Population sequencing of tropically-adapted sheep and sheep with defined or rare phenotypes // Develop genotyping tools for Cameroon sheep as a model for understanding the genetic basis of trypanotolerance in small ruminants in West Africa
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
unavailable
Planned Impact
unavailable
Publications
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 will develop genotyping tools for Cameroon sheep as a model for understanding the genetic basis of trypanotolerance in small ruminants in West Africa. We have generated whole genome Illumina 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 were genotyped on the Ovine 50K SNP Chip to select focal individuals for sequencing. We sequenced the genomes of 48 of the Cameroon sheep in total, at 15x coverage using the Illumina platform. Initial analysis of the Cameroon, Nigeria and Ghana datasets using Principal Component Analysis, with the sheep HAPMAP dataset, revealed that these West African breeds are genetically distinct from East African breeds but are similar to Carribean Hair Sheep. This further enforces a recently published observation, made by our collaborators at the USDA, that the Carribean Hair sheep have West African Ancestry. The West African sheep samples are being analysed particularly for polymorphisms in immune genes as these sheep are anecdotally tolerant to Trypanosomes. We are currently performing a comparative analysis of loci for trypano-tolerance that have been identified in cattle with our dataset from sheep. 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 | Our goal is to use the whole genome sequence information we have generated 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 sheep in West Africa. This dataset has also been used by our collborators at the USDA to identify polymorphisms in immune genes underlying resistance to infection by gastro-intestinal helminths in hair and wool sheep. We are also making all of the whole genome sequence data 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 technology developed by the International Sheep Genomics Consortium. The overall goal of the African sheep sequencing projects 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 |
| 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 | 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 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 | 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 | 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 | 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 | 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 |