Population sequencing of tropically-adapted sheep and sheep with defined or rare phenotypes
Lead Research Organisation:
University of Edinburgh
Department Name: The Roslin Institute
Abstract
Abstracts are not currently available in GtR for all funded research. This is normally because the abstract was not required at the time of proposal submission, but may be because it included sensitive information such as personal details.
Technical Summary
The project aims to provide genomic data on livestock populations in Africa and Asia, and improved genomic references. The aim of our work is to translate modern genomic tools that are widely-applied in genetic improvement in western livestock to cost-effective genotyping tools and breeding strategies for improved animals that can be made available to small-holder farmers.
Planned Impact
unavailable
Organisations
- University of Edinburgh (Lead Research Organisation)
- University of Dschang (Collaboration)
- U.S. Department of Agriculture USDA (Collaboration)
- UNIVERSITY OF NOTTINGHAM (Collaboration)
- Shetland Sheep Society (Collaboration)
- International Livestock Research Institute (ILRI) (Collaboration)
- Cameroonian Academy of Sciences (Collaboration)
- Rare Breeds Survival Trust (RBST) (Collaboration)
- Scotland's Rural College (Collaboration)
People |
ORCID iD |
| Michael Watson (Principal Investigator) |
Publications
Ahbara A
(2022)
Natural adaptation and human selection of northeast African sheep genomes
in Genomics
Nandolo W
(2021)
Detection of copy number variants in African goats using whole genome sequence data.
in BMC genomics
Wiener P
(2021)
Whole-Genome Sequence Data Suggest Environmental Adaptation of Ethiopian Sheep Populations.
in Genome biology and evolution
| Description | This project is split into three parts: 1) Sequencing of East African sheep, 2) Sequencing of West African sheep and 3) Sequencing of sheep with rare phenotypes. For the first part of the project we have generated whole genome sequence data for 130 East African sheep (112 from Ethiopia and 18 from Libya). 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, and from a population of Libyan Barbary sheep 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. The second part of the project is focused on sequencing West African sheep. We have generated whole genome sequence at 15x coverage from 20 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 are being genotyped on the Ovine 50K SNP Chip to select focal individuals for sequencing. In the third part of project we sequenced 50 rare breeds of primitive sheep from phenotypic extremes regarding the timing and duration of breeding season. These were also sequenced at 30x on the HiSeqX. Surprisingly, the strongest signatures of selection we identified were enriched for genes and loci involved in neurological development. This highlights the historic importance of behavioural selection in the domestication of primitive sheep breeds. It also indicates that hypothalamic neural development may have been an important target for the genetic selection of a desirable breeding season in these breeds. Using the whole genome sequencing dataset we have generated we were able to identify 3 million SNPs across 12 Ethiopian sheep populations. We then applied landscape genomics approaches to investigate the association between these variants and environmental variables. Our results indicated that environmental adaptation for precipitation related variables was stronger than that related to other environmental variables including altitude or temperature. We were able to identify a set of genes showing association with environmental variables that were enriched in blood and nerve tissues. The results provide a foundation to investigate further the effects of climatic variables on tropical small ruminant populations |
| Exploitation Route | We have performed whole genome analysis on the East and West African sheep datasets, including genome structure, gene content, gene duplication and copy number variant analysis. Roslin is co-leading a working group within the VarGoats consortium focused on comparative analysis of the goat genome sequence data with other ruminants, which we will facilitate using the African sheep datasets we have generated. The West African sheep samples are being analysed particularly for polymorphisms in immune genes as these sheep are anecdotally tolerant to Trypanosomes. We are making all of the whole genome sequence data for sheep publicly available via the NCBI short read archive, in order that it is included in the next run of variant calling for the sheepgenomesbd.org project. This will greatly increase the variant information currently available for African sheep and ensure they are represented in new genotyping technologies developed by the International Sheep Genomics Consortium. 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. |
