• Habitat Selection by Grazing Animals in Heterogeneous Environments: The Case of Hill Sheep In Western Ireland

      Williams, Bryony; Walls, Sean; Walsh, Michael; Gormally, Michael (Royal Irish Academy, 2012-10-19)
      Uplands and peatlands are of high conservation importance and, while grazing animals are a key management tool for conservation, grazing-related damage can easily occur. Damage to European uplands is most notable in Britain and Ireland, where Scottish Blackface is the dominant hill sheep breed. Therefore, if conservation strategies that address concerns of grazing-related damage are to be strengthened, the Scottish Blackface is a good subject and a better understanding of their resource use would be advantageous. While previous habitat selection studies of hill sheep have depended on direct observation, this particular study uses Global Positioning System tracking collars to determine ewe locations. The study site is on a mountainside in western Ireland that is dominated by blanket bog (52.8%) and wet heath (35.3%). Habitat mapping and ewe range and resource selection analyses indicated that habitat selection was significant (P < 0.05), typically acid grassland is selected most followed by wet heath, with blanket bog habitats selected least. Seasonal variation in habitat selection was also evident. These results (1) corroborate the findings of previous work elsewhere on plant community/habitat selection and (2) provide additional information that can be used to strengthen existing or new hill grazing management models that are used to aid decision-making. In particular, management plans should take into consideration the availability (both in terms of total area and connectivity) of the preferred sheep habitats and specifically consider grazing pressure in and between those habitats.
    • Herd health status and management practices on 16 Irish suckler beef farms

      O'Shaughnessy, James; Mee, John F; Doherty, Michael L; Crosson, Paul; Barrett, Damien; Grady, Luke; Earley, Bernadette; Teagasc Walsh Fellowship Programme (Biomed Central, 2013-11-06)
      Background: There have been few studies published internationally which document herd health management practices in suckler beef herds and no published Irish studies. The study objective was to document herd health status and management practices on sixteen Irish suckler beef herds over a two year period (2009–2010). The farms used in the study were part of the Teagasc BETTER farm beef programme. The mean (s.d.) herd size, stocking rate and farm size was 68 cows (27.6), 2.0 LU/ha (0.3) and 64.3 (21.6) adjusted hectares, respectively. Two questionnaires were designed; 1) a farmer questionnaire to collect information on farm background and current herd health control practices and 2) a veterinary questionnaire to collect information on the extent of animal health advice given by veterinarians to their clients and identification of any on-farm herd health issues. Results: Dystocia, calf pneumonia, and calf diarrhoea, in that order, were identified as the primary herd health issues in these Irish suckler beef herds. In addition, substantial deficiencies in biosecurity practices were also identified on these farms. Conclusions: The findings of this study may serve as the focus for future research in animal health management practices in Irish suckler beef herds.
    • Heritability and impact of environmental effects during pregnancy on antral follicle count in cattle

      Walsh, S.W.; Mossa, F.; Butler, Stephen T.; Berry, Donagh P.; Scheetz, D.; Jimenez-Krassel, F.; Templeman, R.J.; Cater, F.; Lonergan, P.; Evans, A. C. O.; Ireland, J. J.; Department of Agriculture, Food and the Marine, Ireland; RSF-06-328; RSF-06-328 (Elsevier for American Dairy Science Association, 2014-07)
      Previous studies have documented that ovarian antral follicle count (AFC) is positively correlated with number of healthy follicles and oocytes in ovaries (ovarian reserve), as well as ovarian function and fertility in cattle. However, environmental factors (e.g., nutrition, steroids) during pregnancy in cattle and sheep can reduce AFC in offspring. The role that genetic and environmental factors play in influencing the variability in AFC and, correspondingly, the size of the ovarian reserve, ovarian function, and fertility, are, however, poorly understood. The present study tests the hypothesis that variability in AFC in offspring is influenced not only by genetic merit but also by the dam age and lactation status (lactating cows vs. nonlactating heifers) and milk production during pregnancy. Antral follicle count was assessed by ultrasonography in 445 Irish Holstein-Friesian dairy cows and 522 US Holstein-Friesian dairy heifers. Heritability estimates for AFC (± standard error) were 0.31 ± 0.14 and 0.25 ± 0.13 in dairy cows and heifers, respectively. Association analysis between both genotypic sire data and phenotypic dam data with AFC in their daughters was performed using regression and generalized linear models. Antral follicle count was negatively associated with genetic merit for milk fat concentration. Also, AFC was greater in offspring of dams that were lactating (n = 255) compared with nonlactating dams (n = 89) during pregnancy and was positively associated with dam milk fat concentration and milk fat-to-protein ratio. In conclusion, AFC in dairy cattle is a moderately heritable genetic trait affected by age or lactation status and milk quality but not by level of dam’s milk production during pregnancy.
    • High level of treatment failure with commonly used anthelmintics on Irish sheep farms

