• Universally Distributed Single-Copy Genes Indicate a Constant Rate of Horizontal Transfer

      Creevey, Christopher J.; Doerks, Tobias; Fitzpatrick, David; Raes, Jeroen; Bork, Peer (PLOS, 2011-08-05)
      Single copy genes, universally distributed across the three domains of life and encoding mostly ancient parts of the translation machinery, are thought to be only rarely subjected to horizontal gene transfer (HGT). Indeed it has been proposed to have occurred in only a few genes and implies a rare, probably not advantageous event in which an ortholog displaces the original gene and has to function in a foreign context (orthologous gene displacement, OGD). Here, we have utilised an automatic method to identify HGT based on a conservative statistical approach capable of robustly assigning both donors and acceptors. Applied to 40 universally single copy genes we found that as many as 68 HGTs (implying OGDs) have occurred in these genes with a rate of 1.7 per family since the last universal common ancestor (LUCA). We examined a number of factors that have been claimed to be fundamental to HGT in general and tested their validity in the subset of universally distributed single copy genes. We found that differing functional constraints impact rates of OGD and the more evolutionarily distant the donor and acceptor, the less likely an OGD is to occur. Furthermore, species with larger genomes are more likely to be subjected to OGD. Most importantly, regardless of the trends above, the number of OGDs increases linearly with time, indicating a neutral, constant rate. This suggests that levels of HGT above this rate may be indicative of positively selected transfers that may allow niche adaptation or bestow other benefits to the recipient organism.
    • Urine patch distribution under dairy grazing at three stocking rates in Ireland

      Dennis, S.J.; Moir, James L.; Cameron, K.C.; Di, H.J.; Hennessy, Deirdre; Richards, Karl G. (Teagasc (Agriculture and Food Development Authority), Ireland, 2011)
      Nitrate pollution of water is a serious global environmental issue. Grassland agriculture is a major source of diffuse nitrate pollution, with much of this nitrate originating from the urine patches of grazing animals. To study nitrate losses from grassland it is necessary to consider the areas of grassland that are affected by urine separately from the remainder of the pasture. Urine patches can be observed in the field as areas of vigorously growing pasture, however the pasture may continue to respond for several months, making it difficult to determine when the observed patch was actually deposited. A global positioning system was used to record the location of all urine and dung patches in a pasture at every second grazing on an Irish dairy farm during the grazing season. Any patches reappearing were removed from the data, allowing the fresh urine patches to be identified. Dairy cows deposited 0.359 urine patches per grazing hour, a value that may be used to predict the distribution of urine patches under any grazing regime. This equated to 14.1 to 20.7% of the soil surface being wet by urine annually at stocking rates of 2.0 to 2.94 cows per hectare, consistent with previous research. These values may be used in conjunction with values for nitrate loss from urine and non-urine areas to calculate nitrate losses from grazed pasture at a range of stocking rates.
    • Use of different wood types as environmental enrichment to manage tail biting in docked pigs in a commercial fully-slatted system

      Chou, Jen-Yun; D'Eath, Rick B.; Sandercock, Dale A.; Waran, Natalie; Haigh, Amy; O'Driscoll, Keelin; Department of Agriculture, Food and the Marine, Ireland; Teagasc Walsh Fellowship Programme; Scotland's Rural College (Elsevier, 2018-04-07)
      Provision of adequate environmental enrichment on pig farms is a legal requirement under current EU legislation and also alleviates the risk of tail biting. Wood is an organic alternative where loose bedding, which has been identified as the optimal enrichment, is not possible on fully-slatted floors since it may disrupt the slurry system. The study compared four different wood types (beech (Fagus sylvatica), larch (Larix decidua), spruce (Picea sitchensis), and Scots pine (Pinus sylvestris L.)) as enrichment, taking into account the qualities of the wood, economic considerations, and effectiveness at reducing damaging behaviours and lesions. A total of 800 tail docked finisher pigs on an Irish commercial farm were used. Eight pens were provided with each wood type (25 pigs/pen), and the study was conducted over 2 replicates in time. In each pen a single wooden post was presented to the pigs in a metal dispenser with two lateral chains during the finisher period (12–22 weeks of age). The rate of wear, moisture content, and hardness of the wood along with lesion scorings and behavioural observation on pigs were monitored. Spruce was consumed more quickly than other wood types in terms of weight loss and reduction in length (P < 0.001), resulting in a greater cost per pig. Pigs were observed interacting with the spruce more frequently than the other wood types (P < 0.05). Pigs also interacted with the wood more often than the chains in spruce allocated pens (P < 0.001). Overall the interaction with wood posts did not decline significantly across time. However, there was no difference in the frequency of harmful behaviours (tail/ear/flank-biting) observed between wood types, and also no difference in the effectiveness of the different types of wood in reducing tail or ear damage. There was a positive correlation between ear lesion and tear-staining scores (rp= 0.286, P < 0.01), and between tail lesion and tail posture scores (rp= 0.206, P < 0.05). Wood types did not affect visceral condemnation obtained in the slaughterhouse. Wood is a potentially suitable enrichment material, yet the wood species could influence its attractiveness to pigs.
    • The use of subjectively assessed muscular and skeletal traits on live cattle to aid in differentiation between animal genetically divergent in carcass kill out metrics

