The aim of the Teagasc Animal and Grassland Research & Innovation Programme is to increase the profitability, competitiveness and sustainability of Irish livestock production through research and innovation.

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

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

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

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

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

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

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

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

    Argüello, Hector; Garcia Manzanilla, Edgar; Lynch, Helen; Walia, Kavita; Leonard, Finola C.; Egan, John; Duffy, Geraldine; Gardiner, Gillian E.; Lawlor, Peadar G.; Department of Agriculture Food and the Marine; et al. (Frontiers Media SA, 2018-02-15)
    Among the zoonotic pathogens affecting pigs, Salmonella stands out due to the high number of human cases linked to pork consumption. In the last two decades many countries have put considerable effort into the control of the infection by surveillance and control strategies on farm. Despite this effort, many herds still have a high Salmonella prevalence and they require guidance to address this problem. The present study, using the serological surveillance data of finishing pigs from the Irish National pig Salmonella Control Programme, aimed to highlight factors associated with increased risk or that might mitigate Salmonella occurrence on farm. A questionnaire with 33 questions regarding herd characteristics, management, feeding, biosecurity, and health was completed for 61 individual herds. After the multivariate analysis by linear regression, nine variables were retained in the final model and linked to herd seroprevalence. Home produced-feed linked to the use of meal showed an eight points reduction in Salmonella prevalence compared to purchased feed (p = 0.042). Different biosecurity measures were associated to lower seroprevalence. Changing of footwear from outside to inside the farm decreased seroprevalence nearly 20 units (p = 0.014) and policies not permitting access to the farmyard to feed trucks (p = 0.048) or avoiding the presence of cats on the farm (p = 0.05) were estimated in 10 units less of seroprevalence. In contrast, the lack of perimeter fence increased the chance to have higher seroprevalence in five units (p = 0.05). Finally, intestinal diseases such as swine dysentery (p = 0.044) and E. coli diarrhea (p = 0.1) were estimated to increase Salmonella prevalence in ∼20 and 10 units, respectively, demonstrating the importance of controlling other enteric pathogens in an on-farm Salmonella control programme. These results show the usefulness of surveillance data to improve on-farm control and confirm that Salmonella infection in pigs is multi-factorial and the approach to its control should be multifaceted.
  • Divergent functional isoforms drive niche specialisation for nutrient acquisition and use in rumen microbiome

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

    Smith, Paul E; Waters, Sinead M; Kenny, David A; Kirwan, Stuart F; Conroy, Stephen; Kelly, Alan K; FACCE ERA-GAS; European Union; Teagasc Walsh Scholarship Programme; 16/RD/ERAGAS/1RUMENPREDICT-ROI2017; et al. (Oxford University Press, 2021-10-01)
    Residual expressions of enteric emissions favor a more equitable identification of an animal’s methanogenic potential compared with traditional measures of enteric emissions. The objective of this study was to investigate the effect of divergently ranking beef cattle for residual methane emissions (RME) on animal productivity, enteric emissions, and rumen fermentation. Dry matter intake (DMI), growth, feed efficiency, carcass output, and enteric emissions (GreenFeed emissions monitoring system) were recorded on 294 crossbred beef cattle (steers = 135 and heifers = 159; mean age 441 d (SD = 49); initial body weight (BW) of 476 kg (SD = 67)) at the Irish national beef cattle performance test center. Animals were offered a total mixed ration (77% concentrate and 23% forage; 12.6 MJ ME/kg of DM and 12% CP) ad libitum with emissions estimated for 21 d over a mean feed intake measurement period of 91 d. Animals had a mean daily methane emissions (DME) of 229.18 g/d (SD = 45.96), methane yield (MY) of 22.07 g/kg of DMI (SD = 4.06), methane intensity (MI) 0.70 g/kg of carcass weight (SD = 0.15), and RME 0.00 g/d (SD = 0.34). RME was computed as the residuals from a multiple regression model regressing DME on DMI and BW (R2 = 0.45). Animals were ranked into three groups namely high RME (>0.5 SD above the mean), medium RME (±0.5 SD above/below the mean), and low RME (>0.5 SD below the mean). Low RME animals produced 17.6% and 30.4% less (P < 0.05) DME compared with medium and high RME animals, respectively. A ~30% reduction in MY and MI was detected in low versus high RME animals. Positive correlations were apparent among all methane traits with RME most highly associated with (r = 0.86) DME. MY and MI were correlated (P < 0.05) with DMI, growth, feed efficiency, and carcass output. High RME had lower (P < 0.05) ruminal propionate compared with low RME animals and increased (P < 0.05) butyrate compared with medium and low RME animals. Propionate was negatively associated (P < 0.05) with all methane traits. Greater acetate:propionate ratio was associated with higher RME (r = 0.18; P < 0.05). Under the ad libitum feeding regime deployed here, RME was the best predictor of DME and only methane trait independent of animal productivity. Ranking animals on RME presents the opportunity to exploit interanimal variation in enteric emissions as well as providing a more equitable index of the methanogenic potential of an animal on which to investigate the underlying biological regulatory mechanisms.
  • Multiclonal human origin and global expansion of an endemic bacterial pathogen of livestock