      Keane, Orla M; Keegan, Jason D; Good, Barbara; de Waal, Theo; Fanning, June; Gottstein, Michael; Casey, Micheal; Hurley, Christine; Sheehan, Maresa (Biomed Central, 2014-08-03)
      Background: In 2013 a Technology Adoption Program for sheep farmers was established to encourage the implementation of best management practices on sheep farms in Ireland. There were 4,500 participants in this programme in 2013. As part of this programme, farmers had the option to carry out a drench test to establish the efficacy of their anthelmintic treatment. Results: Flock faecal samples were collected before and after treatment administration and gastrointestinal nematode eggs enumerated. In total there were 1,893 participants in the task, however only 1,585 included both a pre- and post-treatment faecal sample. Of those, 1,308 provided information on the anthelmintic product that they used with 46%, 23% and 28% using a benzimidazole (BZ), levamisole (LEV) and macrocyclic lactone (ML) product respectively. The remaining farmers used a product inapplicable for inclusion in the task such as a flukicide or BZ/LEV combination product. Samples were included for analysis of drench efficacy if the pre-treatment flock egg count was ≥200 eggs per gram and the interval post-sampling was 10–14 days for BZ products, 4–7 days for LEV products and 14–18 days for ML products. These criteria reduced the number of valid tests to 369, 19.5% of all tests conducted. If the reduction post-treatment was ≥95% the treatment was considered effective. Only 51% of treatments were considered effective using this criterion. There was a significant difference in efficacy between the anthelmintic drug classes with BZ effective in only 30% of treatments, LEV effective in 52% of cases and ML effective in 76% of cases. Conclusions: Gastrointestinal nematode anthelmintic treatments, as practiced on Irish farms, have a high failure rate. There was a significant difference between the efficacies of the anthelmintic classes with BZ the least effective and ML the most effective.
    • Horizontal transmission of Escherichia coli O157:H7 during cattle housing, survival kinetics in feces and water of Escherichia coli O157:H7 and characterisation of E. coli O157:H7 isolates from cattle faeces and a feedlot environment

      Scott, Lourda; McGee, Philip; Sheridan, Jim; Earley, Bernadette; Leonard, Nola (Teagasc, 2005-12-01)
      Escherichia coli O157:H7 can cause severe illness and in some cases leading to death. Cattle are the main reservoir with transmission to humans occurring through contamination of food or the environment. Improved understanding of the survival and transmission and survival of E. coli O157:H7 on the farm is essential for developing future controls of this pathogen. This study showed that transmission of E. coli O157:H7 can occur rapidly in groups of housed cattle, with contamination of the pens and hides occurring in 24 hrs. The inoculation dose for cattle is lower than previously reported. Ingestion of bacteria from the hide through social grooming is important for pathogen transmission in housed cattle along with faecal contamination of the environment. Sampling hide will improve the estimation of prevalence of E. coli O157:H7 in pens.
    • Horizontal transmission of Escherichia coli O157:H7 during cattle housing, survival kinetics in feces and water of Escherichia coli O157:H7 and characterisation of E. coli O157:H7 isolates from cattle faeces and a feedlot environment.

      Scott, Lourda; McGee, Philip; Sheridan, Jim; Earley, Bernadette; Leonard, Nola (Teagasc, 2005-12-01)
      Ruminant livestock, particularly cattle, are considered the primary reservoir of E. coli O157:H7. This study examined the transmission of E. coli O157:H7 within groups of cattle during winter housing. Holstein Friesian steers were grouped in 6 pens of 5 animals. An animal inoculated with, and proven to be shedding a marked strain of E. coli O157:H7 was introduced into each pen. Fecal (rectal swabs) and hide samples (900cm2 right rump) were taken from the thirty six animals throughout the study. Water, feed and gate/partition samples from each pen were also examined. Within 24h of introducing the inoculated animals into the pens, samples collected from the drinking water, pen barriers and animal hides were positive for the pathogen. Within 48h, the hides of 20 of 30 (66%) cohort animals from the 6 pens were contaminated with E. coli O157:H7. The first positive fecal samples from the non-inoculated cohort animals were detected three days after the introduction of the inoculated steers. Over the 23 days of the study 15 of 30 cohort animals shed the marked E. coli O157:H7 strain in their feces on at least one occasion. Animal behavior in the pens was monitored over a 12h period using CCTV cameras. The camera footage showed an average of 13 instances of animal grooming in each pen per hour. The study suggests that transmission of E. coli O157:H7 between animals may occur following ingestion of the pathogen at low levels, and that animal hide may be an important source of transmission.
    • The host immune response to gastrointestinal nematode infection in sheep

