Animal and Grassland Research and Innovation Center

Athenry, Ireland

Animal and Grassland Research and Innovation Center

Athenry, Ireland
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Brophy C.,National University of Ireland | Dooley A.,National University of Ireland | Kirwan L.,University College Dublin | Finn J.A.,Teagasc | And 5 more authors.
Ecology | Year: 2017

Understanding the biodiversity and ecosystem function relationship can be challenging in species-rich ecosystems. Traditionally, species richness has been relied on heavily to explain changes in ecosystem function across diversity gradients. Diversity–Interactions models can test how ecosystem function is affected by species identity, species interactions, and evenness, in addition to richness. However, in a species-rich system, there may be too many species interactions to allow estimation of each coefficient, and if all interaction coefficients are estimable, they may be devoid of any sensible biological meaning. Parsimonious descriptions using constraints among interaction coefficients have been developed but important variability may still remain unexplained. Here, we extend Diversity–Interactions models to describe the effects of diversity on ecosystem function using a combination of fixed coefficients and random effects. Our approach provides improved standard errors for testing fixed coefficients and incorporates lack-of-fit tests for diversity effects. We illustrate our methods using data from a grassland and a microbial experiment. Our framework considerably reduces the complexities associated with understanding how species interactions contribute to ecosystem function in species-rich ecosystems. © 2017 by the Ecological Society of America

Power C.,Teagasc | Power C.,Cork Institute of Technology | Whelan M.,Teagasc | Danaher M.,Teagasc | And 5 more authors.
Food Additives and Contaminants - Part A Chemistry, Analysis, Control, Exposure and Risk Assessment | Year: 2013

Triclabendazole is a flukicide used in the treatment of liver fluke in cattle. However, its use in the treatment of liver fluke is prohibited in dairy cows. In this work, two independent studies were designed to investigate the persistence of triclabendazole residues in milk following the administration of 10% Fasinex® as dry-cow and lactating-cow treatments. In the dry-cow study, 36 in-calf dairy cows were treated with a commercial product, 10% Fasinex®, at drying-off and three triclabendazole residues (triclabendazole, triclabendazole sulphoxide and triclabendazole sulphone) were monitored in the milk following calving, approximately 60 days post-treatment. No residues were measurable in the milk of the 36 cows tested - the LOQ of the method was 1.00 μg kg-1. In the lactating-cow study, the persistence of four triclabendazole residues was investigated in the milk of six dairy cows. The highest levels of triclabendazole, triclabendazole sulphoxide, triclabendazole sulphone and keto-triclabendazole residues measured in individual milk samples were 244, 525, 1710 and 16 μg kg-1, respectively. Residues of triclabendazole, triclabendazole sulphoxide, triclabendazole sulphone and keto-triclabendazole were detectable in milk for up to 5.5, 15.5, 20 and 5 days post-treatment, respectively. Triclabendazole sulphone was found to be the most important residue, accounting for >87% of marker residues at ≥3.5 days following drug administration. These results indicate that following treatment at drying-off, triclabendazole residues in milk post-calving are well below the current MRL. Therefore, triclabendazole is a suitable flukicide for use during the dry period. © 2013 Copyright Teagasc.

Berry D.P.,Animal and Grassland Research and Innovation Center | Bastiaansen J.W.M.,Wageningen University | Veerkamp R.F.,Animal Breeding and Genomics Center | Wijga S.,Wageningen University | And 3 more authors.
Animal | Year: 2012

