Genetic dissection of complex traits

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

Abstract

This project aims to develop a systems biology approach to dissecting the genetic variation in complex traits. Complex traits are determined by the interaction of genes and the environment. Understanding how genes shape the observed phenotypic variation is relevant for animal breeders, evolutionary biologists, human geneticists and many others. Classical dissection of complex traits has developed techniques that were primarily applied in pursuit of QTL, single loci that explain a large fraction of the genetic variance. Such loci provide natural experiments and could be incorporated into breeding programmes or used to give new insights into treatments for disease. However, emerging from numerous genome-wide association studies in humans and livestock is the issue of the “missing heritability”, where even for strongly heritable traits the large numbers of markers associated with the trait explain only a small fraction of the genetic variation. Responding to this issue raises new questions and requires new approaches to dealing with the challenge of dissecting the genetic variance in complex traits. The direct objectives in this theme will move beyond the locus-centric approach and develop system-centric approaches to dissection. Nevertheless there remains value in identifying classical QTL and there are new sources of data that may offer greater power of detection. Whilst the project is concerned with hypotheses on homology among species in genetic variance and the relative importance of cis/trans and e/m regulatory genetic elements, the novel methodologies developed will be important for those ISP identifying genetic variants. Of particular value across all strategic programmes will be incorporating the use of expression data into the QTL detection.

Organisations

Publications

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Audzevich T (2017) Pre/pro-B cells generate macrophage populations during homeostasis and inflammation. in Proceedings of the National Academy of Sciences of the United States of America

 
Description 1. We reviewed the relevance and evidence for epistasis (gene interactions) in the control of complex traits using humans as a data-rich model and concluded large sample sizes and very dense genomic information, essentially sequence-level, was likely to be necessary for comprehensive evaluation of epistasis.

2. We used computer simulations to investigate the amount of genetic variation for complex traits that can be revealed by single-SNP genome-wide association studies (GWAS) or regional heritability mapping (RHM) analyses based on full genome sequence data or SNP chips. The numbers of variants detected and the fraction of variance explained were broadly similar with no clear advantage to either method. GWAS applied to sequence increased the number of variants by as much as 50% but only modestly increased the fraction of variance explained.

3. We have demonstrated the feasibility of identifying predictive epigenetic markers of disease risk using imputed data, and demonstrated the functionality of this with a readily available data set on Parkinson's Disease.

4. We collaborated in the characterisation and separation of the genetic architecture of human fluid intelligence (the ability to reason in novel situations) and crystallized intelligence (the ability to apply acquired knowledge) by combining gene- and pathway-based approaches.

5. Quantifying skull morphology form computed tomography, we have identified a major locus responsible for canine brachycephaly and have narrowed the precise causal variant to a small number of mutations. In contrast we have shown that two skeletal disorders, canine hip dysplasia and equine osteochondrosis are essentially polygenic in nature, which implies that breeding to reduce the impact of these disorders will require the use of whole genome approaches (e.g. through low density SNP chips combined with imputation) rather than a single gene test. Simulation analyses have subsequently supported the potential utility and value of genotypic imputation within dog breeds. Further work suggests that cross-population reference populations may not be effective for genomic selection against hip dysplasia, possibly due to lack of shared haplotype blocks across separate dog populations, such that genomic prediction will be most successful within populations.

6. We have identified historic selective sweeps that shaped domestication of the pig, and identified candidate regions that remain under selection.

7. We identified lethal recessive mutations causing perinatal mortality in sheep and pig populations using homozygosity mapping, and worked with industry to publish practical guidelines to help breeding organisations across all sectors become proactive in lifting the curse of such lethal recessives.

8. Quantitative trait loci with effects on resistance to Marek's Disease were identified. 1200 F6 animals from a full-sib intercross line, selected for high or low resistance were genotyped with the chicken 600K SNP chip. 10 founder parents were also whole genome sequenced and variants identified. Pools of pedigreed animals from 15 generations were also genotyped and QTLs refined and verified. Fifteen of the most significant QTL regions were annotated for genes and variants. Highly significant genetic associations with MDV survival were found.

9. We have identified regions harbouring putative QTL associated with susceptibility to bovine tuberculosis, including a region on chromosome 23, which contains the coding regions for BoLA loci. We identified putative QTL that differentiate between cases with and without visible lesions, which if confirmed has implications for surveillance programs. However the findings indicate that genetic variation in bTB susceptibility is predominantly polygenic in nature.

10. We have identified genes within QTL with significant effects on growth in poultry (CCKAR) and skeletal quality in laying hens (CBS). These loci have been characterised to the level of changes in gene expression at the largest QTL for growth in poultry and in a QTL for skeletal quality in laying hens. Subsequently efforts have been made to the elucidate the role of the genes in the respective traits. This has led to neural pathways which may be critical to improving efficiency in poultry and to nutritional interventions for bone quality.
Exploitation Route The tools and knowledge generated in this project will enable on-going research in systems biology of complex animal systems, and feed into discussions with breeding organisations on the infrastructure and processes required to establish effective remedial breeding programmes in the skeletal disorders studied. There is also the possibility of commercialising the variant detection models we have developed for predicting complex traits in humans. The work on bTB has supported the implemented polygenic models for the routine publication of expected breeding values for susceptibility/resistance to bTB (TB Advantage) Protocols for lifting the curse of the lethal recessives are already being implemented.
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

URL http://www.signetfbc.co.uk/wp-content/uploads/2014/11/ridgene_manual_digital.pdf
 
Description 1. Brachycephaly is a source of morbidity and a major welfare concern of managed animals including cats and dogs and stimulates public debate as brachycephalic breed animals continue to be among the most popular pets among the general public despite the clear links between skull shape and morbidity. Our findings have been presented at a number of public forums including the British Science Festival 2016, Royal Highland Shows (2015-2016), Midlothian Science Festival (2016) among others and are framing public attitudes to this condition and pedigree breeding in general, and the canine pedigree breeding industry which has substantial economic value. "Saving the British Bulldog", a public TV production that documents our work will air in March 2018. 2. The work identifying lethal recessives has been publicised by industry across multiple sectors and to veterinary surgeons. We ourselves have worked with industry to pursue three such defects. The guide on how to lift the curse was written by the project team and published by industry. [http://www.signetfbc.co.uk/wp-content/uploads/2014/11/ridgene_manual_digital.pdf]. 3. The understanding of the genetic architecture of susceptibility to bovine tuberculosis has been used to integrate selection against susceptibility into breeding indices through TbAdvantage.
First Year Of Impact 2012
Sector Agriculture, Food and Drink,Leisure Activities, including Sports, Recreation and Tourism,Pharmaceuticals and Medical Biotechnology
Impact Types Cultural,Societal,Economic