      Berry, Donagh; Coyne, J. M.; Doyle, J.; Evans, R. D.; Science Foundation Ireland; Department of Agriculture, Food and the Marine; 16/RC/3835 (Elsevier BV, 2020-04)
      Subjective linear scoring of live beef cattle is routinely undertaken as part of breed society regulations or as part of national breeding programs; linear scores describe biological extremes of animals for a range of different traits reflecting muscularity, skeletal development, and functionality. The objective of the present study was to quantify the usefulness of these linear scores measured on live growing beef cattle to predict genetic merit for kill out (KO) percent and the difference between live-weight at slaughter and carcass weight (herein known as KO difference). The data used consisted of linear scores for 16 traits on up to 67,167 cattle as well as KO information on 31,827 cattle; 1,166 animals had records for both sets of traits. Variance components were estimated using univariate animal linear mixed models while covariance components between the linear scores and the KO traits were estimated using a series of bivariate sire linear mixed models. In an additional series of analyses, the KO metrics were adjusted phenotypically for differences in live-weight at slaughter through its inclusion as a covariate in the statistical model. Heritability estimates of the linear scores varied from 0.06 (width at pins) to 0.37 (development of hind-quarter); the heritability of KO percent and KO difference were estimated to be 0.53 and 0.37, respectively. Both the phenotypic and genetic correlations between the muscular type traits and KO percent were moderately positive, albeit the genetic correlations were stronger. The phenotypic correlations ranged from 0.27 (development of inner thigh) to 0.37 (development of hind quarter) while the genetic correlations varied from 0.40 (development of inner thigh and development of loin) to 0.60 (development of hind quarter); in all cases, adjusting for differences in live-weight at slaughter had minimal impact on the estimated correlations. With the exception of depth of rump, the phenotypic and genetic correlations between the skeletal traits with KO percent were all close to zero (≤|0.24|) irrespective of whether or not differences in live-weight at slaughter were accounted for. While the genetic correlations between the muscular traits and KO difference not adjusted for differences in live-weight at slaughter were all close to zero (≤|0.30|), the correlations strengthened (≥|0.39|) once adjusted to a common live-weight at slaughter. The opposite was true for the genetic correlations between the skeletal traits and KO difference. In all, the results suggest that the muscular linear scores assessed subjectively on live animals at, on average, 10 months of age are a useful genetic (and phenotypic) predictor of KO percent at, on average, 21 months of age, but also the quantity of live-weight that does not end up as carcass, once adjusted to a common live-weight.
    • Using models to establish the financially optimum strategy for Irish dairy farms

      Ruelle, Elodie; Delaby, Luc; Wallace, Michael; Shalloo, Laurence; European Union; Department of Agriculture, Food and the Marine; 11/S/132 (Elsevier, 2017-11-02)
      Determining the effect of a change in management on farm with differing characteristics is a significant challenge in the evaluation of dairy systems due to the interacting components of complex biological systems. In Ireland, milk production is increasing substantially following the abolition of the European Union milk quota regime in 2015. There are 2 main ways to increase the milk production on farm (within a fixed land base): either increase the number of animals (thus increasing the stocking rate) or increase the milk production per animal through increased feeding or increased lactation length. In this study, the effect of increased concentrate feeding or an increase in grazing intensity was simulated to determine the effect on the farm system and its economic performance. Four stocking rates (2.3, 2.6, 2.9, and 3.2 cow/ha) and 5 different concentrate supplementation strategies (0, 180, 360, 600, and 900 kg of dry matter/lactation) resulting in 20 different scenarios were evaluated across different milk, concentrate, and silage purchase prices. Each simulation was run across 10 yr of meteorological data, which had been recorded over the period 2004 to 2013. Three models—the Moorepark and St Gilles grass growth model, the pasture-based herd dynamic milk model, and the Moorepark dairy systems model—were integrated and applied to simulate the different scenarios. Overall, this study has demonstrated that the most profitable scenario was a stocking rate of 2.6 cow/ha with a concentrate supplementation of 600 kg of dry matter/cow. The factor that had the greatest influence on profitability was variability of milk price.
    • Using the Biocheck.UGent™ scoring tool in Irish farrow-to-finish pig farms: assessing biosecurity and its relation to productive performance

