Genomics for Triticeae improvement
Lead Research Organisation:
John Innes Centre
Department Name: Contracts Office
Abstract
This project is an international collaboration led by INRA in France (Coordinator Catherine Feuillet) and funded by the EC Framework 7 programme. The project aims to generate physical maps of BACs aligned to wheat and barley group 1 and 3 chromosomes and use this resource to isolate genes and new alleles. The specific objectives of the project are to:
-Construct and anchor physical maps from the wheat and barley group 1 and 3 chromosomes that carry a large number of important agronomic traits (e.g. disease resistance, yield and quality)
-Isolate genes and QTLs underlying disease resistance, yield and quality traits in wheat and barley
-Identify and exploit new alleles for the isolated genes through the use of natural and mutant populations as well as wild germplasm
-Support the development of new varieties that meet farmer and consumer needs through molecular breeding
-Develop new bioinformatic tools to structure, relate and comprehensively analyse the large scale genomics data gathered within the project and
-Lead, coordinate and integrate Triticeae genomics research
The specific role of the JIC (Group Leader, Mike Bevan) is to construct a physical map of chromosome arm 3DL, which is approximately 400 Mb. JIC will be provided with a BAC library constructed from flow- sorted chromosome 3DL and a set of genetic marker sequences from which probes can be made for BAC identification. The BACs will be fingerprinted and placed into pools representing contigs established by FPC. JIC will also align the Brachypodium genome sequence with wheat groups 1 and 3 using COS markers in order to facilitate further integration of wheat physical maps using conserved gene order.
-Construct and anchor physical maps from the wheat and barley group 1 and 3 chromosomes that carry a large number of important agronomic traits (e.g. disease resistance, yield and quality)
-Isolate genes and QTLs underlying disease resistance, yield and quality traits in wheat and barley
-Identify and exploit new alleles for the isolated genes through the use of natural and mutant populations as well as wild germplasm
-Support the development of new varieties that meet farmer and consumer needs through molecular breeding
-Develop new bioinformatic tools to structure, relate and comprehensively analyse the large scale genomics data gathered within the project and
-Lead, coordinate and integrate Triticeae genomics research
The specific role of the JIC (Group Leader, Mike Bevan) is to construct a physical map of chromosome arm 3DL, which is approximately 400 Mb. JIC will be provided with a BAC library constructed from flow- sorted chromosome 3DL and a set of genetic marker sequences from which probes can be made for BAC identification. The BACs will be fingerprinted and placed into pools representing contigs established by FPC. JIC will also align the Brachypodium genome sequence with wheat groups 1 and 3 using COS markers in order to facilitate further integration of wheat physical maps using conserved gene order.
Organisations
- John Innes Centre, United Kingdom (Lead Research Organisation)
- Earlham Institute, NORWICH (Collaboration)
- Institute of Applied Genomics (Collaboration)
- Institute of Zoology (Collaboration)
- Biogemma, France (Collaboration)
- Academy of Sciences of the Czech Republic (Collaboration)
- University of Bologna, Italy (Collaboration)
- French National Institute of Agricultural Research (Collaboration)
- Helmholtz Association of German Research Centres (Collaboration)
- Scottish Crop Research Institute (SCRI) (Collaboration)
- National Institute Of Agricultural Botany (Collaboration)
- Sabanci University (Collaboration)
- University of Milano-Bicocca (Collaboration)
- Haifa University, Israel (Collaboration)
- Leibniz Association (Collaboration)
- University of Western Australia, Australia (Collaboration)
People |
ORCID iD |
| Michael Webster Bevan (Principal Investigator) |
Publications
Luo MC
(2013)
A 4-gigabase physical map unlocks the structure and evolution of the complex genome of Aegilops tauschii, the wheat D-genome progenitor.
in Proceedings of the National Academy of Sciences of the United States of America
Garvin DF
(2010)
An SSR-based genetic linkage map of the model grass Brachypodium distachyon.
in Genome
Bevan MW
(2010)
Brachypodium distachyon genomics for sustainable food and fuel production.
in Current opinion in biotechnology
Thole V
(2010)
Distribution and characterization of more than 1000 T-DNA tags in the genome of Brachypodium distachyon community standard line Bd21.
in Plant biotechnology journal
Bevan M
(2017)
Genomic innovation for crop improvement
in Nature
Bevan M
(2011)
Genomics: endless variation most beautiful.
