Now showing items 1-20 of 1158

    • 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.
    • Study on the Association between Tail Lesion Score, Cold Carcass Weight, and Viscera Condemnations in Slaughter Pigs

      Teixeira, Dayane Lemos; Harley, Sarah; Hanlon, Alison; O’Connell, Niamh Elizabeth; More, Simon John; Manzanilla, Edgar Garcia; Boyle, Laura Ann; Department of Agriculture, Food and the Marine; RSF 11/S/107 (Frontiers Media SA, 2016-03-14)
      The aim of this study was to assess the relationship between tail lesions, cold carcass weight, and viscera condemnations in an Irish abattoir. The following data were collected at the evisceration point from every third pig slaughtered over 7 days: farm identification, sex, tail lesion score, viscera inspection outcome, and cold carcass weight. Tail lesions were scored according to a 5-point scale. Disease lesions responsible for lung (pleurisy, pneumonia, and abscess), heart (pericarditis), and liver (ascariasis) condemnation were recorded based on the decision of the veterinary inspector (VI). Data on 3,143 pigs from 61 batches were available. The relationship between disease lesions, tail lesion score, and cold carcass weight was studied at individual carcass level, while the relationship between disease lesions and tail lesion score was studied at both carcass and batch level. Tail lesions (score ≥1) were found in 72% of the study population, with 2.3% affected by severe tail lesions (scores ≥3). Pleurisy (13.7%) followed by pneumonia (10.4%) showed the highest prevalence, whereas the prevalence of ascariasis showed the greatest variation between batches (0–75%). Tail lesion score, pleurisy, pleuropneumonia, and pericarditis were associated with reductions in carcass cold weight (P ≤ 0.05) ranging from 3 to 6.6 kg. Tail lesion score was associated with condemnations for pleurisy, pneumonia, and pleuropneumonia (P ≤ 0.05) at a batch level. VI shift was associated with condemnations for pneumonia, pleuropneumonia, and pericarditis (P ≤ 0.05) at a carcass level and with pneumonia at a batch level. Sex was not associated with viscera condemnations but males were more likely to be affected by tail lesions. The relationship between overall tail lesion score and the lung diseases at batch level supports the relationship between poor health and poor welfare of pigs on farms. The inclusion of tail lesion scores at post-mortem meat inspection should be considered as a health and welfare diagnostic tool.
    • Responses in lactose yield, lactose percentage and protein-to-protein-plus-lactose ratio from index selection in New Zealand dairy cattle

      Sneddon, NW; Lopez-Villalobos, N; Davis, SR; Hickson, RE; Shalloo, L; Garrick, DJ; Geary, U; Livestock Improvement Corporation Pat Shannon scholarship (Informa UK Limited, 2016-03-16)
      The breeding goal of the New Zealand dairy industry is to improve the genetic capability of cows to convert pasture-based feed into farmer profit. The New Zealand dairy industry exports over 95% of milk produced and the most significant product by export volume is whole milk powder (WMP). The current selection objective, breeding worth (BW), will increase yields of protein and fat, potentially shifting milk composition further from the ideal composition for making WMP. This study aimed to investigate the correlated responses in lactose yield (LY), lactose percentage (LP) and protein-to-protein-plus-lactose ratio (P:P + L) from selection for BW, BW plus LY, BW plus LP and BW plus P:P + L. Selection for BW is predicted to have per-cow responses of 54.92 kg milk/year, 2.22 kg fat/year, 1.78 kg protein/year and 2.84 kg lactose/year. When lactose was included in the selection objective in the form of LY, LP or P:P + L, genetic responses ranged from −59.98 kg to 61.08 kg milk/year and from −2.67 kg to 3.70 kg lactose/year. The industry could reduce imported lactose requirements per tonne of WMP by 6%–11% by including lactose into the selection objective, compared with selection on BW alone.
    • 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.
    • Effect of Freezing Conditions on Fecal Bacterial Composition in Pigs

      Metzler-Zebeli, Barbara; Lawlor, Peadar; Magowan, Elizabeth; Zebeli, Qendrim; European Union; 311794 (Multidisciplinary Digital Publishing Institute, 2016-02-25)
      Sample preservation and recovery of intact DNA from gut samples may affect the inferred gut microbiota composition in pigs. This study aimed to evaluate the effect of the freezing process and storage temperature prior to DNA extraction on DNA recovery and bacterial community composition in pig feces using quantitative PCR. Fresh fecal samples from six growing pigs were collected and five aliquots of each prepared: (1) total DNA extracted immediately; (2) stored at −20 °C; (3) snap frozen and stored at −20 °C; (4) stored at −80 °C; and (5) snap frozen and stored at −80 °C. Results showed that DNA yields from fresh fecal samples were, on average, 25 to 30 ng higher than those from the various stored samples. The DNA extracted from fresh samples had more gene copies of total bacteria and all targeted bacterial groups per gram feces compared to DNA extraction from frozen samples. Data presentation also modified the observed effect of freeze storage; as results for Lactobacillus group, Enterococcus spp., Streptococcus spp., Clostridium cluster IV, Bacteroides-Prevotella-Porphyromonas and Enterobacteriaceae showed the opposite effect when expressed as relative abundance, by being greater in freeze stored feces than in fresh feces. Snap freezing increased the relative proportion of Clostridium cluster IV by 24%. In conclusion, the freezing process affected DNA yield and bacterial abundances, whereas snap freezing and storage temperature had only little influence on abundances of bacterial populations in pig feces.
    • Genetic gain in perennial ryegrass (Lolium perenne) varieties 1973 to 2013