      McRae, Kathryn M.; Stear, Michael J.; Good, Barbara; Keane, Orla M (Wiley, 2015-10-20)
      Gastrointestinal nematode infection represents a major threat to the health, welfare and productivity of sheep populations worldwide. Infected lambs have a reduced ability to absorb nutrients from the gastrointestinal tract, resulting in morbidity and occasional mortality. The current chemo-dominant approach to nematode control is considered unsustainable due to the increasing incidence of anthelmintic resistance. In addition there is growing consumer demand for food products from animals not subjected to chemical treatment. Future mechanisms of nematode control must rely on alternative, sustainable strategies such as vaccination or selective breeding of resistant animals. Such strategies take advantage of the host's natural immune response to nematodes. The ability to resist gastrointestinal nematode infection is considered to be dependent on the development of a protective acquired immune response; although the precise immune mechanisms involved in initiating this process remain to be fully elucidated. In this paper current knowledge on the innate and acquired host immune response to gastrointestinal nematode infection in sheep and the development of immunity is reviewed.
    • How much grassland biomass is available in Ireland in excess of livestock requirements?

      McEniry, Joseph; Crosson, Paul; Finneran, Eoghan; McGee, Mark; Keady, Tim; O'Kiely, Padraig; Department of Agriculture, Food and the Marine; RSF 07 557 (Teagasc (Agriculture and Food Development Authority), Ireland, 2013)
      Grassland is a dominant biomass resource in Ireland and underpins most animal production systems. However, other commercial uses for grassland biomass exist, including, for example, the production of biogas through anaerobic digestion for the generation of heat, electricity and transport fuel. The objective of this study was to estimate the annual grassland resource available in Ireland in excess of livestock requirements under six contrasting scenarios. Under current grassland management and production practices there is an estimated average annual grassland resource of ca. 1.7 million tonnes of dry matter (DM) available in excess of livestock requirements. Only a small proportion of this resource (0.39 million tonnes of DM per annum) would be available if the targets set out in ‘Food Harvest 2020’ were achieved. However, increasing nitrogen (N) fertiliser input (to the limit permitted by the E.U. Nitrates Directive) combined with increasing the grazed grass utilisation rate of cattle (from 0.60 to 0.80 kg DM ingested by livestock per kg DM grown) has the potential to significantly increase this average resource to 12.2 million t DM/annum, even when allowing for achievement of ‘Food Harvest 2020’ targets. Under these scenarios, alternative uses for grassland biomass such as anaerobic digestion and green biorefining would not compete with traditional dairy, beef and lamb production systems, but could provide an alternative enterprise and income to farmers.
    • Identifying Single Copy Orthologs in Metazoa

      Creevey, Christopher J.; Muller, Jean; Doerks, Tobias; Thompson, Julie D.; Arendt, Detlev; Bork, Peer (PLOS, 2011-12-01)
      The identification of single copy (1-to-1) orthologs in any group of organisms is important for functional classification and phylogenetic studies. The Metazoa are no exception, but only recently has there been a wide-enough distribution of taxa with sufficiently high quality sequenced genomes to gain confidence in the wide-spread single copy status of a gene. Here, we present a phylogenetic approach for identifying overlooked single copy orthologs from multigene families and apply it to the Metazoa. Using 18 sequenced metazoan genomes of high quality we identified a robust set of 1,126 orthologous groups that have been retained in single copy since the last common ancestor of Metazoa. We found that the use of the phylogenetic procedure increased the number of single copy orthologs found by over a third more than standard taxon-count approaches. The orthologs represented a wide range of functional categories, expression profiles and levels of divergence. To demonstrate the value of our set of single copy orthologs, we used them to assess the completeness of 24 currently published metazoan genomes and 62 EST datasets. We found that the annotated genes in published genomes vary in coverage from 79% (Ciona intestinalis) to 99.8% (human) with an average of 92%, suggesting a value for the underlying error rate in genome annotation, and a strategy for identifying single copy orthologs in larger datasets. In contrast, the vast majority of EST datasets with no corresponding genome sequence available are largely under-sampled and probably do not accurately represent the actual genomic complement of the organisms from which they are derived.
    • Illumina MiSeq 16S amplicon sequence analysis of bovine respiratory disease associated bacteria in lung and mediastinal lymph node tissue

