• Schmallenberg virus: a systematic international literature review (2011-2019) from an Irish perspective

      Collins, Áine B; Doherty, Michael L; Barrett, Damien J; Mee, John F; Teagasc Walsh Fellowship Programme (Biomed Central, 2019-10-09)
      In Autumn 2011, nonspecific clinical signs of pyrexia, diarrhoea, and drop in milk yield were observed in dairy cattle near the German town of Schmallenberg at the Dutch/German border. Targeted veterinary diagnostic investigations for classical endemic and emerging viruses could not identify a causal agent. Blood samples were collected from animals with clinical signs and subjected to metagenomic analysis; a novel orthobunyavirus was identified and named Schmallenberg virus (SBV). In late 2011/early 2012, an epidemic of abortions and congenital malformations in calves, lambs and goat kids, characterised by arthrogryposis and hydranencephaly were reported in continental Europe. Subsequently, SBV RNA was confirmed in both aborted and congenitally malformed foetuses and also in Culicoides species biting midges. It soon became evident that SBV was an arthropod-borne teratogenic virus affecting domestic ruminants. SBV rapidly achieved a pan-European distribution with most countries confirming SBV infection within a year or two of the initial emergence. The first Irish case of SBV was confirmed in the south of the country in late 2012 in a bovine foetus. Since SBV was first identified in 2011, a considerable body of scientific research has been conducted internationally describing this novel emerging virus. The aim of this systematic review is to provide a comprehensive synopsis of the most up-to-date scientific literature regarding the origin of SBV and the spread of the Schmallenberg epidemic, in addition to describing the species affected, clinical signs, pathogenesis, transmission, risk factors, impact, diagnostics, surveillance methods and control measures. This review also highlights current knowledge gaps in the scientific literature regarding SBV, most notably the requirement for further research to determine if, and to what extent, SBV circulation occurred in Europe and internationally during 2017 and 2018. Moreover, recommendations are also made regarding future arbovirus surveillance in Europe, specifically the establishment of a European-wide sentinel herd surveillance program, which incorporates bovine serology and Culicoides entomology and virology studies, at national and international level to monitor for the emergence and re-emergence of arboviruses such as SBV, bluetongue virus and other novel Culicoides-borne arboviruses.
    • Scientific appraisal of the Irish grass-based milk production system as a sustainable source of premium quality milk and dairy products

      O'Brien, Bernadette; Hennessy, Deirdre (Teagasc (Agriculture and Food Development Authority), Ireland, 2017-12-29)
      The Irish dairy industry is critically important to the economy and general well-being of a large section of the Irish population. Its quality, sustainability and maintenance are the key for a vibrant rural society in the future. Two important elements for the future of this industry include (a) the quality, marketing and sale of dairy products on the export market and (b) sustainability from the perspectives of people, planet and profit. This paper provides a short review of current scientific evidence in relation to a number of topics, each of which is important in maintaining and developing dairy product quality and the sustainability of the Irish dairy industry. The topics addressed in the paper are as follows: the parameters of milk composition; milk processing; hygiene quality and safety; farm management practices and the regulations that govern such practices; animal health and welfare; environmental impacts; economic implications for farm families and rural communities; and the overall future sustainability of the family-based dairy farm structure.
    • Seasonality of nitrogen uptake, apparent recovery of fertilizer nitrogen and background nitrogen supply in two Irish grassland soils

      Murphy, Paul N. C.; O'Connell, K.; Watson, S.; Watson, C. J.; Humphreys, James; Irish National Development Plan; Irish Dairy Levy Research Trust (Teagasc (Agriculture and Food Development Authority), Ireland, 2013)
      Improving fertilizer nitrogen (N) use efficiency is central to sustainable and profitable grassland agriculture. A plot experiment with a control and fertilizer N (calcium ammonium nitrate, 25–50 kg/ha N) applied on nine occasions from February to September 2002 was conducted at two sites in southwest Ireland to assess N uptake and apparent recovery of fertilizer N (ARFN). Apparent recovery of fertilizer N after eight weeks varied from low in February (21%) and March (46%) to high from April to August (69–98%), indicating that high N use efficiency can be achieved in Irish grasslands at these times. Low recovery in spring suggested that N was applied in excess of immediate crop requirements. Note that N uptake and ARFN values from this study are likely to be somewhat conservative, particularly for spring applications. Over the 8 weeks during which growth was monitored, most (70%) of the grass yield and N uptake response to fertilizer N were in weeks 1 to 4 after application; however, a significant (30%) response occurred in weeks 5–8. This suggested that residual N availability following grazing at 4 weeks can be significant and that there may be scope to decrease N application rates in a grazing rotation. This can potentially improve N use efficiency and decrease N surpluses, with associated economic and environmental benefits. Apparent recovery of fertilizer N was closely related to soil temperature, with a 5.8% increase in ARFN with a 1 °C increase in temperature. Background (non-fertilizer) N supply contributed an average of 164 kg/ha per year (49%) taken up by the fertilized sward, highlighting the potential importance of soil N mineralisation to grassland productivity. Note that these results are for one year at two sites and that conditions may vary between years and at other sites and also that the experiment did not reproduce the cumulative effect of repeated fertilizer application over the grazing year.
    • Selection of calibration sub-sets to predict ryegrass quality using principle component analysis for near infrared spectroscopy

