Quantitative Genetics and Population Dynamics
Lead Research Organisation:
University of Edinburgh
Department Name: The Roslin Institute
Abstract
Abstracts are not currently available in GtR for all funded research. This is normally because the abstract was not required at the time of proposal submission, but may be because it included sensitive information such as personal details.
Technical Summary
This project will (i) develop and implement effective models for the delivery of genomic selection and the management of genetic diversity; and (ii) develop and implement a theory of genetic epidemiology that encompasses field disease data. Accelerating the genetic change in populations will require informed utilisation of genomic data. The key challenge is to make accurate predictions of breeding values, most likely an aggregate multi-trait value combining large-scale SNP and sequence data. This technique is known as genomic selection, which is in its infancy with a number of outstanding challenges remaining to be solved. A key biological challenge for genetic improvement is to increase the robustness of populations to disease. To achieve the necessary precision for predicting disease risks, and to do this in relevant populations, it will be necessary to use field data. This offers unique challenges, because assessment of disease prevalence in the field depends upon diagnostic accuracy, and infections rates are strongly influenced by environmental variables. Analysis of such data will require developments in genetic epidemiology – a field in which Roslin scientists are pioneers. The project will develop novel concepts in quantitative genetics and epidemiology. These concepts are fundamental to the understanding of genetic variation in resistance to pathogens addressed in other strategic programmes. The quantitative genetics of using data from systems biology approaches in breeding schemes will also inform and shape the development of work in other strategic programmes.
Planned Impact
unavailable
Organisations
- University of Edinburgh (Lead Research Organisation)
- University of Minnesota (Collaboration)
- Geno Global Ltd. (Collaboration)
- Iowa State University (Collaboration)
- Mars Nutrition Research Council, Mars Incorporated (Collaboration)
- Cyprus University of Technology (Collaboration)
- French National Institute of Agricultural Research (Collaboration)
- University of Rennes 1 (Collaboration)
- U.S. Department of Agriculture USDA (Collaboration)
- Federal University of Minas Gerais (Collaboration)
- University of Ghent (Collaboration)
- University of Helsinki (Collaboration)
- Illumina Inc. (Collaboration)
- UNIVERSITY OF SYDNEY (Collaboration)
- Innovis ltd (Collaboration)
- International Livestock Research Institute (ILRI) (Collaboration)
- Norwegian University of Life Sciences (NMBU) (Collaboration)
- Cherry Valley Farms (Collaboration)
- Sarl Hycole (Collaboration)
- ANIMAL HEALTH TRUST (Collaboration)
- University of Pennsylvania (Collaboration)
- University of California, Davis (Collaboration)
- Ain Shams University (Collaboration)
- North Carolina State University (Collaboration)
- University of Bern (Collaboration)
- University of Saskatchewan (Collaboration)
- WorldFish (Collaboration)
- Axiom (Collaboration)
- University of Liege (Collaboration)
People |
ORCID iD |
| John Woolliams (Principal Investigator) |
Publications
Anacleto O
(2015)
A Novel Statistical Model to Estimate Host Genetic Effects Affecting Disease Transmission
in Genetics
Baillie JK
(2018)
Shared activity patterns arising at genetic susceptibility loci reveal underlying genomic and cellular architecture of human disease.
in PLoS computational biology
Banos G
(2017)
Genetic evaluation for bovine tuberculosis resistance in dairy cattle.
in Journal of dairy science
Battagin M
(2016)
Effect of manipulating recombination rates on response to selection in livestock breeding programs
in Genetics Selection Evolution
Bermingham ML
(2014)
Genome-wide association study identifies novel loci associated with resistance to bovine tuberculosis.
in Heredity
Bessell PR
(2016)
Assessing the potential for Bluetongue virus 8 to spread and vaccination strategies in Scotland.
in Scientific reports
Bishop S
(2012)
A consideration of resistance and tolerance for ruminant nematode infections
in Frontiers in Genetics
Bishop SC
(2014)
Genomics and disease resistance studies in livestock.
in Livestock science
BRAMIS G
(2018)
Predisposing factors and control of bacterial mastitis in dairy ewes
in Journal of the Hellenic Veterinary Medical Society
| Description | The core aims of this theme are to develop the theory and practice of operational genetics and genomics, epidemiology and genetic epidemiology to deliver effective breeding and disease control in populations. 1. We have developed the concept of Genomic Selection 2.0 in which we can cost-effectively generate and utilise huge quantities of genomic sequence data to drive genetic gain and maintenance of genetic variance in livestock breeding programs. We have quantified some of the possible benefits of Genomic Selection 2.0 using simulation. For example, we showed that low-coverage sequence data is as effective as high-coverage sequence data for genomic selection. We have developed theory and methods to maximize genetic gain whilst managing inbreeding and loss of genetic variation, including a demonstration that Genomic Selection 2.0 could enable more response to selection and lower utilisation of genetic variance by allowing the recombination rate to be increased in livestock breeding programs. We have expanded the scope of target traits for genomic selection including the genomic prediction hip dysplasia in dogs and tuberculosis in dairy cattle and sea lice in Atlantic salmon. 2. We have developed a protocol for discovering regions of livestock genomes that harbour lethal recessives affecting embryo survival, and identify the haplotypes involved. Embryos inheriting two copies of these lethal alleles die early in development and reduce the size of litters, although those inheriting a single copy are healthy and cannot be identified without the genomic information; as a consequence of this work the carriers can be identified and selected against. 3. We have developed AlphaGenes, an important software suite and resource to support our vision of Genomic Selection 2.0, and underpin the analysis of vast quantities of sequence data generated from hundreds of thousands of animals at low cost in support of £6M Agri-Tech Catalyst projects. 4. We have modelled the network of livestock movements in the UK as these act as a highway for infectious disease in the course of epidemics. Consequently we have been able to predict proactively the spread of infectious diseases across regions which increases the effectiveness of surveillance and the preparedness of the first line response. 5. We developed efficient Bayesian algorithms to estimate genetic parameters and QTL effects associated with host susceptibility, infectivity and tolerance, from epidemiological data. This will enable us to not only identify individuals of high genetic risk of becoming infected, but also to identify potential genetic super-spreaders, if they exist. Within recently established international collaborations, we are now implementing these algorithms to determine the host genetic influence in the spread and impact of Marek's disease in poultry, porcine reproductive & respiratory syndrome in pigs, scuticociliate infection in turbot, and infectious pancreatic necrosis and amoebic gill disease in salmon. 6. We have developed novel statistical methods for determining how resistance and tolerance, two different strategies of animals to cope with infections, contribute to disease outcome over time. The method is based on tracing individual infection trajectories that capture simultaneously progression of pathogen burden and health over time. Analysis of individual trajectories of mice from different genetic lines infected with Listeria monocytogenes bacteria revealed that individuals that recover or do not recover from infections follow distinct infection paths, and that these are genetically determined. 7. We developed a platform to scan genomic data and identify ancestral haplotypes. This allows the study of selection and evolution in livestock breeds. 8. We expanded an optimum-contribution platform to incorporate genomic data for conservation and genetic improvement programmes. This platform facilitates the balance between genetic gains and inbreeding control (maintaining biodiversity). The platform can accommodate simultaneous selection and gains for genetically antagonistic traits such as production yield and fitness. 9. We have developed genetic models to explore the potential impact of selection for resistance to bTB in cattle and shown that selection is unlikely to change the specificity of SICCT, a key control measure in the fight against the disease. 10. In collaboration with partners, we have partitioned the phenotypic variance in an important commercial population of tilapia, identifying significant components of maternal variance and non-additive genetic variance. |
| Exploitation Route | 1. The findings enable improvements in the accuracy and utility of selective animal breeding and the incorporation of additional traits, such as susceptibility to tuberculosis, into selection indices. Furthermore this work is generic and has been developed further for important plant breeding sectors through collaborations into fruit, crops and forestry, and has applications for overseas development. These applications have been taken forward through an array of commercial funds and partnerships, Innovate UK Agri-tech Catalyst funding, funds from the Bill & Melinda Gates Foundation, and in the extensions to plant breeding through BBSRC Response Mode funding including industrial partnership awards. The findings are directly relevant to any sector which relies on products from managed population where genetics underpins the quantity or quality of the products. 2. The findings allow more effective veterinary surveillance and preparedness in managing the disease threats to UK livestock production, and need to be incorporated into procedures of Defra and its devolved partners.The work on bTB has directly enabled the publication of expected breeding values (EBV) for bTB in cattle (TB Advantage). However work taken forward will involve assessing impact of selection on the sensitivity of SICCT, developing improved genomic EBV, rolling out EBVs to beef breeds, quantifying the genetic variation in infectivity, and building improved genetic impact models to assess future progress. 3. Genomic data was obtained to progress the work on identifying the form of non-additive genetic variance in commercial tilapia to explore the potential for implementation. |