      Johnston, Dayle; Earley, Bernadette; Cormican, Paul; Murray, Gerard; Kenny, David A; Waters, Sinead M.; McGee, Mark; Kelly, Alan K; McCabe, Matthew S (Biomed Central, 2017-05-02)
      Background Bovine respiratory disease (BRD) is caused by growth of single or multiple species of pathogenic bacteria in lung tissue following stress and/or viral infection. Next generation sequencing of 16S ribosomal RNA gene PCR amplicons (NGS 16S amplicon analysis) is a powerful culture-independent open reference method that has recently been used to increase understanding of BRD-associated bacteria in the upper respiratory tract of BRD cattle. However, it has not yet been used to examine the microbiome of the bovine lower respiratory tract. The objective of this study was to use NGS 16S amplicon analysis to identify bacteria in post-mortem lung and lymph node tissue samples harvested from fatal BRD cases and clinically healthy animals. Cranial lobe and corresponding mediastinal lymph node post-mortem tissue samples were collected from calves diagnosed as BRD cases by veterinary laboratory pathologists and from clinically healthy calves. NGS 16S amplicon libraries, targeting the V3-V4 region of the bacterial 16S rRNA gene were prepared and sequenced on an Illumina MiSeq. Quantitative insights into microbial ecology (QIIME) was used to determine operational taxonomic units (OTUs) which corresponded to the 16S rRNA gene sequences. Results Leptotrichiaceae, Mycoplasma, Pasteurellaceae, and Fusobacterium were the most abundant OTUs identified in the lungs and lymph nodes of the calves which died from BRD. Leptotrichiaceae, Fusobacterium, Mycoplasma, Trueperella and Bacteroides had greater relative abundances in post-mortem lung samples collected from fatal cases of BRD in dairy calves, compared with clinically healthy calves without lung lesions. Leptotrichiaceae, Mycoplasma and Pasteurellaceae showed higher relative abundances in post-mortem lymph node samples collected from fatal cases of BRD in dairy calves, compared with clinically healthy calves without lung lesions. Two Leptotrichiaceae sequence contigs were subsequently assembled from bacterial DNA-enriched shotgun sequences. Conclusions The microbiomes of the cranial lung lobe and mediastinal lymph node from calves which died from BRD and from clinically healthy H-F calves have been characterised. Contigs corresponding to the abundant Leptotrichiaceae OTU were sequenced and found not to be identical to any known bacterial genus. This suggests that we have identified a novel bacterial species associated with BRD.
    • Illumina MiSeq Phylogenetic Amplicon Sequencing Shows a Large Reduction of an Uncharacterised Succinivibrionaceae and an Increase of the Methanobrevibacter gottschalkii Clade in Feed Restricted Cattle