      Rodrigues da Costa, Maria; Gasa, Josep; Calderón Díaz, Julia A; Postma, Merel; Dewulf, Jeroen; McCutcheon, Gerard; Manzanilla, Edgar G; Department of Agriculture Food and the Marine; 14/S/832 (Biomed Central, 2019-03-01)
      Background Biosecurity is one of the main factors affecting disease occurrence and antimicrobial use, and it is associated with performance in pig production. However, the importance of specific measures could vary depending on the (national) context. The aim of this study was to describe the biosecurity status in a cohort of Irish pig farms, to investigate which of those biosecurity aspects are more relevant by using the Biocheck.UGent™ scoring system, and to study the impact of such aspects on farm performance. Results External biosecurity score was high compared to most countries due to the characteristics of the Irish pig sector (i.e. purchasing only semen and breeding gilts on farm). The internal biosecurity score was lower and had greater variability among farms than other EU countries. Using multivariable linear regression, the biosecurity practices explained 8, 23, and 16% of variability in piglet mortality, finisher mortality, and average daily gain, respectively. Three clusters of farms were defined based on their biosecurity scores (0 to 100) using principal components and hierarchical clustering analysis. Scores for clusters 1, 2 and 3 were (mean ± SD) 38 ± 7.6, 61 ± 7.0 and 66 ± 9.8 for internal and 73 ± 5.1, 74 ± 5.3 and 86 ± 4.5 for external biosecurity. Cluster 3 had lower piglet mortality (P = 0.022) and higher average daily gain (P = 0.037) when compared to cluster 2. Conclusions Irish farms follow European tendencies with internal biosecurity posing as the biggest liability. Our results suggest that practices related to the environment and region, feed, water and equipment supply, and the management of the different stages, need to be addressed in lower performing farms to improve productive performance. Further studies on the economic impact of these biosecurity practices including complementary data on herd health, gilt rearing, piglet management, vaccination and feeding strategies are needed.
    • Using variable importance measures to identify a small set of SNPs to predict heading date in perennial ryegrass.

      Byrne, Stephen; Conaghan, Patrick; Barth, Susanne; Arojju, Sai Krishna; Casler, Michael; Michel, Thibauld; Velmurugan, Janaki; Milbourne, Dan; E.U. Marie Skłodowska-Curie Fellowship; Teagasc Walsh Fellowship Programme; et al. (Nature, 2017-06-15)
      Prior knowledge on heading date enables the selection of parents of synthetic cultivars that are well matched with respect to time of heading, which is essential to ensure plants put together will cross pollinate. Heading date of individual plants can be determined via direct phenotyping, which has a time and labour cost. It can also be inferred from family means, although the spread in days to heading within families demands roguing in first generation synthetics. Another option is to predict heading date from molecular markers. In this study we used a large training population consisting of individual plants to develop equations to predict heading date from marker genotypes. Using permutation-based variable selection measures we reduced the marker set from 217,563 to 50 without impacting the predictive ability. Opportunities exist to develop a cheap assay to sequence a small number of regions in linkage disequilibrium with heading date QTL in thousands of samples. Simultaneous use of these markers in non-linkage based marker-assisted selection approaches, such as paternity testing, should enhance the utility of such an approach.
    • Validation and Improvement of the Beef Production Sub-index in Ireland for Beef Cattle

      Drennan, Michael J; McGee, Mark; Clarke, Anne Marie; Kenny, David A.; Evans, R. D.; Berry, Donagh (Teagasc, 2009-12-01)
      The objectives of the following study were to: a. Quantify the effect of sire genetic merit for BCI on: 1. feed intake, growth and carcass traits of progeny managed under bull or steer beef production systems. 2. live animal scores, carcass composition and plasma hormone and metabolite concentrations in their progeny. b. Compare the progeny of : 1. Late-maturing beef with dairy breeds and 2. Charolais (CH), Limousin (LM), Simmental (SM) and Belgian Blue (BB) sires bred to beef suckler dams, for feed intake, blood hormones and metabolites, live animal measurements, carcass traits and carcass value in bull and steer production systems.
    • Validation of an Automated Body Condition Scoring System Using 3D Imaging