| Sectors | Agriculture Food and Drink Digital/Communication/Information Technologies (including Software) Leisure Activities including Sports Recreation and Tourism Manufacturing including Industrial Biotechology Pharmaceuticals and Medical Biotechnology Other |
| Description | 1. Genomic selection has had a major impact on selective animal breeding both in the scope of the objectives and in the speed of progress especially in the dairy cattle, pig and poultry sectors. The holistic approaches enabled by genomic selection have increased animal health and productivity, as well as increased economic gains to production industries. Roslin scientists have contributed to the development of the theory and tools to deliver genomic selection. Recent and on-going developments in this project continue to improve the accuracy and utility of genomic selection and have been adopted by commercial partners, particularly in the pig and poultry sectors. 2. The recent release of public genetic evaluations of bovine Tb susceptibility 'TB Advantage' is the fruition of work initiated by Roslin and developed within this project and is a tool made freely available by AHDB to farmers and breeders (and others), to assist in reducing the impact of the current epidemic which has been estimated to cost £100m p.a. 3. Sea lice present the primary constraint to salmon aquaculture in all major salmon producing countries, including the UK, as infestation has negative health and welfare impacts on the fish, and the widespread chemical treatments required to control lice are expensive and damage the environment. The genomic prediction pipeline constructed within this programme for susceptibility to sea lice infestation in salmon has been implemented into the breeding program of Landcatch, and similar genomic selection programs are now run by other salmon breeding companies.. 4. A genomic prediction pipeline has been constructed with support from this project for genomic selection in sheep which is now in operation by Innovis. 5. The work on infectivity modelled has already shaped the design and objectives of challenge trials in fish and poultry breeding companies. As results emerge the estimated breeding values for infectivity will expand their breeding objectives, offer new marketing opportunities, and reduce the impact of epidemics on commercial populations. 6. The predictive model for liver fluke has been adopted by Scotbeef to improve their reporting to farmers, which will assist in on-farm control. 7. The outcomes of the epidemiological models applied to bovine TB in Cameroon have been reported to farmers, the government and butchers in Cameroon about prevalence, strains and risks. This was well-received, particularly by the butchers, but lack of funds and security has limited the support that can be given to develop these outcomes further. |
| Sector | Agriculture, Food and Drink,Leisure Activities, including Sports, Recreation and Tourism,Other |
| Impact Types | Economic |
| Description | Chair of FAO Working Group on "Secondary Guidelines on Management of Small Populations at Risk" |
| Geographic Reach | Multiple continents/international |
| Policy Influence Type | Membership of a guideline committee |
| Impact | Preparation for UN Global Plan of Action for Animal Genetic Resources and Interlaken Declaration in 2007 |
| URL | http://www.fao.org/docrep/010/a1404e/a1404e00.htm |
| Description | EBVs for bTB Next Steps |
| Geographic Reach | Europe |
| Policy Influence Type | Membership of a guideline committee |
| Impact | The improved survival is for CATTLE. The publication of EBVs for resistance to bTB (TB Advantage) has prompted selection for resistance by breeding companies, which is incremental, cumulative and permanent and will lead to reduced numbers of breakdowns, reduced severity of breakdowns, will improve the capacity of UK surveillance (a public service) to suppress the current epidemic and offer a route that is not associated with culling badgers which may contribute to softening teh societal divide on this issue. The guidance committee is an annual meeting with Defra, devolved bodies and AHDB (industry levy board) to monitor progress with TB Advantage and review future actions. It is Europe wide as gene flow and genetic information on genetics of bTB is closely involved with RoI, and the meeting was in RoI with their agriculture ministry participating. |
| URL | https://www.gov.uk/government/publications/a-strategy-for-achieving-bovine-tuberculosis-free-status-... |
| Description | Genomic Selection in Sheep Breeding |
| Geographic Reach | Europe |
| Policy Influence Type | Influenced training of practitioners or researchers |
| Impact | We guided the implementation of genomic selection into a sheep breeding scheme owned by a breeding company. This involved providing a pipeline which took genotypes, carried out imputation, and delivered genomic expected breeding values. |
| Description | Membership of Defra National Consultative Committee on Farm Animal Genetic Resources, 2001 to 2002 |
| Geographic Reach | National |
| Policy Influence Type | Membership of a guideline committee |
| Impact | UK Country Report on Farm Animal Genetic Resources 2002. This was the first time this policy area was addressed and formed an international report to FAO. |
| URL | https://www.gov.uk/government/publications/uk-country-report-on-farm-animal-genetic-resources-2002 |
| Description | Membership of FAO Drafting Group for 3rd Intergovernmental Technical Working Group, 2003 |
| Geographic Reach | Multiple continents/international |
| Policy Influence Type | Membership of a guideline committee |
| Impact | Drafting resolutions for UN inter-governemental meeting on agricultural policies, ultimately leading to UN's Global Plan of Action for Farm Animal Genetic Resources and the Interlaken Agreement in 2007. |
| URL | http://www.fao.org/docrep/010/a1404e/a1404e00.htm |
| Description | Membership of FAO Working Group on Ex Situ Conservation of Livestock |
| Geographic Reach | Multiple continents/international |
| Policy Influence Type | Membership of a guideline committee |
| Impact | Preparation for UN Global Plan of Action for Animal Genetic Resources and the Interlaken Declaration in 2007. |
| URL | http://www.fao.org/docrep/010/a1404e/a1404e00.htm |
| Description | Membership of FAO Working Group on In Situ Conservation of Livestock |
| Geographic Reach | Multiple continents/international |
| Policy Influence Type | Membership of a guideline committee |
| Impact | Preparation for UN Global Plan of Action for Animal Genetic Resources and the Interlaken Declaration in 2007. |
| URL | http://www.fao.org/docrep/010/a1404e/a1404e00.htm |
| Description | Membership of FAO/ISZ Working Group on Implications of Developments in Biotechnology for the Conservation of Animal Genetic Resources at Risk: Reversible DNA Quiescence and Cloning. |
| Geographic Reach | Multiple continents/international |
| Policy Influence Type | Membership of a guideline committee |
| Impact | Informed UN of scientific background to the existing cloning technology, separating fact from fiction. |
| Description | Publication of EBVs on susceptibility to bTB |
| Geographic Reach | National |
| Policy Influence Type | Influenced training of practitioners or researchers |
| Impact | Improvements in survival relates to CATTLE. The publication and uptake of EBVs that are regularly update has enabled genetic progress to reduce suceptibility to bTB in the dairy catt;le population. In reducing susceptibility the number and scale of breakdowns diminish reducing the deleterious economic impact of bTB, improving the capacity to control the ongoing epidemic and is an alternative that does not involve culling of badgers. The need for such culling may not be wholly obviated, however it offers a way forward that softens the societal divide on this issue. Selection is permanent and cumulative, but incremental and the full evidence on benefit will emerge over time. |
| URL | https://www.gov.uk/government/publications/a-strategy-for-achieving-bovine-tuberculosis-free-status-... |
| Description | A global shared data biological sample resource to support productivity improvement for tropical livestock |
| Amount | £5,000,000 (GBP) |
| Organisation | Bill and Melinda Gates Foundation |
| Sector | Charity/Non Profit |
| Country | United States |
| Start | 09/2015 |
| End | 09/2020 |
| Description | AFRI Animal Health and Disease SF424 |
| Amount | $500,000 (USD) |
| Organisation | U.S. Department of Agriculture USDA |
| Department | National Animal Disease Center |
| Sector | Public |
| Country | United States |
| Start | 01/2016 |
| End | 12/2019 |
| Description | BBSRC KTN CASE Studentship |
| Amount | £80,000 (GBP) |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 08/2016 |
| End | 08/2021 |
| Description | BBSRC Responsive Mode |
| Amount | £1,640,000 (GBP) |
| Funding ID | BB/V009818/1 |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 08/2021 |
| End | 08/2025 |
| Description | Dairy Co (now AHDB) grant for bovine tuberculosis genetic evaluations |
| Amount | £100,000 (GBP) |
| Organisation | Agricultural and Horticulture Development Board |
| Sector | Charity/Non Profit |
| Country | United Kingdom |
| Start | 01/2014 |
| End | 12/2015 |
| Description | Development and testing of Operational Models of Bovine Tuberculosis in British Cattle and Badgers |
| Amount | £22,454 (GBP) |
| Organisation | Department For Environment, Food And Rural Affairs (DEFRA) |
| Sector | Public |
| Country | United Kingdom |
| Start | 04/2015 |
| End | 08/2016 |
| Description | Direct funding from Industry (Hendrix Genetics) - Genome editing for resistance to IPNV in salmon |
| Amount | £180,892 (GBP) |
| Organisation | Hendrix Genetics |
| Sector | Private |
| Country | Netherlands |
| Start | 06/2016 |
| End | 03/2019 |
| Description | European Commission Horizon2020 |
| Amount | € 9,000,000 (EUR) |
| Organisation | European Commission |
| Sector | Public |
| Country | European Union (EU) |
| Start | 01/2015 |
| End | 12/2019 |
| Description | Genome Alberta ALGP2 |
| Amount | $500,000 (CAD) |
| Funding ID | ALGP2 024 |
| Organisation | Genome Canada |
| Sector | Charity/Non Profit |
| Country | Canada |
| Start | 03/2015 |
| End | 02/2018 |
| Description | Genomic and nutritional innovations for genetically superior farmed fish to improve efficiency in European aquaculture |
| Amount | € 6,149,963 (EUR) |
| Funding ID | 818367 |
| Organisation | European Union |
| Sector | Public |
| Country | European Union (EU) |
| Start | 01/2019 |
| End | 12/2022 |
| Description | Newton Fund Workshop Brazil |
| Amount | £52,000 (GBP) |