 
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 10/2015 
End 09/2020
 
Description ANIHWA call 2: Better bone quality in laying hens
Amount £836,262 (GBP)
Funding ID BB/M028291/1 
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 06/2015 
End 10/2018
 
Description ANIHWA call1 TURKEYWELFARE
Amount £75,281 (GBP)
Funding ID BB/L012022/1 
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 01/2014 
End 02/2016
 
Description Accelerating advances in animal welfare
Amount $486,594 (USD)
Funding ID 550396 
Organisation Foundation for Food and Agriculture Research 
Start 04/2018 
End 03/2022
 
Description Advancing European Aquaculture by Genome Functional Annotation
Amount € 6,000,000 (EUR)
Organisation European Union 
Sector Public
Country European Union (EU)
Start 05/2019 
End 04/2022
 
Description BBSRC KTN CASE Studentship
Amount £80,000 (GBP)
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 09/2016 
End 08/2021
 
Description BBSRC Responsive Mode
Amount £900,000 (GBP)
Funding ID BB/R008612/1 
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 04/2018 
End 03/2021
 
Description COST Action
Amount € 3,000 (EUR)
Funding ID CA15224 
Organisation European Cooperation in Science and Technology (COST) 
Sector Public
Country European Union (EU)
Start 04/2016 
End 03/2020
 
Description Defining Genetic Causality of Canine Portosystemic Shunts
Amount £20,000 (GBP)
Organisation Dogs Trust 
Sector Charity/Non Profit
Country Unknown
Start 01/2015 
End 03/2016
 
Description Defining Genetic Causality of Canine Tracheal Collapse
Amount £10,000 (GBP)
Organisation Dogs Trust 
Sector Charity/Non Profit
Country Unknown
Start 01/2015 
End 12/2016
 
Description Dogs Trust Bateson Canaine Welfare Grant
Amount £103,114 (GBP)
Organisation Dogs Trust 
Sector Charity/Non Profit
Country Unknown
Start 04/2014 
End 06/2016
 
Description Flexible Talent Mobility Award collaboration on poultry welfare traits
Amount £8,506 (GBP)
Organisation University of Edinburgh 
Sector Academic/University
Country United Kingdom
Start 01/2018 
End 02/2020
 
Description GCRF Data and Resources round 1
Amount £946,000 (GBP)
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 10/2016 
End 07/2017
 
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 Horizon 2020 Call H2020-SFS-2016-2
Amount € 7,000,000 (EUR)
Funding ID 727315 
Organisation European Union 
Sector Public
Country European Union (EU)
Start 05/2017 
End 04/2021
 
Description NERC Aquaculture Innovation Award
Amount £202,253 (GBP)
Funding ID NE/P010695/1 
Organisation Natural Environment Research Council 
Sector Public
Country United Kingdom
Start 01/2017 
End 12/2018
 
Description Newton Fund Workshop Brazil
Amount £52,000 (GBP)
Funding ID 228949780 
Organisation British Council 
Sector Charity/Non Profit
Country United Kingdom
Start 04/2016 
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 04/2017 
End 03/2018
 
Description Newton International Fellowship
Amount £96,501 (GBP)
Funding ID NF160037 
Organisation British Council 
Sector Charity/Non Profit
Country United Kingdom
Start 03/2017 
End 02/2019
 
Description Scottish Aquaculture Innovation Centre
Amount £1,000,000 (GBP)
Organisation Scottish Aquaculture Innovation Centre 
Sector Multiple
Country United Kingdom
Start 04/2018 
End 03/2020
 
Description Solutions-Based Approach to Genetic Diseases in Dogs
Amount £200,000 (GBP)
Organisation Dogs Trust 
Sector Charity/Non Profit
Country Unknown
Start 09/2014 
End 08/2016
 
Description Transcriptomic analysis of the soft palate to investigate the airway inflammatory response of brachycephalic dogs
Amount £5,384 (GBP)
Organisation Ian Finlay Architects 
Sector Private
Country United Kingdom
Start 10/2017 
End 09/2018
 
Description Travel grant from the Universidad Autonoma de Baja California, Mexico
Amount $150,000 (MXN)
Organisation Technological Institute of Baja California 
Start 10/2017 
End 10/2018
 
Description Wellcome Trust-University of Edinburgh Institutional Strategic Support Fund (ISSF2)
Amount £43,641 (GBP)
Organisation University of Edinburgh 
Department Institutional Strategic Support Fund
Sector Charity/Non Profit
Country United Kingdom
Start 03/2015 
End 04/2016
 
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 Better bones 
Description Phenotyped laying hen population with/without DNA for bone quality 
Type Of Material Database/Collection of data 
Year Produced 2015 
Provided To Others? Yes  
Impact Collaboration with colleagues in Germany, Sweden and Spain has resulted in GWAS and other publications 
 
Title Chicken bone RNAseq data used to annotate genome 
Description Chicken bone RNAseq data used to annotate genome 
Type Of Material Database/Collection of data 
Year Produced 2015 
Provided To Others? Yes  
Impact Used for annotation and is available in public database 
 
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 DNAseq data (variants) from dogs 
Description VCF produced from resequenced genomes was contributed (prepublication) to members of the Dog Biomedical Variant Consortium Database. Upon publication by my group, genomes data produced from my group will be deposited in the European Nucleotide Archive for general access. 
Type Of Material Database/Collection of data 
Year Produced 2015 
Provided To Others? Yes  
Impact Publications that utilise this data are pending from my group. Others members of the group have already used this data for their personal research interests. 
 
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 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 Genome-wide pleiotropy and shared biological pathways for resistance to bovine pathogens 
Description The database represents data on disease and production traits in dairy cattle that was the basis or our collaborative research and can be used for further analyses by ourselves and others. 
Type Of Material Database/Collection of data 
Year Produced 2018 
Provided To Others? Yes  
Impact None as yet 
URL https://datashare.is.ed.ac.uk/handle/10283/3040
 
Title India flu - chicken transcriptome 
Description Transcriptomes from brain, lung and ileum tissue from chicken in response to high and low path avian flu 
Type Of Material Database/Collection of data 
Provided To Others? No  
Impact Identification of genes involved in resistance/susceptibility to avian flu 
 
Title India flu - crow transcriptome 
Description Transcriptomes from brain, lung and ileum tissue from crow in response to high and low path avian flu 
Type Of Material Database/Collection of data 
Provided To Others? No  
Impact Identification of genes involved in resistance/susceptibility to avian flu 
 
Title India flu - duck transcriptome 
Description Transcriptomes from brain, lung and ileum tissue from duck in response to high and low path avian flu 
Type Of Material Database/Collection of data 
Provided To Others? No  
Impact Identification of genes involved in resistance/susceptibility to avian flu 
 
Title India flu - goose transcriptome 
Description Transcriptomes from brain, lung and ileum tissue from goose in response to high and low path avian flu 
Type Of Material Database/Collection of data 
Provided To Others? No  
Impact Identification of genes involved in resistance/susceptibility to avian flu 
 