      O’ Leary, Niall O’; Leso, Lorenzo; Buckley, Frank; Kenneally, Jonathon; McSweeney, Diarmuid; Shalloo, Laurence; Science Foundation Ireland; Department of Agriculture, Food and the Marine; 13/IA/1977; 16/RC/3835 (MDPI AG, 2020-06-26)
      Body condition scores (BCS) measure a cow’s fat reserves and is important for management and research. Manual BCS assessment is subjective, time-consuming, and requires trained personnel. The BodyMat F (BMF, Ingenera SA, Cureglia, Switzerland) is an automated body condition scoring system using a 3D sensor to estimate BCS. This study assesses the BMF. One hundred and three Holstein Friesian cows were assessed by the BMF and two assessors throughout a lactation. The BMF output is in the 0–5 scale commonly used in France. We develop and report the first equation to convert these scores to the 1–5 scale used by the assessors in Ireland in this study ((0–5 scale × 0.38) + 1.67 → 1–5 scale). Inter-assessor agreement as measured by Lin’s concordance of correlation was 0.67. BMF agreement with the mean of the two assessors was the same as between assessors (0.67). However, agreement was lower for extreme values, particularly in over-conditioned cows where the BMF underestimated BCS relative to the mean of the two human observers. The BMF outperformed human assessors in terms of reproducibility and thus is likely to be especially useful in research contexts. This is the second independent validation of a commercially marketed body condition scoring system as far as the authors are aware. Comparing the results here with the published evaluation of the other system, we conclude that the BMF performed as well or better.
    • Validation of an ear tag–based accelerometer system for detecting grazing behavior of dairy cows

      Pereira, G.M.; Heins, B.J.; O'Brien, Bernadette; McDonagh, A.; Lidauer, L.; Kickinger, F.; USDA National Institute of Food and Agriculture; Science Foundation Ireland; 2012-51300-20015 (Elsevier, 2020-02-20)
      The objective of the study was to develop a grazing algorithm for an ear tag–based accelerometer system (Smartbow GmbH, Weibern, Austria) and to validate the grazing algorithm with data from a noseband sensor. The ear tag has an acceleration sensor, a radio chip, and temperature sensor for calibration and it can monitor rumination and detect estrus and localization. To validate the ear tag, a noseband sensor (RumiWatch, Itin and Hoch GmbH, Liestal, Switzerland) was used. The noseband sensor detects pressure and acceleration patterns, and, with a software program specific to the noseband, pressure and acceleration patterns are used to classify data into eating, ruminating, drinking, and other activities. The study was conducted at the University of Minnesota West Central Research and Outreach Center (Morris, MN) and at Teagasc Animal and Grassland Research and Innovation Centre (Moorepark, Fermoy, Co. Cork, Ireland). During May and June 2017, observational data from Minnesota and Ireland were used to develop the grazing algorithm. During September 2018, data were collected by the ear tag and noseband sensor from 12 crossbred cows in Minnesota for a total of 248 h and from 9 Holstein-Friesian cows in Ireland for a total of 248 h. A 2-sided t-test was used to compare the percentage of grazing and nongrazing time recorded by the ear tag and the noseband sensor. Pearson correlations and concordance correlation coefficients (CCC) were used to evaluate associations between the ear tag and noseband sensor. The percentage of total grazing time recorded by the ear tag and by the noseband sensor was 37.0% [95% confidence interval (CI): 32.1 to 42.0] and 40.5% (95% CI: 35.5 to 45.6), respectively, in Minnesota, and 35.4% (95% CI: 30.6 to 40.2) and 36.9% (95% CI: 32.1 to 41.8), respectively, in Ireland. The ear tag and noseband sensor agreed strongly for monitoring grazing in Minnesota (r = 0.96; 95% CI: 0.94 to 0.97, CCC = 0.95) and in Ireland (r = 0.92; 95% CI: 0.90 to 0.94, CCC = 0.92). The results suggest that there is potential for the ear tag to be used on pasture-based dairy farms to support management decision-making.
    • Validation of national genetic evaluations for maternal beef cattle traits using Irish field data

