Complex phenotypes and genotype x environment interactions

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

Abstract

This project will examine how the genotype of animals relates to their performance in different environments, for example in relation to behaviour, reproductive efficiency and offspring performance. Such studies will help to ensure that gains in production-relevant traits do not come at the expense of welfare and waste due to reproductive problems. The project also recognises that the attributes of farmed animals are partly determined by their microbiota, particularly in relation to gut health, energy retention and greenhouse gas emissions. Interactions between host genetics and microbiota composition and functions will be dissected. This project aims to enhance efficiency and animal lives.

Organisations

Publications

10 25 50

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Ashworth CJ (2017) Preface. in Molecular reproduction and development

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Auler PA (2017) Testicular parameters and spermatogenesis in different birthweight boars. in Reproduction, fertility, and development

 
Title Exhibition The Pig Park and Other Experiments. The Museum of English Rural Life (MERL) 
Description Film, newspaper and exhibition. The Pig Park and Other Experiments is now open at the Museum of English Rural Life (MERL) and our newspaper and film are on show as part of the exhibition: https://merl.reading.ac.uk/event/the-pig-park/ and https://media.ed.ac.uk/media/Carnevale+/0_p0iqoasy. 
Type Of Art Artistic/Creative Exhibition 
Year Produced 2018 
Impact Public exhibition to raise awareness of positive welfare in pigs. 
URL https://merl.reading.ac.uk/event/the-pig-park/
 
Description Genetic and environmental control of temperament:
• Ecological niche modelling has been used to detect climatic adaptation in Ethiopian chickens. Twenty- five populations of chickens from different regions of Ethiopia have been used to develop a suitability model to describe regions/environments where each breed will thrive. This method could be developed to become applicable to all livestock.
• We used video imaging of social interactions to examine the impact of environmental enrichment (EE) on pig welfare and showed that locomotor play is a sensitive welfare indicator that can be measured automatically. Play behaviour differed between litters, developmental stages (weaning) and when piglets were raised in a free farrowing system, and we are applying for uplift funding to implement remote image analysis in a commercial setting. Social network analysis of the impact of mixing of neonatal pigs on skin lesions, also identified behaviours that contribute to prolonged social instability and aggression.
• In response to EE stimuli, we established that insulin-like growth factor 1 (IGF-1) is markedly upregulated in the brain of neonatal pigs and have since applied RNA sequencing to examine gene expression differences in the frontal cortex linked to active behaviours stimulated by EE, with upregulation of genes involved in synaptic transmission and down-regulation of microglial associated genes during EE.
• With a £58K grant from the University Wellcome Trust Institutional Strategic Support Fund ongoing work is defining the effects of early-rearing environments on neuroinflammation and microglia. Such work will benefit from the availability of novel surgical and neuroimaging modalities of the Large Animal Research & Imaging Facility under construction at Roslin funded by Innovate UK and the University.
• We have shown that stomach ulcers mostly likely caused by fine grinding of feed to increase efficiency are related to behavioural changes which could indicate that gastric ulcers in pigs are painful.
• We have published work suggesting that empathy to animals could affect human-animal interactions is associated with genetic variation on the oxytocin receptor gene.
• We have recently submitted for publication a study showing for the first time that rats can learn to associate odours with playful handling (tickling) by humans (Bombail et al 2019).

The broiler breeder paradox:

• Broiler chickens are feed restricted to control health issues but show behavioural signs of hunger. To understand the basis of satiety and energy homeostasis in broilers, we analysed cholecystokinin (CCK) and gastrin (GAST) transcripts and found that while CCK expression does not respond to acute satiety state, GAST is upregulated under short-term fasting.
• We also analysed the expression of PP-fold peptides in chickens and showed that pancreatic polypeptide is the primary peripheral short-term satiety hormone whereas peptide YY is dependent on longer-term energy state.
• We found sex differences in anorectic and orexigenic gene expression under feed restriction. In an effort to understand the control of food intake we have increased the evidence that there is a strong and potentially causal relationship between the expression of AGRP in the brain and the growth potential of a chicken. We have carried out sex reversal experiments that worked extremely well, with clear phenotypic effects on traits known to be sex steroid dependent such as adult bone strength. It however did not affect the sexual dimorphism of expression of AGRP in the hypothalamus. Suggesting that the sex difference is due to genetic sex and not the hormonal milieu of the animal. The sex difference observations have been extended down the hypothalamo-pituitary axis by measuring GH and TSHb expression, both of which showed strong sexual dimorphism.
• The AGRP neurone may be an important component in the genetic mechanism by which a set point for growth rate and ultimately body weight may be determined, although the genetic effect is not directly on the AGRP gene but rather on the inputs which determine its expression. These can be modified by environment as well as genetics.

Seasonal breeding & maternal behaviour:

• Photoperiodic behaviour underpins the timing of reproduction and breeding success and artificial light is commonly used in chicken production and response to light is an important commercial trait. We have discovered that deep brain rhodopsin photoreceptors maintain gonadal function in ducks.
• We also made the surprising discovery that photoperiod-driven increases in thyroid stimulating hormone (TSHb) show large diurnal variation in the chicken pars tuberalis. Increased TSHb is assumed to be an early step in the neuroendocrine mechanism transducing photoperiodic information to the reproductive axis. TSHbeta expression cycles daily, whether the chicken is photostimulated or not.
• In domesticated chickens the region of the genome containing TSHR and DIO2 and DIO3 has been under intense selection and a genetic association at the locus was observed in a study on incubation behaviour and persistency. Therefore, there may be a link between the locus, photoperiod and reproduction that may have increased fecundity during domestication. The expression of TSHbeta in the pars tuberalis may have an important role beyond the ones currently known in the control of avian reproduction which merit further investigation.
• The neuropeptides oxytocin and vasopressin are important regulators of mammalian social behaviour; playing a crucial role in the onset and maintenance of maternal behaviour. Mesotocin, and the related nonapeptide vasotocin, are synthesized in specific regions of the avian brain including those areas of the neural social network. Our research has demonstrated a role for mesotocin during the expression of chicken broodiness and maternal behaviour. Mesotocin mRNA expression increased during chick rearing however vasotocin mRNA increases were only coincident with egg laying and nest building. Together these data suggest that dynamic changes in the nonapeptide systems may explain the display of incubation and broodiness.
Impact of early life experience:
• In rats we found that brain corticotropin-releasing factor receptors that modulate maternal behaviour and anxiety are dampened during lactation (possibly via an oxytocin-mediated pathway) to ensure appropriate maternal behaviour opening the possibility of therapies for stress-induced maternal neglect.
• Sex differences in hypothalamicpituitaryadrenal (HPA) axis activity are well established in rodents. We have discovered the existence of sex and regional differences in the generation of neuroactive steroids in the brain following acute stress. This suggests that differential neurosteroidogenesis may contribute to sex differences in HPA axis responses to stress.
• Using a foetal growth restriction pig model we are establishing how adverse uterine environments affect the function of mesenchymal precursor cells to explain the reduced carcass quality.
• To model the adverse uterine environment, we established a cell culture system that faithfully recapitulates the reduced muscle/increased adipose phenotype in pig foetal-growth restricted (FGR) littermates. Using RNA sequencing and genetic loss-of-function approaches we have identified genome-wide transcriptome changes associated with FGR in pigs. We have identified the FGF21 receptor, KLB, as a key regulator of adiposity in FGR tissues. We have shown that mesenchymal stem cells from FGR littermates have increased adipogenic capacity but decreased chondrogenic and osteogenic capacities in vitro. In separate studies in cattle we have shown that blood miRNA levels early in life are correlated with later productivity and disease incidence providing an opportunity to use this to improve animal selection and productivity.

Host-microbiome interactions:

• We have developed a non-invasive method to obtain respiratory microbiome data using exhaled breath condensate in sheep, but cautioned that differences from lung microbiota exist. In contrast to humans, we found that the lower respiratory tract microbiota of lambs is dissimilar to that of the upper aerodigestive tract. These baseline data inform ongoing strategically-funded research to understand seasonal outbreaks of respiratory disease in ruminants.
• In chickens we discovered age- and location-specific differences in the respiratory tract microbiome, and ongoing industry-linked work is revealing associations between gut microbiota and broiler phenotypes, including gut health and growth.
• The composition of the commensal microbiota can have a significant influence on the development and function of the microglia in the rodent CNS. Despite this, we have shown that the development of prion disease pathogenesis, neuropathology and microglial activation is not affected in germ-free mice. Aged mice have a significant reduction in antigen-sampling M cells in the epithelia overlying their Peyer's patches. We have shown that the transfer of a young gut microbiota to aged mice can increase the abundance and function of the M cells in the aged recipients. This implies that aging related changes to the gut microbiota can influence the development and function of the gut epithelium.
Advances in understanding of the rumen microbiome.
• The rumen is critical for digestion of plant material to provide energy and nutrients, a process reliant on enzymes encoded by the rumen microbiota and linked to methane emission. While metagenome sequence data for the rumen have been available for some time, fewer than 10% of sequence reads could previously be classified to known taxonomic units.
• Funding from this award supported the generation and analysis of 800 Gb of rumen metagenome data from Scottish cattle. By using Hi-C-based proximity-guided assembly and metagenomics binning strategies, we were able to assemble 913 draft bacterial and archeal genomes, most representing previously unsequenced strains and species. The study enables c. 50% of metagenome sequence reads to be classified to known organisms,
• We have expanded our previous work on the rumen of Scottish cattle, and have now assembled 4941 novel strains of bacteria and archaea from the rumen of 282 cattle raised in Scotland, from four popular beef breeds. These genomes now represent the most comprehensive set of rumen microbial data assembled to date. There are several key findings from the work: the genomes represent 4941 novel strains and 2000 novel species of bacteria and archaea; we reveal the first near-complete genome of a novel lineage of Proteobacteria; we assemble the first fully circularised bacterial chromosomes from a complex metagenomic sample, using long read nanopore sequencing; we published a novel method for assessing how many indels remain in genomic and metagenomic assembly of nanopore data; and we released a novel protein dataset consisting of over 11 million novel rumen proteins that can be used in future proteomic studies.
• The published draft genomes encode >69k proteins predicted to be involved in carbohydrate metabolism, over 90% of which are novel. This provides a powerful resource for industrial biotechnology and further primes our collaborative research with Ingenza to find novel hydrolases for biofuel production.
• In addition to datasets, we published MAGpy, an open source pipeline for the analysis of metagenome-assembled genomes, and PULpy, a pipeline for the prediction of polysaccharide utilisation loci in bacterial and metagenomic datasets to mine novel enzymes. We anticipate that our metagenomic approaches will be applied to other key farm animal species during the programme to drive similar improvements in read classification and identify microbiome and metagenome signatures that contribute to production-relevant phenotypes.
Exploitation Route • Positive Welfare
IIn terms of our play work we now believe that locomotor play would be a sensitive welfare indicator and one that could potentially be measured automatically, hence being a target for remote monitoring technology. Our work on enrichment and growth factors has led us to further investigations of brain effects of enrichment. We currently and we have a BBSRC grant under review on the effects of enrichment on brain health with a focus on microglia. this. In our social science work we are now extending our studies to explore wider perspectives on the concept of positive welfare to better understand how we might promote the concept in practice. We have published 2 briefings on this and are talking to stakeholders interested in expanding the concept of positive welfare in the food chain.
• The broiler breeder paradox:
Understanding the basis of avian satiety and control of food intake is required to devise and assess strategies for feeding broiler breeders. The results obtained are a step towards that and we are studying these factors in experiments with alternative feeding strategies.
• Seasonal breeding and maternal behaviour:
For the TSH beta expression results a much larger study examining the diurnal cycle and how it can be influenced by diet and other environmental factors including entrainment by light may lead to a better understanding of the way reproduction is controlled, if at all by the expression of TSH beta in the pars tuberalis. This will require a grant but has potentially important consequences for the way environmental signals are integrated and ultimately result in successful reproduction.
• Bone Quality Traits: The results on the one of the genetic loci we have characterised underlying bone quality traits in laying hens has led to a hypothesis on nutritional interventions to improve bone quality in laying hens. This is being tested with a feed additive company and the response of different genotypes will be evaluated.
• Sexual Dimorphism in the neural feeding centre: These results on sexual dimorphism in the feeding centre will be a useful starting point for investigating further if AGRP expression is an indicator of growth potential. Understanding the growth potential of a bird could have important applications in the meat industry especially for meat production with chicken meat and eggs providing at least a third of the world's animal protein. This is also of great interest in humans particularly in the context of overconsumption and obesity.