| Funding ID | 228949780 |
| Organisation | British Council |
| Sector | Charity/Non Profit |
| Country | United Kingdom |
| Start | 03/2016 |
| End | 09/2016 |
| Description | Newton Fund Workshop Mexico |
| Amount | £37,550 (GBP) |
| Funding ID | 2016-RLWK7-10399 |
| Organisation | British Council |
| Sector | Charity/Non Profit |
| Country | United Kingdom |
| Start | 03/2017 |
| End | 03/2018 |
| Description | Norwegian research council, Innovation project |
| Amount | kr 8,000,000 (NOK) |
| Organisation | Research Council of Norway |
| Sector | Public |
| Country | Norway |
| Start | 02/2018 |
| End | 01/2021 |
| Description | Personal Award |
| Amount | kr 300,000 (NOK) |
| Organisation | Norwegian University of Life Sciences (NMBU) |
| Sector | Academic/University |
| Country | Norway |
| Start | 08/2014 |
| End | 09/2017 |
| Description | Scottish Government Centre of Expertise in Animal Disease Outbreaks |
| Amount | £10,000,000 (GBP) |
| Organisation | Government of Scotland |
| Sector | Public |
| Country | United Kingdom |
| Start | 03/2016 |
| End | 03/2020 |
| Description | Scottish Government Programmes of Research 2015-21, Strategic Research Programme RD 3 2 2 |
| Amount | £540,000 (GBP) |
| Organisation | Government of Scotland |
| Sector | Public |
| Country | United Kingdom |
| Start | 01/2016 |
| End | 12/2021 |
| Description | Scottish Government Strategic Research Programme (RESAS) |
| Amount | £10,000,000 (GBP) |
| Organisation | Government of Scotland |
| Sector | Public |
| Country | United Kingdom |
| Start | 08/2016 |
| End | 08/2021 |
| Description | The phylogenetics and epidemiology of tuberculosis in cattle and their herders in Cameroon |
| Amount | £397,509 (GBP) |
| Funding ID | WT094945 |
| Organisation | Wellcome Trust |
| Sector | Charity/Non Profit |
| Country | United Kingdom |
| Start | 03/2012 |
| End | 03/2015 |
| Description | Travel grant from the Universidad Autonoma de Baja California, Mexico |
| Amount | $150,000 (MXN) |
| Organisation | Technological Institute of Baja California |
| Sector | Academic/University |
| Country | Mexico |
| Start | 09/2017 |
| End | 10/2018 |
| Description | USDA |
| Amount | $54,000 (USD) |
| Organisation | U.S. Department of Agriculture USDA |
| Sector | Public |
| Country | United States |
| Start | 01/2013 |
| End | 12/2017 |
| Description | Walsh Fellowship for PhD studies |
| Amount | € 90,000 (EUR) |
| Funding ID | 2016140 |
| Organisation | Walsh Fellowship Foundation |
| Sector | Academic/University |
| Country | Ireland |
| Start | 08/2016 |
| End | 08/2020 |
| Description | Walsh Fellowship for PhD studies |
| Amount | € 85,000 (EUR) |
| Funding ID | 2013024 |
| Organisation | Walsh Fellowship Foundation |
| Sector | Academic/University |
| Country | Ireland |
| Start | 09/2013 |
| End | 09/2017 |
| Title | CT-based Morphometrics of the Canine Skull |
| Description | My group has developed methodologies for addressing the extreme size and shape differences of canine skulls to generate phenotypic outcomes in our association studies. |
| Type Of Material | Physiological assessment or outcome measure |
| Year Produced | 2017 |
| Provided To Others? | Yes |
| Impact | The description of our methodology will be released with open-access publication of our study which is review. |
| Title | EBVs for bTB |
| Description | This is a GENETIC assessment, but there is no appropriate menu item. (It could be a model but then so are phyisological assessements!). Expected breeding values for susceptibility/resistance to bTB are published and routinely updated using UK and industry data. |
| Type Of Material | Physiological assessment or outcome measure |
| Year Produced | 2015 |
| Provided To Others? | Yes |
| Impact | Uptake by breeding companies for selective breeding. It also serves as a research tool for the discovery of causal variants underlying bTB susceptibility by researchers. |
| URL | https://dairy.ahdb.org.uk/technical-information/breeding-genetics/tb-advantage/#.XIakQrjgo2w |
| Title | GEBVs |
| Description | Genomic prediction |
| Type Of Material | Physiological assessment or outcome measure |
| Year Produced | 2012 |
| Provided To Others? | Yes |
| Impact | Genomic predictions for use in selection in breeding programmes. |
| Title | Lethals |
| Description | Method for detecting recessive lethals using genomic data. |
| Type Of Material | Physiological assessment or outcome measure |
| Provided To Others? | No |
| Impact | Lethals detected in commercial breeding programme that are now being managed and removed by identifying carriers. |
| Title | Software for conserved genomic regions (ancestral haplotypes) |
| Description | This is a computational tool that detects ancestral haplotypes using genotype phasing by scanning whole animal genomes for any number of generations that are available in the data. The phasing algorithm uses a combination of long range phasing and haplotype library imputation methodologies. Subsequently, the software tracks haplotypes across generations, and computes their average frequency as well as trends for co-ancestry and proportion of segregating ancestral haplotypes across generation. This tool may be applicable to livestock genetic improvement schemes as well as conservation programmes. |
| Type Of Material | Improvements to research infrastructure |
| Provided To Others? | No |
| Impact | Based on this computational platform, a research grant is now being prepared to further extend its utility and application. |
| Title | Addressing individual sensitivity and specificity in disease models |
| Description | A model that incorporates individual sensitivity and specificity as traits with potential genetuc variation, so that potential correlated changes to selection can be assessed. |
| Type Of Material | Data analysis technique |
| Year Produced | 2017 |
| Provided To Others? | Yes |
| Impact | It permitted the initial publication of EBVs for TB Advantage as the potential effects on specifity had been predicted. |
| URL | https://gsejournal.biomedcentral.com/articles/10.1186/s12711-016-0264-3 |
| Title | Chicken LDLA |
| Description | Method for using genomic data in genomic evaluations. |
| Type Of Material | Computer model/algorithm |
| Year Produced | 2012 |
| Provided To Others? | Yes |
| Impact | Provided methodology for incorporating data on ungenotyped animals. |
| Title | Comparison of estimated variances |
| Description | Estimates of pedigree and genomic additive variance are not comparable. This model demonstrates how valid comparisons can be made. |
| Type Of Material | Data analysis technique |
| Year Produced | 2015 |
| Provided To Others? | Yes |
| Impact | Introduced into lecture material. |
| Title | Computational Model to assess the impact of genetic selection for reduced host infectivity and susceptibility to infection |
| Description | A computer model was created to assess the benefits from capturing both host genetic susceptibility and infectivity in genetic evaluations for different selection intensities for and a range of selection accuracies. The code used for the models presented in this paper is available on GitHub (https://github.com/SmaragdaT/GenEpi) and can be adapted to match-specific diseases and population structures. The model is described in the publication Tsairidou S., Anacleto O., Woolliams J.A. & Doeschl-Wilson A.B. 2019. Enhanced genetic disease control with selection for low susceptibility and infectivity. Heredity Jan 16:1 |
| Type Of Material | Computer model/algorithm |
| Year Produced | 2019 |
| Provided To Others? | Yes |
| Impact | The model results form the basis for the perspectives article Tsairidou et al. 2018. Can We Breed Cattle for Lower bovine TB Infectivity? Frontiers in Veterinary Science, 5,310. https://doi.org/10.3389/fvets.2018.00310 and for several collaborative research grants (ISA resistance in Atlantic salmon: Defining new phenotypes for accurate breeding. Norwegian research council, Innovation project for the industrial sector; Investigating infectiousness of pigs selected for multi-factorial resilience or increased resistance to PRRS. Alberta Applied Agricultural Genomics Program (A3GP). |
| URL | https://github.com/SmaragdaT/GenEpi |
| Title | Development of LCSeq |
| Description | LCSeq is a system that we are developing which enables sequence information to be generated for animal breeding populations at low-cost. LCSeq recognises that in livestock populations individuals are highly related and thus share long genome segments (haplotypes). Rather than sequencing individuals at high-coverage aims to sequence the haplotypes that are present in the population by spreading the sequencing resources at low-coverage across many individuals. |
| Type Of Material | Data analysis technique |
| Provided To Others? | No |
| Impact | the research is still on-going, however, one of the softwares that will contribute to this model is AlphaSeqOpt, freely available on the AlphaSuite. |
| URL | http://www.alphagenes.roslin.ed.ac.uk/alphasuite-softwares/alphaseqopt/ |
| Title | DiseaseEBVs |
| Description | A model to simultaneously estimate breeding values for susceptibility and infectivity using genetic epidemiological theory. |
| Type Of Material | Computer model/algorithm |
| Year Produced | 2015 |
| Provided To Others? | Yes |
| Impact | We have introduced a new dimension and capacity to the analysis of disease data populations, however it is too early to assess the impact. |
| Title | Dogslife, a longitudinal study of Labrador Retrievers |
| Description | This database collects life information for Labrador Retrievers from early life onwards. The information is based on owner recording rather than veterinary or insurance records and therefore captures minor illnesses and issues that would not present to the veterinary practice. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2010 |
| Provided To Others? | Yes |
| Impact | There have been a number of research publications about the data, the design of the collection method and more generally about the utility of cohort studies particularly in the dog, and the dog as a model for human and other animal conditions. |
| URL | http://www.dogslife.ac.uk |
| Title | Partition of variance |
| Description | Partition of variance to identify non-additive variance and how the form of non-additive variance affects the inference of additive genetic variance. |
| Type Of Material | Data analysis technique |
| Year Produced | 2018 |
| Provided To Others? | Yes |
| Impact | It allows the reconciliation of pedigree and genomic estimates of heritability. |
| Title | True de-regression |
| Description | The use of de-regressed EBVs is common place for detecting QTL. However they poorly understood and poorly calculated. The model demonstrates, for the first time, how they should be calculated. |