Title India flu - pigeon transcriptome 
Description Transcriptomes from brain, lung and ileum tissue from pigeon in response to high and low path avian flu 
Type Of Material Database/Collection of data 
Provided To Others? No  
Impact Identification of genes involved in resistance/susceptibility to avian flu 
 
Title India flu - turkey transcriptome 
Description Transcriptomes from brain, lung and ileum tissue from turkey in response to high and low path avian flu 
Type Of Material Database/Collection of data 
Provided To Others? No  
Impact Identification of genes involved in resistance/susceptibility to avian flu 
 
Title Mechanistic model for within host PRRS virus infection dynamics 
Description A mechanistic model was developed to assess candidate immune mechanisms responsible for viremia rebound. The model was fitted to viremia data from a large scale PRRS virus infection experiment. The model is published in Go N. et al. 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 
Type Of Material Computer model/algorithm 
Year Produced 2019 
Provided To Others? Yes  
Impact Now collaborative research grant applications 
 
Title PRJEB10338 
Description This collection of data represents whole metagenome sequence data for 8 cattle chosen for low and high methane emissions after matching for breed and diet 
Type Of Material Database/Collection of data 
Year Produced 2016 
Provided To Others? Yes  
Impact This is a critically important dataset for linking genotype to phenotype (methane) in the cattle rumen microbiome. Since its release, the papers based on these data have been cited over 100 times 
URL https://www.ebi.ac.uk/ena/data/view/PRJEB10338
 
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. 
 
Title WGS data related to upper airway study 
Description Whole genome sequencing data related to upper airway study was deposited, prepublication, in the European Nucleotide Archive and shared with members of the Dog Biomedical Variant Database Consortium. 
Type Of Material Database/Collection of data 
Year Produced 2019 
Provided To Others? Yes  
Impact This data is used routinely by members of the DBVDC in separate studies whose focus is to identify the genetic underpinnings of canine genetic diseases: A de novo variant in the ASPRV1 gene in a dog with ichthyosis. Bauer A., Waluk DP., Galichet A., Timm K., Jagannathan V., Sayar BS., Wiener DJ., Dietschi E., Müller EJ., Roosje P., Welle MM., Leeb T. Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern, Switzerland. PLoS Genet. 13(3): e1006651 (2017 Mar) A SINE Insertion in ATP1B2 in Belgian Shepherd Dogs Affected by Spongy Degeneration with Cerebellar Ataxia (SDCA2). Mauri N., Kleiter M., Dietschi E., Leschnik M., Högler S., Wiedmer M., Dietrich J., Henke D., Steffen F., Schuller S., Gurtner C., Stokar-Regenscheit N., O'Toole D., Bilzer T., Herden C., Oevermann A., Jagannathan V., Leeb T. Institute of Genetics, Vetsuisse Faculty, University of Bern, 3001, Switzerland. G3 (Bethesda) 7(8): 2729-2737 (2017 Aug) A GJA9 frameshift variant is associated with polyneuropathy in Leonberger dogs. Becker D., Minor KM., Letko A., Ekenstedt KJ., Jagannathan V., Leeb T., Shelton GD., Mickelson JR., Drögemüller C. Institute of Genetics, Vetsuisse Faculty, University of Bern, 3001, Bern, Switzerland. BMC Genomics 18(1): 662 (2017 Aug) A Large Deletion in the NSDHL Gene in Labrador Retrievers with a Congenital Cornification Disorder. Bauer A., De Lucia M., Jagannathan V., Mezzalira G., Casal ML., Welle MM., Leeb T. Institute of Genetics, Vetsuisse Faculty, University of Bern, 3001, Switzerland. G3 (Bethesda) 7(9): 3115-3121 (2017 Sep) MKLN1 splicing defect in dogs with lethal acrodermatitis. Bauer A., Jagannathan V., Högler S., Richter B., McEwan NA., Thomas A., Cadieu E., André C., Hytönen MK., Lohi H., Welle MM., Roosje P., Mellersh C., Casal ML., Leeb T. Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern, Switzerland. PLoS Genet. 14(3): e1007264 (2018 Mar) 
 
Description Better Bones 
Organisation Swedish University of Agricultural Sciences
Country Sweden 
Sector Academic/University 
PI Contribution Samples, phenotyping and genotyping
Collaborator Contribution GWAS Analysis
Impact Analysis has been completed
Start Year 2013
 
Description Bovine disease resistance 
Organisation Justus Liebig University Giessen
Country Germany 
Sector Academic/University 
PI Contribution Hosting a visiting scientist and collaborating in the analysis of phenotypic data on disease for multiple different infections and parasites in dairy cattle together with genome wide data to estimate heritabilities, genetic correlations and genetic pathways involved in disease.
Collaborator Contribution Collection of data on bovine disease and provision of genomic data. Employment of scientist who visited to analyse the data.
Impact A scientific manuscript has been accepted for publication.
Start Year 2017
 
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 Centre for tropical livestock genetics and health (CTLGH) 
Organisation International Livestock Research Institute (ILRI)
Country Kenya 
Sector Charity/Non Profit 
PI Contribution Mick Watson is co-leading programme 5 (informatics and bioresources) programme of CTLGH which aims to collect data on genotype and phenotype into a central database which can subsequently be mined for useful associations. So far we have ensured that scientists have access to the latest high performance computing environment for research, we have analysed and continue to analyse hundreds of farm animal genomes from LMIC countries, and we have built the data portal (http://data.ctlgh.org)
Collaborator Contribution The partners are involved in all programmes, which include:Program 1: Harnessing genetic variability among indigenous and exotic breeds of cattle (as well as their crosses) to develop genetic and genomic tools that will be used to improve productivity under harsh tropical conditions and to mitigate the impact of cattle on climate change. Program 2: Harnessing genetic variability in tropical productivity and adaptation among various breeds of Chickens. Program 3: Development and application of precision breeding (through novel reproductive and germplasm technologies) to achieve step changes in livestock genetic improvement. Program 4: Understanding the genetic and molecular mechanisms underlying the tolerance of certain cattle and poultry breeds to tropical diseases and pests. Program 5: A shared global data and biological sample resource to support continued research and development on tropical livestock genetics and health.
Impact The data portal so far: http://data.ctlgh.org The collaboration is multi-disciplinary, bringing together geneticists, parasitologists, virologists, epidemiologists and data scientists together.
Start Year 2016
 