• Impact of Early life experience:
The identification of regulatory mechanism involving oxytocin which may serve to counteract the effects of CRF receptor activation, thereby ensuring stable levels of maternal behaviour. This mechanism might be disturbed in mothers showing stress-induced maternal neglect and represents a potential target for treating such malfunctions in the postpartum period.
• Complex Phenotypes:
By deriving physical information from computed tomography, we provide a paradigm of using biomedical imaging for population genetics studies of complex traits.
• Adverse Uterine Environment:
Our findings could significantly facilitate the study of important production traits in livestock as well as novel strategies to ameliorate the effects that foetal growth restriction currently has on the efficiency of meat production as well as on human health, particularly in developing countries
• Sex Determination:
Our greater understanding of the fundamental differences between male and female birds relating to the mechanism of sex determination in birds, will inform approaches to manipulating sex ratios in production chickens. This knowledge will also inform the development of treatments for diseases, for example, due to innate differences in responses of male and female birds. The development of a method for in ovo sexing of chickens may form the basis of a method to sex chickens before hatch.
• Genetic and non-genetic factors associated with behavioural characteristics in dogs:
Results from this study suggest extension to other dog breeds and mixed-breed dogs and further characterisation of the genomic regions identified as being associated with behavioural traits.
• Host-Microbiome interactions:
We believe the 913 genomes we have published from the rumen microbiome will form the basis of hundreds of future studies into the structure and function of the rumen microbiome and how it contributes to beef and dairy production, and animal health and welfare. Our robust methane markers may be used as an intermediary phenotype in selective breeding for lower methane cattle Our AMR work may be used to adjust diets in cattle to help reduce the incidence of anti-microbial resistance genes in the human food chain. Our software could be used by scientists throughout the biological sciences who wish to discover and annotate novel microbial genomes. Impact might include development of probiotics based on beneficial microbial species.
• Lung Microbiome
These studies provide a set of baseline data for these species and describe protocols that can be used to measure that may be useful to others in the field.
Sectors Agriculture, Food and Drink,Education,Environment,Other

URL https://www.ed.ac.uk/roslin/research/isp/improving-animal-production-welfare
 
Description Research conducted under this programme involves significant collaboration with commercial partners to drive genetic gain in their breeding programmes. Commercial partners include Aviagen, PIC, KWS and Monsanto; they visited the Roslin Institute in Spring 2018 to discuss implementation of specific software packages and/or pipelines within their routine breeding programs. The award benefits from strategic platform agreements with Genus (pigs & cattle), Cobb (poultry), WorldFish and Hendrix Genetics (fish) that provide direct funding and access to phenotyped populations and expertise in-kind. Such companies benefit from genomic tools and expertise sustained by this award. We expect such links to grow via the nascent Agri-Tech Centres in which we are key partners (CIEL & Agri-EPI) and following the establishment of Roslin Technologies Ltd and the opening of the Roslin Innovation Centre. • The awards is a platform from which we can attract significant uplift funding. For example xpertise supported by this award and the Core Capability Grant to Roslin were key to securing HM Government funding for data-driven innovation in agriculture as part of the Edinburgh & SE Scotland City Region Deal. This will involve capital investment in world-class data infrastructure and sequencing capacity. • Researchers funded by the programme contribute to our Centre for Tropical Livestock Genetics and Health (CTLGH) to improve the productivity and health of livestock in sub-Saharan Africa by developing and applying the latest genetic and genomics technologies to indigenous breeds, in particular to the benefit of smallholder dairy and poultry farmers. The impact and importance of studying tropical livestock genomes in low and middle income countries is huge and this is recognised by our recently awarded Global Challenges Research Fund Impact Acceleration Accounts (GCRF-IAA) and £4 million Department for International Development (DFID) uplift funding. Such awards provide flexible funding to develop strategies to add value to existing BBSRC investments and generate a wide range of outputs, outcomes and impacts in an international development context. CTLGH is a joint venture launched by the Roslin Institute, Scotland's Rural College (SRUC) and CGIAR - International Livestock Research Institute (ILRI) with two main nodes, one in Edinburgh and one in Nairobi. This award also promotes extensive knowledge exchange with African researchers, primed by a GCRF-STARS award to train early-career researchers from LMICs at Roslin. Moreover, staff funded by the award have visited ILRI to train laboratory staff, for example in bioinformatics, PGC culture and genome editing strategies. The CTLGH has forged close links with the ministries of agriculture in LMIC partner countries to ensure that strategies for achieving genetic gain align with national agricultural development plans. Positive Welfare: Our on-farm assessment of pig welfare, particularly positive welfare, is an important marker for the monitoring of real welfare impacts of any changes in husbandry systems. We have published a book chapter on Positive Welfare in Pigs: https://www.elsevier.com/books/advances-in-pig-welfare/spinka/978-0-08-101012-9 and a chapter on Sustainable Pig Production: https://www.ciwf.org.uk/news/2017/08/the-meat-crisis. We have also presented our work on pig welfare to public audiences: https://www.ed.ac.uk/roslin/news-events/latest-news/animal-welfare-on-easter-bush-campus. The exhibition The Pig Park and Other Experiments is now open at the Museum of English Rural Life (MERL) and a newspaper and film related to environmental enrichment for pigs are on show as part of the exhibition: https://merl.reading.ac.uk/event/the-pig-park/ and https://media.ed.ac.uk/media/Carnevale+/0_p0iqoasy. We have also received acknowledgement of our work from international societies: https://www.ed.ac.uk/roslin/news-events/latest-news/award-professor-animal-behaviour which has been noted by Scottish Government: http://www.parliament.scot/parliamentarybusiness/28877.aspx?SearchType=AdvanceRferenceNumbers=S5M-07396RsultsPerPage=10 and published in the Veterinary record http://veterinaryrecord.bmj.com/content/182/10/275.2.info • Sex Determination: Male meat poultry have a greater food conversion efficiency than female meat birds and are approximately 33% heavier at the time of marketing. A number of commercial enterprises and academic researchers have attempted to increase meat production from female birds by sex-reversing these birds. These efforts have focused on adjusting the hormonal profiles of the birds either by the direct administration of hormones, or by altering the developmental fate of the gonads. To date, these efforts have been unsuccessful. Our findings that the sexual phenotype is cell autonomous should permanently curtail such efforts in endocrine modulation and guide the search for sex determination mechanism to a focus on intracellular factors. We have completed development of an in-ovo sexing assay to determine the sex of chicks before hatch that fully meets the timing and cost requirements of the poultry industry to remove eggs of the unwanted sex before hatch. This assay can identify the sex of chick embryos from nanolitre volumes of whole blood in under five minutes. The assay is currently being tested by industrial partners under commercial production conditions. If this assay can be successfully applied, this procedure will lead to increases in food production and will address a significant poultry welfare issue, the culling of unwanted chicks (mainly males in egg production lines) post-hatch. • Microbiome: Funding from this award has substantially advanced our understanding of the role of microbiomes in health and disease. In particular, our development of tools to assemble whole microbial genomes from rumen metagenome sequence data has transformed our understanding of the microbes present. In turn, these assembled genomes mean that sequence data from microbiome experiments can now be mapped to many more known organisms than before. This is helping us to dissect the basis of greenhouse gas emissions, the mode of action of antibiotic growth promoters and impact of host genetic variation on microbiota, with the longer term aim of rationally manipulating the microbiome. We are also partnered with a biotechnology company to mine the data for enzymes of industrial value and have developed online resources to share microbiome data: https://datashare.is.ed.ac.uk/handle/10283/3009. • The award perpetuates a cadre of highly-skilled research technicians at Roslin with skills required to deliver strategic priorities in Agriculture & Food Security that are not readily recruited. • The award provides a platform to train the next-generation of researchers, with doctoral candidates, MRes students, undergraduate honours students and visitors all attracted to work toward programme objectives. Students are provided training in vulnerable skills and capacities identified in a cross-Council review such as: 1. those required to address global challenges 2.Sophisticated analysis and interpretation of the complex data generated by genomics, proteomics, and metabolomics 3. data analytics, especially bioinformatics 4. skills to work with whole animals and in vivo work and with an holistic understanding of the physiology of laboratory and farmed animals 5. Classical neurophysiological methods 6. Systems biology, particularly the development of integrated optical, electrophysiological, computational, molecular and behavioural approaches to study complex systems in vivo.
First Year Of Impact 2017
Sector Agriculture, Food and Drink,Government, Democracy and Justice
Impact Types Societal,Economic,Policy & public services

 
Description Alistair Lawrence sits on the Coordinating Group of the BBSRC Animal Welfare Research Network
Geographic Reach National 
Policy Influence Type Membership of a guideline committee
URL https://awrn.co.uk/about-us/co-ordinating-group/
 
Description Contribution to Godfray Review of bTB
Geographic Reach National 
Policy Influence Type Gave evidence to a government review
Impact The improved survival is for CATTLE. The publication of EBVs for resistance to bTB (TB Advantage) has prompted selection for resistance by breeding companies, which is incremental, cumulative and permanent and will lead to reduced numbers of breakdowns, reduced severity of breakdowns, will improve the capacity of UK surveillance (a public service) to suppress the current epidemic and offer a route that is not associated with culling badgers which may contribute to softening the societal divide on this issue. The Godfray Review concluded that genetic approaches should be supported and may be expected to contribute to a solution with impact on a par with badger culling.
URL https://www.gov.uk/government/publications/a-strategy-for-achieving-bovine-tuberculosis-free-status-...
 
Description Core Member BBSRC Panel A Response Mode
Geographic Reach National 
Policy Influence Type Membership of a guideline committee
 
Description Deputy Chair BBSRC Response Mode Panel A
Geographic Reach National 
Policy Influence Type Participation in a advisory committee
 
Description EBVs for bTB Next Steps
Geographic Reach Europe 
Policy Influence Type Membership of a guideline committee
Impact The improved survival is for CATTLE. The publication of EBVs for resistance to bTB (TB Advantage) has prompted selection for resistance by breeding companies, which is incremental, cumulative and permanent and will lead to reduced numbers of breakdowns, reduced severity of breakdowns, will improve the capacity of UK surveillance (a public service) to suppress the current epidemic and offer a route that is not associated with culling badgers which may contribute to softening teh societal divide on this issue. The guidance committee is an annual meeting with Defra, devolved bodies and AHDB (industry levy board) to monitor progress with TB Advantage and review future actions. It is Europe wide as gene flow and genetic information on genetics of bTB is closely involved with RoI, and the meeting was in RoI with their agriculture ministry participating.
URL https://www.gov.uk/government/publications/a-strategy-for-achieving-bovine-tuberculosis-free-status-...
 
Description IAIEA-FAO consultancy
Geographic Reach Multiple continents/international 
Policy Influence Type Participation in a advisory committee
 
Description Member of Knowledge Transfer Network Animal Sector Advisory Board
Geographic Reach National 
Policy Influence Type Membership of a guideline committee
URL https://ktn-uk.co.uk/
 
Description Positive farm animal welfare: Something in it for everyone. Policy Briefing on Positive Welfare which has been approved by Scottish Government (RPC RB 2018/01)
Geographic Reach National 
Policy Influence Type Gave evidence to a government review
Impact This briefing paper introduces positive animal welfare and its potential benefits to farmers, retailers, consumers and wider society. It is based on a review of positive welfare, its benefits to animals and its reciprocal human benefits that could help promote positive welfare in practice. ? There are a number of reasons why the idea of positive animal welfare has emerged at this time. For example, people in general are interested in positive aspects of animals' lives in contrast to negative aspects such as animal suffering. This is in line with growing scientific acceptance of animals experiencing positive experiences or emotions. ? Therefore, positive farm animal welfare is in sympathy with public opinion and is supported by science. However for positive welfare to become more central to the production and sale of animal products will require demonstration that it is also of benefit to farmers and retailers. ? The following are examples of potential benefits from positive welfare for suppliers and consumers of animal products: o A focus on positive welfare can produce a distinctive differentiated product that takes standards of animal welfare to higher levels that may not be achievable if the focus is on reducing negative aspects. o There is growing evidence that keeping animals in conditions which promote positive welfare may have benefits to their physical health. o We can use behaviours linked to positive welfare, such as play and grooming behaviour, to provide early indication of production problems. o There is potential to use positive welfare to actively engage with public interests in positive aspects of animals' lives and hence to move consumer sentiment in favour of supporting implementation of positive welfare even where this increases costs. ? In summary positive animal welfare has potential to have multiple benefits for farm animals, farmers and the wider public but further research and practical initiatives will be required to realise this potential.
URL https://www.sruc.ac.uk/downloads/file/3608/positive_farm_animal_welfare_something_in_it_for_everyone
 
Description WPSA European Federation Working Group - WG3 Breeding and Genetics
Geographic Reach Europe 
Policy Influence Type Membership of a guideline committee
URL http://www.wpsa.com/index.php/breeding-and-genetics-wg-3
 
Description World health Organisation global zoonotic tuberculosis road map
Geographic Reach Multiple continents/international 
Policy Influence Type Implementation circular/rapid advice/letter to e.g. Ministry of Health
URL http://www.who.int/tb/publications/2017/zoonotic_TB/en/
 
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 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 CONICYT becas Chile
Amount £179,600 (GBP)
Organisation Government of Chile 
Sector Public
Country Chile
Start 01/2017 
End 12/2021
 
Description CONICYT training grants
Amount £179,600 (GBP)
Organisation National Commission for Scientific and Technological Research (CONICYT) 
Sector Public
Country Chile
Start 01/2017 
End 12/2020
 
Description Center for Tropical Livestock Genetics and Health: Genomic tools to improve the productivity, efficiency, resilience, and health of tropical livestock owned by poor smallholder farmers
Amount £4,541,800 (GBP)
Funding ID R83411 
Organisation Government of the UK 
Department Department for International Development (DfID)
Sector Public
Country United Kingdom
Start 10/2015 
End 09/2020
 
Description Dogs Trust Welfare Grant
Amount £55,092 (GBP)
Organisation Dogs Trust 
Sector Charity/Non Profit
Country Unknown
Start 04/2019 
End 03/2020
 
Description EBI Metagenomics - enabling the reconstruction of microbial populations
Amount £112,997 (GBP)
Funding ID BB/R015023/1 
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 09/2018 
End 09/2021
 
Description European Commission H2020 SMARTER: SMAll RuminanTs breeding for Efficiency and Resilience
Amount € 7,000,000 (EUR)
Funding ID 772787 
Organisation European Union 
Sector Public
Country European Union (EU)
Start 11/2018 
End 10/2022
 
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 2
Amount £220,000 (GBP)
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 10/2017 
End 07/2018
 
