalling axis, resulting in precocious reproductive development in bull calves. Additionally, there is evidence that peptides and hormones produced within adipose tissue depots are also central in mediating the effect of metabolic status with reproductive development. The objective of this study was to undertake gene co-expression analyses on transcriptional data of the HPT and adipose tissues derived from bull calves fed contrasting planes of nutrition up to 18 weeks of life. The relationship between networks of co-expressed genes in each tissue dataset with calf phenotypic data was also assessed using a Pearson correlation analysis. Phenotypic data were related to metabolic status (systemic concentrations of insulin, leptin, adiponectin and IGF-1) reproductive development (systemic concentrations of testosterone, FSH and LH) and markers of testicular development (seminiferous tubule diameter, seminiferous tubule lumen score, spermatogenic cells and Sertoli cells). In the hypothalamus, gene co-expression networks involved in biochemical signalling processes related to gonadotropin-releasing hormone (GnRH) secretion were positively associated (P < 0.05) with systemic concentrations of IGF-1 and insulin. Similarly, a network of gene transcripts involved in GnRH signalling in the anterior pituitary was positively associated (P < 0.05) with systemic concentrations of LH. In the testes and adipose tissues, networks of co-expressed genes implicated in cholesterol and fatty acid biosynthesis were positively associated (P < 0.05) with lumen score, Sertoli cell number, and stage of spermatogenesis. Additionally, gene co-expression networks significantly associated (P < 0.05) with both metabolic and reproductive trait data were found to be enriched (P < 0.05) for biological pathways related to energy production, cellular growth and proliferation, GnRH signalling and cholesterol biosynthesis across multiple tissues examined. Results from this study highlight networks of co-expressed genes directly associated with markers of enhanced metabolic status and subsequent earlier reproductive development. Furthermore, genes involved in biological processes mentioned above may hold potential for informing genomic selection breeding programmes for the selection of calves capable of displaying earlier reproductive development as a consequence of enhanced dietary intake.
  • Insights on meat quality from combining traditional studies and proteomics

    Purslow, Peter P.; Gagaoua, Mohammed; Warner, Robyn D.; Marie Skłodowska-Curie grant agreement; 713654 (Elsevier, 2021-04-30)
    Following a century of major discoveries on the mechanisms determining meat colour and tenderness using traditional scientific methods, further research into complex and interactive factors contributing to variations in meat quality is increasingly being based on data-driven “omics” approaches such as proteomics. Using two recent meta-analyses of proteomics studies on beef colour and tenderness, this review examines how knowledge of the mechanisms and factors underlying variations in these meat qualities can be both confirmed and extended by data-driven approaches. While proteomics seems to overlook some sources of variations in beef toughness, it highlights the role of post-mortem energy metabolism in setting the conditions for development of meat colour and tenderness, and also points to the complex interplay of energy metabolism, calcium regulation and mitochondrial metabolism. In using proteomics as a future tool for explaining variations in meat quality, the need for confirmation by further hypothesis-driven experimental studies of post-hoc explanations of why certain proteins are biomarkers of beef quality in data-driven studies is emphasised.
  • 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, D.P.; Science Foundation Ireland; Irish Department of Agriculture, Food and Marine; European Union; 16/RC/3835 (VistaMilk); 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.
  • Financial benchmarking on dairy farms: Exploring the relationship between frequency of use and farm performance

    Ramsbottom, G.; Läpple, D.; Pierce, K.M. (Elsevier, 2021-03-31)
    The importance of financial benchmarking has increased in recent years as European Union milk quota abolition has facilitated rapid change in the dairy sector. This study evaluates the association between usage frequency of a financial benchmarking tool [Profit Monitor (PM)] and farm changes on spring-calving pasture-based dairy farms. To this end, physical and financial data for 5,945 dairy farms, representing 20,132 farm years, for the years 2010 to 2018 were used. Farms were categorized by frequency of annual financial benchmarking over the 9-yr period into frequent PM users (7–9 yr), infrequent PM users (4–6 yr), low PM users (1–3 yr), and nonusers. We use a mixed model framework and econometric models to characterize farms and to explore characteristics and determinants of economic performance and user groups. The most frequent users of the financial benchmarking tool had the greatest increase in intensification (measured by change in farm stocking rate), productivity (measured by change in milk production per hectare), and financial performance (measured by change in farm gross output and net profit per hectare) across the study period. Infrequent and low PM users of the benchmarking tool were intermediate for all variables measured, whereas nonusers had the least change. Empirical results indicated that economic performance was positively associated with dairy specialization and pasture utilization for all groups. Despite considerable fluctuations over the observation period, the overall change in total farm net profit between 2010 and 2018 was greatest for the frequent PM users (an increase of 70%, or €37,639), followed by farms in the infrequent PM user category (a 71% increase corresponding to an increase of €28,008 in net profit); meanwhile, low PM user and nonuser categories showed increases of 69% (€26,270) and 42% (€10,977), respectively. The results of this study also clearly indicated the existence of a strong positive association between frequency of financial benchmarking and greater technical and financial efficiency. The econometric analysis revealed that financial benchmarking users are more likely than nonusers to have larger herds, and that regional differences exist in usage rates. Finally, the study concludes by suggesting that the development of simplified financial benchmarking technologies and their support are required to increase benchmarking frequency, which may also help to facilitate a more sustainable and resource efficient dairy industry.
  • Effect of dietary restriction and compensatory growth on performance, carcass characteristics, and metabolic hormone concentrations in Angus and Belgian Blue steers

    Keady, S.M.; Keane, M.G.; Waters, S.M.; Wylie, A.R.; O'Riordan, E.G.; Keogh, K.; Kenny, D.A.; Teagasc Walsh Fellowship (Elsevier, 2021-06-30)
    Compensatory growth (CG) is the ability of an animal to undergo accelerated growth after a period of restricted feeding. However, there is a dearth of information in relation to the effect of genotype on CG response, thus the objective of this study was to evaluate CG response in two contrasting breed types, namely Aberdeen Angus (AN) and Belgian Blue (BB). Crossbred AN × Holstein-Friesian or BB × Holstein-Friesian steers were assigned to one of two treatment groups in a two (genotypes) × two (diets) factorial design. For 99 days, one group (11 AN and 12 BB) was offered a high energy control diet (H-H) whereas the second group (11 AN and 12 BB) was offered an energy restricted diet (L-H). At the end of the differential feeding period (99 days), both groups of animals were then offered a high energy control diet for a further 200 days. All animals were then slaughtered on day-299 of the study. During feed restriction, L-H had lower DM intake (DMI), had greater feed conversion ratio (FCR) and lower plasma concentrations of insulin, IGF-1, leptin, glucose, urea, betahydroxybutyrate and smaller M. longissimus thoracis or lumborum muscle and fat depths compared to H-H steers. During realimentation, there was no difference in DMI between diets; however, L-H had greater live weight gain compared to H-H steers. Overall, H-H consumed greater quantities on a DM basis, however, had a higher FCR compared to L-H steers. By the end of the realimentation period, there was no difference in plasma metabolite or hormone concentrations, linear body measurements, ultrasonically scanned fat depths, carcass conformation, dressing percentage or fat class between H-H and L-H steers. At slaughter, carcass weights were affected by diet with greater values for H-H compared to L-H steers. Genotype affected measures associated with body composition including pelvic width and both muscle and fat depths (P < 0.05). Overall, L-H had a CG (or recovery) index of 0.52 and did not make up for the loss of gains during the differential feeding period; however, M. longissimus thoracis et lumborum, a tissue of high economic value, recovered completely making it a target of interest for further investigation.

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