| Type Of Material | Data analysis technique |
| Year Produced | 2016 |
| Provided To Others? | Yes |
| Impact | None to date. |
| Description | Axiom |
| Organisation | Axiom |
| Country | France |
| Sector | Private |
| PI Contribution | We have guided the implementation of Optimum Contribution selection into the pig breeding programme. In the course of which we have supervised an MSc student (2017) using their data. |
| Collaborator Contribution | Provision of data. Opportunities to implement software. |
| Impact | MSc student, full practical testing of software. (Agriculture, Genetics). |
| Start Year | 2016 |
| Description | Centre for Tropical Livestock Genetics and Health |
| Organisation | International Livestock Research Institute (ILRI) |
| Country | Kenya |
| Sector | Charity/Non Profit |
| PI Contribution | This project formed part of the establishment of a joint centre with ILRI to develop new approaches to improving the productivity of African Livestock |
| Collaborator Contribution | There is a formal joint venture |
| Impact | The Centre attracted funding from the Bill and Melinda Gates Foundation. It is too early to identify outcomes, but the centre is fully functional and pursuing multiple collaborative projects |
| Start Year | 2015 |
| Description | Cherry Valley |
| Organisation | Cherry Valley Farms |
| Country | United Kingdom |
| Sector | Private |
| PI Contribution | Supervise MSc students using quantitative genetic models to (i) assess the increase in likelihood of ascites in the breeding population, in particular in relation to selection on live weight and (ii) assess the genetic variation in fertility and its relation to live weight. |
| Collaborator Contribution | Provision of data. |
| Impact | Trained MSc students working in UK breeding industry. Larger scale projects with Roslin colleagues built on initial contacts made with the MSc projects. |
| Start Year | 2015 |
| Description | Dog Biomedical Variant Database Consortium |
| Organisation | Animal Health Trust |
| Country | United Kingdom |
| Sector | Charity/Non Profit |
| PI Contribution | I have contributed variants from 41 prepublication, re-sequenced dog genomes to the database. |
| Collaborator Contribution | To date, the genetic variants from 329 re-sequenced dog genomes have been contributed by the consortium's 19 other members who are located with 13 other institutions and 1 company. |
| Impact | 1.Kinsey, N. A. et al. Canine reference genome accuracy impacts variant calling: Lessons learned from investigating embryonic lethal variants. Anim Genet 53, 706-708 (2022). 2.Jenkins, C. A. et al. Improving the resolution of canine genome-wide association studies using genotype imputation: A study of two breeds. Anim Genet 52, 703-713 (2021). 3.Jagannathan, V. et al. A comprehensive biomedical variant catalogue based on whole genome sequences of 582 dogs and eight wolves. Anim Genet 50, 695-704 (2019). |
| Start Year | 2016 |
| Description | Dog Biomedical Variant Database Consortium |
| Organisation | Mars Nutrition Research Council, Mars Incorporated |
| Country | United States |
| Sector | Private |
| PI Contribution | I have contributed variants from 41 prepublication, re-sequenced dog genomes to the database. |
| Collaborator Contribution | To date, the genetic variants from 329 re-sequenced dog genomes have been contributed by the consortium's 19 other members who are located with 13 other institutions and 1 company. |
| Impact | 1.Kinsey, N. A. et al. Canine reference genome accuracy impacts variant calling: Lessons learned from investigating embryonic lethal variants. Anim Genet 53, 706-708 (2022). 2.Jenkins, C. A. et al. Improving the resolution of canine genome-wide association studies using genotype imputation: A study of two breeds. Anim Genet 52, 703-713 (2021). 3.Jagannathan, V. et al. A comprehensive biomedical variant catalogue based on whole genome sequences of 582 dogs and eight wolves. Anim Genet 50, 695-704 (2019). |
| Start Year | 2016 |
| Description | Dog Biomedical Variant Database Consortium |
| Organisation | North Carolina State University |
| Country | United States |
| Sector | Academic/University |
| PI Contribution | I have contributed variants from 41 prepublication, re-sequenced dog genomes to the database. |
| Collaborator Contribution | To date, the genetic variants from 329 re-sequenced dog genomes have been contributed by the consortium's 19 other members who are located with 13 other institutions and 1 company. |
| Impact | 1.Kinsey, N. A. et al. Canine reference genome accuracy impacts variant calling: Lessons learned from investigating embryonic lethal variants. Anim Genet 53, 706-708 (2022). 2.Jenkins, C. A. et al. Improving the resolution of canine genome-wide association studies using genotype imputation: A study of two breeds. Anim Genet 52, 703-713 (2021). 3.Jagannathan, V. et al. A comprehensive biomedical variant catalogue based on whole genome sequences of 582 dogs and eight wolves. Anim Genet 50, 695-704 (2019). |
| Start Year | 2016 |
| Description | Dog Biomedical Variant Database Consortium |
| Organisation | University of Bern |
| Country | Switzerland |
| Sector | Academic/University |
| PI Contribution | I have contributed variants from 41 prepublication, re-sequenced dog genomes to the database. |
| Collaborator Contribution | To date, the genetic variants from 329 re-sequenced dog genomes have been contributed by the consortium's 19 other members who are located with 13 other institutions and 1 company. |
| Impact | 1.Kinsey, N. A. et al. Canine reference genome accuracy impacts variant calling: Lessons learned from investigating embryonic lethal variants. Anim Genet 53, 706-708 (2022). 2.Jenkins, C. A. et al. Improving the resolution of canine genome-wide association studies using genotype imputation: A study of two breeds. Anim Genet 52, 703-713 (2021). 3.Jagannathan, V. et al. A comprehensive biomedical variant catalogue based on whole genome sequences of 582 dogs and eight wolves. Anim Genet 50, 695-704 (2019). |
| Start Year | 2016 |
| Description | Dog Biomedical Variant Database Consortium |
| Organisation | University of California, Davis |
| Country | United States |
| Sector | Academic/University |
| PI Contribution | I have contributed variants from 41 prepublication, re-sequenced dog genomes to the database. |
| Collaborator Contribution | To date, the genetic variants from 329 re-sequenced dog genomes have been contributed by the consortium's 19 other members who are located with 13 other institutions and 1 company. |
| Impact | 1.Kinsey, N. A. et al. Canine reference genome accuracy impacts variant calling: Lessons learned from investigating embryonic lethal variants. Anim Genet 53, 706-708 (2022). 2.Jenkins, C. A. et al. Improving the resolution of canine genome-wide association studies using genotype imputation: A study of two breeds. Anim Genet 52, 703-713 (2021). 3.Jagannathan, V. et al. A comprehensive biomedical variant catalogue based on whole genome sequences of 582 dogs and eight wolves. Anim Genet 50, 695-704 (2019). |
| Start Year | 2016 |
| Description | Dog Biomedical Variant Database Consortium |
| Organisation | University of Helsinki |
| Country | Finland |
| Sector | Academic/University |
| PI Contribution | I have contributed variants from 41 prepublication, re-sequenced dog genomes to the database. |
| Collaborator Contribution | To date, the genetic variants from 329 re-sequenced dog genomes have been contributed by the consortium's 19 other members who are located with 13 other institutions and 1 company. |
| Impact | 1.Kinsey, N. A. et al. Canine reference genome accuracy impacts variant calling: Lessons learned from investigating embryonic lethal variants. Anim Genet 53, 706-708 (2022). 2.Jenkins, C. A. et al. Improving the resolution of canine genome-wide association studies using genotype imputation: A study of two breeds. Anim Genet 52, 703-713 (2021). 3.Jagannathan, V. et al. A comprehensive biomedical variant catalogue based on whole genome sequences of 582 dogs and eight wolves. Anim Genet 50, 695-704 (2019). |
| Start Year | 2016 |
| Description | Dog Biomedical Variant Database Consortium |
| Organisation | University of Liege |
| Country | Belgium |
| Sector | Academic/University |
| PI Contribution | I have contributed variants from 41 prepublication, re-sequenced dog genomes to the database. |
| Collaborator Contribution | To date, the genetic variants from 329 re-sequenced dog genomes have been contributed by the consortium's 19 other members who are located with 13 other institutions and 1 company. |
| Impact | 1.Kinsey, N. A. et al. Canine reference genome accuracy impacts variant calling: Lessons learned from investigating embryonic lethal variants. Anim Genet 53, 706-708 (2022). 2.Jenkins, C. A. et al. Improving the resolution of canine genome-wide association studies using genotype imputation: A study of two breeds. Anim Genet 52, 703-713 (2021). 3.Jagannathan, V. et al. A comprehensive biomedical variant catalogue based on whole genome sequences of 582 dogs and eight wolves. Anim Genet 50, 695-704 (2019). |
| Start Year | 2016 |
| Description | Dog Biomedical Variant Database Consortium |
| Organisation | University of Minnesota |
| Country | United States |
| Sector | Academic/University |
| PI Contribution | I have contributed variants from 41 prepublication, re-sequenced dog genomes to the database. |
| Collaborator Contribution | To date, the genetic variants from 329 re-sequenced dog genomes have been contributed by the consortium's 19 other members who are located with 13 other institutions and 1 company. |
| Impact | 1.Kinsey, N. A. et al. Canine reference genome accuracy impacts variant calling: Lessons learned from investigating embryonic lethal variants. Anim Genet 53, 706-708 (2022). 2.Jenkins, C. A. et al. Improving the resolution of canine genome-wide association studies using genotype imputation: A study of two breeds. Anim Genet 52, 703-713 (2021). 3.Jagannathan, V. et al. A comprehensive biomedical variant catalogue based on whole genome sequences of 582 dogs and eight wolves. Anim Genet 50, 695-704 (2019). |
| Start Year | 2016 |
| Description | Dog Biomedical Variant Database Consortium |
| Organisation | University of Pennsylvania |
| Country | United States |
| Sector | Academic/University |
| PI Contribution | I have contributed variants from 41 prepublication, re-sequenced dog genomes to the database. |
| Collaborator Contribution | To date, the genetic variants from 329 re-sequenced dog genomes have been contributed by the consortium's 19 other members who are located with 13 other institutions and 1 company. |
