Quantitative Genetics and Population Dynamics

Lead Research Organisation: University of Edinburgh
Department Name: The Roslin Institute

Abstract

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.

Publications

10 25 50
 
Description The core aims of this theme is 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 computational 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.
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.
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. Generically, 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. Therefore the objectives are more holistic improving both health and well-being as well as productivity, and consequently the gains made are economically more valuable. 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. 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. 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. 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.
First Year Of Impact 2014
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 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 EAAP Working Group on Animal Genetic Resources
Geographic Reach Europe 
Policy Influence Type Participation in a advisory committee
Impact Informing EU policy on regulations and incentives for managing farm animal genetic resources.
 
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 AFRI Animal Health and Disease SF424
Amount $147,600 (USD)
Organisation U.S. Department of Agriculture USDA 
Department National Animal Disease Center
Sector Public
Country United States of America
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 of Great Britain & Northern Ireland (UK)
Start 09/2016 
End 08/2021
 
Description Dairy Co (now AHDB) grant for bovine tuberculosis genetic evaluations
Amount £100,000 (GBP)
Organisation Agriculture and Horticulture Development Board (AHDB) 
Sector Multiple
Country Unknown
Start 01/2014 
End 12/2015
 
Description European Commission Horizon2020
Amount € 759,500 (EUR)
Organisation European Commission 
Sector Public
Country European Union (EU)
Start 01/2015 
End 12/2019
 
Description Genome Alberta ALGP2
Amount $60,000 (CAD)
Funding ID ALGP2 024 
Organisation Genome Canada 
Sector Private
Country Canada
Start 03/2015 
End 02/2018
 
Description Newton Fund Workshop Grant
Amount £18,775 (GBP)
Funding ID 2016-RLWK7-10399 
Organisation British Council 
Sector Charity/Non Profit
Country United Kingdom of Great Britain & Northern Ireland (UK)
Start 04/2017 
End 01/2018
 
Description Newton Fund Workshop Grant
Amount £20,823 (GBP)
Funding ID 228949780 
Organisation British Council 
Sector Charity/Non Profit
Country United Kingdom of Great Britain & Northern Ireland (UK)
Start 04/2016 
End 09/2016
 
Description Personal Award
Amount kr 300,000 (NOK)
Organisation Norwegian University of Life Sciences (NMBU) 
Sector Academic/University
Country Norway, Kingdom of
Start 09/2014 
End 09/2017
 
Description Scottish Government Centre of Expertise in Animal Disease Outbreaks
Amount £10,000,000 (GBP)
Organisation Scottish Government 
Sector Public
Country United Kingdom of Great Britain & Northern Ireland (UK)
Start 04/2016 
End 03/2020
 
Description Scottish Government Strategic Research Programme (RESAS)
Amount £540,000 (GBP)
Organisation Scottish Government 
Sector Public
Country United Kingdom of Great Britain & Northern Ireland (UK)
Start 09/2016 
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 of Great Britain & Northern Ireland (UK)
Start 04/2012 
End 03/2015
 
Description USDA
Amount $54,000 (USD)
Organisation U.S. Department of Agriculture USDA 
Sector Public
Country United States of America
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, Republic of
Start 09/2016 
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, Republic of
Start 10/2013 
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 
Provided To Others? No  
Impact The description of our methodology will be released with open-access publication of our study which is review. 
 
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 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 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. 
 
Description Centre for Tropical Livestock Genetics and Health 
Organisation International Livestock Research Institute (ILRI)
Country Kenya, Republic of 
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 Dog Biomedical Variant Database Consortium 
Organisation Animal Health Trust
Country United Kingdom of Great Britain & Northern Ireland (UK) 
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 Publications in preparation.
Start Year 2016
 
Description Dog Biomedical Variant Database Consortium 
Organisation Mars Nutrition Research Council, Mars Incorporated
Country United States of America 
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 Publications in preparation.
Start Year 2016
 
Description Dog Biomedical Variant Database Consortium 
Organisation North Carolina State University
Country United States of America 
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 Publications in preparation.
Start Year 2016
 