Description GCRF-BBR: Beyond the genome: Enabling tropical livestock EWAS of infectious diseases
Amount £60,333 (GBP)
Funding ID BB/P024025/1 
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 07/2017 
End 06/2018
 
Description INSPIRE Small Grants Round 4
Amount £10,000 (GBP)
Organisation Academy of Medical Sciences (AMS) 
Sector Charity/Non Profit
Country United Kingdom
Start 10/2018 
End 10/2019
 
Description Identification of the photoreceptor for light detection in the avian brain
Amount £246,909 (GBP)
Funding ID RPG-2016-392 
Organisation The Leverhulme Trust 
Sector Academic/University
Country United Kingdom
Start 09/2017 
End 09/2020
 
Description Institutional Strategic Support Fund 3
Amount £57,000 (GBP)
Organisation University of Edinburgh 
Sector Academic/University
Country United Kingdom
Start 06/2018 
End 07/2019
 
Description Sub-award from second BBSRC Flexible Talent Mobility Award (BB/S50791X/1). Dr Simone Meddle & Petersome Ltd. 'Understanding appetite in birds to transform food production: When do chicks become hungry after hatch?'.
Amount £23,258 (GBP)
Funding ID BB/S50791X/1 
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 11/2018 
End 03/2021
 
Description he role of interleukin-10 (IL-10) in the regulation of innate immunity in the domestic chicken.
Amount £1,144,442 (GBP)
Funding ID BB/P022049/1 
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 12/2017 
End 12/2020
 
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 Fetal porcine tissue collection 
Description Collection of an array of porcine fetal tissues at different stages of development 
Type Of Material Biological samples 
Year Produced 2017 
Provided To Others? Yes  
Impact Enable initiation of several new collaborative projects in and outwith the Institute 
 
Title MSC lines 
Description We have for the first time isolated native mesenchymal precursor cell populations from tissues of large animal species (pig, horse). We have characterised and successfully expanded these cells in vitro. 
Type Of Material Cell line 
Year Produced 2017 
Provided To Others? Yes  
Impact These novel cell lines have provided novel knowledge on the properties of different perivascular cell populations. Studies are currently underway in our and other laboratories (using cells provided by us) to understand mechanisms of tissue stem cell programing during fetal development. 
 
Title Assembly of 913 microbial genomes from metagenomic sequencing of the cow rumen 
Description This dataset represents 913 draft bacterial and archaeal genomes assembled from over 800 gigabases of rumen metagenomic sequence data derived from 43 Scottish cattle, using both metagenomic binning and Hi-C-based proximity-guided assembly. Most of these genomes represent previously unsequenced strains and species. The draft genomes contain over 1.2 million predicted protein sequences, and 69,000 proteins predicted to be involved in carbohydrate metabolism. ## Relation to earlier versions ## This data is referenced by Watson et al. (In Submission). A previous paper, in bioRXiv, referenced the earlier dataset "Assembly of hundreds of microbial genomes from the cow rumen reveals novel microbial species encoding enzymes with roles in carbohydrate metabolism" https://datashare.is.ed.ac.uk/handle/10283/2772. This in turn was superseded by the more recent version Hi-C genomes from "Assembly of hundreds of microbial genomes from the cow rumen reveals novel microbial species encoding enzymes with roles in carbohydrate metabolism" https://datashare.is.ed.ac.uk/handle/10283/2911. The paper underwent many rounds of review, the first-round revised paper referenced the second (Hi-C) dataset and the final, accepted version will reference the DOI of this dataset. The datasets changed in nature and in name during this process. 
Type Of Material Database/Collection of data 
Year Produced 2017 
Provided To Others? Yes  
Impact The dataset is expected to underpin global rumen microbiome research in the next 5-10 years 
URL https://datashare.is.ed.ac.uk/handle/10283/3009
 
Title Assembly of hundreds of microbial genomes from the cow rumen reveals novel microbial species encoding enzymes with roles in carbohydrate metabolism 
Description The cow rumen is a specialised organ adapted for the efficient breakdown of plant material into energy and nutrients, and it is the rumen microbiome that encodes the enzymes responsible. Many of these enzymes are of huge industrial interest. Despite this, rumen microbes are under-represented in the public databases. Here we present 220 high quality bacterial and archaeal genomes assembled directly from 768 gigabases of rumen metagenomic sequence data. Comparative analysis with current publicly available genomes reveals that the majority of these represent previously unsequenced strains and species of bacteria and archaea. The genomes contain over 13,000 proteins predicted to be involved in carbohydrate metabolism, over 90% of which do not have a good match in the public databases. Inclusion of the 220 genomes presented here improves metagenomic read classification by 2-3-fold, both in our data and in other publicly available rumen datasets. This release improves the coverage of rumen microbes in the public databases, and represents a hugely valuable resource for biomass-degrading enzyme discovery and studies of the rumen microbiome. 
Type Of Material Database/Collection of data 
Year Produced 2017 
Provided To Others? Yes  
Impact This dataset is expected to underpin research in rumen microbiomes over the next 5-10 years 
URL https://datashare.is.ed.ac.uk/handle/10283/2772
 
Title Mathematical model for predicting vaccine effectiveness with accompanied R Shiny app 
Description A mathematical model with an interactive R Shiny app was created to model the epidemiological consequences of vaccination with imperfect vaccines of various types, administered using different strategies to animal herds with different replacement rates and heterogeneity in vaccine responsiveness. 
Type Of Material Computer model/algorithm 
Year Produced 2019 
Provided To Others? Yes  
Impact no impact yet 
URL https://www.wiki.ed.ac.uk/display/saphir/
 
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 PRJEB19199 - Sheep Atlas 438 RNASeq libraries from TxBF Sheep 
Description The raw data, in the form of .fastq files, for the 438 TxBF RNA-Seq libraries generated for the sheep gene expression atlas project is deposited in the European Nucleotide Archive under study accession number PRJEB19199. 
Type Of Material Database/Collection of data 
Year Produced 2017 
Provided To Others? Yes  
Impact This sheep gene expression atlas raw data has been made available publicly under the data sharing agreement of the FAANG consortium. It was the first and largest dataset of it's type to be uploaded to the ENA as a 'FAANG' dataset and was used to test metadata standards and data upload requirements. it provides a valuable information to the livestock genomics community. 
URL http://www.ebi.ac.uk/ena/data/view/PRJEB19199
 
Title PRJEB21624 
Description This is one of the largest rumen metagenomics datasets ever released and represents 43 Scottish cattle from diverse breeds, different in methane emissions and feed conversion ratio. These data were used to assemble over 913 novel rumen microbial genomes. 
Type Of Material Database/Collection of data 
Year Produced 2017 
Provided To Others? Yes  
Impact These data were used to assemble over 913 novel rumen microbial genomes, which are expected to impact global rumen microbiome research over the next 5-10 years 
URL https://www.ebi.ac.uk/ena/data/view/PRJEB21624
 
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 RNASeq wild birds: the transcriptional regulation and climate adaptation of the breeding cycle of Lapland longspur 
Description We sequenced tissues (Heart, Liver, Gonads and Hypothalamus) from Lapland longspur (n=3) birds during arrival and incubation in Alaska during the breeding season. We also sequenced birds during years where they arrived in adverse weather conditions and incubated during a severe storm. 
Type Of Material Database/Collection of data 
Year Produced 2018 
Provided To Others? No  
Impact We are better able to understand the impact of climate change on the transcriptional regulation of the breeding cycle in Lapland longspur. We were able to observe how the different tissues transcriptomes are orchestrated across the breeding cycle. 
 
Title RNASeq: Quail photoperiodism 
Description RNASeq of quail medial basal hypothalamus at ZT4 in long and short photoperiods and at low temperature. BioProject: PRJNA490454 
Type Of Material Database/Collection of data 
Year Produced 2018 
Provided To Others? Yes  
Impact Improved understanding of the seasonal changes in the MBH transcriptomes of quail. Low temperature was confirmed to amplify the transcriptional effect of short photoperiods. 
URL https://www.ncbi.nlm.nih.gov/bioproject/PRJNA490454
 
Title VCF (Variant Call Format) files containing SNPs and Indels calls. 
Description Variants (SNPs and indels) were called using GATK (version 3.7) on 130 WGS indigenous sheep genomes. The East African sheep samples were from populations selected for their tail phenotypes from Ethiopia and from a population of Libyan Barbary sheep adapted to high altitude. 
Type Of Material Database/Collection of data 
Year Produced 2017 
Provided To Others? No  
Impact In collaboration with the University of Nottingham we have generated preliminary analysis to assess population diversity and structure. The data has been used to link tail phenotype to genomic sequence and investigate signatures of selection for adaptation to a tropical environment. This analysis has highlighted several genomic regions of interest including candidate genes associated with fat deposition and metabolism. 
 
Title WGS from 130 East African Sheep 
Description We have generated whole genome sequence data for 130 East African sheep. The DNA samples for the project were provided by our collaborators at the University of Nottingham. These goat genomes were sequenced at 30x coverage on the Illumina HiSeqX platform by Edinburgh Genomics. The East African sheep samples were from populations selected for their tail phenotypes from Ethiopia (118 individuals), and from a population of Libyan Barbary sheep (12 individuals) adapted to high altitude. We have called variants, differences in the sequence of the individuals, on the entire dataset and in collaboration with the University of Nottingham have generated preliminary analysis to assess population diversity and structure. At the University of Nottingham the data is being used to link tail phenotype to genomic sequence and investigate signatures of selection for adaptation to a tropical environment. This analysis has highlighted several genomic regions of interest including candidate genes associated with fat deposition and metabolism. 
Type Of Material Database/Collection of data 
Year Produced 2017 
Provided To Others? No  
Impact The overall goal of the African sheep sequencing project is to translate modern genomic tools, such as whole genome sequencing technology, that are widely-applied in genetic improvement in western livestock, to cost-effective genotyping tools and breeding strategies for improved goats that can be made available to small-holder farmers. 
 
Title WGS from 269 Goats 
Description We have generated whole genome sequence data for 269 goats. The DNA samples for the project were provided by our collaborators at the USDA. These goat genomes were sequenced at 15x coverage on the Illumina HiSeqX platform by Edinburgh Genomics. The majority of the goats we have sequenced are from focal populations of interest to the African Goat Improvement Network (AGIN). They originated from seven different African countries: Mali, Ethiopia, Kenya, Mozambique, Malawi, Tanzania and Zimbabwe. We have also generated sequence data for a small number of goats of interest from Madagascar, New Zealand and the UK. 
Type Of Material Database/Collection of data 
Year Produced 2017 
Provided To Others? Yes  
Impact We intend to do whole genome analysis on the goat dataset, including genome structure, gene content, gene duplication and copy number variant analysis. The goat genome sequence data is being contributed to the "Identification of Variations in Goat genomes related to domestication and adaptation" (VarGoats) Consortium. VarGoats is the first step to a goat 1000 genomes project and is led by INRA, France. Within the consortium there are several working groups focusing on different aspects of data analysis. Roslin is co-leading a working group focused on comparative analysis of the goat genome sequence data with other ruminants. Similarly the data will also be made availale to the African Goat Improvement Network which has 3 key aims: 1) develop village based breeding programs for small holder goats at selected sites in Malawi; 2) select and train one PhD student in village breeding programs and livestock genetics related to genetic improvement; and 3) use DNA tools to analyze founder animals and subsequent improved descendents as well as attempt to facilitate selection of goats within the village breeding programs. 
 
Title WGS from 67 West African Sheep 
Description The second part of the project is focused on sequencing West African sheep. We have generated whole genome sequence at 15x coverage from 67 West African sheep from Ghana and Nigeria, from DNA provided by the USDA. We have also collected a further 108 samples from Cameroon sheep via our collaborators at the University of DSchang in Cameroon. These samples were genotyped on the Ovine 50K SNP Chip to select focal individuals for sequencing. 48 focal individuals from the 108 were sequenced at 15x coverage. 
Type Of Material Database/Collection of data 
Year Produced 2018 
Provided To Others? No  
Impact The West African sheep samples are being analysed particularly for polymorphisms in immune genes as these sheep are anecdotally tolerant to Trypanosomes. Our aim is to use this information to develop a genotyping platform for immune polymorphisms relevant to disease susceptibility that can be applied in the field as a resource to improve sustainable community based breeding programs for these sheep. 
 
Title WGS of Ethiopian chickens 
Description WGS of Ethiopian chickens from 25 different populations (30x coverage) 263 birds in total. 
Type Of Material Database/Collection of data 
Year Produced 2017 
Provided To Others? No  
Impact Data being used for selective sweep analysis, ERV analysis, SNP analysis, CNV analysis etc. by various researchers 
 
Title WGS of Nigerian chickens 
Description WGS of 122 Nigerian chickens (30x coverage) 
Type Of Material Database/Collection of data 
Year Produced 2017 
Provided To Others? No  
Impact Data being analysed for SNPs, ERVs, CNVs, selection signatures etc. by various researchers 
 
Title WGS: Comparing selection in breeds of sheep with long and short breeding seasons 
Description We sequenced 63 individuals from rare breeds of primitive sheep (Shetland, Portland and Herdwick) from phenotypic extremes regarding the timing and duration of breeding season. These were genotyped at 30x on the HiSeqX. 
Type Of Material Database/Collection of data 
Year Produced 2018 
Provided To Others? No  
Impact We identified strong selection signatures on genes, many of which were associated with neurological development. These breeds have not previously been sequenced and are a valuable resource for sheep genetics. 
 
