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

  • Impact of birth and rearing type, as well as inaccuracy of recording, on pre-weaning lamb phenotypic and genetic merit for live weight1

    McHugh, N.; Pabiou, T.; McDermott, K.; Wall, E.; Berry, D. P. (Oxford University Press (OUP), 2017-04-01)
    The objective of the present study was to quantify the impact of the systematic environmental effects of both birth and rearing type on pre-weaning lamb live weight, and to evaluate the repercussions of inaccurate recording of birth and rearing type on subsequent genetic evaluations. A total of 32,548 birth weight records, 35,770 forty-day weight records and 32,548 records for average daily gain (ADG) between birth and 40-day weight from the Irish national sheep database were used. For each lamb, a new variable, birth-rearing type, reflecting both the birth and rearing type of a lamb was generated by concatenating both parameters. The association between birth-rearing type and birth weight, 40-day weight, and ADG was estimated using linear mixed models. The repercussions of inaccurate recording of birth type were determined by quantifying the impact on sire estimated breeding value (EBV; with an accuracy of ≥ 35%), where one of the lambs born in a selection of twin litter births was assumed to have died at birth but the farmer recorded the birth and rearing type as a singleton. The heaviest mean birth weight was associated with lambs born and subsequently reared as singles (5.47 kg); the lightest mean birth weight was associated with lambs born and reared as triplets (4.10 kg). The association between birth-rearing type and 40-day weight differed by dam parity (P < 0.001). Lambs reared by first parity dams as singles, irrespective of birth type were, on average, heavier at 40-day weighing than lambs reared as multiples, but as parity number increased, single-born lambs reared as twins outperformed triplet-born lambs reared as singles. Irrespective of the trait evaluated, the correlation between sire EBV estimated from the accurately recorded data and sire EBV estimated from the data with recording errors was strong ranging from 0.93 (birth weight) to 0.97 (ADG). The EBV for sires with progeny data manipulated were 0.14 kg, 0.34 kg and 5.56 g/d less for birth weight, 40-day weight and ADG, respectively, compared to their equivalent EBV calculated using accurately recorded data. Results from this study highlight the importance of precise recording of birth-rearing type by producers for the generation of accurate genetic evaluations.
  • Is TB Testing Associated With Increased Blood Interferon-Gamma Levels?

    Kennedy, Aideen E.; O’Mahony, Jim; Byrne, Noel; MacSharry, John; Sayers, Riona G. (Frontiers Media SA, 2017-10-23)
    The Republic of Ireland reports a relatively low prevalence of Johne’s disease (JD) compared to international counterparts. Postulated reasons for this include a lower average herd size and a grass-based production system. Ireland also engages in high levels of bovine tuberculosis (bTB) testing. As interferon-gamma (IFN-γ) is believed to play a key role in protecting against JD, it is our hypothesis that administration of purified protein derivative (PPD), as part of the bTB test, is associated with a systemic increase in IFN-γ production, which may potentially limit clinical progression of the disease. We studied 265 cows (202 Friesian and 63 “Non-Friesian,” e.g., JerseyX, Norwegian Red) to assess IFN-γ levels and Mycobacterium avium subspecies paratuberculosis (MAP) antibody response before and after the bTB test. As part of the compulsory annual bTB test, avian and bovine PPD were administered at two separate cervical sites. To assess IFN-γ production, blood samples were taken before and 72 h after PPD administration. MAP antibody response was assessed before and 10 days post-PPD administration. A significant increase in MAP antibody response was identified post-bTB compared to pre-bTB response (p < 0.001). Additionally, IFN-γ production significantly increased at the post-bTB time point (p < 0.001) compared to the pre-bTB test readings. This may indicate a beneficial effect of bTB testing in controlling JD.
  • Genomic identification, expression profiling, and functional characterization of CatSper channels in the bovine†

    Johnson, Gillian P.; English, Anne-Marie; Cronin, Sinead; Hoey, David A.; Meade, Kieran G.; Fair, Sean; Irish Research Council; European Research Council (ERC); Science Foundation Ireland ERC Support Grant SFI; GOIPG/2014/1463; et al. (Oxford University Press (OUP), 2017-07-26)
    Cation channels of sperm (CatSper) are sperm-specific calcium channels with identified roles in the regulation of sperm function in humans, mice, and horses. We sought to employ a comparative genomics approach to identify conserved CATSPER genes in the bovine genome, and profile their expression in reproductive tissue. We hypothesized that CATSPER proteins expressed in bull testicular tissue mediates sperm hyperactivation and their rheotactic response in the reproductive tract of the cow. Bioinformatic analysis identified all four known CATSPER genes (CATSPER 1–4) in the bovine genome, and profiling by quantitative real-time polymerase chain reaction identified site-specific variation in messenger ribonucleic acid (mRNA) expression for all four genes along the reproductive tract of the bull. Using a novel antibody against CATSPER 1, protein expression was confirmed and localized to the principal piece of bull sperm, in agreement with what has been reported in other species. Subsequent treatment of bull sperm with either the calcium chelator ethylene glycol tetraacetic acid; mibefradil, a specific blocker of CatSper channels in human sperm; or CATSPER1 antibody all significantly inhibited caffeine-induced hyperactivation and the rheotactic response, supporting the concept that the calcium influx occurs via CatSper channels. Taken together, the work here provides novel insights into expression and function of CatSper channels in bull testicular tissue and in the function of ejaculated sperm.
  • The creation and evaluation of a model to simulate the probability of conception in seasonal-calving pasture-based dairy heifers