      Burns, G. A.; O'Kiely, Padraig; Gilliland, T. J.; Department of Agriculture, Food and the Marine; RSF –07 526 (British Grassland Society, 2015-09)
      Near infrared reflectance spectroscopy (NIRS) has become the routine method of assessing forage quality on grass evaluation and breeding programmes. NIRS requires predictive calibration models that relate spectral data to reference values developed using a calibration set (Burns et al. 2013). The samples that form the calibration set influence the accuracy and reliability of these models and need to be representative of samples that will likely be analysed (Shenk and Westerhaus, 1991; Burns et al. 2014). Analysing samples from the calibration set using reference techniques has a significant cost and time associated and needs to be considered in the context of the desired accuracy and robustness of calibration models. Calibration selection techniques can therefore maximise the accuracy and robustness of calibration models whilst reducing the number of samples requiring reference analysis. One such method is principal component analysis (PCA; Shenk and Westerhaus, 1991) whereby Shetty et al. (2012) reported that the number of samples could be reduced by up to 80% with a minimal loss in accuracy of calibration model. PCA selects representative calibration sub-sets through plotting all the samples in hyper-dimensional space, based on spectral data, and a sample is selected to represent a local neighbourhood cluster of samples for reference analysis. The aim of this research was to assess the accuracy of NIRS calibration models for buffering capacity, in vitro dry matter digestibility (DMD) and water soluble carbohydrate (WSC) content developed using calibration sub-sets selected by PCA.
    • Sharpea and Kandleria are lactic acid producing rumen bacteria that do not change their fermentation products when co-cultured with a methanogen

      Kumar, Sandeep; Treloar, Bryan P.; Teh, Koon Hoong; McKenzie, Catherine M.; Henderson, Gemma; Attwood, Graeme T.; Waters, Sinead M.; Patchett, Mark L.; Janssen, Peter H.; Teagasc Walsh Fellowship Programme; et al. (Elsevier, 2018-07-25)
      Sharpea and Kandleria are associated with rumen samples from low-methane-emitting sheep. Four strains of each genus were studied in culture, and the genomes of nine strains were analysed, to understand the physiology of these bacteria. All eight cultures grew equally well with d-glucose, d-fructose, d-galactose, cellobiose, and sucrose supplementation. d-Lactate was the major end product, with small amounts of the mixed acid fermentation products formate, acetate and ethanol. Genes encoding the enzymes necessary for this fermentation pattern were found in the genomes of four strains of Sharpea and five of Kandleria. Strains of Sharpea produced traces of hydrogen gas in pure culture, but strains of Kandleria did not. This was consistent with finding that Sharpea, but not Kandleria, genomes contained genes coding for hydrogenases. It was speculated that, in co-culture with a methanogen, Sharpea and Kandleria might change their fermentation pattern from a predominately homolactic to a predominately mixed acid fermentation, which would result in a decrease in lactate production and an increase in formation of acetate and perhaps ethanol. However, Sharpea and Kandleria did not change their fermentation products when co-cultured with Methanobrevibacter olleyae, a methanogen that can use both hydrogen and formate, and lactate remained the major end product. The results of this study therefore support a hypothesis that explains the link between lower methane yields and larger populations of Sharpea and Kandleria in the rumens of sheep.
    • Short communication: Effects of changing teatcup removal and vacuum settings on milking efficiency of an automatic milking system