    Yebra, Gonzalo; Harling-Lee, Joshua D.; Lycett, Samantha; Aarestrup, Frank M.; Larsen, Gunhild; Cavaco, Lina M.; Seo, Keun Seok; Abraham, Sam; Norris, Jacqueline M.; Schmidt, Tracy; et al. (Proceedings of the National Academy of Sciences, 2022-12-05)
    Most new pathogens of humans and animals arise via switching events from distinct host species. However, our understanding of the evolutionary and ecological drivers of successful host adaptation, expansion, and dissemination are limited. Staphylococcus aureus is a major bacterial pathogen of humans and a leading cause of mastitis in dairy cows worldwide. Here we trace the evolutionary history of bovine S. aureus using a global dataset of 10,254 S. aureus genomes including 1,896 bovine isolates from 32 countries in 6 continents. We identified 7 major contemporary endemic clones of S. aureus causing bovine mastitis around the world and traced them back to 4 independent host-jump events from humans that occurred up to 2,500 y ago. Individual clones emerged and underwent clonal expansion from the mid-19th to late 20th century coinciding with the commercialization and industrialization of dairy farming, and older lineages have become globally distributed via established cattle trade links. Importantly, we identified lineage-dependent differences in the frequency of host transmission events between humans and cows in both directions revealing high risk clones threatening veterinary and human health. Finally, pangenome network analysis revealed that some bovine S. aureus lineages contained distinct sets of bovine-associated genes, consistent with multiple trajectories to host adaptation via gene acquisition. Taken together, we have dissected the evolutionary history of a major endemic pathogen of livestock providing a comprehensive temporal, geographic, and gene-level perspective of its remarkable success.
  • Transcriptome characterization and differentially expressed genes under flooding and drought stress in the biomass grasses Phalaris arundinacea and Dactylis glomerata

    Klaas, Manfred; Haiminen, Niina; Grant, Jim; Cormican, Paul; Finnan, John; Arojju, Sai Krishna; Utro, Filippo; Vellani, Tia; Parida, Laxmi; Barth, Susanne; et al. (Oxford University Press (OUP), 2019-06-26)
    Background and Aims Perennial grasses are a global resource as forage, and for alternative uses in bioenergy and as raw materials for the processing industry. Marginal lands can be valuable for perennial biomass grass production, if perennial biomass grasses can cope with adverse abiotic environmental stresses such as drought and waterlogging. Methods In this study, two perennial grass species, reed canary grass (Phalaris arundinacea) and cocksfoot (Dactylis glomerata) were subjected to drought and waterlogging stress to study their responses for insights to improving environmental stress tolerance. Physiological responses were recorded, reference transcriptomes established and differential gene expression investigated between control and stress conditions. We applied a robust non-parametric method, RoDEO, based on rank ordering of transcripts to investigate differential gene expression. Furthermore, we extended and validated vRoDEO for comparing samples with varying sequencing depths. Key Results This allowed us to identify expressed genes under drought and waterlogging whilst using only a limited number of RNA sequencing experiments. Validating the methodology, several differentially expressed candidate genes involved in the stage 3 step-wise scheme in detoxification and degradation of xenobiotics were recovered, while several novel stress-related genes classified as of unknown function were discovered. Conclusions Reed canary grass is a species coping particularly well with flooding conditions, but this study adds novel information on how its transcriptome reacts under drought stress. We built extensive transcriptomes for the two investigated C3 species cocksfoot and reed canary grass under both extremes of water stress to provide a clear comparison amongst the two species to broaden our horizon for comparative studies, but further confirmation of the data would be ideal to obtain a more detailed picture.
  • Pathogens, patterns of pneumonia, and epidemiologic risk factors associated with respiratory disease in recently weaned cattle in Ireland