    Fenlon, Caroline; O’Grady, Luke; Butler, Stephen; Doherty, Michael L.; Dunnion, John; Dairy Research Ireland (Springer Science and Business Media LLC, 2017-11-22)
    Background: Herd fertility in pasture-based dairy farms is a key driver of farm economics. Models for predicting nulliparous reproductive outcomes are rare, but age, genetics, weight, and BCS have been identified as factors influencing heifer conception. The aim of this study was to create a simulation model of heifer conception to service with thorough evaluation. Methods: Artificial Insemination service records from two research herds and ten commercial herds were provided to build and evaluate the models. All were managed as spring-calving pasture-based systems. The factors studied were related to age, genetics, and time of service. The data were split into training and testing sets and bootstrapping was used to train the models. Logistic regression (with and without random effects) and generalised additive modelling were selected as the model-building techniques. Two types of evaluation were used to test the predictive ability of the models: discrimination and calibration. Discrimination, which includes sensitivity, specificity, accuracy and ROC analysis, measures a model’s ability to distinguish between positive and negative outcomes. Calibration measures the accuracy of the predicted probabilities with the Hosmer-Lemeshow goodness-of-fit, calibration plot and calibration error. Results: After data cleaning and the removal of services with missing values, 1396 services remained to train the models and 597 were left for testing. Age, breed, genetic predicted transmitting ability for calving interval, month and year were significant in the multivariate models. The regression models also included an interaction between age and month. Year within herd was a random effect in the mixed regression model. Overall prediction accuracy was between 77.1% and 78.9%. All three models had very high sensitivity, but low specificity. The two regression models were very well-calibrated. The mean absolute calibration errors were all below 4%. Conclusion: Because the models were not adept at identifying unsuccessful services, they are not suggested for use in predicting the outcome of individual heifer services. Instead, they are useful for the comparison of services with different covariate values or as sub-models in whole-farm simulations. The mixed regression model was identified as the best model for prediction, as the random effects can be ignored and the other variables can be easily obtained or simulated.
  • Rapid Communication: Large exploitable genetic variability exists to shorten age at slaughter in cattle

    Berry, D. P.; Cromie, A. R.; Judge, M. M. (Oxford University Press (OUP), 2017-10-01)
    Apprehension among consumers is mounting on the efficiency by which cattle convert feedstuffs into human edible protein and energy as well as the consequential effects on the environment. Most (genetic) studies that attempt to address these issues have generally focused on efficiency metrics defined over a certain time period of an animal’s life cycle, predominantly the period representing the linear phase of growth. The age at which an animal reaches the carcass specifications for slaughter, however, is also known to vary between breeds; less is known on the extent of the within-breed variability in age at slaughter. Therefore, the objective of the present study was to quantify the phenotypic and genetic variability in the age at which cattle reach a predefined carcass weight and subcutaneous fat cover. A novel trait, labeled here as the deviation in age at slaughter (DAGE), was represented by the unexplained variability from a statistical model, with age at slaughter as the dependent variable and with the fixed effects, among others, of carcass weight and fat score (scale 1 to 15 scored by video image analysis of the carcass at slaughter). Variance components for DAGE were estimated using either a 2-step approach (i.e., the DAGE phenotype derived first and then variance components estimated) or a 1-step approach (i.e., variance components for age at slaughter estimated directly in a mixed model that included the fixed effects of, among others, carcass weight and carcass fat score as well as a random direct additive genetic effect). The raw phenotypic SD in DAGE was 44.2 d. The genetic SD and heritability for DAGE estimated using the 1-step or 2-step models varied from 14.2 to 15.1 d and from 0.23 to 0.26 (SE 0.02), respectively. Assuming the (genetic) variability in the number of days from birth to reaching a desired carcass specifications can be exploited without any associated unfavorable repercussions, considerable potential exists to improve not only the (feed) efficiency of the animal and farm system but also the environmental footprint of the system. The beauty of the approach proposed, relative to strategies that select directly for the feed intake complex and enteric methane emissions, is that data on age at slaughter are generally readily available. Of course, faster gains may potentially be achieved if a dual objective of improving animal efficiency per day coupled with reduced days to slaughter was embarked on.
  • Limitation of Grassland Productivity by Low Temperature and Seasonality of Growth