| Sectors | Agriculture Food and Drink |
| Description | A global shared data biological sample resource to support productivity improvement for tropical livestock |
| Amount | £5,000,000 (GBP) |
| Organisation | Bill and Melinda Gates Foundation |
| Sector | Charity/Non Profit |
| Country | United States |
| Start | 09/2015 |
| End | 09/2020 |
| Description | GCRF Data and Resources round 2 |
| Amount | £220,000 (GBP) |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 09/2017 |
| End | 07/2018 |
| Description | GCRF Impact Accelerator |
| Amount | £300,000 (GBP) |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 09/2017 |
| End | 07/2018 |
| Title | Comparing selection in breeds of sheep with long and short breeding season |
| Description | We sequenced 50 individuals from rare breeds of primitive sheep 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. |
| 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 | 2019 |
| Provided To Others? | Yes |
| 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 sheep that can be made available to small-holder farmers. |
| URL | https://www.ncbi.nlm.nih.gov/bioproject/PRJNA523711/ |
| 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 have been sequenced at 15x coverage. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2019 |
| Provided To Others? | Yes |
| 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. |
| URL | https://www.ncbi.nlm.nih.gov/bioproject/PRJNA523711/ |
| Description | Cameroon Academy of Sciences - Cameroon Sheep Project |
| Organisation | Cameroonian Academy of Sciences |
| Country | Cameroon |
| Sector | Academic/University |
| PI Contribution | We are genotyping and sequencing DNA samples from Cameroon sheep collected by collaborators at the University of Dschang and the Cameroonian Academy of Sciences from a diverse set of ecosystems across Cameroon. We will analyse the resulting data with collaborators in Cameroon and at the USDA. |
| Collaborator Contribution | Vincent Tanya at the Cameroon Academy of Sciences both helped to facilitate and also undertook the field work, with collaborators at the University of DSchang, for sample collection of ear notch tissue biopsies from Cameroon sheep from a diverse set of ecosystems across Cameroon. |
| Impact | There no outputs from this project yet. The samples have been collected, DNA extracted and have been shipped to Roslin for genotyping and sequencing. |
| Start Year | 2017 |
| Description | Cameroon Blackbelly Sheep Project |
| Organisation | University of Dschang |
| Country | Cameroon |
| Sector | Academic/University |
| 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 | Centre for tropical livestock genetics and health (CTLGH) |
| Organisation | International Livestock Research Institute (ILRI) |
| Country | Kenya |
| Sector | Charity/Non Profit |
| PI Contribution | Mick Watson is co-leading programme 5 (informatics and bioresources) programme of CTLGH which aims to collect data on genotype and phenotype into a central database which can subsequently be mined for useful associations. So far we have ensured that scientists have access to the latest high performance computing environment for research, we have analysed and continue to analyse hundreds of farm animal genomes from LMIC countries, and we have built the data portal (http://data.ctlgh.org) |
| Collaborator Contribution | The partners are involved in all programmes, which include:Program 1: Harnessing genetic variability among indigenous and exotic breeds of cattle (as well as their crosses) to develop genetic and genomic tools that will be used to improve productivity under harsh tropical conditions and to mitigate the impact of cattle on climate change. Program 2: Harnessing genetic variability in tropical productivity and adaptation among various breeds of Chickens. Program 3: Development and application of precision breeding (through novel reproductive and germplasm technologies) to achieve step changes in livestock genetic improvement. Program 4: Understanding the genetic and molecular mechanisms underlying the tolerance of certain cattle and poultry breeds to tropical diseases and pests. Program 5: A shared global data and biological sample resource to support continued research and development on tropical livestock genetics and health. |
| Impact | The data portal so far: http://data.ctlgh.org The collaboration is multi-disciplinary, bringing together geneticists, parasitologists, virologists, epidemiologists and data scientists together. |
| Start Year | 2016 |
| Description | Centre for tropical livestock genetics and health (CTLGH) |