Description Agricygen 
Organisation Agricultural Research Institute
PI Contribution Use of genomics to optimise sheep and cattle breeding in order to maximise milk production for halloumi cheese
Collaborator Contribution Local livestock expertise and husbandry and nutrition expertise for the optimisation of milk production in Cyprus
Impact Project is in its early stages. No outputs as yet.
Start Year 2017
 
Description Aviagen 
Organisation Aviagen Group
Country United States 
Sector Private 
PI Contribution As a former Aviagen employee I continue to engage with current members of Aviagen's R&D group. Together we have partnered on one unsuccessful research application which would have utilized the NARF avian resources and facilities.
Collaborator Contribution Working with key members of the R&D team at Aviagen, we are able to access commercial know-how and the considerable IP associated with commercial genetic resources.
Impact Grant application BB/R003467/1
Start Year 2016
 
Description Aviagen 
Organisation Aviagen Group
Country United States 
Sector Private 
PI Contribution We are working with Aviagen to explore the role of the chicken gut microbiome in performance of their chickens in diverse environments. So far this includes the placement of one of their staff members in my group for a short period of time for training and development
Collaborator Contribution Aviagen provide access to large commercial flocks of chickens under both controlled and natural environments
Impact No outputs so far
Start Year 2017
 
Description Behavioural neuroendocrinology of rat maternal behaviour Dr Bosch 
Organisation University of Regensburg
Country Germany 
Sector Academic/University 
PI Contribution Expertise, intellectual input and access to facilities.
Collaborator Contribution Expertise, intellectual input and access to facilities.
Impact Douglas AJ, Meddle SL, Kroemer S, Muesch W, Bosch OJ & Neumann ID (2007) Social stress induces hypothalamo-pituitary-adrenal axis responses in lactating rats bred for high trait anxiety. Eur. J. Neuroscience 25: 1599-1603. Douglas AJ, Meddle SL, Toschi N, Bosch OJ & Neumann I.D (2005) Reduced activity of the noradrenergic system in the paraventricular nucleus at the end of pregnancy: implications for stress hyporesponsiveness. J. Neuroendocrinol. 17:40-48. Bosch OJ, Meddle SL, Beiderbeck DI, Douglas AJ & Neuman ID (2005) Brain oxytocin regulates maternal aggression in lactating rats. J. Neuroscience 25:6807-6815.
 
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 CTLGH collaborator -ILRI 
Organisation International Livestock Research Institute (ILRI)
Country Kenya 
Sector Charity/Non Profit 
PI Contribution We are sequencing the chicken samples provided by partners in ILRI
Collaborator Contribution Colleagues in ILRI are collecting DNA samples from indigenous chicken populations
Impact Visits/training between countries; sharing of samples/data; linking genotypes with phenotypes; building of research facilities in Ethiopia Multidisciplinary: Geneticists, bioinformaticians, farmers,
Start Year 2015
 
Description Cameroon Blackbelly Sheep Project 
Organisation University of Dschang
PI Contribution Together with my collaborators in Cameroon I oversaw collection of 108 ear notch biopsy samples and the corresponding metadata from Cameroon Blackbelly sheep populations across Cameroon. These samples have been transferred to the Roslin Institute for genotyping using the Ovine 50K chip and whole genome sequencing. My research team will analyse the data and interpret it in collaboration with collaborators at the University of Dschang, to identify signatures of selection, adaptation to a tropical environment and particularly polymorphisms in immune genes underlying trypanotolerance.
Collaborator Contribution My collaborators at the University of Dschang, Félix Meutchieye and Gustave Simo have contributed their time to this project. Félix Meutchieye planned and oversaw collection of 108 ear notch biopsy samples and the corresponding metadata from Cameroon Blackbelly sheep populations across Cameroon. He has also contributed his knowledge of the Cameroon Blackbelly sheep, including it's population structure and diversity and socio-economic importance in Cameroon. Dr Meutchieye facilitated issuing of collection and export permits for the samples from the Ministry of Agriculture in Cameroon. Gustave Simo undertook the extraction of DNA from the ear notch biopsy samples in laboratory at the University of Dschang and arranged shipping of the samples to Roslin for genotyping and sequencing.
Impact There are no measurable outcomes beyond collection of these samples and generation of data at this stage.
Start Year 2017
 
Description Cattle genomics and diversity 
Organisation International Livestock Research Institute (ILRI)
Country Kenya 
Sector Charity/Non Profit 
PI Contribution We have generated the first African cattle breed (N'dama) reference genome. We are also combining over 4000 Roslin, CTLGH and publically available high coverage genomes to generate the largest publically available set of cattle genetic variants spanning global breeds, which can be exploited for a variety of purposes.
Collaborator Contribution They are providing samples, data and advice on data analysis.
Impact generation of N'dama reference genome
Start Year 2016
 
Description Cattle genomics and diversity 
Organisation University of Nottingham
Country United Kingdom 
Sector Academic/University 
PI Contribution We have generated the first African cattle breed (N'dama) reference genome. We are also combining over 4000 Roslin, CTLGH and publically available high coverage genomes to generate the largest publically available set of cattle genetic variants spanning global breeds, which can be exploited for a variety of purposes.
Collaborator Contribution They are providing samples, data and advice on data analysis.
Impact generation of N'dama reference genome
Start Year 2016
 
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 Charoen Pokphand (CP) group 
Organisation Charoen Pokphand Group
PI Contribution Charoen Pokphand (CP) group are a large Asian conglomerate with an interest in farming, food production and feed additives. They have placed one of their staff members with me for PhD training, fully funded by them. We are training the staff member in laboratory and bioinformatics techniques related to microbiome research in chickens.
Collaborator Contribution CP provide access to large chicken flocks both in at their farms and in their production facility. This enables us to study chicken breeds in the actual environments in which they live throughout Asia.
Impact This is a multi-disciplinary project involving both laboratory and computational techniques. The major outcome so far include a review paper (http://aem.asm.org/content/early/2018/01/29/AEM.02627-17.abstract) and the technology transfer from our group into the commercial partner.
Start Year 2017
 
Description Cherry Valley 
Organisation Cherry Valley Farms
Country United Kingdom 
Sector Private 
PI Contribution Supervise MSc students using quantitative genetic models to (i) assess the increase in likelihood of ascites in the breeding population, in particular in relation to selection on live weight and (ii) assess the genetic variation in fertility and its relation to live weight.
Collaborator Contribution Provision of data.
Impact Trained MSc students working in UK breeding industry. Larger scale projects with Roslin colleagues built on initial contacts made with the MSc projects.
Start Year 2015
 
Description Cherry Valley Farms 
Organisation Cherry Valley Farms
Country United Kingdom 
Sector Private 
PI Contribution There has been an ongoing partnership to develop genomic breeding programme for Cherry Valley Farms (CVF) including strategies to improve the genomic assembly for the Pekin Duck. This collaboration has led to one current grant application (successful Innovate UK) and other planned applications in the future.
Collaborator Contribution Cherry Valley Farms have provided genomic material from within all their current selection lines to enable the analyses of genetic diversity in Pekin Ducks which supply a significant proportion of global commercial duck production.
Impact Generation of significant genomic information; development and production of low density SNP panel; successful Innovate UK funding application.
Start Year 2016
 
Description Collaboration with AB Vista 
Organisation AB Vista
Country United Kingdom 
Sector Private 
PI Contribution We are researching the activity of ovodefensins, naturally-occurring egg peptides with antimicrobial properties. With BBSRC LINK funding we are exploring the activity of diverse ovodefensins from multiple avian species, dissecting their structure and mode of action, and exploring their capacity to act as growth promoters and novel therapeutics.
Collaborator Contribution AB Vista have made a substantial cash contribution to the LINK project (c. £460k) and also provide access to natural populations of broilers for feed trials using diets supplemented (or not) with Trichoderma-expressed ovodefensins. They also support analysis of the impact of such diets on intestinal microbiota and metabolites.
Impact Commercially sensitive and to be disclosed following scrutiny for Intellectual Property.
Start Year 2012
 
Description Collaboration with John Goopy, at ILRI (Kenya): microbial changes in relation to diets in African livestock species 
Organisation International Livestock Research Institute (ILRI)
Country Kenya 
Sector Charity/Non Profit 
PI Contribution Pilot study to investigate the microbial changes in relation to diets in African livestock species
Collaborator Contribution Experimental design was setup by the collaborator in Kenya. All rumen samples were extracted at ILRI and DNA extraction was done on-site.
Impact This collaboration provided pilot data for a future grant application.
Start Year 2017
 
Description Collaboration: The dynamics of antimicrobial resistance gene prevalence on a commercial pig farm: implications for policy 
Organisation University of Edinburgh
Country United Kingdom 
Sector Academic/University 
PI Contribution I am collaborating with data analysis of this project, which give me the opportunity to develop the bioinformatic pipelines needed for analysing my data when it comes. My first publication on AMR from pigs will be published using this data.
Collaborator Contribution This would primarily be computing infra-struction to process the data. It takes about 1.6TB of space to per sample through the pipeline i am using so this sort of data would require significant robust computing infrastructure
Impact Bio-informatic pipeline
Start Year 2017
 
Description Crispr 
Organisation Norwegian University of Life Sciences (NMBU)
Country Norway 
Sector Academic/University 
PI Contribution This is at the start of the collaboration. I will be supervising PhD student and helping to design experiments to investigate new Crispr technology in tilapia.
Collaborator Contribution Research funding, facilities, salaries for student and other members of the research team.
Impact None as yet.
Start Year 2019
 
Description Dr Bas Rodenburg 
Organisation University of Wageningen
Country Netherlands 
Sector Academic/University 
PI Contribution Preparation and submission of grants to BBSRC. Collaborative research in animal welfare/neurobiology and behaviour.
Collaborator Contribution Preparation and submission of grants to BBSRC. Collaborative research in animal welfare/neurobiology and behaviour.
Impact Established collaborations in pigs and chickens. Multidisciplinary research. Behaviour and neuroscience with animal welfare. Joint submission of a BBSRC response mode grant (Jan 2018) and another in the pipeline for submission Set 2018.
Start Year 2017
 
Description Dr Karen Spencer 
Organisation University of St Andrews
Department School of Psychology
Country United Kingdom 
Sector Academic/University 
PI Contribution data generation. Supervision of EastBio DTP student
Collaborator Contribution data generation. Supervision of EastBio DTP student
Impact Presentations at conferences. Training and mentorship of PhD student.
Start Year 2016
 
Description Dr Tyler Stevenson 
Organisation University of Aberdeen
Department School of Biological Sciences Aberdeen
Country United Kingdom 
Sector Academic/University 
PI Contribution Won collaborative grant: The Leverhulme Trust (2016-2019) "Identification of the photoreceptor for light detection in the avian brain" Data generation.
Collaborator Contribution Won collaborative grant: The Leverhulme Trust (2016-2019) "Identification of the photoreceptor for light detection in the avian brain" Data generation.
Impact Data generation. Won collaborative grant: The Leverhulme Trust (2016-2019) "Identification of the photoreceptor for light detection in the avian brain"
Start Year 2016
 
Description Dr Vincent Bombail 
Organisation French National Institute of Agricultural Research
Department Jouy-en-Josas Centre
PI Contribution Collaboration on positive welfare in rats. Behavioural and neurobiological analysis.
Collaborator Contribution Collaboration on positive welfare in rats. Animals and behavioural experiments.
Impact 2 PhD studentships. Presentations and publications. Multidisciplinary research. Behaviour and neuroscience with animal welfare. Currently writing a BBSRC response mode grant.
Start Year 2017
 
Description EBI metagenomics 
Organisation EMBL European Bioinformatics Institute (EMBL - EBI)
Country United Kingdom 
Sector Academic/University 
PI Contribution We have been working with EBI since 2018 on methods and infrastructure around metagenomic data analysis and storage. We have been providing use cases, expertise and biologucal knowledge
Collaborator Contribution EBI provide advice on large scale data analysis and the infrastructure they provide
Impact We were funded by BBSRC BBR in 2018 to continue this collaboration BB/R015023/1
Start Year 2018
 
Description FTMA 
Organisation Lohmann Tierzucht GmbH
PI Contribution This award has funded a number of exchanges between Roslin and Lohmann Tierzucht (LTZ) . We have made good contacts with a new member of staff at LTZ which will lead to new data and publications on bone strength and it will facilitate 2 PhD projects in that area. We have also started a new area of work on hen welfare which we have submitted grant applications and studentships,
Collaborator Contribution We have visited sites and had meetings to understand the problems and have been given assurances of financial support to undertake grant applications.
Impact Grant application Studentship application and studentship Involves animal breeding and developmental biology
Start Year 2018
 
Description Jim Kaufman - MHC 
Organisation University of Cambridge
Country United Kingdom 
Sector Academic/University 
PI Contribution We have collected hundreds of DNA samples from various African chicken populations which have been sent to Prof Jim Kaufman for MHC haplotyping
Collaborator Contribution Prof Kaufman is MHC haplotyping the African birds for which we have collected samples. This will allow us to associate particular MHC haplotypes with disease traits in the bird populations ie. level of robustness
Impact MHC haplotypes have been determined for >20 bird populations from Ethiopia. Work is underway to analyse birds from Nigeria, Oman, Iraq....
Start Year 2017
 
Description Joint PhD student supervision The role of cognitive and affective state during agonistic encounters: Implications for social interactions and animal welfare 
Organisation Scotland's Rural College
Country United Kingdom 
Sector Academic/University 
PI Contribution Mathematical methods for analysis of social interactions
Collaborator Contribution Expertise in Animal Behaviour and Welfare, provision of data
Impact PhD student has only started in October 2018
Start Year 2018
 
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 Agricultural University Plovdiv
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 Monsanto 
Organisation Monsanto
Country United States 
Sector Private 
PI Contribution 1 x post-doc working on
Collaborator Contribution Funding for the post-doc for 3 years plus a contribution towards travel.
Impact Collaboration only began at the end of 2017.
Start Year 2017
 
Description Prof Sue Healy, The University of St Andrews 
Organisation University of St Andrews
Department School of Biology
Country United Kingdom 
Sector Academic/University 
PI Contribution Long term collaborator. Share east BioDTP.
Collaborator Contribution collaboration in data generation.
Impact BBSRC response mode grants. East BioDTP. Publications.
 