Description Centre for tropical livestock genetics and health (CTLGH) 
Organisation Scotland's Rural College
Country United Kingdom 
Sector Academic/University 
PI Contribution Mick Watson is co-leading programme 5 (informatics and bioresources) programme of CTLGH which aims to collect data on genotype and phenotype into a central database which can subsequently be mined for useful associations. So far we have ensured that scientists have access to the latest high performance computing environment for research, we have analysed and continue to analyse hundreds of farm animal genomes from LMIC countries, and we have built the data portal (http://data.ctlgh.org)
Collaborator Contribution The partners are involved in all programmes, which include:Program 1: Harnessing genetic variability among indigenous and exotic breeds of cattle (as well as their crosses) to develop genetic and genomic tools that will be used to improve productivity under harsh tropical conditions and to mitigate the impact of cattle on climate change. Program 2: Harnessing genetic variability in tropical productivity and adaptation among various breeds of Chickens. Program 3: Development and application of precision breeding (through novel reproductive and germplasm technologies) to achieve step changes in livestock genetic improvement. Program 4: Understanding the genetic and molecular mechanisms underlying the tolerance of certain cattle and poultry breeds to tropical diseases and pests. Program 5: A shared global data and biological sample resource to support continued research and development on tropical livestock genetics and health.
Impact The data portal so far: http://data.ctlgh.org The collaboration is multi-disciplinary, bringing together geneticists, parasitologists, virologists, epidemiologists and data scientists together.
Start Year 2016
 
Description Collaboration with Benchmark PLC in salmon gene editing 
Organisation Benchmark Holdings
PI Contribution This collaboration has been to develop a successful Industrial Partnership Award proposal for BBSRC into gene editing for disease resistance in salmon. Our team have developed gene editing facilities and capability in house for salmon (cell culture and embryos), and worked together with Benchmark to codevelop the project which begins on 1 April 2018. The reference code is BB/R008612/1.
Collaborator Contribution The partners are bringing substantial in kind contribution, cash contribution and expertise to the project. This includes access to samples and data from their salmon breeding programme in Norway, and access to year-round salmon gametes for gene editing experiments.
Impact Outputs include the successful award of project BB/R008612/1
Start Year 2017
 
Description Collaboration with Cawthron Institute in New Zealand 
Organisation Cawthron Institute
Country New Zealand 
Sector Charity/Non Profit 
PI Contribution This collaboration is built around a BBSRC partnering award in which I was the UK PI (BB/N022114/1 New Zealand - UK Paterning Award: Breeding for disease resistance in farmed oysters using genomic tools). The idea is to merge the genomic tools and skills that we have developed in the UK with the advanced shellfish selective breeding programmes that Cawthron run in New Zealand. Our research team has, for example, developed a high density SNP genotyping array for farmed oysters - the first of its kind for this species.
Collaborator Contribution Cawthron have world-leading selective breeding programmes for shellfish, including Pacific Oysters. One of the main target traits is to increase resistance to Oyster Herpes Virus (OHV) which can decimate stocks on oyster farms. They are providing our collaborative projects with access to extensive samples and data from their pedigreed oysters which have been challenged with OHV, in addition to their time to manage and run the project and provide intellectual input.
Impact Funded collaborative grant: NE/P010695/1 Application of genetic markers to improve resistance to herpes virus in commercial oyster populations This grant application builds on the BBSRC travel award and will provide funds for genotyping Cawthron's pedigreed oyster material with our high density SNP array developed under the BBSRC Aquaculture Initiative project BB/M026140/1 Investigation of Host Genetic Resistance to Oyster Herpes Virus using a High Density SNP Array. The downstream impact will be improved selective breeding for disease resistance in oysters, and transfer of much needed skills and expertise in advanced shellfish breeding from NZ to the UK. These collaborations also involve the Centre for Environment, Fisheries and Aquaculture Science (Cefas). The collaboration brings together expertise in genomics, sequencing, selective breeding, shellfish biology and virology.
Start Year 2016
 
Description Collaboration with University of Chile and AquaInnovo 
Organisation AquaChile
Country Chile 
Sector Private 
PI Contribution Chile is the second largest producer of Atlantic salmon in the world. This collaboration is based on research projects aimed at improving breeding for disease resistance in Chilean farmed salmon. The collaboration centres around a bilateral Newton project RCUK-CONICYT: Utilising functional genomic variation for improved disease resistance in Chilean salmon aquaculture. In this project, our team will run large-scale genomic analyses on disease challenged salmon samples, including from salmon challenged with sea lice and piscirickettsia salmonis - a major bacterial pathogen of salmon. This will include whole genome resequencing, analyses of differential gene expression profiles between resistant and susceptible fish, and genomic prediction analyses.
Collaborator Contribution The project partners (AquaChile and University of Chile) have provided access to over 5,000 samples from pedigreed Atlantic salmon stocks with associated data on sea lice and P. salmonis resistance. In addition, they provide significant practical and academic expertise to the collaboration.
Impact The outcomes of the collaboration to date have included training of postdoctoral researcher Diego Robledo in University of Chile in January 2017, and publications of peer-reviewed manuscripts: Genomics in aquaculture to better understand species biology and accelerate genetic progress. Jose M. Yáñez, Scott Newman, Ross D. Houston - 01 Apr 2015 - Frontiers in genetics Vol: 6. Genetics and genomics of disease resistance in salmonid species. José M Yáñez, Ross D Houston, Scott Newman - 2014 - Frontiers in genetics Vol: 5 Pages: 415 The future outcomes of the project will be improved methods of breeding for resistance to disease in Chilean salmon aquaculture. The collaboration includes quantitative genetics, disease biology, high throughput genomics / sequencing, and bioinformatics.
Start Year 2014
 
Description Collaboration with University of Chile and AquaInnovo 
Organisation University of Chile
Country Chile 
Sector Academic/University 
PI Contribution Chile is the second largest producer of Atlantic salmon in the world. This collaboration is based on research projects aimed at improving breeding for disease resistance in Chilean farmed salmon. The collaboration centres around a bilateral Newton project RCUK-CONICYT: Utilising functional genomic variation for improved disease resistance in Chilean salmon aquaculture. In this project, our team will run large-scale genomic analyses on disease challenged salmon samples, including from salmon challenged with sea lice and piscirickettsia salmonis - a major bacterial pathogen of salmon. This will include whole genome resequencing, analyses of differential gene expression profiles between resistant and susceptible fish, and genomic prediction analyses.
Collaborator Contribution The project partners (AquaChile and University of Chile) have provided access to over 5,000 samples from pedigreed Atlantic salmon stocks with associated data on sea lice and P. salmonis resistance. In addition, they provide significant practical and academic expertise to the collaboration.
Impact The outcomes of the collaboration to date have included training of postdoctoral researcher Diego Robledo in University of Chile in January 2017, and publications of peer-reviewed manuscripts: Genomics in aquaculture to better understand species biology and accelerate genetic progress. Jose M. Yáñez, Scott Newman, Ross D. Houston - 01 Apr 2015 - Frontiers in genetics Vol: 6. Genetics and genomics of disease resistance in salmonid species. José M Yáñez, Ross D Houston, Scott Newman - 2014 - Frontiers in genetics Vol: 5 Pages: 415 The future outcomes of the project will be improved methods of breeding for resistance to disease in Chilean salmon aquaculture. The collaboration includes quantitative genetics, disease biology, high throughput genomics / sequencing, and bioinformatics.
Start Year 2014
 