| Organisation | Scotland's Rural College |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | Mick Watson is co-leading programme 5 (informatics and bioresources) programme of CTLGH which aims to collect data on genotype and phenotype into a central database which can subsequently be mined for useful associations. So far we have ensured that scientists have access to the latest high performance computing environment for research, we have analysed and continue to analyse hundreds of farm animal genomes from LMIC countries, and we have built the data portal (http://data.ctlgh.org) |
| Collaborator Contribution | The partners are involved in all programmes, which include:Program 1: Harnessing genetic variability among indigenous and exotic breeds of cattle (as well as their crosses) to develop genetic and genomic tools that will be used to improve productivity under harsh tropical conditions and to mitigate the impact of cattle on climate change. Program 2: Harnessing genetic variability in tropical productivity and adaptation among various breeds of Chickens. Program 3: Development and application of precision breeding (through novel reproductive and germplasm technologies) to achieve step changes in livestock genetic improvement. Program 4: Understanding the genetic and molecular mechanisms underlying the tolerance of certain cattle and poultry breeds to tropical diseases and pests. Program 5: A shared global data and biological sample resource to support continued research and development on tropical livestock genetics and health. |
| Impact | The data portal so far: http://data.ctlgh.org The collaboration is multi-disciplinary, bringing together geneticists, parasitologists, virologists, epidemiologists and data scientists together. |
| Start Year | 2016 |
| Description | Collaboration with the Rare Breed Survival Trust (RBST) to study the genetics of rare breeds of sheep |
| Organisation | Rare Breeds Survival Trust (RBST) |
| Country | United Kingdom |
| Sector | Charity/Non Profit |
| PI Contribution | Sampling and resequencing DNA from rare breed sheep. This assists our research into identifying the genetics and selection of seasonal phenotypes and also has a wider impact for RBST, for UK agriculture, and globally in understanding and preserving the genetics of rare breeds. The collaboration also allows us to effectively disseminate the latest research to the rare breeds community via the RBST farmers network and publications. |
| Collaborator Contribution | RBST provide specialist knowledge of the breeds that RSBT manage. An introduction to breeders for obtaining genetics samples. Feedback and consultation on design and ethical evaluation of the research. A network for the dissemination of research finding. |
| Impact | We collected DNA for WGS from rare breed Portland sheep. RBST provided the introduction to relevant breeders and approval and feedback on the letter of introduction and informed consent. RBST recently extended an invitation to publish an article in their breeding magazine to update members on research outcomes. |
| Start Year | 2016 |
| Description | Collaboration with the Shetland Sheep Society (SSS) to study the genetics of rare breeds of sheep |
| Organisation | Shetland Sheep Society |
| Country | United Kingdom |
| Sector | Charity/Non Profit |
| PI Contribution | Sampling and resequencing DNA from rare breed sheep. This assists our research into identifying the genetics and selection of seasonal phenotypes and also has a wider impact for SSS, for UK agriculture, and globally in understanding and preserving the genetics of rare breeds. The collaboration also allows us to effectively disseminate the latest research to the rare breeds community via the SSS farmers network and publications. |
| Collaborator Contribution | SSS provide specialist knowledge of the breeds that SSS manage. An introduction to breeders for obtaining genetics samples. Feedback and consultation on design and ethical evaluation of the research. A network for the dissemination of research finding. |
| Impact | We collected DNA for WGS from rare breed Shetland breed sheep. SSS provided the introduction to relevant breeders. |
| Start Year | 2016 |
| Description | Ethiopian and Libyan Sheep Sequencing |
| Organisation | University of Nottingham |
| Department | Faculty of Medicine & Health Sciences |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | We have sequenced the genomes, at 30x coverage on the Illumina HiSeqX platform, of 120 Ethiopian sheep from several different breeds, including Menz, Bongo and Afar, aswell as 10 Libyan Barbary sheep. We have called variants on this dataset and provided .vcf files to our collaborators. We are analysing the data for gene content, polymorphisms in immune genes, structural variation and comparative analysis with whole genome sequencing data from African goats. |