    Wingler, Astrid; Hennessy, Deirdre (Frontiers Media SA, 2016-07-27)
    The productivity of temperate grassland is limited by the response of plants to low temperature, affecting winter persistence and seasonal growth rates. During the winter, the growth of perennial grasses is restricted by a combination of low temperature and the lack of available light, but during early spring low ground temperature is the main limiting factor. Once temperature increases, growth is stimulated, resulting in a peak in growth in spring before growth rates decline later in the season. Growth is not primarily limited by the ability to photosynthesize, but controlled by active regulatory processes that, e.g., enable plants to restrict growth and conserve resources for cold acclimation and winter survival. An insufficient ability to cold acclimate can affect winter persistence, thereby also reducing grassland productivity. While some mechanistic knowledge is available that explains how low temperature limits plant growth, the seasonal mechanisms that promote growth in response to increasing spring temperatures but restrict growth later in the season are only partially understood. Here, we assess the available knowledge of the physiological and signaling processes that determine growth, including hormonal effects, on cellular growth and on carbohydrate metabolism. Using data for grass growth in Ireland, we identify environmental factors that limit growth at different times of the year. Ideas are proposed how developmental factors, e.g., epigenetic changes, can lead to seasonality of the growth response to temperature. We also discuss perspectives for modeling grass growth and breeding to improve grassland productivity in a changing climate.
  • An ultra-high density genetic linkage map of perennial ryegrass (Lolium perenne) using genotyping by sequencing (GBS) based on a reference shotgun genome assembly

    Velmurugan, Janaki; Mollison, Ewan; Barth, Susanne; Marshall, David; Milne, Linda; Creevey, Christopher J.; Lynch, Bridget; Meally, Helena; McCabe, Matthew; Milbourne, Dan; et al. (Oxford University Press (OUP), 2016-06-06)
    Background and aims: High density genetic linkage maps that are extensively anchored to assembled genome sequences of the organism in question are extremely useful in gene discovery. To facilitate this process in perennial ryegrass (Lolium perenne L.), a high density single nucleotide polymorphism (SNP)- and presence/absence variant (PAV)-based genetic linkage map has been developed in an F2 mapping population that has been used as a reference population in numerous studies. To provide a reference sequence to which to align genotyping by sequencing (GBS) reads, a shotgun assembly of one of the grandparents of the population, a tenth-generation inbred line, was created using Illumina-based sequencing. Methods: The assembly was based on paired-end Illumina reads, scaffolded by mate pair and long jumping distance reads in the range of 3-40 kb, with >200-fold initial genome coverage. A total of 169 individuals from an F2 mapping population were used to construct PstI-based GBS libraries tagged with unique 4-9 nucleotide barcodes, resulting in 284 million reads, with approx. 1·6 million reads per individual. A bioinformatics pipeline was employed to identify both SNPs and PAVs. A core genetic map was generated using high confidence SNPs, to which lower confidence SNPs and PAVs were subsequently fitted in a straightforward binning approach. Key results: The assembly comprises 424 750 scaffolds, covering 1·11 Gbp of the 2·5 Gbp perennial ryegrass genome, with a scaffold N50 of 25 212 bp and a contig N50 of 3790 bp. It is available for download, and access to a genome browser has been provided. Comparison of the assembly with available transcript and gene model data sets for perennial ryegrass indicates that approx. 570 Mbp of the gene-rich portion of the genome has been captured. An ultra-high density genetic linkage map with 3092 SNPs and 7260 PAVs was developed, anchoring just over 200 Mb of the reference assembly. Conclusions: The combined genetic map and assembly, combined with another recently released genome assembly, represent a significant resource for the perennial ryegrass genetics community.
  • Sperm-Coating Beta-Defensin 126 Is a Dissociation-Resistant Dimer Produced by Epididymal Epithelium in the Bovine Reproductive Tract