      Upton, John; Bolona, P. Silva; Reinemann, D. J.; Teagasc Wash Fellowship Programme; University of Wisconsin-Madison; Lely, The Netherlands (Elsevier, 2019-08-22)
      The aim of this experiment was to assess strategies to reduce milking time in a pasture-based automatic milking system (AMS). Milking time is an important factor in automatic milking because any reductions in box time can facilitate more milkings per day and hence higher production levels per AMS. This study evaluated 2 end-of-milking criteria treatments (teatcup removal at 30% and 50% of average milk flowrate at the quarter-level), 2 milking system vacuum treatments (static and dynamic, where the milking system vacuum could change during the peak milk flowrate period), and the interaction of these treatment effects on milking time in a Lely Astronaut A4 AMS (Maassluis, the Netherlands). The experiment was carried out at the research facility at Teagasc Moorepark, Cork, Ireland, and used 77 spring-calved cows, which were managed on a grass-based system. Cows were 179 DIM, with an average parity of 3. No significant differences in milk flowrate, milk yield, box time, milking time, or milking interval were found between treatments in this study on cows milked in an AMS on a pasture-based system. Average and peak milk flowrates of 2.15 kg/min and 3.48 kg/min, respectively, were observed during the experiment. Small increases in maximum milk flowrate were detected (+0.09 kg/min) due to the effect of increasing the system vacuum during the peak milk flow period. These small increases in maximum milk flowrate were not sufficient to deliver a significant reduction in milking time or box time. Furthermore, increasing the removal setting from 30% of the average milk flowrate to 50% of the average milk flowrate was not an effective means of reducing box time, because the resultant increase in removal flowrate of 0.12 kg/min was not enough to deliver practical or statistically significant decreases in milking time or box time. Hence, to make significant reductions in milking time, where cows have an average milk flow of 2 kg/min and yield per milking of 10 kg, end-of-milking criteria above 50% of average milk flowrate at the quarter level would be required.
    • Short Communication: The effect of dry period duration and dietary energy density on the rennet gelation properties of milk in early lactation

      Butler, Stephen T.; de Feu, M.A.; O'Brien, Bernadette; Guinee, Timothy P.; Murphy, J.J.; National Development Plan (Dublin, Ireland) (American Dairy Science Association and Elsevier Inc., 2010-02)
      This study was carried out to examine the effects of decreasing dry period duration (DP) and altering the energy density of the diet during early lactation on the rheological characteristics of milk. Forty mature Holstein-Friesian cows were used in a completely randomized design with a 2 × 2 factorial arrangement of treatments. Cows were randomly assigned to one of two dry period treatments and one of two nutritional treatments. The dry period treatments were continuous milking (CM) or an 8-week standard dry period (SDP), and the nutritional treatments were a standard energy diet (SE) or a high energy diet (HE). Actual dry period lengths were 6.3 ± 1.7 days and 62.1 ± 1.9 days for cows for the CM and SDP treatments, respectively. Milk samples were collected at 2, 6 and 10 weeks postpartum. The concentration of fat, protein and lactose was determined in each sample. The rennet gelation properties were measured at 31 ° C using dynamic low-amplitude strain oscillatory rheometry. The following parameters were obtained from the resultant elastic shear modulus (G′): gelation time (GT), maximum curd firming rate (CFRmax) and gel strength (GS). Reducing dry period duration from 62 to 6 days resulted in increases in milk protein concentration (31.8 vs. 34.7 g/kg; P < 0.001), CFRmax (2.58 vs. 3.60 Pa/min; P < 0.001) and GS (69.4 vs. 90.5 Pa; P = 0.003). Raising the dietary energy density decreased percentage milk fat (43.1 vs. 37.7 g/kg; P < 0.001) but otherwise had no effect. GS was correlated with CFRmax (r = 0.98; P < 0.001), and both variables were correlated with milk protein concentration (r = 0.71; P < 0.001, and r = 0.73; P < 0.001, respectively). The results indicate that decreasing the duration of DP increased milk protein concentration and improved the rennet gelation properties of milk, but that dietary energy density had little effect.
    • Short communication: Uncovering quantitative trait loci associated with resistance to Mycobacterium avium ssp. paratuberculosis infection in Holstein cattle using a high-density single nucleotide polymorphism panel