in Nature
Lu F
(2018)
Independent assessment and improvement of wheat genome sequence assemblies using Fosill jumping libraries
in GigaScience
Idziak D
(2011)
Painting the chromosomes of Brachypodium: current status and future prospects.
in Chromosoma
Allen AM
(2011)
Transcript-specific, single-nucleotide polymorphism discovery and linkage analysis in hexaploid bread wheat (Triticum aestivum L.).
in Plant biotechnology journal
| Description | this project was a collaboration with the Universities of Bristol and Liverpool and focussed on developing useful genomic resources for wheat improvement. we established the first gene set from bread wheat and used this to align a huge set of sequence polymorphisms for marker development |
| Exploitation Route | the data from this project was made available to wheat breeders world-wide for their use in marker design and genome selection models |
| Sectors | Agriculture, Food and Drink |
| URL | http://plants.ensembl.org/Triticum_aestivum/Info/Index |
| Description | The sequence data from this project was provided directly to researchers and wheat breeders so they could identify new markers in wheat genes |
| First Year Of Impact | 2012 |
| Sector | Agriculture, Food and Drink |
| Impact Types | Economic |
| Description | Genomics for Triticeae Improvement |
| Organisation | Academy of Sciences of the Czech Republic |
| Department | Institute of Experimental Botany |
| Country | Czech Republic |
| Sector | Academic/University |
| PI Contribution | We constructed a physical map of Chromosome 3DL of wheat using fingerprinted BACs |
| Collaborator Contribution | The Institute of Experimental Botany in the Czech Republic made a BAC library from purified chromosome 3DL The Instituto di Genomica Applicata in Udine, Italy, carried out fingerprinting of the BACs using double enzyme digestion and fluorescent labelling INRA Toulouse managed the BACS University of Haifa developed a new fingerprinting method At JIC we implemented the fingerprinting of the BACs to generate a physical map of chromosome 3DL. This was integrated with a genetic map from Aegilops tauschii In subsequent work we sequenced and assembled the BACS |
| Impact | physical maps of several wheat chromosomes as part of an international collaboration. These formed the basis of an international effort to sequence the wheat genome. Ultimately this approach was abandoned, after much effort and expenditure |
| Start Year | 2008 |
| Description | Genomics for Triticeae Improvement |
| Organisation | Biogemma |
| Country | France |
| Sector | Private |
| PI Contribution | We constructed a physical map of Chromosome 3DL of wheat using fingerprinted BACs |
| Collaborator Contribution | The Institute of Experimental Botany in the Czech Republic made a BAC library from purified chromosome 3DL The Instituto di Genomica Applicata in Udine, Italy, carried out fingerprinting of the BACs using double enzyme digestion and fluorescent labelling INRA Toulouse managed the BACS University of Haifa developed a new fingerprinting method At JIC we implemented the fingerprinting of the BACs to generate a physical map of chromosome 3DL. This was integrated with a genetic map from Aegilops tauschii In subsequent work we sequenced and assembled the BACS |
| Impact | physical maps of several wheat chromosomes as part of an international collaboration. These formed the basis of an international effort to sequence the wheat genome. Ultimately this approach was abandoned, after much effort and expenditure |
| Start Year | 2008 |
| Description | Genomics for Triticeae Improvement |
| Organisation | French National Institute of Agricultural Research |
| Country | France |
| Sector | Academic/University |
| PI Contribution | We constructed a physical map of Chromosome 3DL of wheat using fingerprinted BACs |
| Collaborator Contribution | The Institute of Experimental Botany in the Czech Republic made a BAC library from purified chromosome 3DL The Instituto di Genomica Applicata in Udine, Italy, carried out fingerprinting of the BACs using double enzyme digestion and fluorescent labelling INRA Toulouse managed the BACS University of Haifa developed a new fingerprinting method At JIC we implemented the fingerprinting of the BACs to generate a physical map of chromosome 3DL. This was integrated with a genetic map from Aegilops tauschii In subsequent work we sequenced and assembled the BACS |
| Impact | physical maps of several wheat chromosomes as part of an international collaboration. These formed the basis of an international effort to sequence the wheat genome. Ultimately this approach was abandoned, after much effort and expenditure |
| Start Year | 2008 |
| Description | Genomics for Triticeae Improvement |
| Organisation | Helmholtz Association of German Research Centres |
| Department | Helmholtz Zentrum Munchen |
| Country | Germany |
