Genetic and non-genetic evaluation tools for accelerating improvement in beef cattle carcass traits within and across country

The main revenue source for beef cattle farmers is the price they are awarded for carcasses based on carcass value (i.e., carcass weight, conformation and fat score) which is influenced by genetic and environmental factors (e.g., herd management). In order to improve profitability, accurate means of evaluating and improving both sets of factors influencing carcass trait performance are necessary. This would entail optimal management of genetic resources and herd practices. Furthermore, access to a large international germplasm pool would facilitate faster genetic gain. The objective of this thesis was to generate tools for the enhancement of carcass trait genetic and herd management evaluations both at a national and international level. The data used in the thesis originated from the Irish and UK national cattle databases and consisted of 336,944 Irish and 147,876 UK cattle of multiple beef and dairy breeds from 9,572 Irish and 3,385 UK commercial herds. Livestock mature at different rates depending on a number of factors including the genetic background; therefore, the optimum age at which to slaughter the progeny of different sires may differ. Chapter 2 examined sire level genetic profiles for three carcass traits (carcass weight, conformation and fat score) in cattle using data from the Republic of Ireland. Variance components for each trait across age at slaughter were estimated using sire random regression models. Heritability estimates of carcass traits across ages at slaughter varied depending on gender (heifers, steers, young bulls) and the trait in question, and ranged from 0.08 (± 0.02) to 0.34 (± 0.02) for carcass weight, from 0.24 (± 0.02) to 0.42 (± 0.02) for conformation score and from 0.16 (± 0.03) to 0.40 (± 0.02) for fat score. Genetic correlations between traits across ages at slaughter were all significantly less than unity, indicating that different genetic mechanisms control these traits across life. The results from chapter 2 show that genetic variability in the progeny growth trajectory of sires exists and that this variability in the growth profiles of sires for carcass traits may be exploited in breeding programmes. As carcass traits are a function of both the genetics of the animal and the environment in which the animal is reared, chapter 3 aimed to quantify the contribution of the herd environment to the same three beef carcass traits, with particular emphasis on generating finishing herd-specific profiles for carcass traits across different ages at slaughter. The data analysed in chapter 3 was from animals slaughtered in UK abattoirs. Genetic and finishing-herd-year of slaughter parameters were generated using random regression analysis. Across slaughter age and gender, the proportion of phenotypic variance accounted for by finishing-herd-year of slaughter variance was between 30.83%-71.48% for carcass weight, 21.38%-26.29% for conformation score and between 10.88%-44.04% for fat score. These parameters indicate that the finishing herd environment is an at least equally important contributor to carcass trait variability as the genetic background of animals, and amenable to improvement with appropriate management practices. The final study of the thesis was to investigate the feasibility of across-country carcass trait genetic evaluations. Examination of the level of genetic connectedness between Ireland and the UK found 225 distinct bulls common to both countries. These common bulls were related to 80,707 Irish and 23,162 UK animals with carcass records in each population. Genetic correlations for carcass traits between Ireland and the UK were almost unity, ranging from 0.92 (± 0.31) for fat score to 0.96 (± 0.17) for carcass weight, indicating that the carcass traits recorded in both countries are genetically essentially equivalent. These strong genetic correlations between carcass traits in both countries enabled the direct pooling of carcass data for the purpose of across-country genetic evaluations (breeding value estimation). An increased rate of genetic gain for carcass traits per generation was predicted from across-country selection compared to within country selection ranging from 2% (conformation score in Ireland) to 33.77% (conformation score in the UK). This improved gain was primarily due to greater intensity of selection and somewhat more accurate estimated breeding values when carcass records and pedigree information from both countries were combined. The results presented in this thesis demonstrate that routinely collected abattoir data in Ireland and the UK can be exploited to produce additional selection and on-farm management tools. The results also show that access to across-country carcass trait genetic evaluations would allow UK and Irish beef farmers to make more informed decisions on the selection of seed stock needed to increase genetic gain and profits. Outcomes of this thesis pave the way to improvements in national carcass traits genetic evaluations in Ireland and the UK based on appropriate age at slaughter and also demonstrate the feasibility of across-country carcass trait genetic evaluations between Ireland and the UK. The scope for further areas of research includes the identification of specific management practices for optimal herd performance for carcass traits. Additionally, across-country carcass trait genetic evaluations based on random regression models across different ages at slaughter would also be of benefit to beef producers in Ireland and the UK. Finally, the viability of across-country genetic evaluations for additional carcass traits, such as carcass cut weights should be explored