      McCabe, Matthew Sean; Cormican, Paul; Keogh, Kate; O'Connor, Aaron; O'Hara, Eoin; Palladino, Rafael Alejandro; Kenny, David A.; Waters, Sinead M. (PLOS, 2015-07-30)
      Periodic feed restriction is used in cattle production to reduce feed costs. When normal feed levels are resumed, cattle catch up to a normal weight by an acceleration of normal growth rate, known as compensatory growth, which is not yet fully understood. Illumina Miseq Phylogenetic marker amplicon sequencing of DNA extracted from rumen contents of 55 bulls showed that restriction of feed (70% concentrate, 30% grass silage) for 125 days, to levels that caused a 60% reduction of growth rate, resulted in a large increase of relative abundance of Methanobrevibacter gottschalkii clade (designated as OTU-M7), and a large reduction of an uncharacterised Succinivibrionaceae species (designated as OTU-S3004). There was a strong negative Spearman correlation (ρ = -0.72, P = <1x10-20) between relative abundances of OTU-3004 and OTU-M7 in the liquid rumen fraction. There was also a significant increase in acetate:propionate ratio (A:P) in feed restricted animals that showed a negative Spearman correlation (ρ = -0.69, P = <1x10-20) with the relative abundance of OTU-S3004 in the rumen liquid fraction but not the solid fraction, and a strong positive Spearman correlation with OTU-M7 in the rumen liquid (ρ = 0.74, P = <1x10-20) and solid (ρ = 0.69, P = <1x10-20) fractions. Reduced A:P ratios in the rumen are associated with increased feed efficiency and reduced production of methane which has a global warming potential (GWP 100 years) of 28. Succinivibrionaceae growth in the rumen was previously suggested to reduce methane emissions as some members of this family utilise hydrogen, which is also utilised by methanogens for methanogenesis, to generate succinate which is converted to propionate. Relative abundance of OTU-S3004 showed a positive Spearman correlation with propionate (ρ = 0.41, P = <0.01) but not acetate in the liquid rumen fraction.
    • Impact of agronomic practices of an intensive dairy farm on nitrogen concentrations in a karst aquifer in Ireland

      Huebsch, Manuela; Horan, Brendan; Blum, P; Richards, Karl G.; Grant, Jim; Fenton, Owen; Teagasc Walsh Fellowship Programme (Elsevier, 24/09/2013)
      Exploring the relationship between agricultural nitrogen loading on a dairy farm and groundwater reactive nitrogen concentration such as nitrate is particularly challenging in areas underlain by thin soils and karstified limestone aquifers. The objective of this study is to relate changes in detailed agronomic N-loading, local weather conditions, hydrogeological and geological site characteristics with groundwater N occurrence over an 11-year period on an intensive dairy farm with free draining soils and a vulnerable limestone aquifer. In addition, the concept of vertical time lag from source to receptor is considered. Statistical analysis used regression with automatic variable selection. Four scenarios were proposed to describe the relationships between paddock and groundwater wells using topographic and hydrogeological assumptions. Monitored nitrate concentrations in the studied limestone aquifer showed a general decrease in the observed time period (2002–2011). Statistical results showed that a combination of improved agronomic practices and site specific characteristics such as thicknesses of the soil and unsaturated zone together with hydrogeological connections of wells and local weather conditions such as rainfall, sunshine and soil moisture deficit were important explanatory variables for nitrate concentrations. Statistical results suggested that the following agronomic changes improved groundwater quality over the 11-year period: reductions in inorganic fertiliser usage, improvements in timing of slurry application, the movement of a dairy soiled water irrigator to less karstified areas of the farm and the usage of minimum cultivation reseeding on the farm. In many cases the explanatory variables of farm management practices tended to become more important after a 1- or 2-year time lag. Results indicated that the present approach can be used to elucidate the effect of farm management changes to groundwater quality and therefore the assessment of present and future legislation implementations.
    • Impact of three inactivated bovine viral diarrhoea virus vaccines on bulk milk p80 (NS3) ELISA test results in dairy herds

      Sayers, Riona; Sayers, Gearoid; Graham, David; Arkins, Sean (Elsevier, 2015-03-25)
      Bovine viral diarrhoea virus (BVDV) is endemic in many countries and vaccines are used as a component of control and eradication strategies. Surveillance programmes to detect exposure to BVDV often incorporate the use of bulk milk (BM) testing for antibodies against BVDV p80 (NS3), but vaccination can interfere with these results. The aim of this study was to evaluate whether BVDV vaccines would confound BM testing for specific antibodies in a nationally representative group of commercial dairy farms in the Republic of Ireland. A total of 256 commercial dairy herds were included in the statistical analysis. Quarterly BM or serum samples from selected weanling heifers (unvaccinated homeborn youngstock) were assessed by ELISA for antibodies against the BVDV p80 subunit and whole virus. Wilcoxon ranksum and receiver operating characteristic (ROC) analyses were used to examine differences among groups vaccinated with one of three commercially available inactivated BVDV vaccines. Two of the three vaccines showed evidence of interference with ELISA testing of BM samples. ROC analysis highlighted that one vaccine did not reduce the discriminatory power of the BVDV p80 ELISA for identification of herds with evidence of recent BVDV circulation, when compared with unvaccinated herds; thus, administration of this vaccine would allow uncomplicated interpretation of BM ELISA test results in vaccinated seropositive herds. Seasonal differences in BM antibody results were identified, suggesting that the latter half of lactation is the most suitable time for sampling dairy herds containing predominantly spring calving cows. The results of the present study are likely to prove useful in countries allowing vaccination during or following BVDV eradication, where BM testing is required as part of the surveillance strategy.
    • Implementing biosecurity measures on dairy farms in Ireland