      Mallikarjunappa, Sanjay; Sargolzaei, Mehdi; Brito, Luiz F.; Meade, Kieran G; Karrow, N. A.; Pant, S. D.; The Semex Alliance; NSERC; the Graham Centre for Agricultural Innovation; Darcy John O'Sullivan Bequest; et al. (Elsevier, 2018-05-10)
      Mycobacterium avium ssp. paratuberculosis (MAP) is the etiological agent of Johne's disease in cattle. Johne's disease is a disease of significant economic, animal welfare, and public health concern around the globe. Therefore, understanding the genetic architecture of resistance to MAP infection has great relevance to advance genetic selection methods to breed more resistant animals. The objectives of this study were to perform a genome-wide association study of previously analyzed 50K genotypes now imputed to a high-density single nucleotide polymorphism panel (777K), aiming to validate previously reported associations and potentially identify additional single nucleotide polymorphisms associated with antibody response to MAP infection. A principal component regression-based genome-wide association study revealed 15 putative quantitative trait loci (QTL) associated with the MAP infection phenotype (serum or milk ELISA tests) on 9 different chromosomes (Bos taurus autosomes 5, 6, 7, 10, 14, 15, 16, 20, and 21). These results validated previous findings and identified new QTL on Bos taurus autosomes 15, 16, 20, and 21. The positional candidate genes NLRP3, IFi47, TRIM41, TNFRSF18, and TNFRSF4 lying within these QTL were identified. Further functional validation of these genes is now warranted to investigate their roles in regulating the immune response and, consequently, cattle resistance to MAP infection.
    • The significance of livestock as a contributor to global greenhouse gas emissions today and in the near future

      O'Mara, Frank P. (Elsevier Inc., 23/06/2011)
      Animal agriculture is responsible for 8–10.8% of global greenhouse gas (GHG) emissions as assessed by IPCC accounting and, on the basis of lifecycle analysis, the contribution of livestock is up to 18% of global emissions. Asia is the source of the most enteric CH4 emissions with Latin America, Africa, Western Europe and North America being significant sources. These emissions are dominated by emissions from cattle. When GHG emissions are related to food production, the four most efficient regions are Eastern and Western Europe, North America, and the non-EU former Soviet Union which produced 46.3% of ruminant meat and milk energy and only 25.5% of enteric CH4 emissions in 2005. In comparison, the three least efficient producers (Asia, Africa, Latin America) produced an equivalent amount (47.1%) of ruminant meat and milk energy, and almost 69% of enteric CH4 emissions in 2005. Livestock related emissions will increase as world population and food demand increases; enteric CH4 emissions are projected to grow by over 30% from 2000 to 2020. There are mitigations available now, but it is imperative to develop new mitigations and ways to implement existing technologies more cost effectively.
    • A Single Dose of Fat-Based Energy Supplement to Light Birth Weight Pigs Shortly After Birth Does Not Increase Their Survival and Growth

      Schmitt, Océane; Baxter, Emma; Lawlor, Peadar G; Boyle, Laura; O'Driscoll, Keelin; Department of Agriculture, Food and the Marine; 13S428 (MDPI AG, 2019-05-09)
      Low birth weight piglets are at high risk of mortality, because of the rapid depletion of their energy reserves after birth. At 3 h postpartum, 405 piglets weighing <1.1 kg were either dosed orally with 2 mL of (1) coconut oil (CO, 74 kJ/2 mL, n = 107 piglets), (2) commercial product (CP, 71 kJ/2 mL, n = 101 piglets), (3) water (W, 0 kJ/2 mL, n = 100 piglets) or (4) were sham-dosed (S, n = 97 piglets). Treatments were applied within litter (97 sows). Before treatment piglets were weighed, scored for vitality and blood glucose concentration (subset: CO = 45 piglets, CP = 38 piglets, W = 49 piglets and S = 44 piglets) and rectal temperature were measured. Rectal temperature was remeasured 1 h post-treatment (4 h postpartum). At 24 h post-treatment (27 h postpartum), vitality, weight and blood glucose were remeasured. Piglets were weighed on D5, D7, D10, D14, D21 and at weaning (27 ± 0.1 day old). Mortality rate and cause were recorded until 24h period post-treatment and until weaning. Data were analysed using Generalised Linear Mixed Models in SAS. There was no overall effect of treatment on any of the parameters measured. In conclusion, a single oral of fat-based energy supplement dose at birth did not improve growth, survival, rectal temperature or vitality of low birth weight piglets.
    • A Single Dose of Fat-Based Energy Supplement to Light Birth Weight Pigs Shortly After Birth Does Not Increase Their Survival and Growth