    Murray, Gerard M.; More, Simon J.; Sammin, Dónal; Casey, Mìcheàl J.; McElroy, Máire C.; O’Neill, Rónan G.; Byrne, William J.; Earley, Bernadette; Clegg, Tracy A.; Ball, Hywel; et al. (SAGE, 2017-01-11)
    We examined the pathogens, morphologic patterns, and risk factors associated with bovine respiratory disease (BRD) in 136 recently weaned cattle (“weanlings”), 6–12 mo of age, that were submitted for postmortem examination to regional veterinary laboratories in Ireland. A standardized sampling protocol included routine microbiologic investigations as well as polymerase chain reaction and immunohistochemistry. Lungs with histologic lesions were categorized into 1 of 5 morphologic patterns of pneumonia. Fibrinosuppurative bronchopneumonia (49%) and interstitial pneumonia (48%) were the morphologic patterns recorded most frequently. The various morphologic patterns of pulmonary lesions suggest the involvement of variable combinations of initiating and compounding infectious agents that hindered any simple classification of the etiopathogenesis of the pneumonias. Dual infections were detected in 58% of lungs, with Mannheimia haemolytica and Histophilus somni most frequently recorded in concert. M. haemolytica (43%) was the most frequently detected respiratory pathogen; H. somni was also shown to be frequently implicated in pneumonia in this age group of cattle. Bovine parainfluenza virus 3 (BPIV-3) and Bovine respiratory syncytial virus (16% each) were the viral agents detected most frequently. Potential respiratory pathogens (particularly Pasteurella multocida, BPIV-3, and H. somni) were frequently detected (64%) in lungs that had neither gross nor histologic pulmonary lesions, raising questions regarding their role in the pathogenesis of BRD. The breadth of respiratory pathogens detected in bovine lungs by various detection methods highlights the diagnostic value of parallel analyses in respiratory disease postmortem investigation.
  • Surgical castration with pain relief affects the health and productive performance of pigs in the suckling period

    Morales, Joaquin; Dereu, Andre; Manso, Alberto; de Frutos, Laura; Piñeiro, Carlos; Garcia Manzanilla, Edgar; Wuyts, Niels; Zoetis Inc. (Springer Science and Business Media LLC, 2017-09-06)
    Background Surgical castration is still practiced in many EU countries to avoid undesirable aggressive behavior and boar taint in male pigs. However, evidence shows that castration is painful and has a detrimental influence on pig health. This study investigated the clinical and productive effects of surgical castration in the suckling period. A total of 3696 male pigs, 3 to 6 days old, comprising of 721 litters from two different farms were included in the study. Within each litter, half of the males were kept as intact males (IM) and half were surgically castrated (CM). Surgical castration was conducted by a trained farmer. Average daily gain (ADG), body weight at weaning (BWW), percentage of pre-weaning mortality (PWM) and antibiotic usage were measured. Pig major acute phase protein (PigMAP) serum concentrations were analyzed prior to castration, and on days 1 and 10 after castration. Productive performance data were analyzed using a linear mixed model. Mortality and percentage of pigs treated with antibiotics were analyzed using the Fisher’s exact test. Results No overall differences in BWW and ADG were observed between the two groups. However, differences were observed when the same effects were analyzed in the 25% lightest, 50% medium and 25% heaviest pigs at birth. PWM was higher in CM than in IM groups (6.3% vs 3.6%; p < 0.001), especially in the light (12.2% vs 6.2%; p = 0.02) and in the medium (5.5% vs 2.7%; p = 0.04) weight groups. In the heaviest pigs group PWM was not affected by castration, but IM tended to show higher ADG (p = 0.06) and showed higher BWW (8.0 kg vs 7.8 kg; p = 0.05) than CM. There were no differences in percentage of pigs treated with antibiotics between the two groups (5.8% vs 5.8%; p = 0.98) in this study. Furthermore, PigMAP was increased in CM the day after castration (0.944 mg/ml vs 0.847 mg/ml; p = 0.025), but there was no difference between CM and IM groups at day 10. Conclusions Surgical castration has a negative impact on production in the suckling period because it causes an increase in PWM, especially in pigs in the three lower quartiles for body weight, and negatively affects the BWW in pigs born in the highest quartile for body weight.
  • The transcriptome of the endometrium and placenta is associated with pregnancy development but not lactation status in dairy cows