| Collaborator Contribution | We are collaborating with Olivier Hanotte and a PhD student Abulgasim Ahbara on this project. Professor Hanotte has a joint appointment with ILRI Ethiopia and was able to obtain permission to collect these samples from Ethiopia and Libya. With the PhD student he oversaw collection of the samples from sheep in Libya and Ethiopia, extraction of the DNA and shipping of the samples to Nottingham then to Roslin. Abulgasim Ahbara has been analysing the whole genome sequencing data using the .vcf files provided by us and has also generated 50K genotyping data from these and a wider subset of samples which will contribute to his PhD thesis. |
| Impact | The PhD student who has been working on this data, Abulgasim Ahbara, has presented some of this data as a poster at the Livestock Genomics Meeting in Cambridge 2016, ISAG Dublin 2017 and Pop Group Bristol 2017. There are no other outputs and outcomes at this stage. |
| Start Year | 2016 |
| Description | ILRI |
| Organisation | International Livestock Research Institute (ILRI) |
| Country | Kenya |
| Sector | Charity/Non Profit |
| PI Contribution | We work with ILRI on all aspects of genomics and data science, including whole genome sequencing of multiple African animals, data recording and database design, web and web content development, and bioinformatics training. |
| Collaborator Contribution | We work with ILRI on all aspects of genomics and data science, including whole genome sequencing of multiple African animals, data recording and database design, web and web content development, and bioinformatics training. |
| Impact | So far we have sequenced the genomes of approx 800 African farm animals from diverse breeds and ecotypes |
| Start Year | 2016 |
| Description | USDA ONT sequencing of sheep and goat genomes |
| Organisation | U.S. Department of Agriculture USDA |
| Department | Beltsville Agricultural Research Center |
| Country | United States |
| Sector | Academic/University |
| PI Contribution | We are working to generate long read genome assemblies for breeds of sheep and goats from across the globe to generate a pan genome. We plan to use Oxford Nanopore technologies and are extracting DNA, preparing sequencing libraries and sequencing ONT libraries at Roslin for this purpose. We plan to use a trio-binning approach and start with the Texel x Scottish Blackface cross. To this end we have brought up ovine embryonic fibroblasts from this cross and frozen cell pellets ready for DNA extraction. |
| Collaborator Contribution | The USDA are coordinating sheep and goat long read genome assembly sequencing efforts and plan to send us flow cells to generate some of these assemblies at Roslin. They are also providing their expertise in the generation of trio-binned assemblies and are facilitating acquiring some of the samples from other partners for sequencing. |
| Impact | No outputs or outcomes to report to date. |
| Start Year | 2021 |
| 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 | CTLGH Annual General Meeting Small Ruminant Functional Genomics Talk |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Other audiences |
| Results and Impact | The Centre for Tropical Livestock Genetics and Health (CTLGH) held it's annual general meeting in Naivasha Kenya in September 2018. Emily Clark gave a presentation on small ruminant functional genomics within CTLGH. The was a panel discussion at the end of the session which covered some of the key points raised by all the speakers in the session and areas for possible development and collaboration. Participants at the meeting including industry representatives, researchers, funders and representatives from government organisations. |
| Year(s) Of Engagement Activity | 2018 |
| Description | CTLGH Annual Meeting - Transformative Technologies for Small Ruminant Breeding |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Other audiences |
| Results and Impact | At the Annual General Meeting for the Centre for Tropical Livestock Genetics and Health in September 2019 Emily Clark in collaboration with Mike Coffey (SRUC) gave a presentation entitled 'Transformative Technologies for Small Ruminant Breeding'. This presentation summarised current projects to investigate loci underlying adaptation to a tropical environment and new concepts for small ruminant breeding including surrogate sire technology. The presentation raised several points for discussion and potential for future collaboration and activity. |
| Year(s) Of Engagement Activity | 2019 |
| Description | CTLGH Small Ruminants Strategy Meeting 2nd - 5th June 2020 |
| Form Of Engagement Activity | A formal working group, expert panel or dialogue |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Other audiences |