      Schmitt, Océane; Baxter, Emma; Lawlor, Peadar; Boyle, Laura; O’Driscoll, Keelin; Department of Agriculture, Food and the Marine; 13S428 (MDPI AG, 2019-05-09)
      Low birth weight piglets are at high risk of mortality, because of the rapid depletion of their energy reserves after birth. At 3 h postpartum, 405 piglets weighing <1.1 kg were either dosed orally with 2 mL of (1) coconut oil (CO, 74 kJ/2 mL, n = 107 piglets), (2) commercial product (CP, 71 kJ/2 mL, n = 101 piglets), (3) water (W, 0 kJ/2 mL, n = 100 piglets) or (4) were sham-dosed (S, n = 97 piglets). Treatments were applied within litter (97 sows). Before treatment piglets were weighed, scored for vitality and blood glucose concentration (subset: CO = 45 piglets, CP = 38 piglets, W = 49 piglets and S = 44 piglets) and rectal temperature were measured. Rectal temperature was remeasured 1 h post-treatment (4 h postpartum). At 24 h post-treatment (27 h postpartum), vitality, weight and blood glucose were remeasured. Piglets were weighed on D5, D7, D10, D14, D21 and at weaning (27 ± 0.1 day old). Mortality rate and cause were recorded until 24h period post-treatment and until weaning. Data were analysed using Generalised Linear Mixed Models in SAS. There was no overall effect of treatment on any of the parameters measured. In conclusion, a single oral of fat-based energy supplement dose at birth did not improve growth, survival, rectal temperature or vitality of low birth weight piglets.
    • Single nucleotide polymorphisms at the imprinted bovine insulin-like growth factor 2 (IGF2) locus are associated with dairy performance in Irish Holstein-Friesian cattle

      Berkowicz, Erik W; Magee, David A; Sikora, Klaudia M; Berry, Donagh P.; Howard, Dawn J.; Mullen, Michael P.; Evans, R. D.; Spillane, Charles; MacHugh, David E (Cambridge University Press: Published for the Institute of Food Research and the Hannah Research Institute, 2010-09)
      The imprinted insulin-like growth factor 2 gene (IGF2) encodes a fetal mitogenic hormone protein (IGF-II) and has previously been shown to be associated with performance in dairy cattle. In this study we assessed genotype-phenotype associations between four single nucleotide polymorphisms (SNPs) located within the bovine IGF2 locus on chromosome 29 and a range of performance traits related to milk production, animal growth and body size, fertility and progeny survival in 848 progeny-tested Irish Holstein-Friesian sires. Two of the four SNPs (rs42196909 and IGF2.g-3815A>G), which were in strong linkage disequilibrium (r 2=0.995), were associated with milk yield (Pf0.01) and milk protein yield (Pf0.05); the rs42196901 SNP was also associated (Pf0.05) with milk fat yield. Associations (Pf0.05) with milk fat percentage and milk protein percentage were observed at the rs42196901 and IGF2.g-3815A>G SNPs, respectively. The rs42196909 and IGF2.g-3815A>G SNPs were also associated with progeny carcass conformation (Pf0.05), while an association (Pf0.01) with progeny carcass weight was observed at the rs42194733 SNP locus. None of the four SNPs were associated with body size, fertility and progeny survival. These findings support previous work which suggests that the IGF2 locus is an important biological regulator of milk production in dairy cattle and add to an accumulating body of research showing that imprinted genes influence many complex performance traits in cattle.
    • Single nucleotide polymorphisms in the insulin-like growth factor 1 (IGF-1) gene are associated with performance in Holstein-Friesian dairy cattle