    Narciandi, F.; Fernandez-Fuertes, B.; Khairulzaman, I.; Jahns, H.; King, D.; Finlay, E. K.; Mok, K. H.; Fair, S.; Lonergan, P.; Farrelly, C. O.; et al. (Oxford University Press (OUP), 2016-10-05)
    Beta-defensins are innate immune molecules, often described as antimicrobial peptides because of their bactericidal activity and are now known to have diverse additional functions, including cell signaling, chemoattraction, immunoregulation, and reproduction. In humans and primates, beta-defensin 126 has been shown to regulate the ability of sperm to swim through cervical mucus and to protect sperm from attack by the female immune system during transit toward the oviduct. Bovine beta-defensin 126 (BBD126) is the ortholog of human defensin 126, and computational analysis here revealed significant conservation between BBD126 and other mammalian orthologs at the N-terminus, although extensive sequence differences were detected at the C-terminus, implying possible species-specific roles for this beta-defensin in reproduction. We had previously demonstrated preferential expression of this and related beta-defensin genes in the bovine male reproductive tract, but no studies of bovine beta-defensin proteins have been performed to date. Here, we analyzed BBD126 protein using a monoclonal antibody (a-BBD126) generated against a 14 amino acid peptide sequence from the secreted fragment of BBD126. The specificity of a-BBD126 was validated by testing against the native form of the peptide recovered from bovine caudal epididymal fluid and recombinant BBD126 generated using a prokaryotic expression system. Western blot analysis of the native and recombinant forms showed that BBD126 exists as a dimer that was highly resistant to standard methods of dissociation. Immunohistochemical staining using a-BBD126 demonstrated BBD126 protein expression by epithelial cells of the caudal epididymis and vas deferens from both mature and immature bulls. BBD126 could also be seen (by confocal microscopy) to coat caudal sperm, with staining concentrated on the tail of the sperm cells. This study is the first to demonstrate beta-defensin 126 protein expression in the bovine reproductive tract and on bull sperm. Its dissociation-resistant dimeric structure is likely to have important functional implications for the role of BBD126 in bovine reproduction.
  • Contextual Hub Analysis Tool (CHAT): A Cytoscape app for identifying contextually relevant hubs in biological networks

    Muetze, Tanja; Goenawan, Ivan H.; Wiencko, Heather L.; Bernal-Llinares, Manuel; Bryan, Kenneth; Lynn, David J.; European Union; FP7-HEALTH-2011-278568 (F1000 Research Ltd, 2016-07-19)
    Highly connected nodes (hubs) in biological networks are topologically important to the structure of the network and have also been shown to be preferentially associated with a range of phenotypes of interest. The relative importance of a hub node, however, can change depending on the biological context. Here, we report a Cytoscape app, the Contextual Hub Analysis Tool (CHAT), which enables users to easily construct and visualize a network of interactions from a gene or protein list of interest, integrate contextual information, such as gene expression or mass spectrometry data, and identify hub nodes that are more highly connected to contextual nodes (e.g. genes or proteins that are differentially expressed) than expected by chance. In a case study, we use CHAT to construct a network of genes that are differentially expressed in Dengue fever, a viral infection. CHAT was used to identify and compare contextual and degree-based hubs in this network. The top 20 degree-based hubs were enriched in pathways related to the cell cycle and cancer, which is likely due to the fact that proteins involved in these processes tend to be highly connected in general. In comparison, the top 20 contextual hubs were enriched in pathways commonly observed in a viral infection including pathways related to the immune response to viral infection. This analysis shows that such contextual hubs are considerably more biologically relevant than degree-based hubs and that analyses which rely on the identification of hubs solely based on their connectivity may be biased towards nodes that are highly connected in general rather than in the specific context of interest.
  • Identification of sperm proteins as biomarkers of field fertility in Holstein-Friesian bulls used for artificial insemination

    Rabaglino, M.B.; Le Danvic, C.; Schibler, L.; Kupisiewicz, K.; Perrier, J.P.; O'Meara, C.M.; Kenny, D.A.; Fair, S.; Lonergan, P.; Science Foundation Ireland; et al. (Elsevier, 2022-12)
    Despite passing stringent quality control, bulls used in artificial insemination can vary significantly in their fertility, emphasizing the need for reliable markers of sperm quality. This study aimed to identify sperm proteins acting as biomarkers of fertility in 2 different populations of dairy bulls classified based on their field fertility. Semen was collected and cryopreserved from: 54 Holstein bulls located in Ireland, classified according to fertility indexes as low fertility (LF, n = 23), medium fertility (n = 14), or high fertility (HF, n = 17); and 18 Holstein bulls located in Denmark, classified as LF (n = 8) or HF (n = 10). The proteome was measured through liquid chromatography-mass spectrometry and data were analyzed with the R software. Differentially abundant proteins between HF and LF bulls and biomarker proteins were determined through a modified t-test and random forest, respectively, selecting 301 differentially abundant proteins and 34 biomarker proteins. The predictive ability of the 34 biomarkers was evaluated employing support vector machine as the classifier, using their abundance levels in the Irish bulls to train the model and in the Danish bulls for validation. The prediction accuracy was 94.4%, with only one HF bull misclassified, corresponding to the lowest fertility index bull in the HF group. The biomarkers more abundant in sperm of HF bulls enriched axoneme assembly and sperm motility (false discovery rate <0.05), according to functional analysis. In conclusion, a robust model coupled with the application of appropriate bioinformatic tools allowed the identification of functionally relevant sperm proteins predictive of the fertility of Holstein bulls used in artificial insemination.