Description Prof. J. Wingfield, UC Davis, USA. 
Organisation University of California, Davis
Country United States 
Sector Academic/University 
PI Contribution Won National Science Foundation, USA 3 year Research Grant (2016-2019) "Modulation of the Adrenocortical Responses to Perturbations of the Environment". Co-Investigator. Grant jointly held with Prof. J. Wingfield, UC Davis, USA. Ongoing data collection, publications and talks
Collaborator Contribution won National Science Foundation, USA 3 year Research Grant (2016-2019) "Modulation of the Adrenocortical Responses to Perturbations of the Environment". Co-Investigator. Grant jointly held with Prof. J. Wingfield, UC Davis, USA.Ongoing data collection, publications and talks
Impact Publications and training of post docs and PhD students. Presentations workshops and conference organisation.
 
Description SLU: genetic and environmental dissection of behavioural traits 
Organisation Swedish University of Agricultural Sciences
Country Sweden 
Sector Academic/University 
PI Contribution We are carrying out a study of genetic and non-genetic factors associated with dog behaviour, incorporating data collection, analysis and interpretation.
Collaborator Contribution Partners: Professor Erling Strandberg, Dr. Per Arvelius. They have contributed samples and data to the study. They are also contributing to the data analysis and interpretation.
Impact No outputs thus far.
Start Year 2017
 
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 collaboration on early life biomarkers in cattle 
Organisation Scotland's Rural College
Country United Kingdom 
Sector Academic/University 
PI Contribution Provided expertise on small RNA analysis in livestock and laboratory facilities for the study
Collaborator Contribution Provided funding, animal samples, and expertise in cattle genetics
Impact Manuscript just submitted to Scientific Reports, Responsive mode BBSRC application in preparation
Start Year 2016
 
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 Saphir - Horizon2020 
Organisation French National Institute of Agricultural Research
Country France 
Sector Public 
PI Contribution I am leader of workpackage 16: Modelling vaccine efficacy
Collaborator Contribution INRA is project leader
Impact -Scientific Publication: Go N., Islam Z., Lunney J., Belloc C., Touzeau S.& Doeschl-Wilson A.B., 2019. How to prevent viremia rebound: evidence from a PRRSv data-supported model of immune response. BMC Systems Biol. https://doi.org/10.1186/s12918-018-0666-7 -Popular article "How to prevent viremia rebound in virus infections? Evidence from a data-driven mathematical model for PRRS". Doeschl-Wilson A., Go N., Touzeau S. SAPHIR newsletter Nov 2017 - Issue 4. Project coordinator statement "A very innovative approach for modelling the immune response has been designed and validated." -Interactive Wiki-website: Vaccine effectiveness in the field. https://www.wiki.ed.ac.uk/display/saphir/ -Conference talks: International Vaccinology Meeting in Edinburgh, May 2018; Annual Meeting for the Society for Mathematical Biology, Sydney Australia, July 2018 and the Conference for Research Workers in Animal Disease, Chicago December 2018
Start Year 2016
 
Description Saphir - Horizon2020 
Organisation University of Ghent
Department Faculty of Veterinary Medicine
Country Belgium 
Sector Academic/University 
PI Contribution I am leader of workpackage 16: Modelling vaccine efficacy
Collaborator Contribution INRA is project leader
Impact -Scientific Publication: Go N., Islam Z., Lunney J., Belloc C., Touzeau S.& Doeschl-Wilson A.B., 2019. How to prevent viremia rebound: evidence from a PRRSv data-supported model of immune response. BMC Systems Biol. https://doi.org/10.1186/s12918-018-0666-7 -Popular article "How to prevent viremia rebound in virus infections? Evidence from a data-driven mathematical model for PRRS". Doeschl-Wilson A., Go N., Touzeau S. SAPHIR newsletter Nov 2017 - Issue 4. Project coordinator statement "A very innovative approach for modelling the immune response has been designed and validated." -Interactive Wiki-website: Vaccine effectiveness in the field. https://www.wiki.ed.ac.uk/display/saphir/ -Conference talks: International Vaccinology Meeting in Edinburgh, May 2018; Annual Meeting for the Society for Mathematical Biology, Sydney Australia, July 2018 and the Conference for Research Workers in Animal Disease, Chicago December 2018
Start Year 2016
 
Description Studies of brain health and neuroinflammation in the pig 
Organisation University of Edinburgh
Department Brain Research Imaging Centre
Country United Kingdom 
Sector Academic/University 
PI Contribution This is a multi-disciplinary team studying neuroimmune processes in the pig - we have provided experience of pig biology and welfare
Collaborator Contribution This is a multi-disciplinary team studying neuroimmune processes in the pig - our collaborators provided expertise in microglia, brain imaging and molecular biology
Impact Multi-disciplinary: - pig biology - pig welfare - brain imaging - cell isolation and sorting - sequencing
Start Year 2018
 
Description Studies of brain health and neuroinflammation in the pig 
Organisation University of Edinburgh
Department Centre for Discovery Brain Sciences
PI Contribution This is a multi-disciplinary team studying neuroimmune processes in the pig - we have provided experience of pig biology and welfare
Collaborator Contribution This is a multi-disciplinary team studying neuroimmune processes in the pig - our collaborators provided expertise in microglia, brain imaging and molecular biology
Impact Multi-disciplinary: - pig biology - pig welfare - brain imaging - cell isolation and sorting - sequencing
Start Year 2018
 
Description Studies of brain health and neuroinflammation in the pig 
Organisation University of Edinburgh
Department Institutional Strategic Support Fund
Country United Kingdom 
Sector Charity/Non Profit 
PI Contribution This is a multi-disciplinary team studying neuroimmune processes in the pig - we have provided experience of pig biology and welfare
Collaborator Contribution This is a multi-disciplinary team studying neuroimmune processes in the pig - our collaborators provided expertise in microglia, brain imaging and molecular biology
Impact Multi-disciplinary: - pig biology - pig welfare - brain imaging - cell isolation and sorting - sequencing
Start Year 2018
 
Description The University of Aberdeen 
Organisation University of Aberdeen
Department Institute of Medical Sciences
Country United Kingdom 
Sector Academic/University 
PI Contribution We have been working with Alan Walker and Tim Snelling in the field of rumen metagenomic profiling
Collaborator Contribution Alan and Tim are experts in rumen microbiology and 16S sequencing, whereas my group is expert in whole-genome-shotgun metagenomics and bioinformatics
Impact As part of a Scottish government project, we have sequenced 90 rumen metagenomes using whole genome sequencing, and almost 300 using 16S profiling. Data analysis is ongoing, but my team have assembled hundreds of microbial genomes from the rumen (10.1101/162578) and written a pipeline for analysiing such data(10.1101/233544)
Start Year 2016
 
Description Tilapia 
Organisation Norwegian University of Life Sciences (NMBU)
Country Norway 
Sector Academic/University 
PI Contribution Superviison and guidance on the partitioning of the observed phenotypic variance to obtain both additive and non-additive components of variance, including design and interpretation of analysis and derivation of key interpretative formulae.
Collaborator Contribution Provision and payment of PhD student, access to data, genotyping and collaborative time from researchers at NMBU.
Impact Paper in scientific press. New PhD graduate. New trained employee entering breeding industry. Knowledge transfer to industry.
Start Year 2014
 
Description USDA Sheep and Goat Sequencing 
Organisation U.S. Department of Agriculture USDA
Country United States 
Sector Public 
PI Contribution Collaborators at the USDA provided DNA from African goats and sheep, I had these samples sequenced using the Illumina HiSeqX platform to produce whole genome sequencing data at 15x coverage. We have shared the goat sequencing data with our collaborators at the USDA and within the IGGC, ADAPTMap, Vargoats and AGIN consortiums. We will contribute to comparative analysis of these genomes with African sheep and analysis of gene content and polymorphisms in immune gene relevant to adaptive immunity. The Dalljonke sheep samples will be analysed with the Cameroon Blackbelly sheep sequencing data and we will provide a comprehensive analysis of the genome structure, gene content and adaptive significance of CNVs in this rare indigenous African sheep breed.
Collaborator Contribution My collaborators Curt Van Tassell, Ben Rosen and Gordon Spangler at U.S. Department of Agriculture USDA, provided DNA samples from approximately 300 goats from African countries for whole genome sequencing. The goat samples selected for sequencing were focal individuals identified in the goat ADAPTMap and AGIN (African Goat Improvement Network) projects using the 50K Chip genotyping data. In addition to the goat samples they have also provided DNA from 20 Dalljonke sheep from Nigeria and Uganda also for whole genome sequencing, these samples were also genotyped on the Ovine 50K Chip, by the USDA, to identify the focal individuals for sequencing.
Impact The first round of data from the goat whole genome sequencing has been shared with the IGGC/ADAPTMap/Vargoats consortium for variant calling and analysis.
Start Year 2017
 
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
 
Description VarGoats Consortium African Goat Sequencing 
Organisation French National Institute of Agricultural Research
Department INRA Toulouse
Country France 
Sector Public 
PI Contribution We have sequenced 300+ genomes from African goats from DNA samples provided by the USDA and contributed the raw sequencing data to INRA for variant calling as our collaborators in the VarGoats consortium. We will contribute to analysis of the genomes including gene content analysis, structural variation, functional analysis and comparative analysis with genomic data generated from African sheep.
Collaborator Contribution VarGoats is the first step of a 1000 goat genomes project and is lead by Gwenola Tosser-Klopp (INRA, France). Our collaborators at INRA are calling variants to generate .vcf files for the goat sequence data we provided. These files will then be provided to the VarGoats consortium for analysis by the various working groups.
Impact We have provided the raw data to INRA who have generated the a set of .vcf files which is the first output from this collaboration. The Vargoats project and Roslin's contribution was presented at the International Goat Genomics Consortium meeting at the Plant and Animal Genomes Conference, San Diego, USA, January 16th 2018.
Start Year 2017
 
Title AlphaSimR 
Description AlphaSimR is a next generation software package in the line of our successful earlier package AlphaSim. The new package is accessible in a user-friendly way via an interface in the public domain environment R. The package is used for stochastic simulations of breeding programs to the level of DNA sequence for every individual. Contained is a wide range of functions for modeling common tasks in a breeding program, such as selection and crossing. These functions allow for constructing simulations of highly complex plant and animal breeding programs via scripting in the R software environment. Such simulations can be used to evaluate overall breeding program performance and conduct research into breeding program design, such as implementation of genomic selection. Included is the 'Markovian Coalescent Simulator' ('MaCS') for fast simulation of biallelic sequences according to a population demographic history [Chen et al. (2009)]. 
Type Of Technology Software 
Year Produced 2018 
Impact This package has rapidly expanded our possibilities to apply breeding simulation in research projects, both in academic research projects and for the breeding industry (most notably Driscolles and Bayer). Several graduate students used the package for their internship projects. 
URL https://alphagenes.roslin.ed.ac.uk/wp/software/alphasimr/
 
Title Den Haag 
Description R package written to simulate populations and the techniques for control of genetic variance as an aid for teaching. 
Type Of Technology Software 
Year Produced 2017 
Impact Used in lectures. 
URL https://github.com/jwoollia/DenHaag/blob/master/DenHaag.pdf
 
Title MAGpy 
Description Recent advances in bioinformatics have enabled the rapid assembly of genomes from metagenomes (MAGs), and there is a need for reproducible pipelines that can annotate and characterise thousands of genomes simultaneously. Here we present MAGpy, a Snakemake pipeline that takes FASTA input and compares MAGs to several public databases, checks quality, assigns a taxonomy and draws a phylogenetic tree. 
Type Of Technology Software 
Year Produced 2017 
Open Source License? Yes  
Impact This software was used to annotate 913 metagenome assembled genomes from the cattle rumen, a dataset which is expected to underpin rumen metagenomics research for the next 5-10 years 
URL https://datashare.is.ed.ac.uk/handle/10283/3009
 
Title PULpy 
Description Polysaccharide utilisation loci (PUL) are regions within bacterial genomes that encode all the necessary machinery for the cleavage of particular carbohydrates. For the Bacteroidetes phylum, prediction of PUL from genomic data alone involves the identification of carbohydrate-active enzymes (CAZymes) co-localised with susCD gene pairs. Here we present the open prediction of PUL in 5414 public Bacteroidetes genomes, and an open-source pipeline to reproduce or extend the results. 
Type Of Technology Software 
Year Produced 2018 
Open Source License? Yes  
Impact We use this software in our metagenomics and microbiome research 
URL https://github.com/WatsonLab/PULpy
 
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 "Amazing Bodies" - Edinburgh Science Festiva 
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 Edinburgh Science Festival and located within the National Museum of Scotland, one of the top tourist attractions within Edinburgh.
Year(s) Of Engagement Activity 2018
URL https://www.sciencefestival.co.uk/festival
 
Description "Studying the microbial communities of livestock" Nuffield Research Placement 
Form Of Engagement Activity Participation in an open day or visit at my research institution
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Schools
Results and Impact "Studying the microbial communities of livestock" Nuffield Research Placement. 4 week laboratory experience placement for high school pupil.
Year(s) Of Engagement Activity 2018
 