      Sayers, Riona; Sayers, Gearoid; Mee, John F; Good, M.; Bermingham, Mairead L; Grant, Jim; Dillon, Pat (Elsevier, 2012-12-29)
      Dairy farms in Ireland are expanding in preparation for a new era of unrestricted milk production with the elimination of the European Union (EU) production quotas in 2015. Countries experiencing a changing agricultural demographic, including farm expansion, can benefit from documenting the implementation of on-farm biosecurity. The objectives of this study were to document and describe influences on biosecurity practices and related opinions on dairy farms. A representative response rate of 64% was achieved to a nationwide telesurvey of farmers. A 20% discrepancy was found between self-declared and truly ‘closed’ herds indicating a lack of understanding of the closed herd concept. Although >72% of farmers surveyed considered biosecurity to be important, 53% stated that a lack of information might prevent them from improving their biosecurity. Logistic regression highlighted regional, age, and farm-size related differences in biosecurity practices and opinions towards its implementation. Farmers in the most dairy cattle dense region were three times more likely to quarantine purchased stock than were their equivalents in regions where dairy production was less intense (P = 0.012). Younger farmers in general were over twice as likely as middle-aged farmers to implement biosecurity guidelines (P = 0.026). The owners of large enterprises were almost five times more likely to join a voluntary animal health scheme (P = 0.003), and were over three times more likely to pay a premium price for health accredited animals (P = 0.02) than were those farming small holdings. The baseline data recorded in this survey will form the basis for more detailed sociological and demographic research which will facilitate the targeting of future training of the farming community in biosecurity.
    • The Imprinted Retrotransposon-Like Gene PEG11 (RTL1) Is Expressed as a Full-Length Protein in Skeletal Muscle from Callipyge Sheep

      Byrne, Keren; Colgrave, Michelle L.; Vuocolo, Tony; Pearson, Roger; Bidwell, Christopher A.; Cockett, Noelle E.; Lynn, David J; Fleming-Waddell, Jolena N.; Tellam, Ross L. (PLOS, 2010-01-08)
      Members of the Ty3-Gypsy retrotransposon family are rare in mammalian genomes despite their abundance in invertebrates and some vertebrates. These elements contain a gag-pol-like structure characteristic of retroviruses but have lost their ability to retrotranspose into the mammalian genome and are thought to be inactive relics of ancient retrotransposition events. One of these retrotransposon-like elements, PEG11 (also called RTL1) is located at the distal end of ovine chromosome 18 within an imprinted gene cluster that is highly conserved in placental mammals. The region contains several conserved imprinted genes including BEGAIN, DLK1, DAT, GTL2 (MEG3), PEG11 (RTL1), PEG11as, MEG8, MIRG and DIO3. An intergenic point mutation between DLK1 and GTL2 causes muscle hypertrophy in callipyge sheep and is associated with large changes in expression of the genes linked in cis between DLK1 and MEG8. It has been suggested that over-expression of DLK1 is the effector of the callipyge phenotype; however, PEG11 gene expression is also strongly correlated with the emergence of the muscling phenotype as a function of genotype, muscle type and developmental stage. To date, there has been no direct evidence that PEG11 encodes a protein, especially as its anti-sense transcript (PEG11as) contains six miRNA that cause cleavage of the PEG11 transcript. Using immunological and mass spectrometry approaches we have directly identified the full-length PEG11 protein from postnatal nuclear preparations of callipyge skeletal muscle and conclude that its over-expression may be involved in inducing muscle hypertrophy. The developmental expression pattern of the PEG11 gene is consistent with the callipyge mutation causing recapitulation of the normal fetal-like gene expression program during postnatal development. Analysis of the PEG11 sequence indicates strong conservation of the regions encoding the antisense microRNA and in at least two cases these correspond with structural or functional domains of the protein suggesting co-evolution of the sense and antisense genes.
    • Improved detection of biomarkers in cervico-vaginal mucus (CVM) from postpartum cattle