    Moore, Stephen G.; McCabe, Matthew S.; Green, Jacob C.; Newsom, Emily M.; Lucy, Matthew C. (Oxford University Press (OUP), 2017-06-19)
    Infertility in lactating dairy cows is explained partially by the metabolic state associated with high milk production. The hypothesis was that lactating and nonlactating cows would differ in endometrial and placental transcriptomes during early pregnancy (day 28 to 42) and this difference would explain the predisposition for lactating cows to have embryonic loss at that time. Cows were either milked or not milked after calving. Reproductive [endometrium (caruncular and intercaruncular) and placenta] and liver tissues were collected on day 28, 35, and 42 of pregnancy. The hypothesis was rejected because no effect of lactation on mRNA abundance within reproductive tissues was found. Large differences within liver demonstrated the utility of the model to test an effect of lactation on tissue gene expression. Major changes in gene expression in reproductive tissues across time were found. Greater activation of the transcriptome for the recruitment and activation of macrophages was found in the endometrium and placenta. Changes in glucose metabolism between day 28 and 42 included greater mRNA abundance of rate-limiting genes for gluconeogenesis in intercaruncular endometrium and evidence for the establishment of aerobic glycolysis (Warburg effect) in the placenta. Temporal changes were predicted to be controlled by CSF1, PDGFB, TGFB1, and JUN. Production of nitric oxide and reactive oxygen species by macrophages was identified as a mechanism to promote angiogenesis in the endometrium. Reported differences in pregnancy development for lactating vs. nonlactating cows could be explained by systemic glucose availability to the conceptus and appeared to be independent of the endometrial and placental transcriptomes.
  • Association between the prion protein genotype and animal performance traits in a large multibreed sheep population

    McHugh, Noirin; O'Brien, A.C.; Pabiou, T.; McDermott, K.; Berry, Donagh; Department of Agriculture, Food and the Marine; 14/S/849 (Elsevier, 2022-07-31)
    Genetic susceptibility to scrapie, a fatal disease of sheep and goats, is modulated by polymorphisms in the prion protein (PrP). Neither the frequency of the PrP genotypes nor their association with animal performance has been investigated in a large multibreed Irish sheep population. Scrapie genotypes were available on 16 416 animals; the breeds represented included purebred Belclare (733), Charollais (333), Suffolk (739), Texel (1 857), Vendeen (191), and crossbreds (12 563). Performance data on lambing, lamb and ewe performance as well as health traits were available. The association between alternative approaches of describing the PrP genotype (i.e. 15 individually called PrP genotypes, five genotype classes representing susceptibility to scrapie, or number of ARR haplotypes) and animal performance were quantified using animal linear mixed models. All 15 of the possible scrapie genotypes were detected, although the frequency differed by breed. The frequency of the five PrP haplotypes in the entire population were 0.70 (ARR), 0.15 (ARQ), 0.11 (ARH), 0.02 (AHQ) and 0.01 (VRQ); the most susceptible haplotype (VRQ) was only detected in purebred Texels and crossbreds. No association was detected between the PrP genotype of either the animal or dam and any of the lambing traits (i.e. lambing difficulty score, perinatal mortality and birth weight). With the exception of ultrasound muscle depth, no association between the PrP genotype and any of the lamb performance traits (i.e. lamb BW and carcass) was observed. Lambs carrying the category four PrP genotype (i.e. ARR/VRQ) had 1.20 (SE = 0.45) mm, 1.38 (SE = 0.12) mm, 1.47 (S = 0.25) mm shallower ultrasound muscle depth relative to lambs of the less susceptible scrapie categories of 1, 2, 3, respectively (P < 0.05). Nonetheless, no association between PrP genotype and lamb carcass conformation, the ultimate end goal of producers, was detected. Ewe litter size, body condition score or lameness did not differ by PrP genotype of the ewe (P > 0.05). For ewe mature BW, ARH/VRQ ewes differed from most other ewe PrP genotypes and were, on average, 3.79 (SE = 1.66) kg heavier than ARR/ARR genotype ewes. Lamb dag score differed by dam PrP genotype (P < 0.05), although the differences were small. Results from this study show that scrapie is segregating within the Irish sheep population, but the PrP genotype was not associated with most traits investigated and, where associations were detected, the biological significance was minimal. This suggests minimal impact of selection on PrP genotype on performance, at least for the traits investigated in the present study.
  • A novel hybrid coagulation-constructed wetland system for the treatment of dairy wastewater