| Sector | Academic/University |
| PI Contribution | We constructed a physical map of Chromosome 3DL of wheat using fingerprinted BACs |
| Collaborator Contribution | The Institute of Experimental Botany in the Czech Republic made a BAC library from purified chromosome 3DL The Instituto di Genomica Applicata in Udine, Italy, carried out fingerprinting of the BACs using double enzyme digestion and fluorescent labelling INRA Toulouse managed the BACS University of Haifa developed a new fingerprinting method At JIC we implemented the fingerprinting of the BACs to generate a physical map of chromosome 3DL. This was integrated with a genetic map from Aegilops tauschii In subsequent work we sequenced and assembled the BACS |
| Impact | physical maps of several wheat chromosomes as part of an international collaboration. These formed the basis of an international effort to sequence the wheat genome. Ultimately this approach was abandoned, after much effort and expenditure |
| Start Year | 2008 |
| Description | Genomics for Triticeae Improvement |
| Organisation | Institute of Applied Genomics |
| Country | Italy |
| Sector | Charity/Non Profit |
| PI Contribution | We constructed a physical map of Chromosome 3DL of wheat using fingerprinted BACs |
| Collaborator Contribution | The Institute of Experimental Botany in the Czech Republic made a BAC library from purified chromosome 3DL The Instituto di Genomica Applicata in Udine, Italy, carried out fingerprinting of the BACs using double enzyme digestion and fluorescent labelling INRA Toulouse managed the BACS University of Haifa developed a new fingerprinting method At JIC we implemented the fingerprinting of the BACs to generate a physical map of chromosome 3DL. This was integrated with a genetic map from Aegilops tauschii In subsequent work we sequenced and assembled the BACS |
| Impact | physical maps of several wheat chromosomes as part of an international collaboration. These formed the basis of an international effort to sequence the wheat genome. Ultimately this approach was abandoned, after much effort and expenditure |
| Start Year | 2008 |
| Description | Genomics for Triticeae Improvement |
| Organisation | Leibniz Association |
| Department | Leibniz Institute of Plant Genetics and Crop Plant Research |
| Country | Germany |
| Sector | Charity/Non Profit |
| PI Contribution | We constructed a physical map of Chromosome 3DL of wheat using fingerprinted BACs |
| Collaborator Contribution | The Institute of Experimental Botany in the Czech Republic made a BAC library from purified chromosome 3DL The Instituto di Genomica Applicata in Udine, Italy, carried out fingerprinting of the BACs using double enzyme digestion and fluorescent labelling INRA Toulouse managed the BACS University of Haifa developed a new fingerprinting method At JIC we implemented the fingerprinting of the BACs to generate a physical map of chromosome 3DL. This was integrated with a genetic map from Aegilops tauschii In subsequent work we sequenced and assembled the BACS |
| Impact | physical maps of several wheat chromosomes as part of an international collaboration. These formed the basis of an international effort to sequence the wheat genome. Ultimately this approach was abandoned, after much effort and expenditure |
| Start Year | 2008 |
| Description | Genomics for Triticeae Improvement |
| Organisation | National Institute Of Agricultural Botany |
| Country | United Kingdom |
| Sector | Private |
| PI Contribution | We constructed a physical map of Chromosome 3DL of wheat using fingerprinted BACs |
| Collaborator Contribution | The Institute of Experimental Botany in the Czech Republic made a BAC library from purified chromosome 3DL The Instituto di Genomica Applicata in Udine, Italy, carried out fingerprinting of the BACs using double enzyme digestion and fluorescent labelling INRA Toulouse managed the BACS University of Haifa developed a new fingerprinting method At JIC we implemented the fingerprinting of the BACs to generate a physical map of chromosome 3DL. This was integrated with a genetic map from Aegilops tauschii In subsequent work we sequenced and assembled the BACS |
| Impact | physical maps of several wheat chromosomes as part of an international collaboration. These formed the basis of an international effort to sequence the wheat genome. Ultimately this approach was abandoned, after much effort and expenditure |
| Start Year | 2008 |
| Description | Genomics for Triticeae Improvement |
| Organisation | Sabanci University |
| Country | Turkey |
| Sector | Academic/University |
| PI Contribution | We constructed a physical map of Chromosome 3DL of wheat using fingerprinted BACs |