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 Publications in preparation.
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 Publications in preparation.
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 Publications in preparation.
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 Publications in preparation.
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 Publications in preparation.
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 Publications in preparation.
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 Publications in preparation.
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 Publications in preparation.
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 Publications in preparation.
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 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 
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 correlations between diseases and production traits in dairy cattle 
Organisation Justus Liebig University Giessen
Country Germany 
Sector Academic/University 
PI Contribution We provided scientific input to a visiting scientist to implement a novel analysis based on human genetic approaches to estimate for the first time the genetic correlations between resistance to various infectious diseases and between diseases and production traits (e.g. early growth, milk production) in dairy cattle. This was the first time that this novel approach which allows genetic estimates of correlations between traits recorded in different animals to be used, had been applied in livestock
Collaborator Contribution The collaborators had collected a very large body of data on diseases and production traits on 20,000 dairy cattle together with whole genome genotypes on the relevant animals. Such data took several years to collect and involved many veterinarians and others to collect and classify disease traits. The genotyping alone of the cattle is likely to have cost 1,000,000 Euros. The data analysis was performed by a PhD student sponsored by the collaborators whilst he was visiting and based in our group in Edinburgh.
Impact The results of the analysis have been published (https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0194374) The data used in the analysis is stored in Edinburgh datashare and is available for our own future analyses and those of others (https://datashare.is.ed.ac.uk/handle/10283/3040) The collaboration involved animal scientists, geneticists and bioinformaticians.
Start Year 2017
 
Description Genetics of one-carbon metabolism 
Organisation University of Nottingham
Country United Kingdom 
Sector Academic/University 
PI Contribution The Roslin Institute partners in this collaboration provide expertise in genome analysis in farmed animal species and expertise in molecular, quantitative and population genetic analyses.
Collaborator Contribution The University of Nottingham group bring expertise in reproductive biology, physiology, epigenetics and bioinformatics as well as the biological questions which the "Genetics of one-carbon metabolism in sheep in relation to productivity, fertility and health" project has been designed to address.
Impact This BBSRC-funded research project (2013-17) supported by grants to University of Nottingham (BB/K017810/1) and The Roslin Institute, University of Edinburgh (BB/K017993/1) is an outcome from this collaborative link that started three years earlier. Whilst this collaboration is multi-disciplinary, the disciplines involved are specialisms within biology: reproductive biology; physiology; genetics; genomics; bioinformatics.
Start Year 2010
 
Description Hy-line 
Organisation Hy-line International
Country United States 
Sector Private 
PI Contribution -Genotyping of DNA from MDV susceptible/resistant birds -Whole genome sequencing of parental birds -Identification of candidate genes/SNPs for MDV resistance
Collaborator Contribution -Provision of DNA samples from 1200 F6 birds, showing susceptibility/resistance to Marek's Disease virus. -Genotyping of candidate SNPs in 10,000 sire-pedigreed birds (15 generations)
Impact Identification of QTLR, genes and SNPs associated with resistance to MDV
Start Year 2013
 
Description Keel bone damage COST action 
Organisation Aarhus University
Country Denmark 
Sector Academic/University 
PI Contribution Ian Dunn is a work group leader and contributed to writing the proposal. We have hosted a number of visits under the scheme and ourselves have taken part in meetings workshops and training activities.
Collaborator Contribution A large number of contributors across Europe with different expertise form the collaboration on keel bone damage. Veterinarians, companies, behaviour specialists and those skilled in measuring damage.
Impact Standardised methodologies, new collaborations, spread of good practice, successful funding applications
Start Year 2016
 
Description Keel bone damage COST action 
Organisation French Agency for Food, Environmental and Occupational Health & Safety (ANSES)
Country France 
Sector Public 
PI Contribution Ian Dunn is a work group leader and contributed to writing the proposal. We have hosted a number of visits under the scheme and ourselves have taken part in meetings workshops and training activities.
Collaborator Contribution A large number of contributors across Europe with different expertise form the collaboration on keel bone damage. Veterinarians, companies, behaviour specialists and those skilled in measuring damage.
Impact Standardised methodologies, new collaborations, spread of good practice, successful funding applications
Start Year 2016
 
Description Keel bone damage COST action 
Organisation Friedrich Loeffler Institute
Country Germany 
Sector Public 
PI Contribution Ian Dunn is a work group leader and contributed to writing the proposal. We have hosted a number of visits under the scheme and ourselves have taken part in meetings workshops and training activities.
Collaborator Contribution A large number of contributors across Europe with different expertise form the collaboration on keel bone damage. Veterinarians, companies, behaviour specialists and those skilled in measuring damage.
Impact Standardised methodologies, new collaborations, spread of good practice, successful funding applications
Start Year 2016
 
Description Keel bone damage COST action 
Organisation Institut de Sélection Animale BV
PI Contribution Ian Dunn is a work group leader and contributed to writing the proposal. We have hosted a number of visits under the scheme and ourselves have taken part in meetings workshops and training activities.
Collaborator Contribution A large number of contributors across Europe with different expertise form the collaboration on keel bone damage. Veterinarians, companies, behaviour specialists and those skilled in measuring damage.
Impact Standardised methodologies, new collaborations, spread of good practice, successful funding applications
Start Year 2016
 
Description Keel bone damage COST action 
Organisation Institute of Animal Biochemistry and Genetics
PI Contribution Ian Dunn is a work group leader and contributed to writing the proposal. We have hosted a number of visits under the scheme and ourselves have taken part in meetings workshops and training activities.
Collaborator Contribution A large number of contributors across Europe with different expertise form the collaboration on keel bone damage. Veterinarians, companies, behaviour specialists and those skilled in measuring damage.
Impact Standardised methodologies, new collaborations, spread of good practice, successful funding applications
Start Year 2016
 
Description Keel bone damage COST action 
Organisation Swedish University of Agricultural Sciences
Country Sweden 
Sector Academic/University 
PI Contribution Ian Dunn is a work group leader and contributed to writing the proposal. We have hosted a number of visits under the scheme and ourselves have taken part in meetings workshops and training activities.
Collaborator Contribution A large number of contributors across Europe with different expertise form the collaboration on keel bone damage. Veterinarians, companies, behaviour specialists and those skilled in measuring damage.
Impact Standardised methodologies, new collaborations, spread of good practice, successful funding applications
Start Year 2016
 