Description 'Cute Egg' activities for P5 school pupils as part of Borders Agricultural Society Show 
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 school pupils at local schools were engaged in an event run by the Borders Agricultural Society involving c. 225 visitors. Our activities built on the BBSRC-funded 'Cute Egg' exhibit, which uses coloured eggs to demonstrate the presence of a cuticle under the shell that protects the egg from spoilage. The scope to measure cuticle thickness as a quantitative trait for genetic selection was described in simple terms.
Year(s) Of Engagement Activity 2017
 
Description 2 Day Mini Science Festival for Primary Schools: Eastgate Theatre, Peebles 
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 school children from P3-P7 from 4 primary schools attended workshops on "Brilliant Biology" activities involving DNA extraction from strawberries, personalised model chromosome building to reflect individual traits such as hair colour, eye colour, and a lung biology activity.
Year(s) Of Engagement Activity 2015,2016,2017,2018
 
Description 2017 Seminar: "Neuroendocrine and environmental interactions underlying reproductive behaviour in birds" The Institute of Biological & Environmental Sciences, The University of Aberdeen, Aberdeen, UK. 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact Talk given at the university and discussions with academics. Has inspired future collaborations with the University of Aberdeen.
Year(s) Of Engagement Activity 2017
 
Description 2017 Speaker: "Rat as a model for studying behaviour" 2nd Edinburgh Rat Genetics Workshop, University of Edinburgh. 17th November, 2017. 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Professional Practitioners
Results and Impact 2017 Speaker: "Rat as a model for studying behaviour" 2nd Edinburgh Rat Genetics Workshop, University of Edinburgh. 17th November, 2017.Provided information regarding behavioural equipment and uses at the Roslin Institute.
Year(s) Of Engagement Activity 2017
 
Description 2019 American Association for the Advancement of Science Annual Conference 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Public/other audiences
Results and Impact Symposium title: Can genome edited livestock transcend GMO regulatory stalemate? world's largest multi-disciplinary science society, fulfilling its mission to advance science, engineering, and innovation throughout the world for the benefit of all people through a broad array of initiatives focused on communication, public engagement, education, scientific responsibility, public policy, and science diplomacy.
Year(s) Of Engagement Activity 2018
URL https://meetings.aaas.org/about-the-meeting/
 
Description A presentation given at the Universities Federation for Animal Welfare (UFAW) Science Symposium, 2017 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Postgraduate students
Results and Impact Title of talk: Positive animal welfare revisited with a focus on the role of behavioural expression. Co-author Professor Peter Sandoe http://www.forskningsdatabasen.dk/en/catalog/2372695868 - the meeting is attended by a range of scientists interested in animal welfare but it also functions as a post-graduate conference with many of the audience studying at for post-graduate degrees - I had a number of discussions with students from various organisations during the meeting
Year(s) Of Engagement Activity 2017
URL https://www.ufaw.org.uk/ufaw-events/measuring-animal-welfare-and-applying-scientific-advances-why-is...
 
Description A talk given at the Annual Meeting of the International Society for Applied Ethology 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Postgraduate students
Results and Impact The Annual Meeting of the ISAE is now recognised as an excellent training for post-graduate students interested in applied animal behaviour and welfare. Following our talk on brain gene expression effects of enrichment I had a number of discussions with students about the work and their own interests. I also was involved in a session entitlied: Meet the Professors where students sign up to discuss their science and careers with a panel of senior scientists in the field.
Year(s) Of Engagement Activity 2017
URL http://conferences.au.dk/isae2017/
 
Description Adebabay training 
Form Of Engagement Activity Participation in an open day or visit at my research institution
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Study participants or study members
Results and Impact Almas Gheyas trained ILRI staff (Adebabay Kebele) on bioinformatics analysis during his visit to the UK and is currently mentoring him on further analysis of the data
Year(s) Of Engagement Activity 2017
 
Description Almas PAG 2018 talk 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Postgraduate students
Results and Impact Talk: "Genomic analysis of African local chickens to elucidate tropical adaptation" in the Animal Genomics and Climate Change Workshop in the PAG 2018 held during 13-18 Jan 2018 in SanDiego, California.
Year(s) Of Engagement Activity 2018
URL http://www.intlpag.org/
 
Description Animal Microbiome Congress London 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Mick Watson presented his work on functional microbiome analysis at the Animal Microbiome Congress London. Attendees included industry/business, farmers, professional practitioners and academics
Year(s) Of Engagement Activity 2017
 
Description Annual Roslin Institute Open Doors Day 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Public/other audiences
Results and Impact The annual Roslin Institute Open Doors day was held on 14 October 2017 and was attended by 491 people. It involved 81 members of staff and students and showcased a wide range of research arising from BBSRC strategic investment, including (but not limited to), food safety, influenza, genetic improvement, DNA, imaging and the ethical treatment of animals in research.
Year(s) Of Engagement Activity 2017
 
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 BBC Country File interview 
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 Supporters
Results and Impact TV interview on genetically engineered pigs on mainstream BBC Country File programme
Year(s) Of Engagement Activity 2013
 
Description BBC Countryfile film related to the work of the Centre for Tropical Livestock Genetics & Health at Roslin 
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 Bill Gates was interviewed by BBC Countryfile on 26 January 2018 in relation to work funded by the Gates Foundation involving Roslin Institute scientists towards the genetic improvement of farmed animals in low- and middle-income countries. The programme aired on 11 February 2018 and reached an estimated audience in excess of 5 million. The interview took place on the same day as the launch of the Global Academy of Agriculture & Food Security, which was attended by the Secretary of State for the Department for International Development the Rt Hon Penny Mordaunt (see separate activity) and generated significant press interest, featuring on BBC Scotland news. Particular emphasis was placed on the work of Roslin scientists to understand the genetic make-up of African diary cattle and chickens and to understand how this relates to performance traits in order to guide breeding decisions.
Year(s) Of Engagement Activity 2018
 
Description BBC at the Edinburgh Festivals: The Human Body. Lung Biology activity 
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 Lung biology activity
Year(s) Of Engagement Activity 2017
 
Description BBSRC Japan Partnering Workshop on Neuroendocrine Control of Reproduction 
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 Japan Partnering Workshop. Invited speaker from Japan. Engaged with staff, post graduate students and undergraduate students. 20 People attended and presented. Much discussion and plans made for further collaboration and visits to Japan in 2019. In addition talks surrounding future careers for post docs and PhD students.
Year(s) Of Engagement Activity 2018
 
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 Bird Stress in your Backyard, Midlothian Science Festival 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Public/other audiences
Results and Impact Bird Stress in your Backyard, Midlothian Science Festival. learn how we can observe, track and help local birds effected by towns, traffic, light and noise pollution. Sparked questions and discussion.
Year(s) Of Engagement Activity 2018
URL https://midlothiansciencefestival.com/event/bird-stress-in-your-backyard-3/
 
Description CMVM Science Insights Research Taster Session: 2 hour lab session for S5 high school pupils 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Schools
Results and Impact The event is the CMVM Science Insights Programme for S5 high school pupils. A week long activity to give interested pupils an insight into a career in science. A small group came to my lab for an afternoon hands-on practical session.
Year(s) Of Engagement Activity 2018
URL https://www.ed.ac.uk/medicine-vet-medicine/outreach/science-insights
 
Description COST Action on harmful social behaviours 
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 Gave talks at 2 PhD training schools: COST Action on harmful social behaviours (Bratislava, October, 2018); Danish PhD school organised by the Aarhus University (November, 2018).
A 3-day Training School on how Breeding and Epigenetics influence the behaviour and welfare of animals, and understanding of neurobiological processes. An opportunity for PhD students and Postdocs to learn about genetics of normal and damaging social behaviour in pigs and laying hens, to discuss the latest science and make new European connections and collaborations.
Year(s) Of Engagement Activity 2018
URL https://www.grouphousenet.eu/Training%20school%202018-1.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 Campus Open Day- Midlothian Science Festival 
Form Of Engagement Activity Participation in an open day or visit at my research institution
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Public/other audiences
Results and Impact The Roslin Institute and Easter Bush Campus Open Day was an event undertaken within the Midlothian Science Festivals. Hands on public activities lead by scientists under "Complex phenotypes and genotype x environment interactions" included Science is for Everyone, Brains and Behaviour, The Genetic Toolbox, Bio-imaging: The Nature of Fluorescence, Cells up close, The Cow Lab, Life through a Lens and Crafty Science.
Year(s) Of Engagement Activity 2018
URL https://www.ed.ac.uk/easter-bush-campus/science-outreach-centre
 
Description Cell Block Science: Chicken behaviour session for female prisoners at HMP Edinburgh 
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 Cell Block Science: Chicken behaviour session for female prisoners at HMP Edinburgh which sparked questions and discussion.
Year(s) Of Engagement Activity 2018
 
Description Cost action Training School for the histological investigation of avian bone 
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 Interest in collaboration and potential links with industry.
Year(s) Of Engagement Activity 2019
URL http://www.keelbonedamage.eu/wp-content/uploads/FlyerTrainingSchool.pdf
 
Description Costing the Earth 
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 BBC radio interview on genetically engineered livestock for BBC Radio 4 Costing the Earcth
Year(s) Of Engagement Activity 2013
 
Description Cutting edge Festival 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Public/other audiences
Results and Impact Talk on genome edited livestock at international science festival
Year(s) Of Engagement Activity 2016
 
Description DBT workshop 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Policymakers/politicians
Results and Impact Indian Department of Biotechnology workshop on GM Livestock in Bangalore
Year(s) Of Engagement Activity 2016
 
Description EBSOC Lead Engagement Activities- Talks/Discussions 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Schools
Results and Impact The Easter Bush Science Outreach Centre (EBSOC) which opened in January 2018 is the first of its kind in Scotland. EBSOC is a unique, purpose-built laboratory space where visitors, including primary and secondary pupils and their teachers, engage with real-life science. Supported by scientists from "Complex phenotypes and genotype x environment interactions", EBSOC's schools workshops enable pupils to meet scientists from The Roslin Institute. As well as supporting scientist-lead workshops both to National and International audiences, scientists undertaking research within "Complex phenotypes and genotype x environment interactions" undertake discussions and talks within these activities on research undertaken within this theme including improving farm animal productivity and health and understanding of animal behaviour.
Year(s) Of Engagement Activity 2018
URL https://www.ed.ac.uk/easter-bush-campus/science-outreach-centre
 
Description EIFF Learning Event ­ Ideas Laboratory Laugh Off 
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 EIFF Learning Event ­ Ideas Laboratory Laugh Off. Opportunity for school pupils to ask scientist questions and discuss ideas. Created interest in science especially for female pupils.
Year(s) Of Engagement Activity 2017
 
Description Easter Bush Campus Open Day - The Roslin Institute 
Form Of Engagement Activity Participation in an open day or visit at my research institution
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Public/other audiences
Results and Impact Over 750 visitors from the general public were able to visit the University of Edinburgh's Easter Bush Campus and see behind the scenes at The Roslin Institute Building, Veterinary Teaching Building and the new Charnock Bradley Building, home of the Easter Bush Science Outreach Centre and the Roslin Innovation Centre.

They were afforded the opportunity to meet scientists and vets from The Roslin Institute, the Royal (Dick) School of Veterinary Studies, Scotland's Rural College and the Roslin Innovation Centre and have a chance to find out about their work and get hands-on with fun activities suitable for all ages.

Families found the experience very positive, with both children and adults relishing the opportunity to get 'hands on' with activities and ask questions about the science of the Institute.

Building tours were available throughout the day.