| Collaborator Contribution | The Institute of Experimental Botany in the Czech Republic made a BAC library from purified chromosome 3DL The Instituto di Genomica Applicata in Udine, Italy, carried out fingerprinting of the BACs using double enzyme digestion and fluorescent labelling INRA Toulouse managed the BACS University of Haifa developed a new fingerprinting method At JIC we implemented the fingerprinting of the BACs to generate a physical map of chromosome 3DL. This was integrated with a genetic map from Aegilops tauschii In subsequent work we sequenced and assembled the BACS |
| Impact | physical maps of several wheat chromosomes as part of an international collaboration. These formed the basis of an international effort to sequence the wheat genome. Ultimately this approach was abandoned, after much effort and expenditure |
| Start Year | 2008 |
| Description | Genomics for Triticeae Improvement |
| Organisation | Scottish Crop Research Institute (SCRI) |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | We constructed a physical map of Chromosome 3DL of wheat using fingerprinted BACs |
| Collaborator Contribution | The Institute of Experimental Botany in the Czech Republic made a BAC library from purified chromosome 3DL The Instituto di Genomica Applicata in Udine, Italy, carried out fingerprinting of the BACs using double enzyme digestion and fluorescent labelling INRA Toulouse managed the BACS University of Haifa developed a new fingerprinting method At JIC we implemented the fingerprinting of the BACs to generate a physical map of chromosome 3DL. This was integrated with a genetic map from Aegilops tauschii In subsequent work we sequenced and assembled the BACS |
| Impact | physical maps of several wheat chromosomes as part of an international collaboration. These formed the basis of an international effort to sequence the wheat genome. Ultimately this approach was abandoned, after much effort and expenditure |
| Start Year | 2008 |
| Description | Genomics for Triticeae Improvement |
| Organisation | University of Bologna |
| Country | Italy |
| Sector | Academic/University |
| PI Contribution | We constructed a physical map of Chromosome 3DL of wheat using fingerprinted BACs |
| Collaborator Contribution | The Institute of Experimental Botany in the Czech Republic made a BAC library from purified chromosome 3DL The Instituto di Genomica Applicata in Udine, Italy, carried out fingerprinting of the BACs using double enzyme digestion and fluorescent labelling INRA Toulouse managed the BACS University of Haifa developed a new fingerprinting method At JIC we implemented the fingerprinting of the BACs to generate a physical map of chromosome 3DL. This was integrated with a genetic map from Aegilops tauschii In subsequent work we sequenced and assembled the BACS |
| Impact | physical maps of several wheat chromosomes as part of an international collaboration. These formed the basis of an international effort to sequence the wheat genome. Ultimately this approach was abandoned, after much effort and expenditure |
| Start Year | 2008 |
| Description | Genomics for Triticeae Improvement |
| Organisation | University of Haifa |
| Country | Israel |
| Sector | Academic/University |
| PI Contribution | We constructed a physical map of Chromosome 3DL of wheat using fingerprinted BACs |
| Collaborator Contribution | The Institute of Experimental Botany in the Czech Republic made a BAC library from purified chromosome 3DL The Instituto di Genomica Applicata in Udine, Italy, carried out fingerprinting of the BACs using double enzyme digestion and fluorescent labelling INRA Toulouse managed the BACS University of Haifa developed a new fingerprinting method At JIC we implemented the fingerprinting of the BACs to generate a physical map of chromosome 3DL. This was integrated with a genetic map from Aegilops tauschii In subsequent work we sequenced and assembled the BACS |
| Impact | physical maps of several wheat chromosomes as part of an international collaboration. These formed the basis of an international effort to sequence the wheat genome. Ultimately this approach was abandoned, after much effort and expenditure |
| Start Year | 2008 |
| Description | Genomics for Triticeae Improvement |
| Organisation | University of Milano-Bicocca |
| Country | Italy |
| Sector | Academic/University |
| PI Contribution | We constructed a physical map of Chromosome 3DL of wheat using fingerprinted BACs |
| Collaborator Contribution | The Institute of Experimental Botany in the Czech Republic made a BAC library from purified chromosome 3DL The Instituto di Genomica Applicata in Udine, Italy, carried out fingerprinting of the BACs using double enzyme digestion and fluorescent labelling INRA Toulouse managed the BACS University of Haifa developed a new fingerprinting method At JIC we implemented the fingerprinting of the BACs to generate a physical map of chromosome 3DL. This was integrated with a genetic map from Aegilops tauschii In subsequent work we sequenced and assembled the BACS |