| Impact | 1.Kinsey, N. A. et al. Canine reference genome accuracy impacts variant calling: Lessons learned from investigating embryonic lethal variants. Anim Genet 53, 706-708 (2022). 2.Jenkins, C. A. et al. Improving the resolution of canine genome-wide association studies using genotype imputation: A study of two breeds. Anim Genet 52, 703-713 (2021). 3.Jagannathan, V. et al. A comprehensive biomedical variant catalogue based on whole genome sequences of 582 dogs and eight wolves. Anim Genet 50, 695-704 (2019). |
| Start Year | 2016 |
| Description | Dog Biomedical Variant Database Consortium |
| Organisation | University of Rennes 1 |
| Country | France |
| Sector | Academic/University |
| PI Contribution | I have contributed variants from 41 prepublication, re-sequenced dog genomes to the database. |
| Collaborator Contribution | To date, the genetic variants from 329 re-sequenced dog genomes have been contributed by the consortium's 19 other members who are located with 13 other institutions and 1 company. |
| Impact | 1.Kinsey, N. A. et al. Canine reference genome accuracy impacts variant calling: Lessons learned from investigating embryonic lethal variants. Anim Genet 53, 706-708 (2022). 2.Jenkins, C. A. et al. Improving the resolution of canine genome-wide association studies using genotype imputation: A study of two breeds. Anim Genet 52, 703-713 (2021). 3.Jagannathan, V. et al. A comprehensive biomedical variant catalogue based on whole genome sequences of 582 dogs and eight wolves. Anim Genet 50, 695-704 (2019). |
| Start Year | 2016 |
| Description | Dog Biomedical Variant Database Consortium |
| Organisation | University of Saskatchewan |
| Country | Canada |
| Sector | Academic/University |
| PI Contribution | I have contributed variants from 41 prepublication, re-sequenced dog genomes to the database. |
| Collaborator Contribution | To date, the genetic variants from 329 re-sequenced dog genomes have been contributed by the consortium's 19 other members who are located with 13 other institutions and 1 company. |
| Impact | 1.Kinsey, N. A. et al. Canine reference genome accuracy impacts variant calling: Lessons learned from investigating embryonic lethal variants. Anim Genet 53, 706-708 (2022). 2.Jenkins, C. A. et al. Improving the resolution of canine genome-wide association studies using genotype imputation: A study of two breeds. Anim Genet 52, 703-713 (2021). 3.Jagannathan, V. et al. A comprehensive biomedical variant catalogue based on whole genome sequences of 582 dogs and eight wolves. Anim Genet 50, 695-704 (2019). |
| Start Year | 2016 |
| Description | Dog Biomedical Variant Database Consortium |
| Organisation | University of Sydney |
| Country | Australia |
| Sector | Academic/University |
| PI Contribution | I have contributed variants from 41 prepublication, re-sequenced dog genomes to the database. |
| Collaborator Contribution | To date, the genetic variants from 329 re-sequenced dog genomes have been contributed by the consortium's 19 other members who are located with 13 other institutions and 1 company. |
| Impact | 1.Kinsey, N. A. et al. Canine reference genome accuracy impacts variant calling: Lessons learned from investigating embryonic lethal variants. Anim Genet 53, 706-708 (2022). 2.Jenkins, C. A. et al. Improving the resolution of canine genome-wide association studies using genotype imputation: A study of two breeds. Anim Genet 52, 703-713 (2021). 3.Jagannathan, V. et al. A comprehensive biomedical variant catalogue based on whole genome sequences of 582 dogs and eight wolves. Anim Genet 50, 695-704 (2019). |
| Start Year | 2016 |
| Description | Genetic studies with colleagues from Cyprus |
| Organisation | Cyprus University of Technology |
| Country | Cyprus |
| Sector | Academic/University |
| PI Contribution | We provided genetic analysis and evaluation expertise. |
| Collaborator Contribution | The partners provided phenotypic and genetic data from a local resource population and interacted with us in the genetic analyses. |
| Impact | Two scientific publications were produced (a peer reviewed journal paper and a conference proceedings contribution) which have been linked to this award. |
| Start Year | 2015 |
| Description | Hycole OCS |
| Organisation | Sarl Hycole |
| Country | France |
| Sector | Private |
| PI Contribution | Plan and guide the implementartion of Optimum Contribution selection into the rabbit breeding programme. In the course of which we supervised an MSc student using practical data. |
| Collaborator Contribution | Data, opportunity to test software in practice and learn about challenges of rabbit breeding. |
| Impact | Opportunity to test software in practice with practical constraints in a novel species with unusual breeding structure. |
| Start Year | 2016 |
| Description | Innovis |
| Organisation | Innovis ltd |
| Country | United Kingdom |
| Sector | Private |
| PI Contribution | We carried out bioinformatic processing, genomic analyses and the construction of a pipeline for the companty to enable them to process genomic data independently for routine evaluations. |
| Collaborator Contribution | Provision of phenotypic data, genotypes, pedigree, and funding. |
| Impact | Trained post doc. Implementation of genomic selection. Capacity building of company. |
| Start Year | 2013 |
| Description | Newton Fund Travel Award Saif Agha |
| Organisation | Ain Shams University |
| Department | Faculty of Engineering |
| Country | Egypt |
| Sector | Academic/University |
| PI Contribution | Hosted Dr. Saif Agha, Egyptian researcher for 6 months; Joint research project on genotype by environmental interactions and resilience in farm animals |
| Collaborator Contribution | GxE datasets for tilapia; genetic analyses of GxE; took lead in writing the paper and presenting results |
| Impact | Agha S., Mekkawy W., Ibanez-Escriche N., Lind C.E., Kumar J., Mandal A., Benzie J., Doeschl-Wilson A. B. 2017. Breeding for robustness: Investigating genotype by environment interactions and micro- environmental sensitivity of Genetically Improved Farmed Tilapia (GIFT) (Oreochromis niloticus). Animal Breeding and Genetics. Under Review (2) Agha S., Mekkawy W., Ibanez-Escriche N., Lind C.E., Kumar J., Mandal A., Benzie J., Doeschl-Wilson A. B. Investigating the macro- and micro- environmental sensitivity of Genetically Improved Farmed Tilapia (GIFT). Poster presentation at the EAAP 2017. |
| Start Year | 2015 |
| Description | Newton Fund Travel Award Saif Agha |
| Organisation | Worldfish |
| Country | Malaysia |
| Sector | Charity/Non Profit |
| PI Contribution | Hosted Dr. Saif Agha, Egyptian researcher for 6 months; Joint research project on genotype by environmental interactions and resilience in farm animals |
| Collaborator Contribution | GxE datasets for tilapia; genetic analyses of GxE; took lead in writing the paper and presenting results |
| Impact | Agha S., Mekkawy W., Ibanez-Escriche N., Lind C.E., Kumar J., Mandal A., Benzie J., Doeschl-Wilson A. B. 2017. Breeding for robustness: Investigating genotype by environment interactions and micro- environmental sensitivity of Genetically Improved Farmed Tilapia (GIFT) (Oreochromis niloticus). Animal Breeding and Genetics. Under Review (2) Agha S., Mekkawy W., Ibanez-Escriche N., Lind C.E., Kumar J., Mandal A., Benzie J., Doeschl-Wilson A. B. Investigating the macro- and micro- environmental sensitivity of Genetically Improved Farmed Tilapia (GIFT). Poster presentation at the EAAP 2017. |
| Start Year | 2015 |
| Description | PRRS Host Genetics Consortium |
| Organisation | Iowa State University |
| Country | United States |
| Sector | Academic/University |
| PI Contribution | Genetic analysis of infectious disease data and mathematical modelling of PRRS infection dynamics; Contribution to experimental design of PRRS challenge and field experiments and sampling; |
| Collaborator Contribution | Access to data; access to statistical models; scientific advice for model assumptions |
| Impact | Joint manuscripts and publications: 1. Go N., Islam Z., Lunney J., Belloc C., Touzeau S.& Doeschl-Wilson A.B., 2017. Neutralizing antibodies prevent PRRS viremia rebound: evidence from a data-supported model of the immune response. PloS Comp. Biol. Under review 2. Lough G., Hess A., Dekkers JCM, Hess M., Kyriazakis I., Mulder H., Lunney J, Rowland BB, Doeschl-Wilson A.B. 2017. Harnessing longitudinal information to identify genetic variation in tolerance of pigs to Porcine Reproductive and Respiratory Syndrome virus. Genetics Selection Evolution. Under review 3. Lough G., Rashidi H., Kyriazakis I., Dekkers JCM, Hess AS, Hess MK, Deeb N, Kause A., Lunney J, Rowland BB, Mulder H and Doeschl-Wilson A.B. 2017. Use of multi-trait and random regression models to identify genetic variation in tolerance to Porcine Reproductive and Respiratory Syndrome virus. Genetics Selection Evolution, 49(1)37. 3. 4. Hess, A.S., Islam, Z., Hess, M.K., Rowland, R.R., Lunney, J.K., Doeschl-Wilson, A., Plastow, G.S. and Dekkers, J.C., 2016. Comparison of host genetic factors influencing pig response to infection with two North American isolates of porcine reproductive and respiratory syndrome virus. Genetics Selection Evolution, 48(1), p.1.18. 5. Islam Z.U., Bishop S.C., Savill N.J. , Rowland R.R.R., Lunney J.K., Trible B and Doeschl-Wilson A.B. 2013. Quantitative analysis of Porcine Reproductive and Respiratory Syndrome (PRRS) viremia profiles from experimental infection: a statistical modelling approach. PLoS One, DOI: 10.1371/journal.pone.0083567. ( |
| Start Year | 2012 |
| Description | Partnership with Geno Global |
| Organisation | Geno Global Ltd. |
| Country | Norway |
| Sector | Private |
| PI Contribution | In this partnership we will work together to develop and implement genotyping, sequencing and imputation strategies and tools in the Norwegian Red population central to Geno Global. The work seeks to integrate AlphaImpute, our imputation software, into the routine breeding value estimation pipeline at Geno. We will also perform analysis of the resulting data to aid the use of genomic prediction methods in the Geno breeding program and to help the discovery of causal variants that segregate in the Norwegian Red population. |
| Collaborator Contribution | Geno has provided historical data form their herd and made it available to develop and train new imputation strategies. |
| Impact | Developed an imputation strategy with Geno. |
| Start Year | 2016 |
| Description | Saphir - Horizon2020 |
| Organisation | French National Institute of Agricultural Research |
| Country | France |
| Sector | Academic/University |
| PI Contribution | I am leader of workpackage 16: Modelling vaccine efficacy |
| Collaborator Contribution | INRA is project leader |