      Mullen, Michael P.; Berry, Donagh P.; Howard, Dawn J.; Diskin, Michael G.; Lynch, Ciaran Oliver; Giblin, Linda; Kenny, David A.; Magee, David A; Meade, Kieran G; Waters, Sinead M.; et al. (Frontiers Media SA, 16/02/2011)
      Insulin-like growth factor 1 (IGF-1) has been shown to be associated with fertility, growth, and development in cattle. The aim of this study was to (1) identify novel single nucleotide polymorphisms (SNPs) in the bovine IGF-1 gene and alongside previously identified SNPs (2) determine their association with traits of economic importance in Holstein-Friesian dairy cattle. Nine novel SNPs were identified across a panel of 22 beef and dairy cattle by sequence analysis of the 5′ promoter, intronic, and 3′ regulatory regions, encompassing ∼5 kb of IGF-1. Genotyping and associations with daughter performance for milk production, fertility, survival, and measures of body size were undertaken on 848 Holstein-Friesian AI sires. Using multiple regression analysis nominal associations (P < 0.05) were identified between six SNPs (four novel and two previously identified) and milk composition, survival, body condition score, and body size. The C allele of AF017143 a previously published SNP (C-512T) in the promoter region of IGF-1 predicted to introduce binding sites for transcription factors HSF1 and ZNF217 was associated (P < 0.05) with increased cow carcass weight (i.e., an indicator of mature cow size). Novel SNPs were identified in the 3′ region of IGF-1 were associated (P < 0.05) with functional survival and chest width. The remaining four SNPs, all located within introns of IGF-1 were associated (P < 0.05) with milk protein yield, milk fat yield, milk fat concentration, somatic cell score, carcass conformation, and carcass fat. Results of this study further demonstrate the multifaceted influences of IGF-1 on milk production and growth related traits in cattle.
    • Six-year longitudinal study of Fasciola hepatica bulk milk antibody ELISA in the dairy dense region of the Republic Ireland

      Munita, Maria P; Rea, Rosemary; Bloemhoff, Yris; Byrne, Nicky; Martinez-Ibeas, Ana M; Sayers, Riona; Irish Dairy Levy (Elsevier, 2016-09-28)
      Completion of the F. hepatica lifecycle is dependent on suitable climatic conditions for development of immature stages of the parasite, and its snail intermediate host. Few investigations have been conducted regarding temporal variations in F. hepatica status in Irish dairy herds. The current study aimed to conduct a longitudinal study examining annual and seasonal trends in bulk milk seropositivity over six years, while also investigating associations with soil temperature, rainfall and flukicide treatment. Monthly bulk milk samples (BTM) were submitted by 28 herds between March 2009 and December 2014. In all, 1337 samples were analysed using a Cathepsin L1 ELISA. Soil temperature, rainfall and management data were obtained for general estimating equation and regression analyses. A general decrease in milk seropositivity was observed over the six year study period and was associated with an increased likelihood of treating for liver fluke (OR range = 2.73–6.96). Annual and seasonal analyses of rainfall and F. hepatica BTM status yielded conflicting results. Higher annual rainfall (>1150 mm) yielded a lower likelihood of being BTM positive than annual rainfall of <1000 mm (OR = 0.47; P = 0.036). This was most likely due to farmers being more proactive in treating for F. hepatica in wetter years, although a ‘wash effect’ by high rainfall of the free living stages and snails cannot be ruled out. Higher seasonal rainfall (>120 mm), however, was associated with increased ELISA S/P% values (Coefficient = 9.63S/P%; P = 0.001). Soil temperature was not found to influence F. hepatica to the same extent as rainfall and may reflect the lack of severe temperature fluctuations in Ireland. Flukicides active against both immature and mature F. hepatica were approximately half as likely to record a positive F. hepatica herd BTM status than a flukicide active against only the mature stage of the parasite (OR ≅ 0.45; P < 0.01). This study highlights the importance of examining both annual and seasonal F. hepatica data, which can vary significantly. Additionally, it highlights the progress that can be achieved in fluke control by application of a continuous BTM monitoring program.
    • SNP variation in the promoter of the PRKAG3 gene and association with meat quality traits in pig