| Impact | physical maps of several wheat chromosomes as part of an international collaboration. These formed the basis of an international effort to sequence the wheat genome. Ultimately this approach was abandoned, after much effort and expenditure |
| Start Year | 2008 |
| Description | Genomics for Triticeae Improvement |
| Organisation | University of Zurich |
| Country | Switzerland |
| Sector | Academic/University |
| PI Contribution | We constructed a physical map of Chromosome 3DL of wheat using fingerprinted BACs |
| Collaborator Contribution | The Institute of Experimental Botany in the Czech Republic made a BAC library from purified chromosome 3DL The Instituto di Genomica Applicata in Udine, Italy, carried out fingerprinting of the BACs using double enzyme digestion and fluorescent labelling INRA Toulouse managed the BACS University of Haifa developed a new fingerprinting method At JIC we implemented the fingerprinting of the BACs to generate a physical map of chromosome 3DL. This was integrated with a genetic map from Aegilops tauschii In subsequent work we sequenced and assembled the BACS |
| Impact | physical maps of several wheat chromosomes as part of an international collaboration. These formed the basis of an international effort to sequence the wheat genome. Ultimately this approach was abandoned, after much effort and expenditure |
| Start Year | 2008 |
| 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 | Newspaper commentaries about wheat genome sequencing progress |
| Form Of Engagement Activity | A press release, press conference or response to a media enquiry/interview |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Public/other audiences |
| Results and Impact | Mike Bevan provided newspaper commentaries about wheat genome sequencing progress. |
| Year(s) Of Engagement Activity | 2012 |
| URL | http://online.wsj.com/article/SB10001424127887324205404578147823815273136.html |
| Description | Presentation at PAG conference San Diego USA |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | I presented our latest data on comparative gene expression between diploid and hexaploid wheat lines |
| Year(s) Of Engagement Activity | 2019 |
| Description | Press article entitled: 'Wheat genome sequence analysis.' |
| Form Of Engagement Activity | A press release, press conference or response to a media enquiry/interview |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Media (as a channel to the public) |
| Results and Impact | Mike Bevan wrote a press article entitled: 'Wheat genome sequence analysis.' |
| Year(s) Of Engagement Activity | 2012 |
| URL | http://www.sciencedaily.com/releases/2012/11/121128143545.htm |
| Description | Press article for BBC entitled: 'Wheat genome's key parts unlocked in new study.' |
| Form Of Engagement Activity | A press release, press conference or response to a media enquiry/interview |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Public/other audiences |
| Results and Impact | Mike Bevan wrote a press article for the BBC entitled: 'Wheat genome's key parts unlocked in new study.' |
| Year(s) Of Engagement Activity | 2012 |
| Description | Press article in Farmers Weekly |
| Form Of Engagement Activity | A press release, press conference or response to a media enquiry/interview |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Industry/Business |
| Results and Impact | Mike Bevan wrote a press article in Farmers Weekly entitled:'Wheat genome breakthrough offers food security boost'. |
| Year(s) Of Engagement Activity | 2012 |
| URL | http://www.fwi.co.uk/articles/29/11/2012/136475/wheat-genome-breakthrough-offers-food-security-boost... |
| Description | Press article in National Association of Wheat Growers |
| Form Of Engagement Activity | A press release, press conference or response to a media enquiry/interview |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Industry/Business |
| Results and Impact | Mike Bevan wrote a press article in National Association of Wheat Growers entitled: 'Scientists announce stride towards wheat genome sequence'. |
| Year(s) Of Engagement Activity | 2012 |
| URL | http://www.wheatworld.org/news-events/2012/11/scientists-announce-strides-toward-wheat-genome-sequen... |
| Description | Press release in National Science Foundation entitled: 'International team generates major breakthrough in deciphering bread wheat's genetic code'. |
| Form Of Engagement Activity | A press release, press conference or response to a media enquiry/interview |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Policymakers/politicians |
| Results and Impact | Mike Bevan participated in a press release in National Science Foundation entitled: 'International team generates major breakthrough in deciphering bread wheat's genetic code'. |
| Year(s) Of Engagement Activity | 2012 |
| URL | http://www.nsf.gov/news/news_summ.jsp?cntn_id=126008 |