Developing a research network for the application of wheat genomics in the UK and China
Lead Research Organisation:
John Innes Centre
Department Name: Cell and Develop Biology
Abstract
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Organisations
- John Innes Centre (Lead Research Organisation)
- Natural History Museum (Collaboration)
- National Institute of Agricultural Botany (Collaboration)
- University of Western Australia (Collaboration)
- University of Saskatchewan (Collaboration)
- Helmholtz Zentrum München (Collaboration)
- French National Institute of Agricultural Research (Collaboration)
- EMBL European Bioinformatics Institute (EMBL - EBI) (Collaboration)
- Chinese Academy of Sciences (Collaboration)
- University of Zurich (Collaboration)
- Leibniz Association (Collaboration)
- John Innes Centre (Collaboration)
- University of California, Davis (Collaboration)
- EARLHAM INSTITUTE (Collaboration)
- Shanghai Institutes for Biological Sciences (Project Partner)
People |
ORCID iD |
| Michael Bevan (Principal Investigator) |
Publications
Bevan MW
(2017)
Genomic innovation for crop improvement.
in Nature
Lu FH
(2018)
Independent assessment and improvement of wheat genome sequence assemblies using Fosill jumping libraries.
in GigaScience
Luo MC
(2017)
Genome sequence of the progenitor of the wheat D genome Aegilops tauschii.
in Nature
| Description | The purpose of this travel award is to explore opportunities for coordinating research in wheat genomics and genetics between the JIC and Chinese laboratories. Various meetings have been held here, in China and at PAG in the USA where most academics in the field congregate. As this grant still has a year to run more work needs to be done to help coordinate work among potential Chinese partners. In the meantime excellent progress in genomics and assessing sequence variation in wheat diversity lines is being made that can form the foundations of association studies of complex traits such as yield As we could not get access to Chinese wheat germplasm we have focussed on accessing and using germplasm from our own collections. The work involves optimising low-coverage sequencing for accessing genetic variation, and relating this to traits, both through classical genetic mapping and QTL analyses, and using association studies |
| Exploitation Route | The point of this project is to help align wheat genetic and genomic research between the UK and China. So there will be mutual benefit to several UK and and Chinese labs when the coordination activities have reached a successful conclusion |
| Sectors | Agriculture, Food and Drink |
| Description | This project is still going on. The current activities in research coordination will probably not lead directly to new research collaborations, but they will help raise awareness of our long-term plans and capabilities. The best outcome would be a joint project exploring genetic variation in European and Chinese wheat varieties. Update 2018: DNA of Chinese and UK landraces have been exchanged for genotyping and exome capture. It is not clear if we will be able to get seeds from the Chinese collections. A joint paper on Ae tauschii genome was published It has proved to be impossible to obtain wheat lines from China despite reaching an agreement to do so with CAAS scientists. This limits the extent of the collaboration. We have therefore focussed on an international collection we have at JIC that contains a broad diversity of wheat genetic variation |
| First Year Of Impact | 2018 |
| Sector | Agriculture, Food and Drink |
| Description | Outcomes of plans to analyse Chinese and European wheat varieties using common standards |
| Geographic Reach | Asia |
| Policy Influence Type | Influenced training of practitioners or researchers |
| Impact | The objectives of this collaboration have yet to be realised due to difficulties in sharing Chinese marker details, DNA samples and germplasm. This mens the proposed collaboration will not work |
| Description | Chinese Academy of Sciences Newton Award |
| Organisation | Chinese Academy of Sciences |
| Department | Institute of Genetics & Developmental Biology |
| Country | China |
| Sector | Academic/University |
| PI Contribution | At JIC we are providing in-depth understanding of a mechanism controlling organ and seed size in Arabidopsis in a collaboration with Yunhai Li at IGDB. We are currently working on experiments to finalise the resubmission of a joint paper |
| Collaborator Contribution | Dr Li's lab contributes genetic analyses of interacting proteins and measurements of growth for our joint publication |
| Impact | We are still working on revising a joint publication on growth control. The disciplines involved are genetics, biochemistry, cell biology |
| Start Year | 2009 |
| Description | New marker technologies for wheat using Illumina sequencing |
| Organisation | Earlham Institute |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | The overall aim of the partnership with EI is to develop a new set of sequencing technologies for high-throughput genotyping of wheat using the power of Illumina sequencing. JIC is providing ideas and concepts and wheat DNA samples for analyses and coordinates the project; UPDATE: NIAB is providing access to populations for genotyping |
| Collaborator Contribution | The EI provides sequencing and analyses and interpretation in the partnership. NIAB provide lines for testing genotyping and assistance with analysis of data. |