Genome-wide association studies for difficult-to-measure traits are generally limited by the sample population size with accurate phenotypic data. The objective of this study was to utilise data on primiparous Holstein-Friesian cows from experimental farms in Ireland, the United Kingdom, the Netherlands and Sweden to identify genomic regions associated with traditional measures of fertility, as well as a fertility phenotype derived from milk progesterone profiles. Traditional fertility measures investigated were days to first heat, days to first service, pregnancy rate to first service, number of services and calving interval (CI); post-partum interval to the commencement of luteal activity (CLA) was derived using routine milk progesterone assays. Phenotypic and genotypic data on 37 590 single nucleotide polymorphisms (SNPs) were available for up to 1570 primiparous cows. Genetic parameters were estimated using linear animal models, and univariate and bivariate genome-wide association analyses were undertaken using Bayesian stochastic search variable selection performed using Gibbs sampling. Heritability estimates of the traditional fertility traits varied from 0.03 to 0.16; the heritability for CLA was 0.13. The posterior quantitative trait locus (QTL) probabilities, across the genome, for the traditional fertility measures were all <0.021. Posterior QTL probabilities of 0.060 and 0.045 were observed for CLA on SNPs each on chromosome 2 and chromosome 21, respectively, in the univariate analyses; these probabilities increased when CLA was included in the bivariate analyses with the traditional fertility traits. For example, in the bivariate analysis with CI, the posterior QTL probability of the two aforementioned SNPs were 0.662 and 0.123. Candidate genes in the vicinity of these SNPs are discussed. The results from this study suggest that the power of genome-wide association studies in cattle may be increased by sharing of data and also possibly by using physiological measures of the trait under investigation. © Copyright The Animal Consortium 2012.

Beecher C.,Teagasc | Beecher C.,University College Cork | Daly M.,Teagasc | Childs S.,Teagasc | And 4 more authors.
BMC Genetics | Year: 2010

Background: Mastitis, an inflammation of the mammary gland, is a major source of economic loss on dairy farms. The aim of this study was to quantify the associations between two previously identified polymorphisms in the bovine toll-like receptor 2 (TLR2) and chemokine receptor 1 (CXCR1) genes and mammary health indictor traits in (a) 246 lactating dairy cow contemporaries representing five breeds from one research farm and (b) 848 Holstein-Friesian bulls that represent a large proportion of the Irish dairy germplasm. To expand the study, a further 14 polymorphisms in immune genes were included for association studies in the bull population.Results: TLR4-2021 associated (P < 0.05) with both milk protein and fat percentage in late lactation (P < 0.01) within the cow cohort. No association was observed between this polymorphism and either yield or composition of milk within the bull population. CXCR1-777 significantly associated (P < 0.05) with fat yield in the bull population and tended to associate (P < 0.1) with somatic cell score (SCS) in the cows genotyped. CD14-1908 A allele was found to associate with increased (P < 0.05) milk fat and protein yield and also tended to associate with increased (P < 0.1) milk yield. A SERPINA1 haplotype with superior genetic merit for milk protein yield and milk fat percentage (P < 0.05) was also identified.Conclusion: Of the sixteen polymorphisms in seven immune genes genotyped, just CXCR1-777 tended to associate with SCS, albeit only in the on-farm study. The lack of an association between the polymorphisms with SCS in the Holstein-Friesian data set would question the potential importance of these variants in selection for improved mastitis resistance in the Holstein-Friesian cow. © 2010 Beecher et al; licensee BioMed Central Ltd.

Harley S.,University College Dublin | More S.J.,University College Dublin | O'Connell N.E.,Queen's University of Belfast | Hanlon A.,University College Dublin | And 2 more authors.
Veterinary Record | Year: 2012

Despite extensive utilisation in epidemiological investigations of animal health, to date there has been little consideration of the value of abattoir meat inspection as a pig welfare surveillance tool. This study measured the prevalence of tail-docking, tail biting, carcase condemnations and associated financial losses of the latter (Northern Ireland only) in 36,963 pigs slaughtered in six abattoirs from the Republic of Ireland and Northern Ireland in July and August 2010. Over 99 per cent of inspected pigs had been tail-docked, while 58.1 per cent and 1.03 per cent had detectable and severe tail lesions, respectively. Producer losses resulting from carcase condemnation were estimated to be €0.37 per pig slaughtered. Enhanced capture and utilisation of meat inspection data for use in animal welfare surveillance schemes has the potential to drive improvements in production efficiency and animal welfare. However, significant differences were detected in the prevalence of carcase condemnation conditions between abattoirs and judiciaries (Republic and Northern Ireland). This reflects variation in the criteria and methods of data capture used in meat inspection in different abattoirs. Thus, the meat inspection process needs to be standardised and reformed before it can be reliably utilised in large-scale pig welfare surveillance schemes.