Vaccine effectiveness of live attenuated and trivalent inactivated influenza vaccination in 2010/11 to 2015/16:the SIVE II record linkage study

Background: There is good evidence of vaccine effectiveness in healthy individuals but less robust evidence for vaccine effectiveness in the populations targeted for influenza vaccination. The live attenuated influenza vaccine (LAIV) has recently been recommended for children in the UK. The trivalent influenza vaccine (TIV) is recommended for all people aged≥65 years and for those aged<65 years who are at an increased risk of complications from influenza infection (e.g. people with asthma). Objective: To examine the vaccine effectiveness of LAIV and TIV. Design: Cohort study and test-negative designs to estimate vaccine effectiveness. A self-case series study to ascertain adverse events associated with vaccination. Setting: A national linkage of patient-level general practice (GP) data from 230 Scottish GPs to the Scottish Immunisation & Recall Service, Health Protection Scotland virology database, admissions to Scottish hospitals and the Scottish death register. Participants: A total of 1,250,000 people. Interventions: LAIV for 2- to 11-year-olds and TIV for older people (aged≥65 years) and those aged<65 years who are at risk of diseases, from 2010/11 to 2015/16. Main outcome measures: The main outcome measures include vaccine effectiveness against laboratory-confirmed influenza using real-time reverse-transcription polymerase chain reaction (RT-PCR), influenza-related morbidity and mortality, and adverse events associated with vaccination. Results: Two-fifths (40%) of preschool-aged children and three-fifths (60%) of primary school-aged children registered in study practices were vaccinated. Uptake varied among groups [e.g. most affluent vs. most deprived in 2- to 4-year-olds, odds ratio 1.76, 95% confidence interval (CI) 1.70 to 1.82]. LAIV-adjusted vaccine effectiveness among children (aged 2-11 years) for preventing RT-PCR laboratoryconfirmed influenza was 21% (95% CI -19% to 47%) in 2014/15 and 58% (95% CI 39% to 71%) in 2015/16. No significant adverse events were associated with LAIV. Among at-risk 18- to 64-year-olds, significant trivalent influenza vaccine effectiveness was found for four of the six seasons, with the highest vaccine effectiveness in 2010/11 (53%, 95% CI 21% to 72%). The seasons with non-significant vaccine effectiveness had low levels of circulating influenza virus (2011/12, 5%; 2013/14, 9%). Among those people aged≥65 years, TIV effectiveness was positive in all six seasons, but in only one of the six seasons (2013/14) was significance achieved (57%, 95% CI 20% to 76%). Conclusions: The study found that LAIV was safe and effective in decreasing RT-PCR-confirmed influenza in children. TIV was safe and significantly effective in most seasons for 18- to 64-year-olds, with positive vaccine effectiveness in most seasons for those people aged≥65 years (although this was significant in only one season). Future work: The UK Joint Committee on Vaccination and Immunisation has recommended the use of adjuvanted injectable vaccine for those people aged≥65 years from season 2018/19 onwards. A future study will be required to evaluate this vaccine. Trial registration: Current Controlled Trials ISRCTN88072400

Seasonal influenza vaccine effectiveness in people with asthma: a national test-negative design case-control study