| Impact | It is too early for any outputs of the project. We have done extensive computational analyses of 10 sequenced and assembled wheat varieties and identified vast numbers of variety-specific polymorphisms. These have been mapped to the reference assembly. A set of 1000 polymorphic regions mapped to each Mb of group 3 chromosomes was identified and gene capture probes designed. DNA from a wide variety of testing lines has been made. In the coming months this DNA will be genotyped to test the method. Future goals are to refine the method to make it cost effective for application in pedigree breeding |
| Start Year | 2017 |
| Description | New marker technologies for wheat using Illumina sequencing |
| Organisation | National Institute Of Agricultural Botany |
| Country | United Kingdom |
| Sector | Private |
| PI Contribution | The overall aim of the partnership with EI is to develop a new set of sequencing technologies for high-throughput genotyping of wheat using the power of Illumina sequencing. JIC is providing ideas and concepts and wheat DNA samples for analyses and coordinates the project; UPDATE: NIAB is providing access to populations for genotyping |
| Collaborator Contribution | The EI provides sequencing and analyses and interpretation in the partnership. NIAB provide lines for testing genotyping and assistance with analysis of data. |
| Impact | It is too early for any outputs of the project. We have done extensive computational analyses of 10 sequenced and assembled wheat varieties and identified vast numbers of variety-specific polymorphisms. These have been mapped to the reference assembly. A set of 1000 polymorphic regions mapped to each Mb of group 3 chromosomes was identified and gene capture probes designed. DNA from a wide variety of testing lines has been made. In the coming months this DNA will be genotyped to test the method. Future goals are to refine the method to make it cost effective for application in pedigree breeding |
| Start Year | 2017 |
| Description | New marker technologies for wheat using Illumina sequencing |
| Organisation | Natural History Museum |
| Country | United Kingdom |
| Sector | Public |
| PI Contribution | The overall aim of the partnership with EI is to develop a new set of sequencing technologies for high-throughput genotyping of wheat using the power of Illumina sequencing. JIC is providing ideas and concepts and wheat DNA samples for analyses and coordinates the project; UPDATE: NIAB is providing access to populations for genotyping |
| Collaborator Contribution | The EI provides sequencing and analyses and interpretation in the partnership. NIAB provide lines for testing genotyping and assistance with analysis of data. |
| Impact | It is too early for any outputs of the project. We have done extensive computational analyses of 10 sequenced and assembled wheat varieties and identified vast numbers of variety-specific polymorphisms. These have been mapped to the reference assembly. A set of 1000 polymorphic regions mapped to each Mb of group 3 chromosomes was identified and gene capture probes designed. DNA from a wide variety of testing lines has been made. In the coming months this DNA will be genotyped to test the method. Future goals are to refine the method to make it cost effective for application in pedigree breeding |
| Start Year | 2017 |
| Description | Wheat Genomics in China |
| Organisation | Chinese Academy of Sciences |
| Department | Shanghai Institute of Plant Physiology and Ecology |
| Country | China |
| Sector | Academic/University |
| PI Contribution | The collaboration aims to develop wheat genomics within the framework of CAS in China. Various meetigns have been held to try and coordinate research in genomics and association studies with CAS |
| Collaborator Contribution | The main foundation for this attempted collaboration was the exciting association studies in rice conducted by Bin Han and colleagues in Shanghai. The initial aim was to replicate these studies in wheat using exome capture sequence of landraces. However, CAS turned out not to be the optimal partner, and they do not have Chinese germplasm. Recently collaboration has been initiated with the Chinese Academy of Agricultural Sciences, who have an extensive germplasm collection. We have initiated a new collaboration with them, initially involving exchange of DNA, while we work out the exchange of germplasm |
| Impact | Limited outcomes working with CAS, but very promising opportunities with CAAS |
| Start Year | 2015 |
| Description | Wheat genome sequencing |
| Organisation | Earlham Institute |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | We are working together to sequence and annotate multiple wheat genomes. This involves its applications to wheat improvement by engagement with international wheat improvement organisations, principally CIMMYT and the International Wheat Yield Programme. One goal goal is to provide genomics expertise for these groups to accelerate their breeding programmes. We also work directly with UK wheat breeders. |
| Collaborator Contribution | TGAC provide the lion's share of the expertise and sequencing capacity. I provide connections and strategy. |
| Impact | Too soon to tell, but has led to a joint applications to ODA and Grand Challenge Funds with international wheat breeders and researchers to support breeding |
| Start Year | 2015 |
| Description | Wheat genome sequencing |
| Organisation | University of Western Australia |
| Country | Australia |
| Sector | Academic/University |
| PI Contribution | We are working together to sequence and annotate multiple wheat genomes. This involves its applications to wheat improvement by engagement with international wheat improvement organisations, principally CIMMYT and the International Wheat Yield Programme. One goal goal is to provide genomics expertise for these groups to accelerate their breeding programmes. We also work directly with UK wheat breeders. |