      McHugh, Noirin; Cromie, A. R.; Evans, R. D.; Berry, Donagh (American Society of Animal Science, 2014-11-24)
      Genetic evaluations provide information to aid in breeding decisions that increase long-term performance of animals and herds. However, to date no study has been undertaken to investigate the accuracy of the Irish maternal genetic evaluations in beef cattle. The objective, therefore, of this study was to quantify the relationship between phenotypic performance and measures of genetic merit for predominantly maternal-related traits in Irish beef cattle. The association between animal EBV for calving interval, age at first calving, and both direct and maternal weaning weight with the respective phenotypic performance was quantified using a fixed effects model; the expectation for the regression coefficient of phenotypic performance on EBV was one. The association between genetic merit for cow survival, perinatal mortality, calving assistance, and calving dystocia with the log of the odds of the respective trait was quantified using logistic regression. The association analyses were conducted using field data on up to 38,619 records from 5,236 herds. Age at first calving increased linearly by 0.32 ± 0.15 (P = 0.03) days per day increase in EBV for age at first calving. Calving interval increased by, on average, 0.58 ± 0.16 (P = 0.002) days per day increase in EBV for calving interval although the association differed by parity with a greater association in pluriparae. Weaning weight increased linearly by 1.74 ± 0.09 and 0.84 ± 0.16 kg (P < 0.001) per kilogram increase in EBV for direct and maternal weaning weight, respectively. The log of the odds of a cow surviving to next lactation increased linearly by 0.16 ± 0.03 (P < 0.001) per unit increase in EBV for cow survival. The log of the odds of an assisted calving or dystocia both increased linearly by 0.21 ± 0.01 and 0.24 ± 0.01, respectively, per unit increase in EBV for direct calving difficulty (P < 0.001). The log of the odds of a dead calf at birth increased linearly by 0.93 ± 0.13 (P < 0.001) per unit increase in EBV for calf mortality. Results from this study show that selection of breeding animals for favorable maternal genetic attributes will result in favorable improvements in performance and profitability.
    • Variability in greenhouse gas emission intensity of semi-intensive suckler cow beef production systems

      Samsonstuen, Stine; Åby, Bente A.; Crosson, Paul; Beauchemin, Karen A.; Wetlesen, Marit S.; Bonesmo, Helge; Aass, Laila; Norwegian University of Life Sciences and Department of Animal and Aquacultural Sciences; The Agriculture and Food Industry Research Funds; Geno Breeding and AI Association; et al. (Elsevier BV, 2020-09)
      Emission intensities from beef production vary both among production systems (countries) and farms within a country depending upon use of natural resources and management practices. A whole-farm model developed for Norwegian suckler cow herds, HolosNorBeef, was used to estimate GHG emissions from 27 commercial beef farms in Norway with Angus, Hereford, and Charolais cattle. HolosNorBeef considers direct emissions of methane (CH4), nitrous oxide (N2O) and carbon dioxide (CO2) from on-farm livestock production and indirect N2O and CO2 emissions associated with inputs used on the farm. The corresponding soil carbon (C) emissions are estimated using the Introductory Carbon Balance Model (ICBM). The farms were distributed across Norway with varying climate and natural resource bases. The estimated emission intensities ranged from 22.5 to 45.2 kg CO2 equivalents (eq) (kg carcass)−1. Enteric CH4 was the largest source, accounting for 44% of the total GHG emissions on average, dependent on dry matter intake (DMI). Soil C was the largest source of variation between individual farms and accounted for 6% of the emissions on average. Variation in GHG intensity among farms was reduced and farms within region East, Mid and North re-ranked in terms of emission intensities when soil C was excluded. Ignoring soil C, estimated emission intensities ranged from 21.5 to 34.1 kg CO2 eq (kg carcass)−1. High C loss from farms with high initial soil organic carbon (SOC) content warrants further examination of the C balance of permanent grasslands as a potential mitigation option for beef production systems.
    • Variance components for bovine tuberculosis infection and multi-breed genome-wide association analysis using imputed whole genome sequence data

      Ring, Siobhan C.; Purfield, Deirdre C; Good, Margaret; Breslin, P.; Ryan, Eoin; Blom, A.; Evans, R. D.; Doherty, M. L.; Bradley, Daniel G; Berry, Donagh; et al. (Public Library of Science (PLoS), 2019-02-14)
      Bovine tuberculosis (bTB) is an infectious disease of cattle generally caused by Mycobacterium bovis, a bacterium that can elicit disease humans. Since the 1950s, the objective of the national bTB eradication program in Republic of Ireland was the biological extinction of bTB; that purpose has yet to be achieved. Objectives of the present study were to develop the statistical methodology and variance components to undertake routine genetic evaluations for resistance to bTB; also of interest was the detection of regions of the bovine genome putatively associated with bTB infection in dairy and beef breeds. The novelty of the present study, in terms of research on bTB infection, was the use of beef breeds in the genome-wide association and the utilization of imputed whole genome sequence data. Phenotypic bTB data on 781,270 animals together with imputed whole genome sequence data on 7,346 of these animals’ sires were available. Linear mixed models were used to quantify variance components for bTB and EBVs were validated. Within-breed and multi-breed genome-wide associations were undertaken using a single-SNP regression approach. The estimated genetic standard deviation (0.09), heritability (0.12), and repeatability (0.30) substantiate that genetic selection help to eradicate bTB. The multi-breed genome-wide association analysis identified 38 SNPs and 64 QTL regions associated with bTB infection; two QTL regions (both on BTA23) identified in the multi-breed analysis overlapped with the within-breed analyses of Charolais, Limousin, and Holstein-Friesian. Results from the association analysis, coupled with previous studies, suggest bTB is controlled by an infinitely large number of loci, each having a small effect. The methodology and results from the present study will be used to develop national genetic evaluations for bTB in the Republic of Ireland. In addition, results can also be used to help uncover the biological architecture underlying resistance to bTB infection in cattle.
    • Variance components for bovine tuberculosis infection and multi-breed genome-wide association analysis using imputed whole genome sequence data

