Generate high quality reference genome for the Indian water buffalo, and population sequencing to inform new genetic tools
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
People |
ORCID iD |
| Michael Watson (Principal Investigator) |
Publications
Dutta P
(2020)
Whole genome analysis of water buffalo and global cattle breeds highlights convergent signatures of domestication.
in Nature communications
Talenti A
(2022)
A cattle graph genome incorporating global breed diversity.
in Nature communications
| Description | We participated in the generation of a new high-quality reference genome for the water buffalo through this grant and the sequencing of multiple animals of various Indian buffalo breeds to study breed diversity and the evolutionary basis of domestication. A high-quality genome is essential to understand the biology of any species and to understanding the function of each gene of the genome. |
| Exploitation Route | We participated in the generation of a new reference genome for the water buffalo and contributed data to annotate that genome. This will provide providing valuable information on where genes are expressed in the body and their functions This data will help both biologists and farmers, as a high-quality reference genome is necessary to understand the biology of a species, manage genetic diversity and, in the case of livestock, to apply genomic selection for genetic improvement. |
| Sectors | Agriculture Food and Drink |
| Description | The annotated reference genome was published in Nature Communications in January 2019 (https://www.nature.com/articles/s41467-018-08260-0). This genome was used to align the Indian buffalo genomes used in the study below. The sequence data we generated from Indian buffalo breeds was used in a study of the evolutionary basis of domestication in cattle and buffalo and published in Nature Communications in September 2020 (https://www.nature.com/articles/s41467-020-18550-1). More people globally depend on the water buffalo than any other domesticated species, and as the most closely related domesticated species to cattle they can provide important insights into the shared evolutionary basis of domestication. The genomes of 79 water buffalo across seven breeds were compared for patterns of between breed selective sweeps with those seen for 294 cattle genomes representing 13 global breeds. The genomic regions under selection between cattle breeds significantly overlap regions linked to stature in human genetic studies, with a disproportionate number of these loci also shown to be under selection between water buffalo breeds. Investigation of potential functional variants in the water buffalo genome identifies a rare example of convergent domestication down to the same mutation having independently occurred and been selected for across domesticated species. Cross-species comparisons of recent selective sweeps can consequently help identify and refine important loci linked to domestication. |
| First Year Of Impact | 2019 |
| Sector | Agriculture, Food and Drink |
| Impact Types | Cultural Economic |
| 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 |
| 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 | 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 | 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 | Talk and poster presentation at ISAG 2017 conference in Dublin |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Other audiences |
| Results and Impact | Rachel Young presented a talk and poster at the International Society for Animal Genetics on work on buffalo genomics. Interest was generated in the types of techniques developed in livestock species at Roslin and the data generated by this. This conference was mainly attended by academics in the animal genetics and genomics field as well as industry. |
| 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 |