    Keenan, D.F.; Hayes, J.E.; Kenny, T.A.; Kerry, J.P.; Department of Agriculture, Food and Rural Development (Wiley, 2015-11-03)
    Eating quality, processing and storage attributes were examined in hot- and cold-boned beef (90 min and 24 h postmortem, respectively) post from two muscles (M. biceps femoris [BF] and M. pectoralis profundus [PP]) injected with curing brines at conventionally chilled (2–4C) and elevated temperature (15–17C) curing brines, stored over 21 days (4C). The pH/temperature profiles showed all hot-boned experimental treatments were outside of the reported ranges for the occurrence of cold or heat shortening. Hot-boned beef did not exhibit any significant added or reduced functionality compared to conventionally-boned beef i.e., cook loss and final yield unaffected in BF and PP muscles. Cold-boned BF products were harder (P < 0.05) than hot-boned; however, this was not supported by sensory analysis. Samples prepared with elevated brine temperatures had a detrimental effect on the sensory characteristics of PP hams. Principal component and hierarchical cluster analyses (PCA and HCA, respectively) were used to better visualize the underlying structure between the quality measurements and samples, showing gradual product deterioration over storage. Although the combination of hot boning and higher brine temperature led to expected higher bacterial numbers, microbial stability of the product was maintained after 21 days.
  • Acquisition of the yeast Kluyveromyces marxianus from unpasteurised milk by a kefir grain enhances kefir quality

    Gethins, Loughlin; Rea, Mary C.; STANTON, CATHERINE; Ross, R. Paul; Kilcawley, Kieran; O'Sullivan, Maurice; Crotty, Suzanne; Morrissey, John P.; Teagasc Walsh fellowship; EU Marie-Curie Programme EU FP7; et al. (PubMed, 2016-07-01)
    Kefir is a fermented milk beverage consumed for nutritional and health tonic benefits in many parts of the world. It is produced by the fermentation of milk with a consortium of bacteria and yeast embedded within a polysaccharide matrix. This consortium is not well defined and can vary substantially between kefir grains. There are little data on the microbial stability of kefir grains, nor on interactions between microbes in the grain and in the milk. To study this, a grain was split, with one half of each stored at −20°C and the other half passaged repeatedly in whole unpasteurised milk. Grains passaged in the unpasteurised milk recovered vigour and acquired the yeast Kluyveromyces marxainus from the milk which was confirmed to be the same strain by molecular typing. Furthermore, these passaged grains produced kefir that was distinguished chemically and organoleptically from the stored grains. Some changes in ultrastructure were also observed by scanning electron microscopy. The study showed that kefir grains can acquire yeast from their environment and the final product can be influenced by these newly acquired yeasts. Kluyveromyces marxianus is considered to be responsible for some of the most important characteristics of kefir so the finding that this yeast is part of the less stable microbiota is significant.
  • Cauda Epididymis-Specific Beta-Defensin 126 Promotes Sperm Motility but Not Fertilizing Ability in Cattle

    Fernandez-Fuertes, B.; Narciandi, F.; O'Farrelly, C.; Kelly, A. K.; Fair, S.; Meade, K. G.; Lonergan, P. (PubMed, 2016-10-05)
    Bovine beta-defensin 126 (BBD126) exhibits preferential expression for the cauda epididymis of males, where it is absorbed onto the tail and postacrosomal region of the sperm. The aim of this study was to examine the role of BBD126 in bull sperm function. Fresh and frozen-thawed semen were incubated in the presence of different capacitating agents as well as with phosphatidylinositol-specific phospholipase C. These treatments, which have been successful in releasing beta-defensin 126 from macaque sperm, proved to be ineffective in bull sperm. This finding suggests that the protein behaves in a different manner in the bovine. The lack of success in removing BBD126 led us to use corpus epididymis sperm, a model in which the protein is not present, to study its functional role. Corpus sperm were incubated with cauda epididymal fluid (CEF) in the absence or presence of BBD126 antibody or with recombinant BBD126 (rBBD126). Confocal microscopy revealed that rBBD126 binds to corpus sperm with the same pattern observed for BBD126 in cauda sperm, whereas an aberrant binding pattern is observed when sperm are subject to CEF incubation. Addition of CEF increased motility as well as the number of corpus sperm migrating through cervical mucus from estrus cows. However, it decreased the ability of sperm to fertilize in vitro matured oocytes. The presence of the antibody failed to abrogate these effects. Furthermore, when rBBD126 was added in the absence of other factors and proteins from the CEF, an increase in motility was also observed and no negative effects in fertility were seen. These results suggest that BBD126 plays a key role in the acquisition of sperm motility in the epididymis.
  • Fatty acid composition, shelf-life and eating quality of beef from steers fed corn or wheat dried distillers' grains with solubles in a concentrate supplement to grass silage