Financial support. The work was funded by the Chief Scientist Office of the Scottish Government under the grant (AUKCAR/14/03) and the NIHR–Health Technology Assessment (HTA) Programme (13/34/14) for the Seasonal Influenza Vaccination Effectiveness II (SIVE II) study. As principal investigator, C. R. S. received a grant for the SIVE-II project from the NIHR HTA. This work was carried out with the support of the Asthma UK Centre for Applied Research (AUK-AC-2012-01), the Farr Institute (MR/M501633/2), Health Data Research UK (an initiative funded by UK Research and Innovation, Department of Health and Social Care England and the devolved administrations and leading medical research charities), the European Union’s Horizon 2020 research and innovation programme (under grant agreement No 634446) and European Centre for Disease Prevention and Control (Influenza-Monitoring Vaccine Effectiveness). Acknowledgments. The authors thank and acknowledge all colleagues at the Asthma UK Centre for Applied Research for their support in this study. Disclaimer. The funding bodies had no role in the design of the study, review process, analysis, interpretation, or reporting of data. The views and opinions expressed herein are those of the authors and do not necessarily reflect those of the Health Technology Assessment Programme, National Institute for Health Research (NIHR), National Health Service, or the Department of Health. Potential conflicts of interest. The authors: No reported conflicts of interest. All authors have submitted the ICMJE Form for Disclosure of Potential Conflicts of Interest. Conflicts that the editors consider relevant to the content of the manuscript have been disclosed.Peer reviewedPublisher PDFPublisher PD

Peripheral and gastrointestinal immune systems of healthy cattle raised outdoors at pasture or indoors on a concentrate-based ration

peer-reviewedBackground: Despite an increasing preference of consumers for beef produced from more extensive pasture-based production systems and potential human health benefits from the consumption of such beef, data regarding the health status of animals raised on pasture are limited. The objective of this study was to characterise specific aspects of the bovine peripheral and the gastrointestinal muscosal immune systems of cattle raised on an outdoor pasture system in comparison to animals raised on a conventional intensive indoor concentrate-based system. Results: A number of in vitro functional tests of immune cells suggested subtle differences between the animals on the outdoor versus indoor production systems. There was a decrease in the number of neutrophils and monocytes engaged in phagocytosis in outdoor cattle (P < 0.01 and P < 0.05, respectively) in comparison to those indoors. Following mitogen stimulation, a lower level of interferon-γ was produced in leukocytes from the outdoor animals (P < 0.05). There was evidence of a gastrointestinal nematode infection in the outdoor animals with elevated levels of serum pepsinogen (P < 0.001), a higher number of eosinophils (P < 0.05) and a higher level of interleukin-4 and stem cell factor mRNA expression (P < 0.05) in the outdoor animals in comparison to the indoor animals. Lower levels of copper and iodine were measured in the outdoor animals in comparison to indoor animals (P < 0.001). Conclusion: Despite distinctly contrasting production systems, only subtle differences were identified in the peripheral immune parameters measured between cattle raised at pasture in comparison to animals raised on a conventional intensive indoor concentrate-based production system

Herd-specific random regression carcass profiles for beef cattle after adjustment for animal genetic merit

Abattoir data are an important source of information for the genetic evaluation of carcass traits, but also for onfarm management purposes. The present study aimed to quantify the contribution of herd environment to beef carcass characteristics (weight, conformation score and fat score) with particular emphasis on generating finishing herd-specific profiles for these traits across different ages at slaughter. Abattoir records from 46,115 heifers and 78,790 steers aged between 360 and 900 days, and from 22,971 young bulls aged between 360 and 720 days, were analysed. Finishing herd-year and animal genetic (co)variance components for each trait were estimated using random regression models. Across slaughter age and gender, the ratio of finishing herd-year to total phenotypic variance ranged from 0.31 to 0.72 for carcass weight, 0.21 to 0.57 for carcass conformation and 0.11 to 0.44 for carcass fat score. These parameters indicate that the finishing herd environment is an important contributor to carcass trait variability and amenable to improvement with management practices