| Impact | -Scientific Publication: Go N., Islam Z., Lunney J., Belloc C., Touzeau S.& Doeschl-Wilson A.B., 2019. How to prevent viremia rebound: evidence from a PRRSv data-supported model of immune response. BMC Systems Biol. https://doi.org/10.1186/s12918-018-0666-7 -Popular article "How to prevent viremia rebound in virus infections? Evidence from a data-driven mathematical model for PRRS". Doeschl-Wilson A., Go N., Touzeau S. SAPHIR newsletter Nov 2017 - Issue 4. Project coordinator statement "A very innovative approach for modelling the immune response has been designed and validated." -Interactive Wiki-website: Vaccine effectiveness in the field. https://www.wiki.ed.ac.uk/display/saphir/ -Conference talks: International Vaccinology Meeting in Edinburgh, May 2018; Annual Meeting for the Society for Mathematical Biology, Sydney Australia, July 2018 and the Conference for Research Workers in Animal Disease, Chicago December 2018 |
| Start Year | 2016 |
| Description | Saphir - Horizon2020 |
| Organisation | University of Ghent |
| Department | Faculty of Veterinary Medicine |
| Country | Belgium |
| Sector | Academic/University |
| PI Contribution | I am leader of workpackage 16: Modelling vaccine efficacy |
| Collaborator Contribution | INRA is project leader |
| Impact | -Scientific Publication: Go N., Islam Z., Lunney J., Belloc C., Touzeau S.& Doeschl-Wilson A.B., 2019. How to prevent viremia rebound: evidence from a PRRSv data-supported model of immune response. BMC Systems Biol. https://doi.org/10.1186/s12918-018-0666-7 -Popular article "How to prevent viremia rebound in virus infections? Evidence from a data-driven mathematical model for PRRS". Doeschl-Wilson A., Go N., Touzeau S. SAPHIR newsletter Nov 2017 - Issue 4. Project coordinator statement "A very innovative approach for modelling the immune response has been designed and validated." -Interactive Wiki-website: Vaccine effectiveness in the field. https://www.wiki.ed.ac.uk/display/saphir/ -Conference talks: International Vaccinology Meeting in Edinburgh, May 2018; Annual Meeting for the Society for Mathematical Biology, Sydney Australia, July 2018 and the Conference for Research Workers in Animal Disease, Chicago December 2018 |
| Start Year | 2016 |
| Description | Sequencing of beef cattle in Ireland |
| Organisation | Illumina Inc. |
| Department | Illumina |
| Country | United Kingdom |
| Sector | Private |
| PI Contribution | The objectives of this project is to generate large data set for the Irish beef and cattle market, analyse it and obtain insights into the mechanics of the resulting predictions underlying the biology of the beef and dairy population. The AlphaSuite is a collection of software that we have developed to perform many of the common tasks in animal breeding, plant breeding, and human genetics including genomic prediction, breeding value estimation, variance component estimation, GWAS, imputation, phasing, optimal contributions, simulation, field trial designs, and various data recoding and handling tools. |
| Collaborator Contribution | Illumina is providing the DNA sequencing data on more than 1000 cattle. |
| Impact | At this stage of the collaboration the outputs have not been generated. |
| Start Year | 2016 |
| Description | The Evolution of Mycobacterium bovis evolution in Africa |
| Organisation | U.S. Department of Agriculture USDA |
| Country | United States |
| Sector | Public |
| PI Contribution | We have made available a collection of Mycobacterium isolates from cattle from across Africa that the BBSRC funded plus one has coordinated. |
| Collaborator Contribution | The USDA have sequenced these isolates using their WGS pipeline. |
| Impact | work is still in progress |
| Start Year | 2016 |
| Description | Tilapia |
| Organisation | Norwegian University of Life Sciences (NMBU) |
| Country | Norway |
| Sector | Academic/University |
| PI Contribution | Superviison and guidance on the partitioning of the observed phenotypic variance to obtain both additive and non-additive components of variance, including design and interpretation of analysis and derivation of key interpretative formulae. |
| Collaborator Contribution | Provision and payment of PhD student, access to data, genotyping and collaborative time from researchers at NMBU. |
| Impact | Paper in scientific press. New PhD graduate. New trained employee entering breeding industry. Knowledge transfer to industry. |
| Start Year | 2014 |
| Description | Universidade Federal de Minas Gerais, Pampulha - Belo Horizonte |
| Organisation | Federal University of Minas Gerais |
| Department | Department Of Animal Science |
| Country | Brazil |
| Sector | Academic/University |
| PI Contribution | Hosted Dr. Fabio Luiz Buranelo Toral; joint research collaboration on disease resistance and tolerance of Brazilian cattle; provided statistical expertise and computing facilities |
| Collaborator Contribution | Dedicated full time researcher Dr. Buranelo Toral to this joint collaboration; datasets |
| Impact | Too early |
| Start Year | 2017 |
| Title | AlphaImpute |
| Description | Imputation can cost-effectively generate high-density genotypes of many individuals. Typical genotyping strategies involve genotyping a small number of individuals with expensive high-density marker panels, and a large number of individuals with cheaper low-density panels. Imputation is the used to infer the un-typed high-density markers in the individuals genotyped at low-density. AlphaImpute is a flexible tool that imputes genotypes and alleles accurately and quickly for datasets with large pedigrees and large numbers of genotyped markers. It combines basic rules of Mendelian inheritance, probabilistic inferences of genotypes, phasing of long stretches of haplotypes, and imputation of genotypes from a haplotype library. AlphaImpute consists of a single program however it calls both AlphaPhase1.1 and GeneProbForAlphaImpute. All information on the model of analysis, input files and their layout, is specified in a single parameter file. |
| Type Of Technology | Software |
| Year Produced | 2016 |
| Impact | The AlphaImpute package is freely available in AlphSuite and includes supporting manual, and access to technical support with the aim of benefiting the academic research community in animal breeding. The program has been downloaded over 200 times in recent years, attracting users from a number of different academic institutions internationally. AlphaImpute has supported collaboration with a number of industrial partner. One such example is the Innovate UK funded project in collaboration with PIC. This project has accelerated the rate of genetic gain by 35% in pigs, enabled by AlphaImpute. Major emphasis has been put on making AlphaImpute more computationally effective and accessible to small animal breeding operation and/or academic institutions, we have succeeded in improved the computing time by 75%. |
| URL | http://www.alphagenes.roslin.ed.ac.uk/alphasuite-softwares/ |
| Title | AlphaPhase |
| Description | The use of phased sequencing data has been shown to significantly increase the accuracy of imputation. AlphaPhase has been used as part of an imputation pipeline. Existing programs for phasing, have generally scaled poorly to large datasets with long and expensive burden in the computational resources available. Additionally, the increasing production of large sequencing data bundles and its heterogeneity complicate the phasing process. The current version of AlhaPhase implements methods to determine phase using an extended Long Range Phasing and Haplotype Library Imputation. |
| Type Of Technology | Software |
| Year Produced | 2016 |
| Impact | The AlphaPhase package is freely available in AlphSuite and includes supporting manual, and access to technical support with the aim of benefiting the academic research community in animal breeding. Since its recent publication in the AlphaSuite, AlphaPhase have been downloaded 5 times. The AlphaPhase program is closely related to AlphaImpute, and is playing a key role in the Innovate UK funded project in collaboration with PIC, Innovate UK, Aviangen Innovate UK and ICBF. |
| URL | http://www.alphagenes.roslin.ed.ac.uk/alphasuite-softwares/ |
| Title | AlphaSeqOpt |
| Description | With improving technologies and decreasing costs, it is now possible and much more informative to collect genomic data by whole genome sequencing. However, sequencing all individuals at high coverage in a large population is not feasible. Instead, we can harness the fact that individuals within a population are related and thus share sections of the genome. If we can identify and sequence individuals that share more of their genome with a large number of individuals in the population then we can pass on the generated sequence data to other individuals that share the same regions of the genome as the sequenced individual, a process known as imputation. AlphaSeqOpt is a software tool that enables researchers and breeders to define a minimal set of individuals that share more of their genomes with a large number of individuals in the population. AlphaSeqOpt also provides the sequencing investment required for a key individual in order to generate accurate and high quality sequence data that can be used to impute sequence for other individuals in the population. |
| Type Of Technology | Software |
| Year Produced | 2016 |
| Impact | The AlphaSeqOpt package is freely available in AlphSuite and includes supporting manual, and access to technical support with the aim of benefiting the academic research community in animal breeding, and expect to have the publication accepted in the near future. AlphaSeqOpt is a key element on the Innovate UK funded project with PIC and Innovate UK Aviagen, and ICBF project. |
| URL | http://www.alphagenes.roslin.ed.ac.uk/alphasuite-softwares/alphaseqopt/ |
| Title | AlphaSim |
| Description | One of the fundamental questions in populations dynamic is assessing how changes in the current structure and environment affect the structure composition in both the short and long-term. Plant and animal breeding programs benefits from having a tool to evaluate the potential of different selection strategies or new emerging technologies to improve population performance. Empirical datasets to assess the effect of different factors on one population are difficult to collect, since they require substantial financial and time investments and are subject to noise and error. Simulation is a key tool for both researchers and breeders to assess the impact of different factors given a known historical and current population structure prior to implementation within a real-life setting. AlphaSim is a fast and flexible software tool that enables researchers and breeders to do this. Unlike other simulation tools, AlphaSim has the functionality to manipulate fine details of the population structure in order to simulate realistic scenarios and provides detailed outputs for use in downstream analyses. |