    Salami, Saheed A.; O'Grady, Michael N.; Luciano, Giuseppe; Priolo, Alessandro; McGee, Mark; Moloney, Aidan P.; Kerry, Joseph P.; European Commission; Department of Agriculture, Food and the Marine; 11/S/122, FEFAN (Elsevier, 2021-03)
    Thirty-six steers were randomly assigned to one of three dietary treatments fed ad libitum grass silage and concentrate supplements containing either barley/soybean meal (CON), 80% DM corn (CDGS)- or 80% DM wheat (WDGS)-dried distillers' grains with solubles for 124 days pre-slaughter. Chemical and fatty acid composition, shelf-life, and eating quality of longissimus thoracis muscle were determined. Dietary CDGS and WDGS increased the proportion of conjugated linoleic acids (P < 0.05) and tended to increase C18:3n-3 (P = 0.075) and total polyunsaturated fatty acids (P = 0.060) relative to the CON. Feeding diets containing distillers' grains reduced the lipid and colour stability of fresh beef patties stored in modified atmosphere packs (MAP), with CDGS exhibiting an intermediate effect between CON and WDGS. Diet did not negatively influence the texture profile parameters and eating quality attributes of beef stored in MAP. The inclusion of CDGS or WDGS in supplementary concentrates may improve the fatty acid profile but decreased the shelf-life of beef.
  • Cross-sectional analyses of a national database to determine if superior genetic merit translates to superior dairy cow performance

    Ring, S.C.; Evans, R.D.; Cromie, A.R.; Berry, D.P.; Science Foundation Ireland; Department of Agriculture, Food and the Marine (Dublin, Ireland); 16/RC/3835 (VistaMilk) (Elsevier, 2021-07)
    Various studies have validated that genetic divergence in dairy cattle translates to phenotypic differences; nonetheless, many studies that consider the breeding goal, or associated traits, have generally been small scale, often undertaken in controlled environments, and they lack consideration for the entire suite of traits included in the breeding goal. Therefore, the objective of the present study was to fill this void, and in doing so, provide producers with confidence that the estimated breeding values (EBV) included in the breeding goal do (or otherwise) translate to desired changes in performance among commercial cattle; an additional outcome of such an approach is the identification of potential areas for improvements. Performance data on 536,923 Irish dairy cows (and their progeny) from 13,399 commercial spring-calving herds were used. Association analyses between the cow's EBV of each trait included in the Irish total merit index for dairy cows (which was derived before her own performance data accumulated) and her subsequent performance were undertaken using linear mixed models; milk production, fertility, calving, maintenance (i.e., liveweight), beef, health, and management traits were all considered in the analyses. Results confirm that excelling in EBV for individual traits, as well as on the total merit index, generally delivers superior phenotypic performance; examples of the improved performance for genetically elite animals include a greater yield and concentration of both milk fat and milk protein, despite a lower milk volume, superior reproductive performance, better survival, improved udder and hoof health, lighter cows, and fewer calving complications; all these gains were achieved with minimal to no effect on the beef merit of the dairy cow's progeny. The associated phenotypic change in each performance trait per unit change in its respective EBV was largely in line with the direction and magnitude of expectation, the exception being for calving interval. Per unit change in calving interval EBV, the direction of phenotypic response was as anticipated but the magnitude of the response was only half of what was expected. Despite the deviation from expectation between the calving interval EBV and its associated phenotype, a superior total merit index or a superior fertility EBV was indeed associated with an improvement in all detailed fertility performance phenotypes investigated. Results substantiate that breeding is a sustainable strategy of improving phenotypic performance in commercial dairy cattle and, by extension, profit.
  • Effect of ovulation synchronization program and season on pregnancy to timed artificial insemination in suckled beef cows