      McDonagh, J.; O’Donovan, M.; McEvoy, M.; Gilliland, T. J. (Springer Science and Business Media LLC, 2016-08-10)
      Perennial ryegrass (Lolium perenne) forms the basis of grassland production in temperate pastures and is globally one of the most important forage grasses. Consequently, there has been large plant breeding industry investment over the past 40 years in producing new varieties and independent testing systems designed to identify and list those with the most improved performances. This study was conducted at the Plant Testing Station, Crossnacreevy, Northern Ireland and compared the DM yield and sward density of new varieties submitted from 1973 to 2013 and grass digestibility from 1980 to 2013, under conservation and simulated grazing managements. A variety × years matrix was compiled for each parameter and comparable means between varieties never in side by side performance trials were produced. Dry matter yields showed an overall significant (p < 0.001) average annual increase of 0.52 % under conservation and 0.35 % under simulated grazing, with similar gain levels within maturity groups or ploidies. These rates were not constant over time, and periods of no gain occurred in various variety groupings. Sward density of the examined varieties did not change significantly. Herbage digestibility showed no improvement over the timeframe but had the largest differences between concurrent varieties, indicating that improvements were possible in the future. The study indicated that plant breeding gains were primarily DM yield focused with sward density remaining stagnant over the 40 years, while the lack of grass digestibility improvement appeared to only require more time to overcome. Evidence of benefits and risks of variety testing influences on plant breeding objectives was discussed.
    • Effect of mechanical premilking stimulation on milking duration in late lactation

      Upton, J.; Browne, M.; Silva Bolona, P.; Science Foundation Ireland (SFI); Department of Agriculture, Food and Marine; Dairymaster, Causeway, Ireland; 16/RC/3835 (Elsevier, 2022-11)
      This study documents the effect of mechanical prestimulation on the milking duration of pasture-based cows in late lactation to better harness increased capacity of automation in the milk harvesting process. Premilking stimulation, provided via manual or mechanical means, has been shown to promote the milk letdown reflex and assist in achieving quick, comfortable, and complete milk removal from the udder. The literature is lacking knowledge on the effect of mechanical premilking stimulation on milking duration, especially in late lactation and in pasture-based systems, and many pasture-based farms do not practice a full premilking routine because of a lack of labor availability. The current study addresses this gap in knowledge. In this study, we tested 2 treatments: (1) the No Stim treatment used normal farm milking settings with no premilking preparation and (2) the Stim treatment used 60 s of mechanical premilking stimulation, with a rate of 120 cycles per minute and a pulsator ratio of 30:70 on cluster attachment. Once the 60 s of stimulation had elapsed, normal milking settings resumed for the remainder of the milking. Sixty cows were enrolled in the study, which ran for 20 d. The effect of treatment on a.m. milking duration was significant, a.m. milking duration for Stim was 12 s shorter than that of No Stim. The effect of treatment on p.m. milk duration was not significant. Treatment had no effect on a.m./p.m. milk yields, average milk flowrates or peak milk flowrates. Significant differences emerged between treatments on a.m. and p.m. dead time (time from cluster attachment to reach a milk flowrate of 0.2 kg/min). The a.m. and p.m. dead times were 6 s shorter for Stim compared with No Stim. The time taken to achieve peak milk flowrate (time to peak) at morning milking was 7 s shorter for Stim compared with No Stim, and treatment yielded no significant effects on time to peak at p.m. milkings. Treatment also had no significant effect on log10 somatic cell count. Although the percentage of congested teat-ends and teat-barrels was numerically lower for Stim versus No Stim, no statistical differences were detected across these measures. Based on the results of the study, we found merit in applying 60 s of mechanical pre-stimulation at a.m. milking from a milking duration perspective. However, the strategy was not as successful for the p.m. milking. Analysis of the milk flowrate profiles recorded during the study suggest potential utility in employing different machine settings for various milkings based on anticipated yield and level of udder fill.
    • 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.
    • Improved representation of cattle herd dynamics for bio-physical modelling of pathways to a climate neutral land sector