    Mohamed, A.Y.A.; Siggins, A.; Healy, M.G.; Ó hUallacháin, Daire; Fenton, Owen; Tuohy, P.; Teagasc Walsh Fellowship; RMIS-0386 (Elsevier, 2022-07-29)
    Constructed wetlands (CWs) are a cost-effective and sustainable treatment technology that may be used on farms to treat dairy wastewater (DWW). However, CWs require a large area for optimal treatment and have poor long-term phosphorus removal. To overcome these limitations, this study uses a novel, pilot-scale coagulation-sedimentation process prior to loading CWs with DWW. This hybrid system, which was operated on an Irish farm over an entire milking season, performed well at higher hydraulic loading rates than conventional CWs, and obtained removal efficiencies ≥99 % for all measured water quality parameters (chemical oxygen demand, total nitrogen and phosphorus, total suspended solids and turbidity), which complied with EU directives concerning urban wastewater treatment. Overall, the hybrid coagulation-CW is a promising technology that requires a smaller area than conventional CWs and minimal operator input, and produces high effluent quality.
  • An evaluation of four private animal health and welfare standards and associated quality assurance programmes for dairy cow production

    More, S.J.; Marchewka, J.; Hanlon, A.; Balzani, A.; Boyle, Laura Ann; Department of Agriculture, Food and the Marine; RSF 17/S/230 (Elsevier, 2021-12-31)
    Private standards in animal health and welfare (AHW) and associated quality assurance (QA) programmes are an important instrument for food policy with the potential to substantially improve AHW. However, there are concerns that they do not necessarily do so. In this study, we evaluated four private AHW standards and associated QA programmes for dairy cow production, from Denmark, Ireland, the Netherlands and the United Kingdom, using an existing (but adapted) conceptual framework. The framework considers criteria relating to programme goals including relevance to AHW, programme beneficiaries, effectiveness, efficiency and transparency. The current study focused on information that was publicly available online. We found limited objective information to support programme claims, although there were considerable differences between programmes. Across all programmes, problems were identified with respect to transparency, and attempts to scrutinise claims would not be a straightforward process for most consumers. Among the programmes, there were notable examples of best-practice in AHW, relating to science-based evidence, separation of risk assessment and risk management, animal-based measures, farm benchmarking, ongoing programme-level metrics and measurement, and ongoing programme review. There is a need for careful scrutiny of private standards and QA programmes, to provide consumers with assurance with respect to programme effectiveness and transparency. Further, it is important that programme efficiencies are maximised. There is a strong case for regulatory oversight of private standards in AHW and associated QA programmes. This could be within existing or defined policy instruments, both to facilitate the positive impact of these programmes and to build confidence among consumers of the validity of programme claims.
  • Application of machine-learning methods to milk mid-infrared spectra for discrimination of cow milk from pasture or total mixed ration diets

    Frizzarin, Maria; O'Callaghan, Tom; Murphy, T.B.; Hennessey, Deirdre; Casa, A.; Science Foundation Ireland; Department of Agriculture, Food and the Marine; 16/RC/3835; 18/SIRG/5562 (Elsevier, 2021-12-31)
    The prevalence of “grass-fed” labeled food products on the market has increased in recent years, often commanding a premium price. To date, the majority of methods used for the authentication of grass-fed source products are driven by auditing and inspection of farm records. As such, the ability to verify grass-fed source claims to ensure consumer confidence will be important in the future. Mid-infrared (MIR) spectroscopy is widely used in the dairy industry as a rapid method for the routine monitoring of individual herd milk composition and quality. Further harnessing the data from individual spectra offers a promising and readily implementable strategy to authenticate the milk source at both farm and processor levels. Herein, a comprehensive comparison of the robustness, specificity, and accuracy of 11 machine-learning statistical analysis methods were tested for the discrimination of grass-fed versus non-grass-fed milks based on the MIR spectra of 4,320 milk samples collected from cows on pasture or indoor total mixed ration–based feeding systems over a 3-yr period. Linear discriminant analysis and partial least squares discriminant analysis (PLS-DA) were demonstrated to offer the greatest level of accuracy for the prediction of cow diet from MIR spectra. Parsimonious strategies for the selection of the most discriminating wavelengths within the spectra are also highlighted.

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