| Type Of Technology | Software |
| Year Produced | 2016 |
| Impact | AlphaSim is a freely available software package that simulates genetic population and can assess breeding programs. The AlphaSim package includes a manual, tutorial, and access to technical support with the aim of benefiting the academic research community in animal breeding. This software package has already attracted users from a number of different academic institutions and has supported a number of peer-reviewed academic publications. These publications include: Potential of gene drives with genome editing to increase genetic gain in livestock breeding programs. 2017. Gonen, S, J. Jenko, G. Gorjanc, A.J. Mileham, C.B.A. Whitelaw, J.M. Hickey. Genetics Selection Evolution, 49:3. AlphaSim: Software for Breeding Program Simulation. 2016. Faux A. M., G. Gorjanc, R. C. Gaynor , M. Battagin, S. M. Edwards, D. L. Wilson, Sarah J. Hearne, S. Gonen, and J. M. Hickey. The Plant Genome vol. 9, no.3. AlphaSim is not only used in academic research, but has also attracted industrial collaborations. One such example is our recently awarded Innovate UK grant in collaboration with Driscoll's. |
| URL | http://www.alphagenes.roslin.ed.ac.uk/alphasuite-softwares/alphasim/ |
| Title | AlphaSim GUI |
| Description | In an effort to improve the accessibility and usability of our AlphaSim software, we have developed a graphical user interface (GUI), which uses the Java runtime environment (JRE). By increasing the usability of our software, we hope that the impact of these programs will be even greater, especially for people where available resources are at a premium. Tthe AlphaSim GUI is freely available on the AlphaGenes webpage, and includes video tutorials, practical exercises and support. |
| Type Of Technology | Webtool/Application |
| Year Produced | 2016 |
| Impact | Currently we do not have noticeable impacts, as the GUI has been only available for a few months. |
| URL | http://www.alphagenes.roslin.ed.ac.uk/alphasuite-softwares/alphasim/ |
| Title | Den Haag |
| Description | R package written to simulate populations and the techniques for control of genetic variance as an aid for teaching. |
| Type Of Technology | Software |
| Year Produced | 2017 |
| Impact | Used in lectures. |
| URL | https://github.com/jwoollia/DenHaag/blob/master/DenHaag.pdf |
| Description | Big Data in Agriculture, Part of the DuPont Pioneer Plant Sciences Symposia Series, at Roslin Institute, 14-15 May 2018 |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Other audiences |
| Results and Impact | Symposium held at the Roslin institute, organised by members of my group, sponsored by third parties from the breeding industry |
| Year(s) Of Engagement Activity | 2018 |
| Description | Biology Teachers CPD Event |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Professional Practitioners |
| Results and Impact | Talk and discussions with 20 Higher Biology teachers about science, specifically about next generation sequence analysis technology and how that is being applied to address many different scientific questions |
| Year(s) Of Engagement Activity | 2018 |
| Description | British Science Festival |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Public/other audiences |
| Results and Impact | I spoke at a section about the genetics of dog morphology, artificial selection, and animal welfare. Approximately 75 persons were in the audience. Following the talk, I gave a podcast interview. |
| Year(s) Of Engagement Activity | 2016 |
| URL | http://www.britishscienceassociation.org/Event/british-science-festival-2016 |
| Description | Citizen Science Project for Beekeepers |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Professional Practitioners |
| Results and Impact | This was a course run over a weekend for 8 beekeepers in the Easterbush Science Outreach Centre. The idea was to engage beekeepers to think about how science might help in maintaining bee health. During the weekend they took in a project looking at varroa mite loads in apiaries and using PCR to ask the question, does high use of propolis by honey bees correlate with low numbers of trypanosmes. Feedback from the course/workshop was excellent. This workshop was organised and delievered by Drs Mark Barnett and Tim Regan. |
| Year(s) Of Engagement Activity | 2018 |
| Description | Community event |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Public/other audiences |
| Results and Impact | Gave a talk on the role of genetics in controlling disease in livestock at the Midlothian "Science in the Saddle" event, with subsequent discussion |
| Year(s) Of Engagement Activity | 2014,2015,2016 |
| Description | Contribution to the New York Time article: Open Season Is Seen in Gene Editing of Animals |
| Form Of Engagement Activity | A magazine, newsletter or online publication |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Public/other audiences |
| Results and Impact | Open Season Is Seen in Gene Editing of Animals was a feature article on gene Editing by Amy Harmon. Professor John Hickey was interviewed as specialist in the Quantitative Genetic field. |
| Year(s) Of Engagement Activity | 2016 |
| URL | https://www.nytimes.com/2015/11/27/us/2015-11-27-us-animal-gene-editing.html?_r=0 |
| Description | Discussion panel with farmers |
| Form Of Engagement Activity | A formal working group, expert panel or dialogue |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Professional Practitioners |
| Results and Impact | I was one of the panel members of a national farmers workshop on the topic "alternative approaches to the use of antibiotics" |
| Year(s) Of Engagement Activity | 2017 |
| Description | Easter Bush Campus Open Day 2018 |
| Form Of Engagement Activity | Participation in an open day or visit at my research institution |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Public/other audiences |
| Results and Impact | The group ran two stands at this event, one on our work with honey bees including general interest items about beekeeping and bees, another was a display of the network analysis tools we have developed initially through BBSRC funding and more laterally as part of the spinout company Kajeka Ltd. Presenters Dr Mark Barnett and Prof Tom Freeman |
| Year(s) Of Engagement Activity | 2018 |
| URL | https://www.ed.ac.uk/roslin/community-engagement/public-events/campus-open-day-2018 |
| Description | Edinburgh Alliance for Complex Trait Genetics |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Professional Practitioners |
| Results and Impact | Co-organise a twice-yearly meeting to coordinate complex trait genetic research focussed on Edinburgh but with national participation. |
| Year(s) Of Engagement Activity | 2011,2012,2013,2014,2015,2016,2017,2018,2019,2020 |
| URL | https://www.wiki.ed.ac.uk/display/eactg/Edinburgh+Alliance+for+Complex+Trait+Genetics |
| Description | Genome Science conference (Liverpool, UK) |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Professional Practitioners |
| Results and Impact | I was an invited speaker to this conference. The conference was attended by peers interested in a variety of cutting-edge Genomics applications. |
| Year(s) Of Engagement Activity | 2016 |
| Description | Guest Lecturer on Canine Quantitative Genetics and Welfare (Programme in Quantitative Genetics and Genome Analysis/UoE School of Biological Sciences) |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Postgraduate students |
| Results and Impact | Provided guest lecturer to MSc students enrolled in the Programme in Quantitative Genetics and Genome Analysis. |
| Year(s) Of Engagement Activity | 2015,2016,2017,2018 |
| Description | Guest Lecturer on Canine Quantitative Genetics and Welfare (Roslin Institute/UoE Animal Biosciences) |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Postgraduate students |
| Results and Impact | Annual lecture to MSc students to provide examples of genetic and genomic studies to canine traits and diseases. |
| Year(s) Of Engagement Activity | 2014,2015,2016,2017 |
| Description | Highland Show |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Public/other audiences |
| Results and Impact | Institute stand at the Royal Highland Show. Demonstrating focussed activity and discussing the work of the University and the institute in relation to food safety, farm animal welfare, production efficiency, disease resistance etc. |
| Year(s) Of Engagement Activity | 2018 |
| Description | Interactive presentations at the Royal Highland Show |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Public/other audiences |
| Results and Impact | I supported the Roslin Institute's interactive presentation at the Royal Highland Show. Topics we covered were widely varied, including genetics and genomics, infection and immunity, farm animal health, and companion animal welfare. |
| Year(s) Of Engagement Activity | 2014,2015 |
| URL | http://royalhighlandshow.org |
| Description | Invited talk at symposium |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Industry/Business |
| Results and Impact | North American PRRS symposium. Chicago, USA, Dec 2017. Novel insights about host response to PRRS from data driven mathematical models. Invited talk. |
| Year(s) Of Engagement Activity | 2017 |
| Description | John Hickey Guest in Farming Today (BBC Radio 4) |
| Form Of Engagement Activity | A broadcast e.g. TV/radio/film/podcast (other than news/press) |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Public/other audiences |
| Results and Impact | On Monday 26th September, The BBC Radio 4 Farming Today had Professor John Hickey as specialist scientist on the subject of breeding programs and scientific impact. |
| Year(s) Of Engagement Activity | 2016 |
| URL | http://www.bbc.co.uk/programmes/b07w5xxq |
| Description | Meet The Scientists |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Schools |
| Results and Impact | Visit to a local primary school to engage with a questions and answers session about science and science careers |
| Year(s) Of Engagement Activity | 2018 |
| Description | Modern plant and animal applied genomics driven by genotype and sequence data, University of Zagreb, Croatia, 17-19 July 2018 |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Postgraduate students |
| Results and Impact | Workshop organised and given by me and two other members of my group. |
| Year(s) Of Engagement Activity | 2018 |