Description Dog Biomedical Variant Database Consortium 
Organisation University of Bern
Country Switzerland, Swiss Confederation 
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 Publications in preparation.
Start Year 2016
 
Description Dog Biomedical Variant Database Consortium 
Organisation University of California, Davis
Country United States of America 
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 Publications in preparation.
Start Year 2016
 
Description Dog Biomedical Variant Database Consortium 
Organisation University of Helsinki
Country Finland, Republic of 
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 Publications in preparation.
Start Year 2016
 
Description Dog Biomedical Variant Database Consortium 
Organisation University of Liege
Country Belgium, Kingdom of 
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 Publications in preparation.
Start Year 2016
 
Description Dog Biomedical Variant Database Consortium 
Organisation University of Minnesota
Country United States of America 
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 Publications in preparation.
Start Year 2016
 
Description Dog Biomedical Variant Database Consortium 
Organisation University of Pennsylvania
Country United States of America 
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 Publications in preparation.
Start Year 2016
 
Description Dog Biomedical Variant Database Consortium 
Organisation University of Rennes 1 (Université de Rennes 1)
Country France, French Republic 
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 Publications in preparation.
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 Publications in preparation.
Start Year 2016
 
Description Dog Biomedical Variant Database Consortium 
Organisation University of Sydney
Country Australia, Commonwealth of 
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 Publications in preparation.
Start Year 2016
 
Description Genetic studies with colleagues from Cyprus 
Organisation Cyprus University of Technology
Country Cyprus, Republic of 
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 Partnership with Geno Global 
Organisation Geno Global Ltd.
Country Norway, Kingdom of 
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 We expect to build on a longterm relationship with Geno, and currently we are discussing the future of this collaboration.
Start Year 2016
 
Description Saphir - Horizon2020 
Organisation French National Institute of Agricultural Research
Country France, French Republic 
Sector Public 
PI Contribution I am leader of workpackage 16: Modelling vaccine efficacy
Collaborator Contribution INRA is project leader
Impact no publications yet
Start Year 2016
 
Description Saphir - Horizon2020 
Organisation Genus plc
Country United Kingdom of Great Britain & Northern Ireland (UK) 
Sector Private 
PI Contribution I am leader of workpackage 16: Modelling vaccine efficacy
Collaborator Contribution INRA is project leader
Impact no publications yet
Start Year 2016
 
Description Saphir - Horizon2020 
Organisation Iowa State University
Department Electrical Engineering
Country United States of America 
Sector Academic/University 
PI Contribution I am leader of workpackage 16: Modelling vaccine efficacy
Collaborator Contribution INRA is project leader
Impact no publications yet
Start Year 2016
 
Description Saphir - Horizon2020 
Organisation NOFIMA, Ås Norway
Country Norway, Kingdom of 
Sector Private 
PI Contribution I am leader of workpackage 16: Modelling vaccine efficacy
Collaborator Contribution INRA is project leader
Impact no publications yet
Start Year 2016
 
Description Saphir - Horizon2020 
Organisation U.S. Department of Agriculture USDA
Country United States of America 
Sector Public 
PI Contribution I am leader of workpackage 16: Modelling vaccine efficacy
Collaborator Contribution INRA is project leader
Impact no publications yet
Start Year 2016
 
Description Saphir - Horizon2020 
Organisation University of Alberta
Department Department of Agricultural, Food and Nutritional Science (AFNS)
Country Canada 
Sector Academic/University 
PI Contribution I am leader of workpackage 16: Modelling vaccine efficacy
Collaborator Contribution INRA is project leader
Impact no publications yet
Start Year 2016
 
Description Sequencing of beef cattle in Ireland 
Organisation Illumina
Country United Kingdom of Great Britain & Northern Ireland (UK) 
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 of America 
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
 
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 173 time in recent years, attracting users from a number of different academic institutions. 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/alphaimpute/
 
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/alphaphase/
 
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/
 
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 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 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
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
 
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
 
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 John hickey Guest in Framing 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 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 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 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 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...