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.

Publications

10 25 50
 
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 French National Institute of Agricultural Research
Country France 
Sector Public 
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 Public 
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 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 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