| Collaborator Contribution | TGAC provide the lion's share of the expertise and sequencing capacity. I provide connections and strategy. |
| Impact | Too soon to tell, but has led to a joint applications to ODA and Grand Challenge Funds with international wheat breeders and researchers to support breeding |
| Start Year | 2015 |
| Description | Wheat genomics collaboration |
| Organisation | EMBL European Bioinformatics Institute (EMBL - EBI) |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | In the framework of the international wheat pan genome project we contribute 5 wheat genome assemblies, annotation pipelines, and transcriptome data for gene annotation and gene expression measurements. |
| Collaborator Contribution | The partnership brings together several groups who are assembling and annotating wheat genomes, primarily as part of national programmes. The plan is to develop approaches to comparing wheat genomes to identify how breeding has influenced the composition of gene families, gene expression and genome structures |
| Impact | The project has only recently been initiated. Major progress is expected in mid 2017, with joint annotations forming and long-range scaffolding providing the foundations of analyses |
| Start Year | 2017 |
| Description | Wheat genomics collaboration |
| Organisation | Earlham Institute |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | In the framework of the international wheat pan genome project we contribute 5 wheat genome assemblies, annotation pipelines, and transcriptome data for gene annotation and gene expression measurements. |
| Collaborator Contribution | The partnership brings together several groups who are assembling and annotating wheat genomes, primarily as part of national programmes. The plan is to develop approaches to comparing wheat genomes to identify how breeding has influenced the composition of gene families, gene expression and genome structures |
| Impact | The project has only recently been initiated. Major progress is expected in mid 2017, with joint annotations forming and long-range scaffolding providing the foundations of analyses |
| Start Year | 2017 |
| Description | Wheat genomics collaboration |
| Organisation | French National Institute of Agricultural Research |
| Country | France |
| Sector | Academic/University |
| PI Contribution | In the framework of the international wheat pan genome project we contribute 5 wheat genome assemblies, annotation pipelines, and transcriptome data for gene annotation and gene expression measurements. |
| Collaborator Contribution | The partnership brings together several groups who are assembling and annotating wheat genomes, primarily as part of national programmes. The plan is to develop approaches to comparing wheat genomes to identify how breeding has influenced the composition of gene families, gene expression and genome structures |
| Impact | The project has only recently been initiated. Major progress is expected in mid 2017, with joint annotations forming and long-range scaffolding providing the foundations of analyses |
| Start Year | 2017 |
| Description | Wheat genomics collaboration |
| Organisation | Helmholtz Zentrum München |
| Country | Germany |
| Sector | Academic/University |
| PI Contribution | In the framework of the international wheat pan genome project we contribute 5 wheat genome assemblies, annotation pipelines, and transcriptome data for gene annotation and gene expression measurements. |
| Collaborator Contribution | The partnership brings together several groups who are assembling and annotating wheat genomes, primarily as part of national programmes. The plan is to develop approaches to comparing wheat genomes to identify how breeding has influenced the composition of gene families, gene expression and genome structures |
| Impact | The project has only recently been initiated. Major progress is expected in mid 2017, with joint annotations forming and long-range scaffolding providing the foundations of analyses |
| Start Year | 2017 |
| Description | Wheat genomics collaboration |
| Organisation | John Innes Centre |
| Department | The Sainsbury Laboratory |
| Country | United Kingdom |
| Sector | Charity/Non Profit |
| PI Contribution | In the framework of the international wheat pan genome project we contribute 5 wheat genome assemblies, annotation pipelines, and transcriptome data for gene annotation and gene expression measurements. |
| Collaborator Contribution | The partnership brings together several groups who are assembling and annotating wheat genomes, primarily as part of national programmes. The plan is to develop approaches to comparing wheat genomes to identify how breeding has influenced the composition of gene families, gene expression and genome structures |
| Impact | The project has only recently been initiated. Major progress is expected in mid 2017, with joint annotations forming and long-range scaffolding providing the foundations of analyses |
| Start Year | 2017 |
| Description | Wheat genomics collaboration |
| Organisation | Leibniz Association |
| Department | Leibniz Institute of Plant Genetics and Crop Plant Research |
| Country | Germany |
| Sector | Charity/Non Profit |
| PI Contribution | In the framework of the international wheat pan genome project we contribute 5 wheat genome assemblies, annotation pipelines, and transcriptome data for gene annotation and gene expression measurements. |