      Ring, S. C.; Purfield, D. C.; Good, M.; Breslin, P.; Ryan, E.; Blom, A.; Evans, R. D.; Doherty, M. L.; Bradley, D. G.; Berry, Donagh; et al. (Public Library of Science (PLoS), 2019-02-14)
      Bovine tuberculosis (bTB) is an infectious disease of cattle generally caused by Mycobacterium bovis, a bacterium that can elicit disease humans. Since the 1950s, the objective of the national bTB eradication program in Republic of Ireland was the biological extinction of bTB; that purpose has yet to be achieved. Objectives of the present study were to develop the statistical methodology and variance components to undertake routine genetic evaluations for resistance to bTB; also of interest was the detection of regions of the bovine genome putatively associated with bTB infection in dairy and beef breeds. The novelty of the present study, in terms of research on bTB infection, was the use of beef breeds in the genome-wide association and the utilization of imputed whole genome sequence data. Phenotypic bTB data on 781,270 animals together with imputed whole genome sequence data on 7,346 of these animals’ sires were available. Linear mixed models were used to quantify variance components for bTB and EBVs were validated. Within-breed and multi-breed genome-wide associations were undertaken using a single-SNP regression approach. The estimated genetic standard deviation (0.09), heritability (0.12), and repeatability (0.30) substantiate that genetic selection help to eradicate bTB. The multi-breed genome-wide association analysis identified 38 SNPs and 64 QTL regions associated with bTB infection; two QTL regions (both on BTA23) identified in the multi-breed analysis overlapped with the within-breed analyses of Charolais, Limousin, and Holstein-Friesian. Results from the association analysis, coupled with previous studies, suggest bTB is controlled by an infinitely large number of loci, each having a small effect. The methodology and results from the present study will be used to develop national genetic evaluations for bTB in the Republic of Ireland. In addition, results can also be used to help uncover the biological architecture underlying resistance to bTB infection in cattle.
    • Variance components for susceptibility to Mycobacterium bovis infection in dairy and beef cattle

      Richardson, Ian W.; Bradley, Daniel G; Higgins, Isabella; More, Simon J; McClure, Jennifer; Berry, Donagh (Biomed Central, 2014-11-18)
      Background Infection of livestock with bovine tuberculosis (bTB; Mycobacterium bovis) is of major economical concern in many countries; approximately 15 000 to 20 000 cattle are infected per year in Ireland. The objective of this study was to quantify the genetic variation for bTB susceptibility in Irish dairy and beef cattle. Methods A total of 105 914 cow, 56 904 heifer and 21 872 steer single intra-dermal comparative tuberculin test records (i.e., binary trait) collected from the years 2001 to 2010 from dairy and beef herds were included in the analysis. Only animal level data pertaining to periods of herd bTB infection were retained. Variance components for bTB were estimated using animal linear and threshold mixed models and co-variances were estimated using sire linear mixed models. Results Using a linear model, the heritability for susceptibility to bTB in the entire dataset was 0.11 and ranged from 0.08 (heifers in dairy herds) to 0.19 (heifers in beef herds) among the sub-populations investigated. Differences in susceptibility to bTB between breeds were clearly evident. Estimates of genetic correlations for bTB susceptibility between animal types (i.e., cows, heifers, steers) were all positive (0.10 to 0.64), yet different from one. Furthermore, genetic correlations for bTB susceptibility between environments that differed in herd prevalence of bTB ranged from 0.06 to 0.86 and were all different from one. Conclusions Genetic trends for bTB susceptibility observed in this study suggest a slight increase in genetic susceptibility to bTB in recent years. Since bTB is of economic importance and because all animals are routinely tested at least once annually in Ireland and some other countries, the presence of genetic variation for bTB susceptibility suggests that bTB susceptibility should be included in a national breeding program to halt possible deterioration in genetic susceptibility to bTB infection.
    • The variation in morphology of perennial ryegrass cultivars throughout the grazing season and effects on organic matter digestibility