| Description | Organised talk with general public about companion animal welfare and research. |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Public/other audiences |
| Results and Impact | Midlothian Science Festival "Walkie Talkie" companion animal welfare and research talk in regional park. General public and their pets were attended. |
| Year(s) Of Engagement Activity | 2019 |
| Description | Phenotyping in genomic evaluations |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | The presentation took place on November 9, 2015, at the Università Cattolica del Sacro Cuore, Piacenza, Italy. The presentation and ensuing discussion were geared towards the use of conventional and novel phenotypes within a livestock genomic evaluation context. The event was attended by about 50 scientists from many European countries including the UK. |
| Year(s) Of Engagement Activity | 2015 |
| Description | Pint of Science talk, 'Pollination in in the genes' |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Public/other audiences |
| Results and Impact | The Pint of Science is a UK wide initiative aimed at popularising science by holding talks in public houses. The talk covering our work on honey bees was delivered by Drs Mark Barnett and Tim Regan |
| Year(s) Of Engagement Activity | 2018 |
| URL | https://pintofscience.co.uk/ |
| Description | Plenary talk |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Industry/Business |
| Results and Impact | Disease in aquaculture workshop, Universidad Autónoma de Baja California, Ensenada Mexico, October 2017. Genetic resistance and vaccination analysis on infectious disease genetics and genetic-epidemiological modelling in aquatic animals. Keynote presentation. |
| Year(s) Of Engagement Activity | 2017 |
| Description | Presentation at the Edinburgh Alliance for Complex Trait Genetics meeting |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | The presentation took place on March 9, 2016, and focused on the new genetic and genomic evaluation system for bovine Tuberculosis. The event was attended by approx. 100 Edinburgh-based scientists and international visitors at the time. |
| Year(s) Of Engagement Activity | 2016 |
| Description | Press release and wide press coverage for PLoS Genetics 12(2): e1005804 |
| Form Of Engagement Activity | A press release, press conference or response to a media enquiry/interview |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Media (as a channel to the public) |
| Results and Impact | A press release was issued for Xia et al. PLoS Genetics 12(2): e1005804 (http://www.eurekalert.org/pub_releases/2016-02/uoe-clc022216.php) The piece was reported in more than 130 English-language media (European, Asian and Australian) and several websites in other languages. |
| Year(s) Of Engagement Activity | 2016 |
| URL | https://news.google.com/news/story?cf=all&hl=en&pz=1&ned=uk&q=obesity+edinburgh&scoring=d&cf=all&ncl... |
| Description | Press release based on Nature Genetics publication |
| Form Of Engagement Activity | A press release, press conference or response to a media enquiry/interview |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Media (as a channel to the public) |
| Results and Impact | A press release was made describing our paper: "Evaluating the contribution of genetic and familial shared environment to common disease using the UK Biobank Munoz, M., Pong-Wong, R., Canela-Xandri, O., Rawlik, K., Haley, C. & Tenesa, A. Sep 2016 In : Nature Genetics. 48, 9, p. 980-983". This resulted in articles in several daily newspapers in the UK as well as overseas. |
| Year(s) Of Engagement Activity | 2016 |
| Description | Primary School "Big Science" visit |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Schools |
| Results and Impact | Visit to local primary school as part of their Big Science activity. Discussing science and scientific careers with the pupils and presenting awards to them based on a science project they had recently completed. |
| Year(s) Of Engagement Activity | 2018 |
| Description | Public lecture |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Public/other audiences |
| Results and Impact | Public lecture about clinical and basic research involving companion animals. |
| Year(s) Of Engagement Activity | 2019 |
| URL | https://www.ed.ac.uk/medicine-vet-medicine/news-events/college-events/let-s-talk-about-health-lectur... |
| Description | Question of Taste PCR Masterclass |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Schools |
| Results and Impact | Practical workshop run by the Roslin Institute public engagement outreach team to allow High School pupils to run PCRs and investigate the genetics of a specific taste receptor. |
| Year(s) Of Engagement Activity | 2018 |
| Description | Researcher Links workshop at CNRG, INIFAP, Tepatitlán and Guadalajara, Mexico, 3-7 February 2018 |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Postgraduate students |
| Results and Impact | Workshop organised and given by me and the members of my group |
| Year(s) Of Engagement Activity | 2018 |
| Description | School visit |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Schools |
| Results and Impact | I presented career options for mathematicians in biology at a local high school |
| Year(s) Of Engagement Activity | 2017 |
| Description | Scottish Native Honey Bee Society Inaugural Meeting (1 April 2017) |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Professional Practitioners |
| Results and Impact | A talk was presented by Dr Mark Barnett entitled 'Mapping honey bee health and genetic diversity in the UK' |
| Year(s) Of Engagement Activity | 2017 |
| URL | http://www.fifebeekeepers.co.uk/?p=1001 |
| Description | Short course in Evolutionary Quantitative Genetics |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Study participants or study members |
| Results and Impact | Evolutionary Quantitative Genetics course was a comprehensive review of modern concepts in Evolutionary Quantitative Genetics. The contents of the course are basic statistics, population genetics, quantitative genetics, evolutionary response in quantitative traits, estimating the fitness of traits and mixed models and their extensions. the instructor was Dr Bruce Walsh, Department of Ecology Evolutionary Biology, University of Arizona, and co-author of Genetics and Analysis of Quantitative Traits. The Course was hosted by Professor John Hickey at the Roslin Institute. |
| Year(s) Of Engagement Activity | 2016 |
| URL | http://www.alphagenes.roslin.ed.ac.uk/bruce-walsh-visit/ |
| Description | Skull Morphology and Health (Royal Highland Show) |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Public/other audiences |
| Results and Impact | Members of my group and I presented an educational event over two days that explained canine health and welfare, focussing on skull morphology and its effects on breathing in dogs. The event was hosted by the the Royal Highland Show, the premier farm show in Scotland. |
| Year(s) Of Engagement Activity | 2018 |
| URL | https://www.royalhighlandshow.org |
| Description | Summer course |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Postgraduate students |
| Results and Impact | Armidale Animal Breeding Summer Course 2018: Mathematical modeling of infection dynamics in genetically diverse livestock populations Teachers: Andrea Doeschl-Wilson and Osvaldo Anacleto Dates: Monday 5 February 2018 (9am) - Thursday 8 February 2018 (4pm) Venue: University of New England, Armidale, NSW Australia; ~40 post-graduate students, academics and industrial researcher attended the workshop in modelling. Based on the positive course evaluation, the course sparked new research in the important field of mathematical modelling of infection dynamics and genetics |
| Year(s) Of Engagement Activity | 2018 |
| URL | https://jvanderw.une.edu.au/aabc2018.htm |
| Description | Talk at the Eden Project |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Public/other audiences |
| Results and Impact | This was a meeting of individuals interested in honey bees and the conservation of native black bees. Our recently published work on honey bees was presented by Dr Mark Barnett. |
| Year(s) Of Engagement Activity | 2019 |
| URL | https://www.edenproject.com/media/2018/02/event-at-eden-to-look-at-future-of-honey-bees |
| Description | Teaching course: Next Generation Plant and Animal Breeding Programs, Animal Science Department, University of Nebraska, Lincoln. |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Postgraduate students |
| Results and Impact | Series of the lectures and workshops on Plant and Animal Breeding Programs exploring current practices and future areas of research. The course was designed and imparted by John Hickey and key members of his team. |
| Year(s) Of Engagement Activity | 2016 |
| URL | http://animalscience.unl.edu/next-generation-plant-and-animal-breeding-programs |
| Description | The Expert Working Group on Wheat Breeding Methods and Strategies |
| Form Of Engagement Activity | A formal working group, expert panel or dialogue |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Expert Working Group on Wheat Breeding Methods and Strategies seeks to exchange breeding methods research information and germ plasm to expert build capacity and support in wheat breeding programs, with more efficient breeding methods consistent with the latest scientific advances. The EWG is working on activities such us workshops, training courses, communications, and sharing of germplasm and information to reach larger pool of wheat breeders and trained in state-of-the-art breeding methods. |
| Year(s) Of Engagement Activity | 2015,2016,2017 |
| URL | http://www.wheatinitiative.org/activities/expert-working-groups/wheat-breeding-methods-and-strategie... |
| Description | Visiting Sawmill |
| Form Of Engagement Activity | A formal working group, expert panel or dialogue |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Industry/Business |
| Results and Impact | Visit to modern working sawmill to discuss the Sitka Spruced objectives, understand industry perspectives on further progress and how industry infrastructure would influence feasibility of future objectives. |
| Year(s) Of Engagement Activity | 2019 |
| URL | https://sitkaspruced.web.ox.ac.uk/home |
| Description | Wild Science Vogrie Country Park (8th Oct 2017), part of the Midlothian Science Festival |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Public/other audiences |
| Results and Impact | Manned a stand including honey tasting, a display of beekeeping equipment, microscopes to look at bees and posters of our scientific studies on bees. Presenters Drs Mark Barnett and Tim Regan. |
| Year(s) Of Engagement Activity | 2017 |
| URL | https://midlothiansciencefestival.com/event/wild-science/ |