| Results and Impact | The Centre for Tropical Livestock Genetics and Health (CTLGH) Small Ruminants Strategy Meeting, held as a zoom tele-conference, 2nd - 5th June 2020. The overall objective of the meeting was "to have initiated the development of a strategy for the CLTGH Small Ruminants Programme for the next 10 years". There were 32 attendees from across the globe. The meeting was organized by the CTLGH small ruminant programme, Emily Clark and Appolinaire Djikeng, and facilitated by Mike Coffey. The next step of the meeting will be to determine a plan of action for small ruminants to better identify fundable projects of significant scale, building on ideas from this meeting and elsewhere, and develop these. |
| Year(s) Of Engagement Activity | 2020 |
| Description | Easter Bush Research Seminar The Sheep Gene Expression Atlas |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Postgraduate students |
| Results and Impact | In April 2019 Emily Clark was invited to give the Easter Bush Campus Research Seminar at the Roslin Institute. She gave a seminar entitled 'The sheep gene expression atlas project and beyond'. During the seminar she described the sheep gene expression atlas project and work in CTLGH sequencing the genomes of tropically adapted sheep and goats. In the audience were researchers from the Roslin Institute, postgraduate and undergraduate students and some clinicians, as well as researchers from the Moredun Institute. There were a number of questions, relating to transcriptomics in sheep and goats and a number of opportunities for further collaboration were discussed. |
| Year(s) Of Engagement Activity | 2019 |
| URL | https://www.ed.ac.uk/roslin/news-events/scientific-events/archive/building-model-transcriptome-rumin... |
| Description | Ethiopian Sheep - 5th Annual Danish Bioinformatics Conference |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Postgraduate students |
| Results and Impact | Pam Wiener gave a presentation on the 22nd of August 2019 at the 5th Annual Danish Bioinformatics Conference entitled 'Probing the genome to investigate history and phenotype using informed experimental design'. This presentation included analysis of signatures of selection, population diversity and adaptation using the whole genome sequencing dataset we generated for Ethiopian sheep. |
| Year(s) Of Engagement Activity | 2019 |
| Description | International Sheep Veterinary Society 2017 CTLGH |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Emily Clark, Bruce Whitelaw and Peter Freeman gave an overview of the small ruminant genetics and genomics projects within the Centre for Tropical Livestock Genetics and Health at the International Sheep Veterinary Society Conference held in Harrogate, UK. They were asked by the organiser of the session to give an overview how genetics and genomics can be applied in community based breeding programs for sheep and goats and to highlight new and proposed projects that might be of interest to delegates at the conference. The session included some debate on the barriers to implementing community based breeding programmes for small ruminants in Africa and Asia and potential strategies to over come these. There was a strong veterinary perspective and the focus of the session was on downstream impact. |
| Year(s) Of Engagement Activity | 2017 |
| Description | Plant and Animal Genome XXVII Conference 2019 Small Ruminant Functional Genomics within CTLGH |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Other audiences |
| Results and Impact | Emily Clark gave an overview of functional genomics in small ruminants at the Roslin Institute and within the Centre for Tropical Livestock Genetics and Health at the International Goat Genomics Workshop at the Plant and Animal Genomes Conference 2019. She described how the Centre for Tropical Livestock Genetics and Health supports programs that improve livestock-based livelihoods in the tropics and how through the CTLGH partnership we are utilizing available resources to apply functional genomics to tropically adapted sheep and goats. Participants in the VarGoats, African Goat Improvement Network and ADAPTMAP projects were present and there were some discussions around gaps in the sampling and plans to include Asian animals in future activity. |
| Year(s) Of Engagement Activity | 2019 |
| URL | https://pag.confex.com/pag/xxvii/meetingapp.cgi/Paper/37370 |
| Description | Presentation to Gates Foundation and DfID |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Policymakers/politicians |
| Results and Impact | Mick Watson presented work on African farm animal genomics and data science to attendees from the Bill and Melinda Gates Foundation (BMGF) and the department for international development (DfID) |
| Year(s) Of Engagement Activity | 2017 |
| 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 | Research Seminar Royal Veterinary College Ruminant Transcriptomics |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Other audiences |