      Beecher, Marion; Hennessy, Deirdre; Boland, T. M.; McEvoy, Mary; O'Donovan, Michael; Lewis, Eva (Wiley, 2013-09-19)
      The grass plant comprises leaf, pseudostem, true stem (including inflorescence) and dead material. These components differ in digestibility, and variations in their relative proportions can affect sward quality. The objective of this study was to determine the change in the proportion and organic matter digestibility (OMD) of leaf, pseudostem, true stem and dead components of four perennial ryegrass cultivars (two tetraploids: Astonenergy and Bealey and two diploids: Abermagic and Spelga) throughout a grazing season. The DM proportions and in vitro OMD of leaf, pseudostem, true stem and dead in all cultivars were determined during ten grazing rotations between May 2011 and March 2012. There was an interaction between rotation and cultivar for leaf, pseudostem, true stem and dead proportions. In May and June, Astonenergy had the highest leaf and lowest true stem proportion (P < 0·05). From July onwards, there was no difference in leaf or true stem proportion between cultivars. Bealey had the highest annual mean OMD (752 g kg−1) and Spelga the lowest (696 g kg−1; P < 0·05). The OMD followed the order leaf > pseudostem > true stem > dead. Bealey had the highest combined leaf and pseudostem proportion 0·92, which explains why it had the highest OMD. In this study, the tetraploid cultivars had the highest leaf and pseudostem proportion and OMD. For accurate descriptions of a sward in grazing studies and to accurately determine sward morphological composition, pseudostem should be separated from true stem, particularly during the reproductive stage when true stem is present.
    • Variation in the Ovine Abomasal Lymph Node Transcriptome between Breeds Known to Differ in Resistance to the Gastrointestinal Nematode

      Ahmed, Albin M.; Good, Barbara; Hanrahan, James P; McGettigan, Paul; Browne, John A; Keane, Orla M; Bahar, Bojlul; Mehta, Jai; Markey, Bryan; Lohan, Amanda; et al. (PLoS, 2015-05-15)
      Texel lambs are known to be more resistant to gastrointestinal nematode (GIN) infection than Suffolk lambs, with a greater ability to limit infection. The objectives of this study were to: 1) profile the whole transcriptome of abomasal lymph node tissue of GIN-free Texel and Suffolk lambs; 2) identify differentially expressed genes and characterize the immune-related biological pathways and networks associated with these genes. Abomasal lymph nodes were collected from Texel (n = 6) and Suffolk (n = 4) lambs aged 19 weeks that had been GIN-free since 6 weeks of age. Whole transcriptome profiling was performed using RNA-seq on the Illumina platform. At the time of conducting this study, a well annotated Ovine genome was not available and hence the sequence reads were aligned with the Bovine (UMD3.1) genome. Identification of differentially expressed genes was followed by pathway and network analysis. The Suffolk breed accounted for significantly more of the differentially expressed genes, (276 more highly expressed in Suffolk v 162 in Texel; P < 0.001). The four most significant differentially expressed pathways were all related to immunity and were classified as: Role of Pattern Recognition Receptors in Recognition of Bacteria and Viruses, Activation of IRF by Cytosolic Pattern Recognition Receptors, Role of RIG-I-like Receptors in Antiviral Innate Immunity, and Interferon Signaling. Of significance is the fact that all of these four pathways were more highly expressed in the Suffolk. These data suggest that in a GIN-free environment, Suffolk lambs have a more active immune profile relative to the Texel: this immune profile may contribute to the poorer efficiency of response to a GIN challenge in the Suffolk breed compared to the Texel breed.
    • Variations in travel time for N loading to groundwaters in four case studies in Ireland:Implications for policy makers and regulators