    Randi, Federico; Kelly, Alan K.; Parr, Mervyn H.; Diskin, Michael G.; Lively, Francis; Lonergan, Patrick; Kenny, David A.; Irish Department of Agriculture, Food and the Marine; 13-S-515 (Elsevier, 2021-09)
    This study was conducted to (i) evaluate the requirement for the administration of GnRH coincident with insertion of a progesterone-releasing intravaginal device (PRID) and (ii) the effect of supplementing with 400 IU eCG at PRID removal on pregnancy per AI (P/AI) in spring and autumn calving suckled beef cows, subjected to a 7-d CO-Synch + PRID timed artificial insemination (TAI) program. Suckled beef cows (n = 1408) on 62 commercial farms were enrolled and randomly assigned to either of three treatments: 1) cows received a PRID and 100 μg GnRH on Day −10, followed by 25 mg PGF2α at PRID removal (Day −3) and 100 μg GnRH 72 h later (Day 0) at TAI (Treatment 1; n: spring = 236, autumn = 248); 2) as Treatment 1, but without GnRH at PRID insertion on Day −10 (Treatment 2; n: spring = 232, autumn = 227); 3) as Treatment 1, but cows also received 400 IU eCG at PRID removal on Day −3 (Treatment 3; n: spring = 233, autumn = 232). At Day −10, ovaries were examined by ultrasonography to evaluate the presence or absence of a corpus luteum (CL) and follicle(s) ≥ 10 mm in diameter. Body condition score (BCS) was assessed on a scale of 1–5. Pregnancy diagnosis was carried out 30–35 d after TAI by transrectal ultrasonography. Data were analyzed using the GENMOD and LOGISTIC procedures of SAS. There was a treatment by season interaction for P/AI (P < 0.001). In spring, overall P/AI was 59.1% (414/701) and was affected by treatment (59.3 v 49.6 v 68.2%, for Treatments 1, 2 and 3, respectively P < 0.05). In contrast, in autumn, overall P/AI (51.5%, 364/707) was unaffected (P > 0.05) by treatment (50.1 v 53.7 v 48.7% for Treatments 1, 2 and 3, respectively). Overall, eCG had a positive effect on P/AI for cows lacking a CL at treatment initiation (P < 0.05). In addition, in cows with low BCS (≤2.25), eCG supplementation tended (P = 0.09) to improve P/AI. Seasonal differences in response to synchronization treatment may be reflective of different management regimens (grazing v confinement) and breed type and remain to be elucidated.
  • The immune response in bovine primary dermal fibroblasts is influenced by Interleukin 8 promoter haplotype and vitamin D

    O’Brien, Megan B.; Beynon, Charlotte L.; McLoughlin, Rachel M.; Meade, Kieran G.; Teagasc Walsh Scholarship; 0005GE (Elsevier, 2021-08)
    Interleukin-8 (IL-8) is a potent inflammatory chemokine, and two gene promoter haplotypes have been previously reported to segregate in cattle populations. Our earlier work showed how these divergent IL8 genotypes influence IL-8 expression and other immune response parameters at a systemic level. Here we extend that work to characterise the influence of haplotype on the local immune response – in primary bovine dermal fibroblasts. Furthermore, we also investigated how this response is modulated by 1,25-dihydroxyvitamin D3 (1,25(OH)2D3). Significant induction of IL8 expression was observed in cells from both haplotypes at 3 and 24 h post-stimulation with the TLR1/2 ligand, Pam3CSK4 and with the TLR4 ligand, LPS. IL8 expression was elevated in response to both LPS and Pam3CSK4 in fibroblasts carrying the IL8-h1 haplotype and this result was supported by significantly enhanced IL-8 protein secretion. Gene expression profiles for other known fibroblast immune mediators (SAA3 and CCL20) did not show significant differences between haplotypes but NOS2 gene expression was significantly elevated in response to vitamin D, even above the level detected in response to both TLR ligands. In conclusion, this work has demonstrated that the IL-8 response of dermal fibroblasts is dependent on IL8 haplotype and that the immune response profile in these cells is significantly differentially regulated by 1,25(OH)2D3. Fibroblasts have important immune response capacity and their function in driving inflammatory responses (including iNOS) is underappreciated. Understanding the relationship between cattle genotype and immune function is critically important for uncovering sustainable solutions for animal disease.
  • Diagnosis of sheep fasciolosis caused by Fasciola hepatica using cathepsin L enzyme-linked immunosorbent assays (ELISA)

    López Corrales, Jesús; Cwiklinski, Krystyna; De Marco Verissimo, Carolina; Dorey, Amber; Lalor, Richard; Jewhurst, Heather; McEvoy, Amanda; Diskin, Michael; Duffy, Catherine; Cosby, S. Louise; et al. (Elsevier, 2021-10)
    Fasciolosis, a global parasitic disease of agricultural livestock, is caused by the liver fluke Fasciola hepatica. Management and strategic control of fasciolosis on farms depends on early assessment of the extent of disease so that control measures can be implemented quickly. Traditionally, this has relied on the detection of eggs in the faeces of animals, a laborious method that lacks sensitivity, especially for sub-clinical infections, and identifies chronic infections only. Enzyme linked immunosorbent assays (ELISA) offer a quicker and more sensitive serological means of diagnosis that could detect early acute infection before significant liver damage occurs. The performance of three functionally-active recombinant forms of the major F. hepatica secreted cathepsins L, rFhCL1, rFhCL2, rFhCL3, and a cathepsin B, rFhCB3, were evaluated as antigens in an indirect ELISA to serologically diagnose liver fluke infection in experimentally and naturally infected sheep. rFhCL1 and rFhCL3 were the most effective of the four antigens detecting fasciolosis in sheep as early as three weeks after experimental infection, at least five weeks earlier than both coproantigen and faecal egg tests. In addition, the rFhCL1 and rFhCL3 ELISAs had a very low detection limit for liver fluke in lambs exposed to natural infection on pastures and thus could play a major role in the surveillance of farms and a ‘test and treat’ approach to disease management. Finally, antibodies to all three cathepsin L proteases remain high throughout chronic infection but decline rapidly after drug treatment with the flukicide, triclabendazole, implying that the test may be adapted to trace the effectiveness of drug treatment.
  • Effects of faba bean, blue lupin and rapeseed meal supplementation on nitrogen digestion and utilization of dairy cows fed grass silage-based diets