      Henn, Daniel; Humphreys, James; Duffy, Colm; Gibbons, James; Styles, David; Irish Cattle Breeding Federation (Elsevier BV, 2023-12)
      Livestock production contributes to food security and livelihood improvement globally but places a significant burden on the environment. In Ireland, an ongoing transition towards highly profitable dairy production after the phasing out of EU milk quotas has changed the composition of the national cattle herd with more dairy and fewer beef cows. This shift impacts greenhouse gas (GHG) accounting across different cattle cohorts, e.g. increasing the proportion of calves from the dairy herd. Dairy x beef crossbreeds (DxB) increasingly contribute to national beef output, leveraging larger average daily liveweight gain (ADG) traits from beef breeding bulls. OBJECTIVE Prospective modelling of climate and land consequences arising from alternative cattle production strategies requires more accurate simulation of cohort-specific ADG and associated feed requirements and GHG emissions. METHODS A new COHORTS model was developed to improve national climate scenario mitigation modelling. COHORTS is capable of simulating 21 genetics-gender-age cohorts calibrated to Irish performance, using just a few basic input parameters (at minimum dairy- and beef-cow numbers). A cohort specific ADG and average standing liveweight is estimated for each genetic (pure dairy calves, DxB and pure beef calves), gender and age combination, enabling more accurate calculation of energy requirements and enteric fermentation emissions based on IPCC Tier 2 calculations. RESULTS AND CONCLUSIONS National simulation of cattle numbers, enteric fermentation emissions and beef outputs were validated against relevant Irish inventories. For the period between 2006 and 2020, simulations resulted in total cattle numbers, emissions and beef production within 4%, 1.8% and 0.5%, respectively, of officially reported data. Our results indicate that climate projections based on average emission factors for pre-adult cattle cohorts may overestimate emissions in scenarios with projected growing dairy calf numbers and declining beef calf numbers. SIGNIFICANCE Validation using a 15-year data time series provides a high degree of confidence that COHORTS can be used to represent future herd dynamics in a wide range of scenarios, supporting robust policy regarding GHG mitigation, livestock production and land use – distinguishing between different levels of dairy or beef specialisation and across different levels of performance to predict forage (land) requirements and GHG emissions more accurately. COHORTS can be easily adapted for other countries, even when limited data are available.
    • EFFECT OF HOT BONING AND ELEVATED BRINE TEMPERATURE ON THE PROCESSING, STORAGE AND EATING QUALITY OF CURED BEEF HINDQUARTER (M. BICEPS FEMORIS) AND FOREQUARTER (M. PECTORALIS PROFUNDUS) MUSCLES

      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.
    • The effect of fertilizer nitrogen input to grass-clover swards and calving date on the productivity of pasture-based dairy production

      Scully, K.M.; Keogh, B.; O' Brien, B.; Casey, I.A.; Humphreys, J.; Department of Agriculture, Food and the Marine; Walsh Scholarship; RSF 07-511; EAPA_304/2016 (Elsevier, 2021-08)
      The objective of this systems-scale study was to investigate grazing season timeframes on pasture and milk production and on milk processability of dairy systems with compact spring-calving dairy cows grazing white clover (Trifolium repens L.) based grassland. Fifty-four primiparous and multiparous Holstein-Friesian dairy cows were used in a one-factor study with 3 systems (n = 18) and repeated over 2 yr (2008/09 and 2009/10). The 3 systems were: early spring calving with annual fertilizer N input of 100 kg·ha−1 applied in spring (ES100N; 2.1 cows·ha−1; grazing February to November), early spring calving without fertilizer N (ES0N; 1.6 cows·ha−1; grazing February to November) and late spring calving without fertilizer N (LS0N; 1.53 cows·ha−1; grazing April to January). Annual pasture production was affected by an interaction between grazing system and year: Mean annual pasture yields for 2008 and 2009 were ES100N; 10.35 and 9.88, ES0N; 8.88 and 8.63, LS0N; 9.18 and 10.31 t of dry matter (DM)·ha−1 (SEM 0.39). LS0N had higher pasture DM yield in 2009 due to higher clover DM production and biological N fixation compared with the other systems. Clover stolon and root mass in the following February was correlated with stolon and root mass in the previous November with 64% of stolon mass present on LS0N in February (R2 = 0.84). There were no detectable differences in per-lactation milk yield (6,335 kg·cow−1), fat, protein and lactose yields (271, 226, 297 kg·cow−1, respectively), cow liveweight (585 kg) or body condition score (3.02). Although winter grazing favored subsequent clover DM production, biological N fixation and pasture DM production, delaying calving date in spring and extending lactation into the following winter led to inefficient use of this pasture by the grazing herd and lowered the quality of late-lactation milk for processing purposes. Hence, a mean calving date in mid- to late-February is recommended for zero-fertilizer N input clover-based grassland.