      Adnane, Mounir; Kelly, Paul; Chapwanya, Aspinas; Meade, Kieran G; O’Farrelly, Cliona; The Algerian Ministry for High Education and Scientific Research; University of Tiaret, Algeria; Department of Agriculture, Food and the Marine, Ireland; ofarrecl-HRB-HRA_POR/2012/37; 13/S/472 (Biomed Central, 2018-09-29)
      Background In the postpartum cow, early diagnosis of uterine disease is currently problematic due to the lack of reliable, non-invasive diagnostic methods. Cervico-vaginal mucus (CVM) is an easy to collect potentially informative source of biomarkers for the diagnosis and prognosis of uterine disease in cows. Here, we report an improved method for processing CVM from postpartum dairy cows for the measurement of immune biomarkers. CVM samples were collected from the vagina using gloved hand during the first two weeks postpartum and processed with buffer alone or buffer containing different concentrations of the reducing agents recommended in standard protocols: Dithiothriotol (DTT) or N-Acetyl-L-Cysteine (NAC). Total protein was measured using the bicinchoninic acid (BCA) assay; interleukin 6 (IL-6), IL-8 and α1-acid glycoprotein (AGP) were measured by ELISA. Results We found that use of reducing agents to liquefy CVM affects protein yield and the accuracy of biomarker detection. Our improved protocol results in lower protein yields but improved detection of cytokines and chemokines. Using our modified method to measure AGP in CVM we found raised levels of AGP at seven days postpartum in CVM from cows that went on to develop endometritis. Conclusion We conclude that processing CVM without reducing agents improves detection of biomarkers that reflect uterine health in cattle. We propose that measurement of AGP in CVM during the first week postpartum may identify cows at risk of developing clinical endometritis.
    • Improvement of dry-cured Iberian ham sensory characteristics through the use of a concentrate high in oleic acid for pig feeding

      Jurado, A.; Garcia, C.; Timon, M.L.; Carrapiso, A.I. (Teagasc, Oak Park, Carlow, Ireland, 2008)
      The aim of this study was to investigate the sensory characteristics of dry-cured hams from confined Iberian pigs fed on a high oleic (HO) concentrate (HO-Pienso hams), and to study how different the characteristics of these hams are from those of Iberian hams from the best grade (Montanera hams, from extensively reared pigs). Nearly half of the fatty acids studied were similar in HO-Pienso and Montanera hams. No differences were found for 18:1, but some major fatty acids of subcutaneous fat of Iberian hams were different between the HO-Pienso and the Montanera hams (C16:0, C18:0, C18:2). The descriptive test revealed that 15 of the 23 sensory characteristics were not significantly different between both groups of hams. No sensory differences appeared for fat appearance or lean texture characteristics, but lean appearance, oiliness, saltiness and the most intensively perceived characteristics of odour and flavour were significantly different. These differences in the sensory traits between Montanera and Pienso hams were not as marked as found in previous studies. Therefore, the use of a concentrate high in oleic acid enables simulation, at least in part, of the sensory characteristics, especially texture.
    • Imputation of genotypes from low- to high-density genotyping platforms and implications for genomic selection

      Berry, Donagh P.; Kearney, J. F. (Cambridge University Press, 2011-02)
      The objective of this study was to quantify the accuracy achievable from imputing genotypes from a commercially available low-density marker panel (2730 single nucleotide polymorphisms (SNPs) following edits) to a commercially available higher density marker panel (51 602 SNPs following edits) in Holstein–Friesian cattle using Beagle, a freely available software package. A population of 764 Holstein–Friesian animals born since 2006 were used as the test group to quantify the accuracy of imputation, all of which had genotypes for the high-density panel; only SNPs on the low-density panel were retained with the remaining SNPs to be imputed. The reference population for imputation consisted of 4732 animals born before 2006 also with genotypes on the higher density marker panel. The concordance between the actual and imputed genotypes in the test group of animals did not vary across chromosomes and was on average 95%; the concordance between actual and imputed alleles was, on average, 97% across all SNPs. Genomic predictions were undertaken across a range of production and functional traits for the 764 test group animals using either their real or imputed genotypes. Little or no mean difference in the genomic predictions was evident when comparing direct genomic values (DGVs) using real or imputed genotypes. The average correlation between the DGVs estimated using the real or imputed genotypes for the 15 traits included in the Irish total merit index was 0.97 (range of 0.92 to 0.99), indicating good concordance between proofs from real or imputed genotypes. Results show that a commercially available high-density marker panel can be imputed from a commercially available lower density marker panel, which will also have a lower cost, thereby facilitating a reduction in the cost of genomic selection. Increased available numbers of genotyped and phenotyped animals also has implications for increasing the accuracy of genomic prediction in the entire population and thus genetic gain using genomic selection.
    • Imputation of ungenotyped parental genotypes in dairy and beef cattle from progeny genotypes