The Royal Society of Biology Scotland Branch Annual Symposium was hosted at the same event. This featured a series of short talks on the cutting-edge science of Genome Editing/CRISPR aimed at senior high school students, teachers and adults with an interest in new developmental biology.
Year(s) Of Engagement Activity 2017,2018
URL https://www.ed.ac.uk/roslin/community-engagement/public-events/campus-open-day-2018
 
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 Evonik research day 
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 my work on precision analysis of microbiomes to Evonik, an international company with over 13000 employees and with interests in chemical and food production. This was part of a one day workshop with Evonik, hosted by Roslin and focused on microbiomes
Year(s) Of Engagement Activity 2018
 
Description Exhibition 
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 The exhibition The Pig Park and Other Experiments is now open at the Museum of English Rural Life (MERL) and our newspaper and film are on show as part of the exhibition: https://merl.reading.ac.uk/event/the-pig-park/ and https://media.ed.ac.uk/media/Carnevale+/0_p0iqoasy.
Year(s) Of Engagement Activity 2018
URL https://merl.reading.ac.uk/event/the-pig-park/
 
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 Hendrix Genetcic workshop 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Industry/Business
Results and Impact Closed industry workshop on application of genetic engineering technology
Year(s) Of Engagement Activity 2016
 
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 Hosted female German Erasmus exchange student on 3 month work experience 'researcher shadowing' in my lab. 
Form Of Engagement Activity Participation in an open day or visit at my research institution
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Postgraduate students
Results and Impact Hosted female German Erasmus exchange student on 3 month work experience 'researcher shadowing' in my lab. Following her research experience she is going to apply for a masters or PhD program.
Year(s) Of Engagement Activity 2017
 
Description ISAG 2017 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Mick Watson presented work on cutting edge techniques that can be used to analyse metagenomics sequence data. ISAG is the international society for animal genetics and this was the very first microbiome session. In attendance were industry practitioners and academics
Year(s) Of Engagement Activity 2017
URL http://www.isag.us/2017/
 
Description Industry Insights Day for Women in STEM 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Undergraduate students
Results and Impact Opportunity for female undergraduate students considering a career in academia to be inspired by women in STEM. Talk and Q&A session.
Year(s) Of Engagement Activity 2018
 
Description Interview for Vet Record 
Form Of Engagement Activity A magazine, newsletter or online publication
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact News and reports in the Veterinary Record. Can play time on the farm promote animal health? (2018) Veterinary Record 182, 275.
Published online 9 March 2018.http://veterinaryrecord.bmj.com/content/182/10/275.2.info









.
Year(s) Of Engagement Activity 2018
URL http://veterinaryrecord.bmj.com/content/182/10/275.2.info
 
Description Introduction to the Research of the Roslin Institute - Royal Society of Biology Scottish Branch Annual Symposium 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Professional Practitioners
Results and Impact Professor Stevens provided an overview of the research of The Roslin Institute to members of the public and the Royal Society of Biology, who convened for the annual symposium of the RSB Scottish Branch on 14 October 2017 at Roslin. The event coincided with the annual Roslin 'Open Doors' day and featured BBSRC-funded research.
Year(s) Of Engagement Activity 2017
 
Description Invited speaker - Avian Genetics and Immunity Symposium 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Research on Avian Genetics and Immunity (RAGI) has been established to strengthen global partnerships and links between academic researchers, students and the poultry professionals working on the genetics of avian immunity. The purpose of the symposium was to provide a forum for discussion and exchange of ideas around the single theme of exploiting available opportunities in ultimately dealing emerging and existing infectious avian diseases in poultry production systems and to safeguard food supplies and human health.
The purpose of KW talk was to overview the current situation in industry for breeding for disease resistance and introduce the NARF. The overview of NARF included a review of facilities, lines available and current work being carried out using NARF avian lines. The presentation stimulated significant discussion.
Year(s) Of Engagement Activity 2017
URL http://geneticsandimmunity.com/
 
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 Jedburgh Grammar: CF Gene Therapy Lecture to Higher/Advanced Higher Biology Pupils 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Schools
Results and Impact Presentation about genetic mutations, genotypes & phenotypes and advances in gene therapy for CF
Year(s) Of Engagement Activity 2015,2016,2017,2018
 
Description Maths and biology. James Gillespies' High School 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Schools
Results and Impact 20-30 pupils and 3-4 teachers attended for presentations from my lab on how numerical skills (mathematics and computing) are applied in biological settings. One of these students, now at University has visited since the Roslin Institute to speak to other researchers.
Year(s) Of Engagement Activity 2018
 
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 Meet the Cows, Midlothian Science Festival Langhill Farm tour 
Form Of Engagement Activity Participation in an open day or visit at my research institution
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Public/other audiences
Results and Impact Meet the Cows, Midlothian Science Festival Langhill Farm tour for visitors to see the cows on the farm.
Year(s) Of Engagement Activity 2017
 
Description Meet the Cows: Midlothian Science Festival Langhill Farm Tour 
Form Of Engagement Activity Participation in an open day or visit at my research institution
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Public/other audiences
Results and Impact Meet the Cows: Midlothian Science Festival Langhill Farm Tour. Public interactions with scientists and seeing animal/farm facilities.
Year(s) Of Engagement Activity 2017
 
Description Michigan State University 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Michigan University Research Seminars with a wide variety of audience ranging from animal breeders and quantitative geneticists to medical doctors.
Year(s) Of Engagement Activity 2017
 
Description Midlorthian Science Festival Debate 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? Yes
Geographic Reach Local
Primary Audience Public/other audiences
Results and Impact Constructive and lengthy debate

Invited back to next festival
Year(s) Of Engagement Activity 2014
 
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 National Autonomous University of Mexico Webinar 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Undergraduate students
Results and Impact National Autonomous University of Mexico Webinar on Positive Animal Welfare Practices to Vet Students and Staff
Year(s) Of Engagement Activity 2018
 
Description Needle Felting with The Roslin Institute at Mini Maker Faire, EISF 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Schools
Results and Impact 150 pupils attended. Opportunity for pupils to meet with scientists to ask questions and engage in discussion. Too early to determine impact.
Year(s) Of Engagement Activity 2017
 
Description Open doors day 
Form Of Engagement Activity Participation in an open day or visit at my research institution
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Public/other audiences
Results and Impact Over 200 members of the public attended which sparked questions and discussion regarding our research
Year(s) Of Engagement Activity 2012,2013,2014,2015,2016
 
Description Oral presentation at CTLGH Annual Scientific Conference: The tropical bovine rumen metagenome associated with feed restricted diets 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Christelle Robert's talk presented the results of a pilot study focusing on the tropical bovine rumen metagenome associated with feed restricted diets. This talk led to further discussions with peers and provided scope for potential future partnerships.
Year(s) Of Engagement Activity 2018
 
Description Our Changing World Series 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Public/other audiences
Results and Impact University of Edinburgh showcase lecture on genome editing animals for food security
Year(s) Of Engagement Activity 2016
 
Description PAG 2017 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Mick Watson gave a talk at PAG 2017 on Comparison of Methods for Functional and Phylogenetic Characterisation of Rumen Metagenomic Data. Attendees include industry, professional practitioners and academics
Year(s) Of Engagement Activity 2017
 
Description PAG 2018 microbiome talk 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact I gave a talk on microbiome bioinformatics at PAG 2018 in San Diego in the microbiome session. PAG includes attendees from industry, farming and academia.
Year(s) Of Engagement Activity 2018
 
Description PCR: A Question of Taste workshop for S5 Jedburgh Grammar pupils 
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 PCR: A Question of Taste workshop for S5 Jedburgh Grammar school pupils. school pupils discussed science and asked questions.
Year(s) Of Engagement Activity 2018
 
Description Peebles High School Careers Event 
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 Sessions with individual or groups of pupils interested in careers in science. Advice on subject choices, degree programmes and shared my own experience in terms of pathways to current position.
Year(s) Of Engagement Activity 2013,2014,2015,2016,2017
 
Description Pint of Science public lecture on 'The nine months that made you, you' by Dr Paula Brunton. 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Public/other audiences
Results and Impact Pint of Science public lecture on the effect of prenatal stress and positive behaviour on offspring performance by Dr Paula Brunton at The City Café, Edinburgh, on 15 May 2017. The informal lecture was attended by approximately 40 members of the public. Although the title attracted those interested in human foetal development, the presentation highlighted ISP-funded research at Roslin using rat and pig models of prenatal stress to study trans-generational effects on offspring behaviour. An opportunity for Q&A was provided.
Year(s) Of Engagement Activity 2017
 
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 during "Africa Week" SABI event: Changes in microbial composition and functional potential associated with sub-optimal feeding in African Zebu cattle 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Professional Practitioners
Results and Impact Dr Toby Wilkinson presented a poster on the changes in microbial composition and functional potential associated with sub-optimal feeding in African Zebu cattle. This was associated with a 5-mn talk to show case the study and key findings to the audience. Very engaging audience with may discussions afterwards.
Year(s) Of Engagement Activity 2018
 
Description Presentation to USA academic visiting group 
Form Of Engagement Activity Participation in an open day or visit at my research institution
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Undergraduate students
Results and Impact Presentation of scientific work to USA agricultural faculty and students visiting Roslin Institute
Year(s) Of Engagement Activity 2017
 
Description Press release - Hair colour 
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 The story collected over 127 pieces of coverage with a potential reach of around 9 million in the UK alone. There was quite a bit of pick up in Australia too but we weren't able to get stats from there. The paper has been tweeted about more than 350 times and is still growing. The Altmetric score is already in the top 1% of all papers tracked, and is currently 14th of all Nature Communications papers.
Year(s) Of Engagement Activity 2018
URL https://www.nature.com/articles/s41467-018-07691-z/metrics
 
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 Projects Update Meeting regarding Circannual Clock in Lake District (With collaborators in University of Manchester, The Arctic University of Norway, and various interested emeritus professors) 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact Two days of talks, discussions and planning meetings with participants and scientific advisors regarding progress on sheep circannual related projects.
Year(s) Of Engagement Activity 2018
 
Description Public Event- Cute Egg 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Schools
Results and Impact Cute Egg has been developed at The Roslin Institute and taken to a wide range of events including Campus Open Day Events, Agricultural Shows and school visits, Primary school pupils and members of the public took part in this hands-on activity which reveals the invisible cuticle layer on hen's eggs and the links to current research at The Roslin Institute. Participants were encouraged to make predictions about the outcome of their egg dyeing experiment and measure the outcomes, highlighting the process and importance of the scientific method. The activity also highlighted connections between fundamental research and improved food safety.
Year(s) Of Engagement Activity 2018
URL https://www.ed.ac.uk/easter-bush-campus/science-outreach-centre
 
Description Question of Taste PCR Masterclass 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Schools
Results and Impact Practical workshop run by the Roslin Institute public engagement outreach team to allow High School pupils to run PCRs and investigate the genetics of a specific taste receptor.
Year(s) Of Engagement Activity 2018
 
Description Researcher Links workshop at CNRG, INIFAP, Tepatitlán and Guadalajara, Mexico, 3-7 February 2018 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Postgraduate students
Results and Impact Workshop organised and given by me and the members of my group
Year(s) Of Engagement Activity 2018
 
Description Roslin Doors Open Day 
Form Of Engagement Activity Participation in an open day or visit at my research institution
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Public/other audiences
Results and Impact Volunteer at Campus open day - Almas Gheyas. Describing CTLGH work to general public.
Year(s) Of Engagement Activity 2018
 
Description Roslin Institute Doors Open Day 
Form Of Engagement Activity Participation in an open day or visit at my research institution
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Public/other audiences
Results and Impact Volunteered at The Roslin Institute Doors Open Day with a CTLGH-dedicated activity (poster-based activity) describing the CTLGH objectives, work achieved within the center and future strategies.
Year(s) Of Engagement Activity 2018
 
Description Roslin Open door day 
Form Of Engagement Activity Participation in an open day or visit at my research institution
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Public/other audiences
Results and Impact Open day to public to show case the work of the institute
Year(s) Of Engagement Activity 2018
 
Description Royal Highland Show, Roslin Institute Stand 
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 Flu-fighters and Genetic Toolbox activities that highlight ongoing research at Roslin Institute
Year(s) Of Engagement Activity 2014,2017
 
Description Rumen microbiome article in Farmer's Weekly 
Form Of Engagement Activity A magazine, newsletter or online publication
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact Mick Watson was personally interviewed for an article in Farmer's weekly on the potential impact of our rumen microbiome work (doi:10.1038/s41467-018-03317-6) on breeding for production traits in beef and dairy cattle.
Year(s) Of Engagement Activity 2018
URL http://www.fwi.co.uk/livestock/rumen-genotyping-advances-enhance-cattle-breeding.htm
 
Description Rumen microbiome work in the national press (print editions) 
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 Various articles about our rumen microbiome work appeared in the national press, including: Scottish Daily Express, Scottish Sun, The Scotsman and the Press and Journal
Year(s) Of Engagement Activity 2018
URL https://www.pressandjournal.co.uk/fp/business/farming/1427948/cow-digestion-discovery-could-boost-pr...
 
Description Rumen microbiome work on National Public Radio (NPR) in the USA 
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 Our rumen microbiome work was featured on NPR.org, (National Public Radio), a US news network that has over 7 million followers on Twitter and reaches millions of people online and via radio. The article was immediately syndicated across an additional ~40 NPR-associated websites
Year(s) Of Engagement Activity 2018
URL https://www.npr.org/sections/thesalt/2018/03/06/589997622/mysteries-of-the-moo-crobiome-could-tweaki...
 