Description Keel bone damage COST action 
Organisation University of Bern
Country Switzerland 
Sector Academic/University 
PI Contribution Ian Dunn is a work group leader and contributed to writing the proposal. We have hosted a number of visits under the scheme and ourselves have taken part in meetings workshops and training activities.
Collaborator Contribution A large number of contributors across Europe with different expertise form the collaboration on keel bone damage. Veterinarians, companies, behaviour specialists and those skilled in measuring damage.
Impact Standardised methodologies, new collaborations, spread of good practice, successful funding applications
Start Year 2016
 
Description Keel bone damage COST action 
Organisation University of Granada
Country Spain 
Sector Academic/University 
PI Contribution Ian Dunn is a work group leader and contributed to writing the proposal. We have hosted a number of visits under the scheme and ourselves have taken part in meetings workshops and training activities.
Collaborator Contribution A large number of contributors across Europe with different expertise form the collaboration on keel bone damage. Veterinarians, companies, behaviour specialists and those skilled in measuring damage.
Impact Standardised methodologies, new collaborations, spread of good practice, successful funding applications
Start Year 2016
 
Description Keel bone damage COST action 
Organisation University of Wageningen
Country Netherlands 
Sector Academic/University 
PI Contribution Ian Dunn is a work group leader and contributed to writing the proposal. We have hosted a number of visits under the scheme and ourselves have taken part in meetings workshops and training activities.
Collaborator Contribution A large number of contributors across Europe with different expertise form the collaboration on keel bone damage. Veterinarians, companies, behaviour specialists and those skilled in measuring damage.
Impact Standardised methodologies, new collaborations, spread of good practice, successful funding applications
Start Year 2016
 
Description Newton Fund Travel Award Saif Agha 
Organisation Ain Shams University
Department Faculty of Engineering
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 Rabbit Genomics 
Organisation Polytechnic University of Valencia
Country Spain 
Sector Academic/University 
PI Contribution Collaborative analysis of data on intramuscular fat and uterine capacity together with whole genome SNP data in commercial rabbit populations
Collaborator Contribution Generation of rabbit populations and genomic data and employment of a scientist visiting Edinburgh to undertake analyses.
Impact Training of visiting scientist. A scientific publication is in preparation.
Start Year 2017
 
Description Regional heritability analysis in Japanese dairy cattle 
Organisation Nihon University
Country Japan 
Sector Academic/University 
PI Contribution Collaboration on regional heritability analyses of milk production traits in dairy cattle
Collaborator Contribution Analysis and provision of data
Impact A publication has bee published (Gervais et al., 2017)
Start Year 2015
 
Description SRUC - Rainer Roehe 
Organisation Scotland's Rural College
Country United Kingdom 
Sector Academic/University 
PI Contribution We have collaborated with Rainer Roehe at SRUC since 2011, and we provide expertise in genomics, DNA sequencing, metagenomics and bioinformatics. We use this to investigate the role of the microbiome in methane emissions and feed conversion ratio.
Collaborator Contribution The SRUC partners provide expertise in rumen biology and function, alongside samples collected and measured for methane emissions and feed conversion ratio
Impact • Rumen metagenomics: we have sequenced the rumen metagenome of 8 cattle selected for high- and low- methane emissions, matched for breed and diet; and we have demonstrated that high methane emitters are enriched for (i) methanogenic Archaea and (ii) enzymes involved in the methane production pathway. Of the latter, we show that there exists over 5000 novel versions of known enzymes involved in methane production. We have made available a database of over 1.9 million proteins, the majority of them novel, as part of this study (10.1186/s12864-015-2032-0) • Host control of the microbiome: using the same dataset, we demonstrate that largely speaking the rumen microbiome structure and function if under genetic control; and can be significantly associated with both methane emissions and feed-conversion-ratio (FCR) (journal.pgen.1005846) • We have subsequently sequenced over 300 Scottish cattle rumens as part of a project funded by BBSRC. These ruminant metagenomes have resulted in the assembly and publication of several hundred novel rumen microbial genomes (10.1101/162578), publication of a novel pipeline for annotating such genomes (10.1101/233544), publication of robust methane markers in across multiple breeds (10.3389/fmicb.2017.02642) and associations between diet, rumen microbes and anti-microbial resistance (10.1186/s40168-017-0378-z)
Start Year 2011
 
Description SRUC: genetic and environmental dissection of behavioural traits 
Organisation Scotland's Rural College
Country United Kingdom 
Sector Academic/University 
PI Contribution We are managing a study of genetic and non-genetic factors associated with behaviour in dogs, incorporating data collection, analysis and interpretation. Funded by the Dogs Trust, we are employing a postdoctoral researcher to carry out the research.
Collaborator Contribution They provide expertise in animal behaviour and are collaborating on data collection, analysis and interpretation.
Impact Several publications have resulted from this collaboration and further funding has been secured. This multi-disciplinary collaboration involves genetics and animal behaviour.
Start Year 2012
 
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 Strategic research partnership with WorldFish 
Organisation Worldfish
Country Malaysia 
Sector Charity/Non Profit 
PI Contribution A strategic research partnership has been established between Roslin and WorldFish. This partnership is initially focussed on use of advanced genetic and genomic technology to improve selective breeding of tilapia - one of the world's most important foodfish. Our contribution has included development of a research programme that builds on research performed in Atlantic salmon to inform strategies and techniques to implement genomic selection in WorldFish tilapia breeding programme.
Collaborator Contribution WorldFish run a family based selective breeding programme for tilapia and will provide data and samples from this programme to inform the research.
Impact This is a multidisciplinary partnership involving researchers involved in tilapia health, genetics, molecular biology and bioinformatics.
Start Year 2017
 
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 Universidad de León: signatures of selection in sheep 
Organisation University of Leon
Country Spain 
Sector Academic/University 
PI Contribution We have contributed to the identification of selected regions in domestic sheep from genomic data.
Collaborator Contribution They are carrying out large-scale studies of domestication and selection in domestic sheep.
Impact Two papers have been published on the identification of signatures of selection in domestic sheep. The results of these analyses suggest convergent selection for dairy traits in cattle and sheep and also confirm strong signatures of selection on several genes associated with carcass composition and growth.
Start Year 2012
 
Description Universidade Federal de Minas Gerais, Pampulha - Belo Horizonte 
Organisation Federal University of Minas Gerais
Department Department Of Animal Science
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 REACTA: Regional Heritability Advanced Complex Trait Analysis 
Description Developed under a collaboration between EPCC and The Roslin Institute, Regional Heritability Advanced Complex Trait Analysis (REACTA) is a modified version of GCTA with improved computational performance, support for Graphics Processing Units (GPUs), and additional features. REACTA was formerly known as ACTA. The purpose of REACTA is to quantify the contribution of genetic variation to phenotypic variation for complex traits. 
Type Of Technology Software 
Year Produced 2012 
Open Source License? Yes  
Impact Two associated publications to date. Used for analyses of the genetics of complex traits 
URL http://www.epcc.ed.ac.uk/projects-portfolio/reacta#
 
Title resSpecies 
Description Database and associated web interface to handle pedigree populations, genotypes and phenotypes for genetic linkage mapping and quantitative trait linkage mapping studies. System checks inheritance of markers and formats/reformats data in readiness for import into common analysis programs. 
Type Of Technology Webtool/Application 
Year Produced 2008 
Impact Non computer-literate scientists can manipulate data - error free - within minutes rather than days 
URL http://www.resspecies.org/
 
Description Improving egg quality; win - win traits 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Industry/Business
Results and Impact Presentation to breeders and geneticists from main breeding companies . X European Symposium on Poultry Genetics
Year(s) Of Engagement Activity 2017
URL http://www.wpsa.com/index.php/publications/wpsa-proceedings/2017/x-european-symposium-on-poultry-gen...
 