      Berry, Donagh P.; McParland, Sinead; Kearney, J.F.; Sargolzaei, M.; Mullen, Michael P.; Department of Agriculture, Food and the Marine, Ireland; Science Foundation Ireland; European Union; RSF-06-0353; RSF-06-0428; 1/SF/311; 09/IN.1/B2642 (Cambridge University Press, 2014-04-09)
      The objective of this study was to quantify the accuracy of imputing the genotype of parents using information on the genotype of their progeny and a family-based and population-based imputation algorithm. Two separate data sets were used, one containing both dairy and beef animals (n = 3122) with high-density genotypes (735 151 single nucleotide polymorphisms (SNPs)) and the other containing just dairy animals (n = 5489) with medium-density genotypes (51 602 SNPs). Imputation accuracy of three different genotype density panels were evaluated representing low (i.e. 6501 SNPs), medium and high density. The full genotypes of sires with genotyped half-sib progeny were masked and subsequently imputed. Genotyped half-sib progeny group sizes were altered from 4 up to 12 and the impact on imputation accuracy was quantified. Up to 157 and 258 sires were used to test the accuracy of imputation in the dairy plus beef data set and the dairy-only data set, respectively. The efficiency and accuracy of imputation was quantified as the proportion of genotypes that could not be imputed, and as both the genotype concordance rate and allele concordance rate. The median proportion of genotypes per animal that could not be imputed in the imputation process decreased as the number of genotyped half-sib progeny increased; values for the medium-density panel ranged from a median of 0.015 with a half-sib progeny group size of 4 to a median of 0.0014 to 0.0015 with a half-sib progeny group size of 8. The accuracy of imputation across different paternal half-sib progeny group sizes was similar in both data sets. Concordance rates increased considerably as the number of genotyped half-sib progeny increased from four (mean animal allele concordance rate of 0.94 in both data sets for the medium-density genotype panel) to five (mean animal allele concordance rate of 0.96 in both data sets for the medium-density genotype panel) after which it was relatively stable up to a half-sib progeny group size of eight. In the data set with dairy-only animals, sufficient sires with paternal half-sib progeny groups up to 12 were available and the withinanimal mean genotype concordance rates continued to increase up to this group size. The accuracy of imputation was worst for the low-density genotypes, especially with smaller half-sib progeny group sizes but the difference in imputation accuracy between density panels diminished as progeny group size increased; the difference between high and medium-density genotype panels was relatively small across all half-sib progeny group sizes. Where biological material or genotypes are not available on individual animals, at least five progeny can be genotyped (on either a medium or high-density genotyping platform) and the parental alleles imputed with, on average, ⩾96% accuracy.
    • Increased detection of mastitis pathogens by real-time PCR compared to bacterial culture

      Keane, Orla M; Budd, Kathleen E; Flynn, James; McCoy, Finola (British Veterinary Association, 2013-08-23)
      Rapid and accurate identification of mastitis pathogens is important for disease control. Bacterial culture and isolate identification is considered the gold standard in mastitis diagnosis but is time consuming and results in many culture-negative samples. Identification of mastitis pathogens by PCR has been proposed as a fast and sensitive alternative to bacterial culture. The results of bacterial culture and PCR for the identification of the aetiological agent of clinical mastitis were compared. The pathogen identified by traditional culture methods was also detected by PCR in 98 per cent of cases indicating good agreement between the positive results of bacterial culture and PCR. A mastitis pathogen could not be recovered from approximately 30 per cent of samples by bacterial culture, however, an aetiological agent was identified by PCR in 79 per cent of these samples. Therefore, a mastitis pathogen was detected in significantly more milk samples by PCR than by bacterial culture (92 per cent and 70 per cent, respectively) although the clinical relevance of PCR-positive culture-negative results remains controversial. A mixed infection of two or more mastitis pathogens was also detected more commonly by PCR. Culture-negative samples due to undetected Staphylococcus aureus infections were rare. The use of PCR technology may assist in rapid mastitis diagnosis, however, accurate interpretation of PCR results in the absence of bacterial culture remains problematic.