| Results and Impact | In February 2019 Emily Clark was asked to give the research seminar at the Royal Veterinary College. She gave a seminar entitled 'The sheep gene expression atlas project - building a model transcriptome for ruminants'. In the audience were researchers from the Royal Veterinary College and some clinicians. There were a number of questions and a number of opportunities for further collaboration particularly relating to innate immunity and disease phenotypes in sheep and goats were identified. |
| Year(s) Of Engagement Activity | 2019 |
| 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 | Ruminant Functional Genomics Research Group Website |
| Form Of Engagement Activity | Engagement focused website, blog or social media channel |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Media (as a channel to the public) |
| Results and Impact | In 2019 we launched webpages for the ruminant functional genomics research group at the Roslin Institute led by Emily Clark. These pages were put together by Mazdak Salavati and Emily Clark to represent the research programme and some key projects including the sheep gene expression atlas and population sequencing of tropically adapted sheep and goats. The reach of web pages should be international and they have led to several enquiries from visiting scientists and other requests for further information. |
| Year(s) Of Engagement Activity | 2019 |
| URL | https://www.ed.ac.uk/roslin/ruminant-functional-genomics |
| Description | SEBI Africa Week - The Million Bucks Concept |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Other audiences |
| Results and Impact | Emily Clark in collaboration with Mike Coffey (SRUC) gave a short presentation of the 'million bucks' concept for delivering transformative goat breeding without disrupting the existing infrastructure in Sub-Saharan Africa. This was part of SEBI's Africa Week Event which included other short presentations on potential transformative ideas in this space. There were policy makers, industry representatives and other academics in the audience. There were several questions which raised interesting points and plans were made to develop the concept further. |
| Year(s) Of Engagement Activity | 2019 |
| Description | Small Ruminants Workshop at CTLGH AGM 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 | During the Centre for Tropical Livestock Genetics and Health annual general meeting in Naivasha Kenya Emily Clark and Appolinaire Djikeng organised a short workshop focused on small ruminants. This workshop included speakers from across the globe and covered community based breeding programmes, communities of practice, socio-economics, health interventions and genetics. A panel discussion was held at the end and there were many points raised related to strategic development and collaboration in this space. |
| Year(s) Of Engagement Activity | 2018 |
| Description | Society for Research on Biological Rhythms (SRBR) meeting 2018 poster presentation (Amelia Island, FL, USA) |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Poster presentation entitled: Genome-wide changes in DNA methylation mark the changing seasons in mammalian calendar cells. Reported on progress in seasonal changes in DNA CpH methylation determined by RRBS. |
| Year(s) Of Engagement Activity | 2018 |
| URL | https://srbr.org/meetings/upcoming-meeting/ |
| Description | TAGC 2020 Poster Exploring genomic signatures of environmental adaptation in Ethiopian sheep |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Other audiences |
| Results and Impact | Pam Wiener gave a poster presentation entitled 'Exploring genomic signatures of environmental adaptation in Ethiopian sheep' at the virtual TAGC (The Allied Genetics Conference), April 2020. She described our analysis of whole genome sequencing data from Ethiopian sheep populations with climate data to identify signatures of selection for adaptation to the diverse ecosystems in Ethiopia. |
| Year(s) Of Engagement Activity | 2020 |
| 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 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: Epigenetics and seasonal biology at Wild Clocks Conference (Munich, Germany) |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Invited by session chair to talk about our work on circannual ovine DNA methylation in the PT. There were many questions on the talk and considerable interest in our findings. |
| Year(s) Of Engagement Activity | 2018 |
| URL | https://www.orn.mpg.de/wild-clocks-conference |
| 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 | Visit of Bill Gates |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Policymakers/politicians |
| Results and Impact | Bill Gates and Penny Mordaunt visited the Easter Bush campus to open the new Global Academy for Food Security. At that event, I presented our work on african farm animal genomes and programme 5 of the CTLGH. |
| Year(s) Of Engagement Activity | 2018 |
| URL | https://www.gov.uk/government/speeches/penny-mordaunt-speech-at-edinburgh-university-with-bill-gates |