      Ryan, Marion T; Hamill, Ruth M; O'Halloran, Aisling M; Davey, Grace C; McBryan, Jean; Mullen, Anne Maria; McGee, Chris; Gispert, Marina; Southwood, Olwen I; Sweeney, Torres; et al. (Biomed Central, 25/07/2012)
      Background: The PRKAG3 gene encodes the γ3 subunit of adenosine monophosphate activated protein kinase (AMPK), a protein that plays a key role in energy metabolism in skeletal muscle. Non-synonymous single nucleotide polymorphisms (SNPs) in this gene such as I199V are associated with important pork quality traits. The objective of this study was to investigate the relationship between gene expression of the PRKAG3 gene, SNP variation in the PRKAG3 promoter and meat quality phenotypes in pork. Results: PRKAG3 gene expression was found to correlate with a number of traits relating to glycolytic potential (GP) and intramuscular fat (IMF) in three phenotypically diverse F1 crosses comprising of 31 Large White, 23 Duroc and 32 Pietrain sire breeds. The majority of associations were observed in the Large White cross. There was a significant association between genotype at the g.-311A>G locus and PRKAG3 gene expression in the Large White cross. In the same population, ten novel SNPs were identified within a 1.3 kb region spanning the promoter and from this three major haplotypes were inferred. Two tagging SNPs (g.-995A>G and g.-311A>G) characterised the haplotypes within the promoter region being studied. These two SNPs were subsequently genotyped in larger populations consisting of Large White (n = 98), Duroc (n = 99) and Pietrain (n = 98) purebreds. Four major haplotypes including promoter SNP’s g.-995A>G and g.-311A>G and I199V were inferred. In the Large White breed, HAP1 was associated with IMF% in the M. longissmus thoracis et lumborum (LTL) and driploss%. HAP2 was associated with IMFL% GP-influenced traits pH at 24 hr in LTL (pHULT), pH at 45 min in LTL (pH45LT) and pH at 45 min in the M. semimembranosus muscle (pH45SM). HAP3 was associated with driploss%, pHULT pH45LT and b* Minolta. In the Duroc breed, associations were observed between HAP1 and driploss% and pHUSM. No associations were observed with the remaining haplotypes (HAP2, HAP3 and HAP4) in the Duroc breed. The Pietrain breed was monomorphic in the promoter region. The I199V locus was associated with several GP-influenced traits across all three breeds and IMF% in the Large White and Pietrain breed. No significant difference in promoter function was observed for the three main promoter haplotypes when tested in vitro. Conclusion: Gene expression levels of the porcine PRKAG3 are associated with meat quality phenotypes relating to glycolytic potential and IMF% in the Large White breed, while SNP variation in the promoter region of the gene is associated with PRKAG3 gene expression and meat quality phenotypes.
    • Snpdat: Easy and rapid annotation of results from de novo snp discovery projects for model and non-model organisms

      Doran, Anthony G; Creevey, Christopher J. (Biomed Central, 2013-02-08)
      Background: Single nucleotide polymorphisms (SNPs) are the most abundant genetic variant found in vertebrates and invertebrates. SNP discovery has become a highly automated, robust and relatively inexpensive process allowing the identification of many thousands of mutations for model and non-model organisms. Annotating large numbers of SNPs can be a difficult and complex process. Many tools available are optimised for use with organisms densely sampled for SNPs, such as humans. There are currently few tools available that are species non-specific or support non-model organism data. Results: Here we present SNPdat, a high throughput analysis tool that can provide a comprehensive annotation of both novel and known SNPs for any organism with a draft sequence and annotation. Using a dataset of 4,566 SNPs identified in cattle using high-throughput DNA sequencing we demonstrate the annotations performed and the statistics that can be generated by SNPdat. Conclusions: SNPdat provides users with a simple tool for annotation of genomes that are either not supported by other tools or have a small number of annotated SNPs available. SNPdat can also be used to analyse datasets from organisms which are densely sampled for SNPs. As a command line tool it can easily be incorporated into existing SNP discovery pipelines and fills a niche for analyses involving non-model organisms that are not supported by many available SNP annotation tools. SNPdat will be of great interest to scientists involved in SNP discovery and analysis projects, particularly those with limited bioinformatics experience.
    • Snpdat: Easy and rapid annotation of results from de novo snp discovery projects for model and non-model organisms

      Doran, Anthony G; Creevey, Christopher J. (Biomed Central, 2013-02-08)
      Background: Single nucleotide polymorphisms (SNPs) are the most abundant genetic variant found in vertebrates and invertebrates. SNP discovery has become a highly automated, robust and relatively inexpensive process allowing the identification of many thousands of mutations for model and non-model organisms. Annotating large numbers of SNPs can be a difficult and complex process. Many tools available are optimised for use with organisms densely sampled for SNPs, such as humans. There are currently few tools available that are species non-specific or support non-model organism data. Results: Here we present SNPdat, a high throughput analysis tool that can provide a comprehensive annotation of both novel and known SNPs for any organism with a draft sequence and annotation. Using a dataset of 4,566 SNPs identified in cattle using high-throughput DNA sequencing we demonstrate the annotations performed and the statistics that can be generated by SNPdat. Conclusions: SNPdat provides users with a simple tool for annotation of genomes that are either not supported by other tools or have a small number of annotated SNPs available. SNPdat can also be used to analyse datasets from organisms which are densely sampled for SNPs. As a command line tool it can easily be incorporated into existing SNP discovery pipelines and fills a niche for analyses involving non-model organisms that are not supported by many available SNP annotation tools. SNPdat will be of great interest to scientists involved in SNP discovery and analysis projects, particularly those with limited bioinformatics experience.
    • Social network properties predict chronic aggression in commercial pig systems