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 School Visit (Dunbar primary School) summer school workshop "Animals Inside and Out" for disadvantaged children 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Schools
Results and Impact Animals Inside out. Summer workshop for disadvantaged school pupils at Dunbar Primary School about animals. 15 school pupils aged 8 to 10.
The school reported a keen interest by the pupils and a request was received to run the workshop again next year.
Year(s) Of Engagement Activity 2018
 
Description School Workshop- DNA Profiling: The Great Escape 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Schools
Results and Impact This workshop was developed and run at the Easter Bush Science Outreach Centre where pupils aged 13-18 took part in this hands-on, researcher-supported workshop linking the techniques of DNA extraction and gel electrophoresis to research on animal behaviour. Participants gained an insight into real-life research and a chance to meet scientists as part of the session and reported an increased interest in science after the session.
Year(s) Of Engagement Activity 2018,2019
URL https://www.ed.ac.uk/easter-bush-campus/science-outreach-centre
 
Description Science Insights for Schools 
Form Of Engagement Activity Participation in an open day or visit at my research institution
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Schools
Results and Impact We ran our Science Insights work experience programme for local school pupils July 2018. 5 pupils attended, 20 of whom worked in the Roslin Institute for 2 days alongside BBSRC-supported researchers from this ISP, including our core-funded staff scientists. All pupils had a tour of the Langhill farm and attended a presentation and debate about the use of animals in research. Pupils ad the opportunity to discuss career paths and what it is like to work as a research scientist.
Year(s) Of Engagement Activity 2018
 
Description Science Insights work experience for S5 school pupils 
Form Of Engagement Activity Participation in an open day or visit at my research institution
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Schools
Results and Impact We ran our Science Insights work experience programme for local school pupils on 24-28 July 2017. 38 S5 pupils attended, 20 of whom worked in the Roslin Institute for 2 days alongside BBSRC-supported researchers from this ISP, including our core-funded staff scientists. All 38 students also had a tour of the Langhill farm and attended a presentation and debate about the use of animals in research. Students also had the opportunity to discuss career paths and what it is like to work as a research scientist.
Year(s) Of Engagement Activity 2017
URL https://www.ed.ac.uk/roslin/working/opportunities/young-people/science-insights
 
Description Seminar - MRC Centre for Neuropsychiatric Genetics and Genomics 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact Part of research institution seminar series
Year(s) Of Engagement Activity 2017
 
Description Seminar: "Neuroendocrine and environmental interactions underlying reproductive behaviour in birds" The Department of Zoology and Physiology, The University of Wyoming, Laramie, USA. 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Seminar: "Neuroendocrine and environmental interactions underlying reproductive behaviour in birds" The Department of Zoology and Physiology, The University of Wyoming, Laramie, USA. Inspired women in STEm. This has sparked an exchange partnership between University of Wyoming and Roslin. I hosted a visiting group composed of undergraduate students in Jan 2018 from University of Wyoming.
Year(s) Of Engagement Activity 2017
 
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 Stand at the Royal Highland Show, including Genetic Toolbox exhibit. 
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 Roslin Institute stand at the Royal Highland Show 22-25 June 2017. Approximately 25 Roslin Institute staff and students were involved. Exhibits of relevance to this ISP included A Genetic Toolbox exhibit, highlighting the heritable nature of traits and how these can be selected or changed.
Year(s) Of Engagement Activity 2017
 
Description Student visit from the University of Wyoming USA 
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 18 students and staff from the University of Wyoming (Honours year, Hope College) attended an afternoon discussion on research at the Roslin Institute. A tour of the Institute and outreach centre was also given. There was much discussion and questions. The was a request to run the event again next year and students reported that this was the best visit out off their whole visit to Europe.
Year(s) Of Engagement Activity 2018
 
Description Summer course 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Postgraduate students
Results and Impact Armidale Animal Breeding Summer Course 2018: Mathematical modeling of infection dynamics in genetically diverse livestock populations
Teachers: Andrea Doeschl-Wilson and Osvaldo Anacleto
Dates: Monday 5 February 2018 (9am) - Thursday 8 February 2018 (4pm)
Venue: University of New England, Armidale, NSW Australia; ~40 post-graduate students, academics and industrial researcher attended the workshop in modelling. Based on the positive course evaluation, the course sparked new research in the important field of mathematical modelling of infection dynamics and genetics
Year(s) Of Engagement Activity 2018
URL https://jvanderw.une.edu.au/aabc2018.htm
 
Description TEDx Talk by Professor Helen Sang on 'Why do we need GM chickens?' 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Public/other audiences
Results and Impact Professor Helen Sang delivered a Tedx Talk in Glasgow on 2 June 2017 on 'Why do we need GM chickens?'. The event was attended by approximately 1700 people and has been shared online with over 900 views. It highlighted the challenge of achieving global food security and the potential of BBSRC-funded research to improve poultry, including via genetic alteration. Examples for ongoing research using GM poultry in this programme were shared.
Year(s) Of Engagement Activity 2017
URL https://www.youtube.com/watch?v=DUbqrh5otWs
 
Description Talk ISGC workshop PAGXXV, San Diego, CA, USA, 2017 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact A talk on "Genome Wide Transcript and Methylation Changes in the Sheep Seasonal Clock" to the workshop organized by the International Sheep Genome Consortium. This included an update on the current progress on genotyping/resequencing exotic breeds with seasonal phenotypes. There were a number of questions and discussion as to how seasonal biology could be important in other agricultural traits (e.g. seasonal epigenetic control of salmon maturation).
Year(s) Of Engagement Activity 2017
URL http://www.intlpag.org/2017/program/workshop-list-xxv
 
Description Talk at One health models of Infectious disease workshop 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Professional Practitioners
Results and Impact A. Wilson provided invited talk on Statistical modelling of health trajectories. The purpose of the talk was to demonstrate the power of collecting longitudinal health data in model species, outbred livestock populations and humans.
Year(s) Of Engagement Activity 2018
 
Description Talk at the Roslin Computational Genetics Discussion Group 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Professional Practitioners
Results and Impact Talk entitled "Genome Wide Transcript and Methylation Changes in the Sheep Seasonal Clock". There were useful questions on the status of EYA3 as a candidate seasonal regulator and discussion on the application of the work to breeding for seasonal phenotypes. An overview of the progress on resequencing exotic breeds was also discussed, which was of particular relevance to the genetics audience.
Year(s) Of Engagement Activity 2017
URL https://www.wiki.ed.ac.uk/display/RCG/Computational+Genetics+Discussion+Group
 
Description Talk: Compassion in World Farming 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Public/other audiences
Results and Impact Talk; compassion in world farming. large group of academics from fields as varied as environment, philosophy and literature add weight and credibility to list of Vision signatories:
Year(s) Of Engagement Activity 2019
URL https://www.ciwf.org.uk/about-us/patrons-and-high-profile-supporters/visionaries/academia/professor-...
 
Description Talks and tour of Roslin for visiting US Agriculture Undergraduate Students 
Form Of Engagement Activity Participation in an open day or visit at my research institution
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Undergraduate students
Results and Impact Talks and tour of Roslin for visiting US Agriculture Undergraduate Students sparking discussion and questions.
Year(s) Of Engagement Activity 2017
 
Description The Food Chain 
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 BBC World Service radio interview on genetically engineered livestock for The Food Chain
Year(s) Of Engagement Activity 2018
 
Description 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 Royal Highland Show, Cute Egg: Providing a safe supply of eggs to hatch the next generation of chickens.
Activity over 4 days of the Royal Highland Show in Edinburgh. It sparked questions and discussions and the visitors reported increased interest in the subject.
Year(s) Of Engagement Activity 2018
URL https://www.ed.ac.uk/roslin/community-engagement/resources/cute-egg
 
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 USDA Visit July 2017 - African Sheep and Goat Projects 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Other audiences
Results and Impact In July 2017 Ben Rosen and Gordon Spangler from the United States Department for Agriculture, Beltsville Agricultural Research Center (USDA ARS) visited the Roslin Institute to give a seminar hosted by the Centre for tropical Livestock Genetics and Health. The titles of the seminars were as follows: Gordon Spangler "The Role of Small Ruminants in the Face of Global Climate Change" and Ben Rosen "African Goat Improvement Network: Community-Based Breeding Programs for the Genetic Improvement of Goats in Small-holder Communities". Both scientists based in Curt Van Tassell's research group have been involved in large genetics and genomics projects, developing new tools and resources for small ruminants, including the new de novo assembly of the domestic goat https://www.nature.com/ng/journal/v49/n4/full/ng.3802.html, varGoats http://www.goatgenome.org/vargoats.html and the African Goat Improvement Network (AGIN) https://www.ars.usda.gov/office-of-international-research-programs/ftf-livestock-improvement/ . The visit highlighted significant potential collaboration on the African goat and sheep whole genome sequencing projects from the Data and Resources grants awarded to Roslin.
Year(s) Of Engagement Activity 2017
 
Description University visit (Nottingham) 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Undergraduate students
Results and Impact Gave a talk on Positive Animal Welfare to veterinary and animal science students and staff at The University of Nottingham
Year(s) Of Engagement Activity 2018
 
Description University visit (Vienna) 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Undergraduate students
Results and Impact Seminar on Positive Animal Welfare practices to veterinary and animal science students and staff at The University of Vienna, Austria.
Year(s) Of Engagement Activity 2018
 
Description Various articles on rumen microbiome work 
Form Of Engagement Activity A magazine, newsletter or online publication
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Various online websites picked up our press release on our rumen microbiome work (doi:10.1038/s41467-018-03317-6) including:
https://phys.org/news/2018-02-dna-cow-stomachs-aid-meat.html
https://www.sciencedaily.com/releases/2018/02/180228085347.htm
http://www.labmanager.com/news/2018/02/dna-study-of-cow-stomachs-could-aid-meat-and-dairy-production#.WpwhWOjFLZs
https://www.technologynetworks.com/genomics/news/cows-guts-could-hold-secrets-to-more-meat-and-milk-298080
http://www.sciencenewsline.com/news/2018030111510072.html
https://www.eurekalert.org/pub_releases/2018-02/uoe-dso022718.php
http://biofuelsdigest.com/nuudigest/2018/02/28/cow-stomach-microbes-could-hold-key-for-increased-food-and-biofuel-production/
Year(s) Of Engagement Activity 2018
URL https://www.sciencedaily.com/releases/2018/02/180228085347.htm
 
Description Visit by Bill Gates and the Secretary of State for the Department of International Development 
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 Public/other audiences
Results and Impact Bill Gates and the Secretary of State for the Department of International Development (DfID; Rt Hon Penny Mordaunt) visited The Roslin Institute on 26 January 2018. This involved separate sessions with the Gates Foundation and DfID to learn about the research undertaken by the Centre for Tropical Livestock Genetics & Health (CTLGH), in which the Roslin Institute is a major partner and researchers in the Institute Strategic Programmes are heavily involved. DfID announced £4m of funding for the CTLGH, adding to £10m already received from the Gates Foundation. In the presence of the Principal of the University of Edinburgh, Bill Gates and the Rt Hon Penny Mordaunt formally opened the Global Academy for Agriculture & Food Security which will provide undergraduate and postgraduate training in sustainable agriculture. The event took place in the new Campus Innovation Building (which received BBSRC strategic funding). The University of Edinburgh press office tracked the following activity related to the visit, in which many participants in the ISPs were involved:

• 109 individual articles and broadcast pieces that mentioned the University with regards to the visit, with an estimated potential reach of more than 7 million people.

• Of these, more than half of the coverage mentioned one of more of the Global Academy of Agriculture & Food Security, the Centre for Tropical Livestock Genetics & Health, SEBI, the Royal (Dick) School of Veterinary Studies, Roslin or the Easter Bush Campus in addition to name checking the University.

• In addition to the UK, we also attracted press coverage in the USA, France, New Zealand, China, Zimbabwe, South Africa, Botswana, Taiwan and Egypt.

• Across social media, we reached more than 1.4 million people with 14k+ engagements (likes, shares, retweets etc). Of these, 99.8% were positive.

• The Facebook Live streaming alone reached more than 100k people. More than 18k people have watched the video.

• Our news videos have garnered more than 35k views across platforms.

• We tracked a spike in traffic to the Global Academy website on the day of the visit - 1405 visits (11 times the average for the previous month).
Year(s) Of Engagement Activity 2018
 
Description Visit to Iowa State University to give talk and discuss my research 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Postgraduate students
Results and Impact On October 8th 2018 I gave a talk to approx. 100 post-graduate students at Iowa State University in the Immunology and Neurobiology research programmes. I also attended small workshop group sessions with the students to discuss my science and also give career advice etc.
Year(s) Of Engagement Activity 2018
 
Description Wellcome Trust Schools Symposium 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Schools
Results and Impact Opening speaker in the Wellcome Trust Summer Symposium for school students (penultimate year of school), discussed the use of genetic techniques in agriculture and how my career developed in science.
Year(s) Of Engagement Activity 2018
 
Description Why use animals in research, Campus open day. 
Form Of Engagement Activity Participation in an open day or visit at my research institution
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Public/other audiences
Results and Impact discussion regarding animal use in research stand as part of the Campus open day
Year(s) Of Engagement Activity 2017
 
Description Wiki-website for vaccine effectiveness in the field 
Form Of Engagement Activity Engagement focused website, blog or social media channel
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact A wiki-website was developed at the University of Edinburgh wiki-server under the link: https://www.wiki.ed.ac.uk/display/saphir/ as an outcome of the H2020 project Saphir. The wiki-website outlines risk factors that compromise vaccine effectiveness in the field, with a specific emphasis on PRRS. The website includes a user friendly modelling app based on a predictive model created as part of the Saphir project that predicts the impact of vaccination, that will help a wide range or people interested in vaccine effectivenes in the field to extract conclusions regarding the factors that put in risk the infection invasion in a herd and the factors that mitigate disease spread and pathogen evolution in farm animal populations.
Year(s) Of Engagement Activity 2019
URL https://www.wiki.ed.ac.uk/display/saphir/
 
Description Working group meeting on the causes of keel bone damage 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Industry/Business
Results and Impact featured a mixture of talks about environmental, genetic, and nutritional causes of keel bone fracture alongside speakers on the etiology and pathology of
fractures. In addition to lectures, the meeting will be organized as a workshop allowing for discussion with planned deliberations intended to produce a review of the field.
Year(s) Of Engagement Activity 2019
URL http://www.keelbonedamage.eu/wp-content/uploads/Flyer-Working-Group-Meeting.pdf
 
Description article around a novem method to monitor blood flow in pregnant pigs 
Form Of Engagement Activity A magazine, newsletter or online publication
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Industry/Business
Results and Impact article around a novel method to monitor blood flow in pregnant pigs appeared on Roslin Institute webpages, plus departmental webpages of University of Edinburgh plus as an article in various industry publications
Year(s) Of Engagement Activity 2018
URL https://doi.org/10.1071/RD17298
 
Description article around gene expression and sex differences 
Form Of Engagement Activity A magazine, newsletter or online publication
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Other audiences
Results and Impact article around gene expression and sex differences appeared on Roslin Institute webpages and University of Edinburgh departmental webpages plus also appeared in a food industry publication
Year(s) Of Engagement Activity 2018
URL https://doi.org/10.1186/s13293-018-0178-6
 
Description named biotechnology speaker on US Ste |Department Economic Bureau Outreach Fund 
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 International workshop top engage stakeholders in genetic engineering technology and applications
Year(s) Of Engagement Activity 2015