| Collaborator Contribution | The partnership brings together several groups who are assembling and annotating wheat genomes, primarily as part of national programmes. The plan is to develop approaches to comparing wheat genomes to identify how breeding has influenced the composition of gene families, gene expression and genome structures |
| Impact | The project has only recently been initiated. Major progress is expected in mid 2017, with joint annotations forming and long-range scaffolding providing the foundations of analyses |
| Start Year | 2017 |
| Description | Wheat genomics collaboration |
| Organisation | University of California, Davis |
| Country | United States |
| Sector | Academic/University |
| PI Contribution | In the framework of the international wheat pan genome project we contribute 5 wheat genome assemblies, annotation pipelines, and transcriptome data for gene annotation and gene expression measurements. |
| Collaborator Contribution | The partnership brings together several groups who are assembling and annotating wheat genomes, primarily as part of national programmes. The plan is to develop approaches to comparing wheat genomes to identify how breeding has influenced the composition of gene families, gene expression and genome structures |
| Impact | The project has only recently been initiated. Major progress is expected in mid 2017, with joint annotations forming and long-range scaffolding providing the foundations of analyses |
| Start Year | 2017 |
| Description | Wheat genomics collaboration |
| Organisation | University of Saskatchewan |
| Country | Canada |
| Sector | Academic/University |
| PI Contribution | In the framework of the international wheat pan genome project we contribute 5 wheat genome assemblies, annotation pipelines, and transcriptome data for gene annotation and gene expression measurements. |
| Collaborator Contribution | The partnership brings together several groups who are assembling and annotating wheat genomes, primarily as part of national programmes. The plan is to develop approaches to comparing wheat genomes to identify how breeding has influenced the composition of gene families, gene expression and genome structures |
| Impact | The project has only recently been initiated. Major progress is expected in mid 2017, with joint annotations forming and long-range scaffolding providing the foundations of analyses |
| Start Year | 2017 |
| Description | Wheat genomics collaboration |
| Organisation | University of Western Australia |
| Country | Australia |
| Sector | Academic/University |
| PI Contribution | In the framework of the international wheat pan genome project we contribute 5 wheat genome assemblies, annotation pipelines, and transcriptome data for gene annotation and gene expression measurements. |
| Collaborator Contribution | The partnership brings together several groups who are assembling and annotating wheat genomes, primarily as part of national programmes. The plan is to develop approaches to comparing wheat genomes to identify how breeding has influenced the composition of gene families, gene expression and genome structures |
| Impact | The project has only recently been initiated. Major progress is expected in mid 2017, with joint annotations forming and long-range scaffolding providing the foundations of analyses |
| Start Year | 2017 |
| Description | Wheat genomics collaboration |
| Organisation | University of Zurich |
| Country | Switzerland |
| Sector | Academic/University |
| PI Contribution | In the framework of the international wheat pan genome project we contribute 5 wheat genome assemblies, annotation pipelines, and transcriptome data for gene annotation and gene expression measurements. |
| Collaborator Contribution | The partnership brings together several groups who are assembling and annotating wheat genomes, primarily as part of national programmes. The plan is to develop approaches to comparing wheat genomes to identify how breeding has influenced the composition of gene families, gene expression and genome structures |
| Impact | The project has only recently been initiated. Major progress is expected in mid 2017, with joint annotations forming and long-range scaffolding providing the foundations of analyses |
| Start Year | 2017 |
| Description | Attended San Diego Plant and Animal genome Meeting |
| 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 | Prof Bevan discussed wheat pan-genomics with international group wheat genomics with Chinese colleagues to identify future potential collaborations. |
| Year(s) Of Engagement Activity | 2017 |
| Description | Discussions on wheat genomics in Shanghai and Beijing |
| Form Of Engagement Activity | A formal working group, expert panel or dialogue |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Prof Bevan had discussions in Shanghai and Beijing about future wheat work with CAAS colleagues. |
| Year(s) Of Engagement Activity | 2016 |
| Description | JIC-in-China symposium |
| 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 | Prof Bevan attended the JIC-in-China symposium in 2015 for discussions of potential collaborations and gave a talk. |
| Year(s) Of Engagement Activity | 2015 |
| Description | San Diego Plant and Animal Genome Meeting |
| 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 | During this meeting Prof Bevan discussed wheat genomics with Chinese colleagues. |
| Year(s) Of Engagement Activity | 2016 |
| Description | planning wheat genome analyses |
| Form Of Engagement Activity | A formal working group, expert panel or dialogue |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | An annual meeting to plan multiple aspects of wheat genome and epigenome sequencing |
| Year(s) Of Engagement Activity | 2018 |