      Foister, Simone; Doeschl-Wilson, Andrea; Roehe, Rainer; Arnott, Gareth; Boyle, Laura; Turner, Simon; Teagasc Walsh Fellowship Programme; Scottish Government; 2015004 (Public Library of Science (PLoS), 2018-10-04)
      Post-mixing aggression in pigs is a harmful and costly behaviour which negatively impacts both animal welfare and farm efficiency. There is vast unexplained variation in the amount of acute and chronic aggression that dyadic behaviours do not fully explain. This study hypothesised that certain pen-level network properties may improve prediction of lesion outcomes due to the incorporation of indirect social interactions that are not captured by dyadic traits. Utilising current SNA theory, we investigate whether pen-level network properties affect the number of aggression-related injuries at 24 hours and 3 weeks post-mixing (24hr-PM and 3wk-PM). Furthermore we compare the predictive value of network properties to conventional dyadic traits. A total of 78 pens were video recorded for 24hr post-mixing. Each aggressive interaction that occurred during this time period was used to construct the pen-level networks. The relationships between network properties at 24hr and the pen level injuries at 24hr-PM and 3wk-PM were analysed using mixed models and verified using permutation tests. The results revealed that network properties at 24hr could predict long term aggression (3wk-PM) better than dyadic traits. Specifically, large clique formation in the first 24hr-PM predicted fewer injuries at 3wk-PM and high betweenness centralisation at 24hr-PM predicted increased rates of injury at 3wk-PM. This study demonstrates that network properties present during the first 24hr-PM have predictive value for chronic aggression, and have potential to allow identification and intervention for at risk groups.
    • Soil Properties and their Influence on Grassland Production under Low Input and Organic Farming Conditions

      Leonard, C.; Mullen, G.J.; Culleton, Noel; Breen, J.; Teagasc Walsh Fellowship Programme (Teagasc, 2006-01-01)
      This project set out to identify soil properties that most influence grassland production under low mineral nitrogen input conditions. Sixteen farms were selected in Counties Limerick and Clare and the soil sampled. Soil physical and chemical characteristics and soil biological aspects involved in the carbon and nitrogen cycles were studied in the laboratory. Nutrient additions to farms as well as the nature of grazing by livestock (numbers, types of grazing animals, grazing practices), grassland management, and production from the farms were recorded.
    • Spatial patterns of Fasciola hepatica and Calicophoron daubneyi infections in ruminants in Ireland and modelling of C. daubneyi infection

      Naranjo-Lucena, Amalia; Munita, Maria P; Martinez-Ibeas, Ana M; McGrath, Guy; Murray, Gerard; Casey, Micheal; Good, Barbara; Sayers, Riona; Mulcahy, Grace; Zintl, Annetta; et al. (Biomed Central, 2018-09-29)
      Background Fasciola hepatica has always represented a threat to Irish livestock because the Irish climate is highly suitable for the main local intermediate host of the parasite, the snail Galba truncatula. The recent clinical emergence of infections due to Calicophoron daubneyi has raised the question of whether the two parasites, which share a niche during part of their life-cycles, interact in some way. Here, we used geographical information systems (GIS) to analyse the distribution of both parasites in cattle and sheep. We also developed the first predictive model of paramphistomosis in Ireland. Results Our results indicated that, in cattle, liver fluke infection is less common than rumen fluke infection and does not exhibit the same seasonal fluctuations. Overall, we found that cattle had a higher likelihood of being infected with rumen fluke than sheep (OR = 3.134, P < 0.01). In addition, infection with one parasite increased the odds of infection with the other in both host species. Rumen fluke in cattle showed the highest spatial density of infection. Environmental variables such as soil drainage, land cover and habitat appeared to be the most important risk factors for C. daubneyi infection, followed by rainfall and vegetation. Overall the risk of infection with this parasite was predicted to be higher in the west of the country. Conclusions This study shows differences between the infection rates and spatial patterns of bovine and ovine infections with F. hepatica and C. daubneyi in Ireland. Whether the reasons for this are due to susceptibility, exposure and/or management factors is yet to be determined. Furthermore, the rumen fluke model indicates distinct risk factors and predicted distribution to those of F. hepatica, suggesting potential biological differences between both parasite species.