Moloney A.P.,Animal and Grassland Research and Innovation Center
Lipid Technology | Year: 2012

Medical authorities recommend that energy intake from saturated fatty acids (SFA) should not exceed 10% of total energy intake. Milk and meat, because of their relatively high SFA concentration and level of consumption, make a large contribution to human SFA consumption. Strategies to decrease the SFA content in meat and milk include inclusion of forage in the ration of ruminants and supplementation of dietary intake of ruminants and monogastrics with unsaturated fatty acid-rich oilseeds, fish oil or marine algae. The influences of these manipulations will be illustrated and the likely future trends in the SFA content of meat and milk will be suggested. © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Amdi C.,Animal and Grassland Research and Innovation Center | Amdi C.,Teagasc | Amdi C.,Royal Veterinary College | Giblin L.,Teagasc | And 3 more authors.
Animal | Year: 2014

A commercial pig spends nearly half of its life in utero and its nutrition during this time can influence birth weight and postnatal growth. We hypothesised that postnatal growth is increased in pigs raised by sows with a high backfat depth and high level of energy intake during gestation compared with sows with a low backfat depth and low level of energy intake during gestation. This was tested in a 2×3 factorial design experiment with 2 factors for gilt backfat depth (Thin and Fat) and 3 factors for gestation feed allowance (Restricted, Control and High). Between d 25 and d 90 of gestation, Thin gilts (n=68; 12±0.6 mm P2 backfat) and Fat gilts (n=72; 19±0.6 mm P2 backfat) were randomly allocated, as individuals, to a gestation diet (6.19 g/kg lysine, 13.0 MJ DE/kg) at the following feed allowances: 1.8 kg/day (Restricted); 2.5 kg/day (Control) and 3.5 kg/day (High). For the remainder of gestation and during lactation all gilts were treated similarly. At weaning (day 28), 155 piglets were sacrificed and 272 were individually housed and followed through to slaughter (day 158). At day 80 of gestation, fasted Thin Restricted gilts had lower serum IGF-1 concentrations than Thin High or Thin Control fed gilts (P<0.001). Pigs born from Fat gilts had greater backfat depths (P<0.05), a lower lean meat yield (P<0.05) and were heavier (P<0.05) at slaughter than pigs born from Thin gilts. Gilt gestation feed allowance had only transitory effects on average daily gain and feed conversion efficiency and had no effect on pig weight at slaughter (P>0.05) or lean meat yield (P>0.05). In conclusion, gilts with a backfat depth of ~19 mm at insemination produced pigs that were heavier and fatter at ~158 days of age than those born from gilts with ~12 mm backfat depth at insemination. Maternal body condition during gestation had a more predominant influence on growth parameters of the offspring, such as weight at slaughter and backfat depth, than did feed level during gestation. © 2013 The Animal Consortium.

Faulkner S.,Animal and Grassland Research and Innovation Center | Faulkner S.,University College Dublin | Elia G.,University College Dublin | O'Boyle P.,Animal and Grassland Research and Innovation Center | And 2 more authors.
Proteomics | Year: 2013