      Fenton, Owen; Coxon, Catherine E.; Haria, Atul H.; Horan, Brendan; Humphreys, James; Johnston, Paul; Murphy, Paul N. C.; Necpalova, Magdalena; Premrov, Alina; Richards, Karl G. (School of Agriculture, Food Science and Veterinary Medicine, University College Dublin in association with Teagasc, 2009)
      Mitigation measures to protect waterbodies must be implemented by 2012 to meet the requirements of the EU Water Framework Directive. The efficacy of these measures will be assessed in 2015. Whilst diffuse N pathways between source and receptor are generally long and complex, EU legislation does not account for differences in hydrological travel time distributions that may result in different water quality response times. The “lag time” between introducing mitigation measures and first improvements in water quality is likely to be different in different catchments; a process that should be considered by policy makers and catchment managers. Many examples of travel time variations have been quoted in the literature but no Irish specific examples are available. Lag times based on initial nutrient breakthrough at four contrasting sites were estimated to a receptor 500 m away from a source. Vertical travel times were estimated using a combination of depth of infiltration calculations based on effective rainfall and subsoil physical parameters and existing hydrological tracer data. Horizontal travel times were estimated using a combination of Darcian linear velocity calculations and existing tracer migration data. Total travel times, assuming no biogeochemical processes, ranged from months to decades between the contrasting sites; the shortest times occurred under thin soil/subsoil on karst limestone and the longest times through thick low permeability soils/subsoils over poorly productive aquifers. Policy makers should consider hydrological lag times when assessing the efficacy of mitigation measures introduced under the Water Framework Directive. This lag time reflects complete flushing of a particular nutrient from source to receptor. Further research is required to assess the potential mitigation of nitrate through denitrification along the pathway from source to receptor.
    • Veterinary dairy herd fertility service provision in seasonal and non-seasonal dairy industries - a comparison

      Mee, John F (Biomed Central, 2010-04-01)
      The decline in dairy herd fertility internationally has highlighted the limited impact of traditional veterinary approaches to bovine fertility management. Three questionnaire surveys were conducted at buiatrics conferences attended by veterinary practitioners on veterinary dairy herd fertility services (HFS) in countries with a seasonal (Ireland, 47 respondents) and non-seasonal breeding model (The Netherlands, 44 respondents and Portugal, 31 respondents). Of the 122 respondents, 73 (60%) provided a HFS and 49 (40%) did not. The majority (76%) of all practitioners who responded stated that bovine fertility had declined in their practice clients' herds with inadequate cow management, inadequate nutrition and increased milk yield as the most important putative causes. The type of clients who adopted a herd fertility service were deemed more educated than average (70% of respondents), and/or had fertility problems (58%) and/or large herds (53%). The main components of this service were routine postpartum examinations (95% of respondents), fertility records analysis (75%) and ultrasound pregnancy examinations (69%). The number of planned visits per annum varied between an average of four in Ireland, where breeding is seasonal, and 23 in Portugal, where breeding is year-round. The benefits to both the practitioner and their clients from running a HFS were cited as better fertility, financial rewards and job satisfaction. For practitioners who did not run a HFS the main reasons given were no client demand (55%) and lack of fertility records (33%). Better economic evidence to convince clients of the cost-benefit of such a service was seen as a major constraint to adoption of this service by 67% of practitioners.
    • Visual drainage assessment: A standardised visual soil assessment method for use in land drainage design in Ireland

      Tuohy, Patrick; Humphreys, James; Holden, Nicholas M.; O'Loughlin, James; Reidy, Brian; Fenton, Owen (Teagasc (Agriculture and Food Development Authority), Ireland, 20/08/2016)
      The implementation of site-specific land drainage system designs is usually disregarded by landowners in favour of locally established ‘standard practice’ land drainage designs. This is due to a number of factors such as a limited understanding of soil–water interactions, lack of facilities for the measurement of soil’s physical or hydrological parameters and perceived time wastage and high costs. Hence there is a need for a site-specific drainage system design methodology that does not rely on inaccessible, time-consuming and/or expensive measurements of soil physical or hydrological properties. This requires a standardised process for deciphering the drainage characteristics of a given soil in the field. As an initial step, a new visual soil assessment method, referred to as visual drainage assessment (VDA), is presented whereby an approximation of the permeability of specific soil horizons is made using seven indicators (water seepage, pan layers, texture, porosity, consistence, stone content and root development) to provide a basis for the design of a site-specific drainage system. Across six poorly drained sites (1.3 ha to 2.6 ha in size) in south-west Ireland a VDA-based design was compared with (i) an ideal design (utilising soil physical measurements to elucidate soil hydraulic parameters) and (ii) a standard design (0.8 m deep drains at a 15 m spacing) by model estimate of water table control and rainfall recharge/drain discharge capacity. The VDA method, unlike standard design equivalents, provided a good approximation of an ideal (from measured hydrological properties) design and prescribed an equivalent land drainage system in the field. Mean modelled rainfall recharge/drain discharge capacity for the VDA (13.3 mm/day) and ideal (12.0 mm/day) designs were significantly higher (P < 0.001, s.e. 1.42 mm/day) than for the standard designs (0.5 mm/day), when assuming a design minimum water table depth of 0.45 m.