Description Aviagen / CP workshop 
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 I presented our work on functional microbiome analysis during a one-day workshop which I set up and organised at The Roslin Institute. In attendance were employees of CP (a large Asian conglomerate) and Aviagen (one of the world's largest chicken breeding companies). The focus of the workshop was animal genetics and microbiome.
Year(s) Of Engagement Activity 2010,2017
 
Description BUAS Schools Countryside Day 
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 Primary 5 children and teachers from the entire Scottish Borders region. Ran activities around the cuticle and its importance.
Year(s) Of Engagement Activity 2017
URL http://www.buas.org/calendar/buas_schools_countryside_day_23_may_17.html
 
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 CUTE EGG: PROVIDING A SAFE SUPPLY OF EGGS TO HATCH THE NEXT GENERATION OF CHICKENS 
Form Of Engagement Activity A magazine, newsletter or online publication
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Industry/Business
Results and Impact Article on Cute egg featured in LOHMANN TIERZUCHT "Poultry News". Reaches huge number of farmers across the world
Year(s) Of Engagement Activity 2017
URL http://www.ltz.de/de-wAssets/docs/poultry-news/2017/Poultry-News-02-2017.pdf
 
Description CUTICLE DEPOSITION DOES NOT AFFECT WATER VAPOUR CONDUCTANCE AND CAN BE MEASURED IN HATCHING EGGS WITHOUT COMPROMISING EMBRYO DEVELOPMENT 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Industry/Business
Results and Impact Presentation to specialists in egg science, breeders and state veterinarians, an industry Science meeting. XVIIth European Symposium on the Quality of Eggs and Egg Products, XXIIIth European Symposium on the Quality of Poultry Meat. Increases awareness across Europe of applications in poultry science.
Year(s) Of Engagement Activity 2017
URL http://www.wpsa.com/index.php/publications/wpsa-proceedings/2017/xxiii-european-symposium-on-the-qua...
 
Description CUTICLE DEPOSITION ENHANCES THE EGGS NATURAL DEFENCE AND IS A TRAIT WHICH DOES NOT TEND TO DECREASE WITH BIRD AGE 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Industry/Business
Results and Impact Presentation to specialists in egg science, breeders and state veterinarians, an industry Science meeting. XVIIth European Symposium on the Quality of Eggs and Egg Products, XXIIIth European Symposium on the Quality of Poultry Meat. Increases awareness across Europe of applications in poultry science.
Year(s) Of Engagement Activity 2017
URL http://www.wpsa.com/index.php/publications/wpsa-proceedings/2017/xxiii-european-symposium-on-the-qua...
 
Description CUTICLE QUALITY GENETICS IN LAYERS AND BROILERS 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Industry/Business
Results and Impact Presentation to specialists in egg science, breeders and state veterinarians, an industry Science meeting. XVIIth European Symposium on the Quality of Eggs and Egg Products, XXIIIth European Symposium on the Quality of Poultry Meat. Increases awareness across Europe of applications in poultry science.
Year(s) Of Engagement Activity 2017
URL http://www.wpsa.com/index.php/publications/wpsa-proceedings/2017/xxiii-european-symposium-on-the-qua...
 
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 DETECTION AND CHARACTERISATION OF A GENETIC ASSOCIATION WITH NORWICH TERRIER UPPER AIRWAY SYNDROME 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Supporters
Results and Impact Invited to give a talk to the Dogs Trust director and board of trustees. Meeting was attended by peers in the research community whose interests include canine research, genetics, improving animal welfare, and sociology of human-canine relationships.
Year(s) Of Engagement Activity 2017
 
Description Development of New Tools for Genetic Selection for a Sustainable Poultry Industry 
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 Presented a talk: Development of New Tools for Genetic Selection for a Sustainable Poultry Industry (2014), Veterinary Advances in Animal Health and Welfare Research - Impact and Opportunities, Feb 20-24, 2014, NIANP Auditorium, Adugodi, Bangalore, India
Year(s) Of Engagement Activity 2014
 
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 Edinburgh scientists working to create safer eggs 
Form Of Engagement Activity A broadcast e.g. TV/radio/film/podcast (other than news/press)
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Public/other audiences
Results and Impact News coverage of egg cuticle story. 'Cute egg'
Year(s) Of Engagement Activity 2018
URL https://www.bbc.co.uk/news/uk-scotland-edinburgh-east-fife-43605254
 
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 ISAG Conference 2012. Talk: NGS of multiple chicken lines and development of a high-density 600K SNP genotyping array, 16-20 July, Cairns, Australia 2012. 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Presented a talk at ISAG Conference 2012. Talk: NGS of multiple chicken lines and development of a high-density 600K SNP genotyping array, 16-20 July, Cairns, Australia 2012.
Year(s) Of Engagement Activity 2012
 
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 New tools and prospects for chicken genomics 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Talk at Genetics Society of Australia (GSA), July 2015, University of Adelaide, Australia
Year(s) Of Engagement Activity 2015
 
Description Newsletter entries for Self Help Queensland 
Form Of Engagement Activity A magazine, newsletter or online publication
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Public/other audiences
Results and Impact Bimonthly newsletter article under the heading "Genetic Matters" for newsletter distributed to members and organisers of support groups; article is often based on questions to the group and is said to be well received.
Year(s) Of Engagement Activity Pre-2006,2006,2007,2008,
URL http://www.selfhelpqld.org.au/content/newsletters
 
Description Next Generation Sequencing of multiple chicken lines reveals a rich source of Single nucleotide polymorphisms for high resolution genetic studies 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Talk at The 1st International Conference on Genomics in the Americas. Talk: Next Generation Sequencing of multiple chicken lines reveals a rich source of Single nucleotide polymorphisms for high resolution genetic studies, 27-28 Sept, Philadelphia, USA.
Year(s) Of Engagement Activity 2012
 