Early embryonic loss accounts for over 70% of total embryonic and foetal loss in dairy cattle. Early embryonic development and survival is associated with the concentration of systemic progesterone. To determine if the uterine proteome is influenced by stage of cycle or systemic progesterone concentrations, uterine flushings were collected from the ipsi- and contralateral uterine horns of beef heifers on Days 7 (n = 10) and 15 (n = 10) of the oestrous cycle. Animals were separated into low or high progesterone groups based on plasma progesterone concentrations on Day 5 of the cycle. Samples were albumin depleted before iTRAQ® labeling and subsequent strong cation exchange-LC-MS/MS analyses. A total of 20 proteins were up to 5.9-fold higher (p < 0.05) and 20 were up to 2.3-fold lower on Day 15 compared to Day 7. In addition, the expression of a number of proteins on Day 7 and/or 15 of the cycle was correlated with progesterone concentrations during Days 3-7 or the rate of change in progesterone between Days 3 and 7. This study highlights the dynamic changes occurring in the microenvironment surrounding the embryo during this period. The findings here also support the hypothesis that progesterone supports embryonic development by altering the maternal uterine environment. © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Berry D.P.,Animal and Grassland Research and Innovation Center | Mcclure M.C.,Irish Cattle Breeding Federation | Mullen M.P.,Animal and Grassland Research and Innovation Center
Journal of Animal Breeding and Genetics | Year: 2014

Summary: The objective of this study was to evaluate, using three different genotype density panels, the accuracy of imputation from lower- to higher-density genotypes in dairy and beef cattle. High-density genotypes consisting of 777 962 single-nucleotide polymorphisms (SNP) were available on 3122 animals comprised of 269, 196, 710, 234, 719, 730 and 264 Angus, Belgian Blue, Charolais, Hereford, Holstein-Friesian, Limousin and Simmental bulls, respectively. Three different genotype densities were generated: low density (LD; 6501 autosomal SNPs), medium density (50K; 47 770 autosomal SNPs) and high density (HD; 735 151 autosomal SNPs). Imputation from lower- to higher-density genotype platforms was undertaken within and across breeds exploiting population-wide linkage disequilibrium. The mean allele concordance rate per breed from LD to HD when undertaken using a single breed or multiple breed reference population varied from 0.956 to 0.974 and from 0.947 to 0.967, respectively. The mean allele concordance rate per breed from 50K to HD when undertaken using a single breed or multiple breed reference population varied from 0.987 to 0.994 and from 0.987 to 0.993, respectively. The accuracy of imputation was generally greater when the reference population was solely comprised of the breed to be imputed compared to when the reference population comprised of multiple breeds, although the impact was less when imputing from 50K to HD compared to imputing from LD. © 2013 Blackwell Verlag GmbH.

PubMed | Animal and Grassland Research and Innovation Center, Agrocampus Ouest and Northumbria University
Type: Journal Article | Journal: Animal : an international journal of animal bioscience | Year: 2016

The herd dynamic milk (HDM) model is a dynamic model capable of simulating the performance of individual dairy animals (from birth to death), with a daily time step. Within this study, the HDM model is described and evaluated in relation to milk production, body condition score (BCS) and BCS change throughout lactation by comparing model simulations against data from published experimental studies. The models response to variation in genetic potential, herbage allowance and concentrate supplementation was tested in a sensitivity analysis. Data from experiments in Ireland and France over a 3-year period (2009-11) were used to complete the evaluation. The aim of the Irish experiment was to determine the impact of different stocking rates (SRs) (SR1: 3.28 cow/ha, SR2: 2.51 cow/ha) on key physical, biological and economic performance. The aim of the French experiment was to evaluate over a prolonged time period, the ability of two breeds of dairy cows (Holstein and Normande) to produce and to reproduce under two feeding strategies (high level and low level) in the context of compact calving. The model evaluation was conducted at the herd level with separate evaluations for the primiparous and multiparous cows. The evaluation included the two extreme SRs for the Irish experiment, and an evaluation at the overall herd and individual animal level for the different breeds and feeding levels for the French data. The comparison of simulation and experimental data for all scenarios resulted in a relative prediction error, which was consistently <15% across experiments for weekly milk production and BCS. In relation to BCS, the highest root mean square error was 0.27 points of BCS, which arose for Holstein cows in the low feeding group in late lactation. The model responded in a realistic fashion to variation in genetic potential for milk production, herbage allowance and concentrate supplementation.

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