    Kuoppala, K.; Jaakkola, S.; Garry, B.; Ahvenjärvi, S.; Rinne, M.; Teagasc Walsh Fellowship; Strategic Research Program of the Academy of Finland; no293045 and 314243; Novel protein Sources of Food Security (Elsevier, 2021-07)
    There is increasing interest in using locally produced protein supplements in dairy cow feeding. The objective of this experiment was to compare rapeseed meal (RSM), faba beans (FBs) and blue lupin seeds (BL) at isonitrogenous amounts as supplements of grass silage and cereal based diets. A control diet (CON) without protein supplement was included in the experiment. Four lactating Nordic Red cows were used in a 4 × 4 Latin Square design with four 21 d periods. The milk production increased with protein supplementation but when expressed as energy corrected milk, the response disappeared due to substantially higher milk fat concentration with CON compared to protein supplemented diets. Milk protein output increased by 8.5, 4.4 and 2.7% when RSM, FB and BL were compared to CON. The main changes in rumen fermentation were the higher propionate and lower butyrate proportion of total rumen volatile fatty acids when the protein supplemented diets were compared to CON. Protein supplementation also clearly increased the ruminal ammonia N concentration. Protein supplementation improved diet organic matter and NDF digestibility but efficiency of microbial protein synthesis per kg organic matter truly digested was not affected. Flow of microbial N was greater when FB compared to BL was fed. All protein supplements decreased the efficiency of nitrogen use in milk production. The marginal efficiency (amount of additional feed protein captured in milk protein) was 0.110, 0.062 and 0.045 for RSM, FB and BL, respectively. The current study supports the evidence that RSM is a good protein supplement for dairy cows, and this effect was at least partly mediated by the lower rumen degradability of RSM protein compared to FB and BL. The relatively small production responses to protein supplementation with simultaneous decrease in nitrogen use efficiency in milk production suggest that economic and environmental consequences of protein feeding need to be carefully considered.
  • Effect of dietary restriction and subsequent realimentation on hepatic oxidative phosphorylation in cattle

    Keogh, K.; McKenna, C.; Porter, R.K.; Waters, S.M.; Kenny, D.A.; Science Foundation Ireland; 09/RFP/GEN2447 (Elsevier, 2021-01)
    Compensatory growth (CG) is a naturally accelerated growth which occurs upon realimentation, following a prior period of dietary restriction. The process is harnessed worldwide as a management practice to reduce feed costs in beef cattle production. The objective of this study was to assess the potential contribution of hepatic cellular mitochondrial capacity to CG through global hepatic oxidative phosphorylation gene expression analyses as well as functional mitochondrial enzyme activity assays. Holstein–Friesian bulls were separated into two groups: (i) restricted feed allowance for 125 days (Period 1) (RES; n = 30) followed by ad-libitum feeding for 55 days (Period 2) or (ii) ad-libitum access to feed throughout (Periods 1 and 2) (ADLIB; n = 30). At the end of each period, 15 animals from each treatment group were slaughtered and hepatic tissue was collected. Tissue samples were subjected to RNAseq and spectrophotometric analysis for the functional assessment of mitochondria. RES and ADLIB groups grew at 0.6 kg/day and 1.9 kg/day, respectively, during Period 1. During Period 2, the RES group underwent CG growing at 2.5 kg/day, with ADLIB animals gaining 1.4 kg/day. Oxidative phosphorylation genes were differentially expressed in response to both dietary restriction and CG. Spectrophotometric assays indicated that mitochondrial abundance was greater in animals undergoing dietary restriction at the end of Period 1 and subsequently reduced during realimentation (P < 0.02). Results indicate that mitochondrial capacity may be enhanced during dietary restriction to more effectively utilize diet-derived nutrients. However, enhanced mitochondrial capacity does not appear to be directly contributing to CG in cattle.

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