Description Organised a British Council Researcher Links conference in Mexico 
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 Co-organised a Researcher Links conference about Genomics in Aquaculture in Merida, Mexico in January 2017. This 5 day event featured around 40 scientists, with a mix of young researchers and mentors from both the UK and Mexico. This has already led to several collaborative links between UK and Mexico in this field.
Year(s) Of Engagement Activity 2017
URL https://sites.google.com/site/genomicsinaquaculturemxuk/home
 
Description Past, Present and Future of Genomics in Poultry Breeding. 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Talk: Past, Present and Future of Genomics in Poultry Breeding. 25th World's Poultry Congress, Beijing, 5-9 September, 2016.
Year(s) Of Engagement Activity 2016
 
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 British NeuroEndocrine Group (Glasgow) CCKAR 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Other audiences
Results and Impact Communication with a wide range of non-avian scientists working on appetite
Year(s) Of Engagement Activity 2016
 
Description Presentation at European Poultry Genetics Symposium (Tuusula, Finland) Bone 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Industry/Business
Results and Impact Talk to audience of the majority of Poultry breeders in the world, Interest from breeders and from other scientists in possible application.
Year(s) Of Engagement Activity 2015
URL http://www.epgs2015.com/program.html
 
Description Presentation at IX European Symposium on Poultry Welfare (Uppsala, Sweden) Bone 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Industry/Business
Results and Impact Talk on our work to generate markers which improve bone strength to improve welfare. Much interest has resulted from groups working in this field in Europe
Year(s) Of Engagement Activity 2013
URL http://www.research.ed.ac.uk/portal/en/publications/genetic-markers-for-the-improvement-of-bone-stre...
 
Description Presentation at International Symposium Avian Endocrinology (Niagara on the Lake) CCKAR 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Other audiences
Results and Impact Communication beyond poultry to wild bird and ecological researchers
Year(s) Of Engagement Activity 2016
URL http://www.isae2016.ca/
 
Description Presentation at International Symposium Avian Endocrinology (Niagara on the Lake) MSH 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Other audiences
Results and Impact Communication beyond poultry to wild bird and ecological researchers
Year(s) Of Engagement Activity 2016
URL http://www.isae2016.ca/
 
Description Presentation at International Symposium Avian Endocrinology (Niagara on the Lake) Sex 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Other audiences
Results and Impact Communication beyond poultry to wild bird and ecological researchers
Year(s) Of Engagement Activity 2016
URL http://www.isae2016.ca/
 
Description Presentation at World Poultry Congress (Beijing) Incubation behaviour 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Largest Poultry science conference >4000 people. 50% industry Interest engendered from researchers.
Year(s) Of Engagement Activity 2016
URL http://www.wpc2016.cn/uploadfiles/2016-9/The%20Proceedings%20of%20WPC2016-Abstracts-20160920.pdf
 
Description Presentation at World Poultry Science UK spring meeting (Chester) Bone 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Industry/Business
Results and Impact Identification of genetic markers for the improvement of bone strength in poultry

Interst from industry and welfare organisations
Year(s) Of Engagement Activity 2016
 
Description Presentation at World Poultry Science UK spring meeting (Chester) CCKAR 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Industry/Business
Results and Impact A logical approach to understanding physiological mechanisms underpinning growth efficiency in broilers explained by a single selected genetic locus

Presentation of effect of the CCKAR locus, interest from industry and how it might be used.
Year(s) Of Engagement Activity 2016
 
Description Presentation on research to Pastoral Breeds Health Foundation 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Study participants or study members
Results and Impact Presented a talk about our research into genetics of glaucoma in the Border Collie. This was to inform people who had donated samples for DNA extraction from their dogs, and to update on progress towards a genetic test. This was followed by extensive questions and answers and continued engagement of dog owners and breeders in our project. It also led to an invitation to speak with the British Veterinary Association Eye Panel.
Year(s) Of Engagement Activity 2017
 
Description Presentation to British Veterinary Association Eye Panel 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact Made a presentation of recent research into the genetics of glaucoma in the Border Collie to veterinary ophthalmologists, Kennel Club and Animal Health Trust. Extensive debate about the results afterwards, with greater understanding of the genetics by the audience and elucidation of the clinical situation by the professionals, which was helpful in further interpretation of the results.
Year(s) Of Engagement Activity 2017
 
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 Production Animal Health and Welfare Research: Impacts and Opportunities. 
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 Talk at Production Animal Health and Welfare Research: Impacts and Opportunities. 19-20 Feb, 2015, Indian Council for Agricultural Research (ICAR), New Delhi, India
Year(s) Of Engagement Activity 2015
 
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 Saving the British Bulldog 
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 I was interviewed to provide expert opinion of the health challenges facing the British bulldog. Topic ranged from morphology, genetics, disease, and welfare. At the time submitting this report, the episode has not been released (scheduled to do so March 2018). I am unaware of a public impact just yet.
Year(s) Of Engagement Activity 2017
 
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 Structural aspects of genomes across species 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Presented a talk at The 8th European Poultry Genetics Symposium. Talk: Structural aspects of genomes across species. 25-27 Sept, Venice Italy, 2013.
Year(s) Of Engagement Activity 2013
 
Description Teaching Animal Body 1 Lectures (R(D)SVS) on Cell and Molecular Biology 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Undergraduate students
Results and Impact Starting in 2016 I give lecturers and administer exams to first year veterinary medicine students. Classes size is approximately 110 students. The topics I cover include cell and molecular biology and I incorporate medically relevant examples of genetic conditions that affect livestock and companion animals.
Year(s) Of Engagement Activity 2016,2017
 
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...
 
Description The chicken genome 10 years on. 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Keynote lecture: chicken genome - 10 years on. Avian Model Systems - the 8th International Meeting, Cold Spring Harbour, USA, 4-8th March, 2014.

CSHL Leading Strand - Keynote Lecture Series (http://theleadingstrand.cshl.edu/Course/Keynote/2014/AVIAN/150

The chicken genome 10 years on - BBSRC (http://www.bbsrc.ac.uk/news/events/1403-chicken-genome.aspx)
Year(s) Of Engagement Activity 2014
 
Description Tissue distribution and dynamic regulation of chicken peptide YY (PYY) 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact 18th International Congress of Comparative Endocrinology , Communication of work by PhD student which as will be apparent from the URL was a great learning and confidence building experience
Year(s) Of Engagement Activity 2017
URL https://goabroadfund.wordpress.com/2017/10/23/18th-international-congress-of-comparative-endocrinolo...
 
Description Visit of Bill Gates 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Policymakers/politicians
Results and Impact Bill Gates and Penny Mordaunt visited the Easter Bush campus to open the new Global Academy for Food Security. At that event, I presented our work on african farm animal genomes and programme 5 of the CTLGH.
Year(s) Of Engagement Activity 2018
URL https://www.gov.uk/government/speeches/penny-mordaunt-speech-at-edinburgh-university-with-bill-gates