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The Defra Wheat Genetic Improvement Network - AR0709

Description
The UK government is committed to the sustainable development of agriculture. Wheat is grown on a larger area and is more valuable than any other arable crop in the UK. The genetic improvement of wheat has the potential to make a very significant contribution to the sustainable development of the arable sector. The overall aim of this project is to provide the core management and research facility of the Defra Wheat Genetic Improvement Network and to generate pre-breeding material carrying novel traits to breeders of wheat grown in the UK. This project will also provide access to advanced breeding technologies thereby ensuring the means are available to produce new, improved varieties.

The Wheat Genetic Improvement Network (WGIN) of which this project will be the core will unite the UK public-sector research activity on genetic improvement of wheat. The WGIN will aim to promote a close working relationship between researchers and “end users”. The WGIN will ensure that UK researchers have a shared objective to promote the sustainable development of the sector.

The core project will be managed by the research partners in conjunction with Defra. They will form a project board which will also include ex-officio representatives of breeders. The project management team will ensure the project and its outputs are communicated to the wider scientific and end user communities, via a web site, an electronic newsletter, a stakeholders’ forum, focused meetings, peer reviewed publications and the provision of germplasm and breeding facilities. The WGIN will ensure collaborations with equivalent operations overseas to ensure the Network as a whole is internationally competitive.

Core project objectives will be pursued in seven main activities

Activity 1. The provision and evaluation of key wheat genetic stocks will underpin most of the WGIN projects. These stocks will be held within the National Wheat Collection at the John Innes Centre (JIC).

Activity 2. Two key mapping populations will be established and populated to high resolution with PCR-based molecular markers. The chosen mapping populations and marker types will reflect both the short and longer term needs of many projects. The availability of molecular markers will improve the efficiency of plant selection by wheat breeders and provide researchers with the tools for gene discovery and isolation.

Activity 3. A hexaploid genotypic diversity screen will be performed to determine the total diversity available in elite North European winter wheat germplasm. This will assist the breeders in the selection of parents with potential novel traits or variant alleles.

Activity 4. The identification and characterisation of traits especially important for sustainable agriculture and knowledge on their inter-dependence, will be pursued within a joint annual field experiment, involving JIC, RRes, UoN and ADAS. A central, searchable database using a controlled vocabulary will be established, to combine existing prior knowledge on specific traits of interest with the new data generated within WGIN.

Activity 5. A related diploid wheat species will be exploited to identify novel sources of resistance to all the major UK fungal and viral pathogens.The novel traits and genes identified can be exploited through introgression breeding and/or through the molecular identification of the comparable allele in hexaploid wheat.

Activity 6. A large mutagenised hexaploid wheat population will be generated, to provide an immediate source of trait diversity to wheat breeders. This population will also permit researchers to identify novel variant alleles of key genes of interest for functional evaluation.

Activity 7. The PCR TILLING technique will be used in both diploid and hexaploid wheat to identify variant alleles of specific genes either arising naturally or via induced mutation. The Rht dwarfing genes and three global regulators of disease resistance will initially be examined for variant allele –novel trait associations. Once other genes of high value to sustainable agriculture are identified, the same approach will be pursued to provide breeders with a wide repertoire of novel trait variants.

Three activities of short duration will also occur within the WGIN. Firstly, there will be an annual donation of F1 wheat seed and the two parental stocks by breeders to the National Wheat Collection. This will reduce substantially the lead-in time for new genetic analysis projects. Secondly, grain will be achieved for 1-2 years from the traits field trial. This would provide researchers working on non-core projects, adequate materials for analyses. Thirdly, and only when appropriate, bioinformatics analyses will be undertaken to exploit micro-synteny between rice, barley, maize and wheat and thereby identify tightly linked markers and candidate genes sequences for important traits.

Objective
We propose the wheat genetic improvement network (WGIN), core project to have three activities. Firstly, a closely interactive and tightly knit group that will comprise the WGIN Management Team. This Team will meet together at quarterly intervals in year 1 and thereafter every 6 months and will be responsible for strategic direction and all operational activities. Secondly, the core infrastructural scientific activities of the network to be undertaken, at least initially, by the consortium members (RRes and JIC). Thirdly, liaison and communication activities by various methods to unite the wheat genetic improvement network (WGIN). A collaborative “Stakeholders’ Forum” will be formed comprising a wide network of interested parties including members of the consortium, research customers and end users.

Part 1. Project Management

Objective 1 Project management (RRes)
The WGIN will succeed in achieving its objectives only if its activities are closely managed and well integrated with the needs of both the commercial sector and funding agencies (including Defra and BBSRC). The responsibilities and objectives of the management team are as follows:

Objective 1.1 To establish the scientific strategy and research programme for the core project activity.

Objective 1.2 To ensure that all the UK wheat research community is aware of the resources emerging from the core programme.

Objective 1.3 To provide a central focus for wider studies of wheat genetic improvement in the UK, funded by BBSRC and other bodies.

Objective 1.4 To facilitate liaison between public sector research on wheat genetic improvement and stakeholders’ in the plant breeding and food industries.

Objective 1.5 To represent UK research on wheat genetic improvement in the wide international arena.

Objective 1.6 To meet at quarterly intervals during the first year and then every six months to achieve the above.

Objective 1.7 Responsible management of budget.

Objective 1.8 To develop a process for the release of new germplasm and other resources to the commercial sector.

Objective 1.9 To develop a process for ensuring the acknowledgement of core project resources by other researchers (both national and international) and to ensure appropriate recognition of efforts is made in their publications.

Objective 1.10 To provide secretarial and administrative support to the core project. Included in the core project budget is a salary to provide eight hours of secretarial/administrative support each week. This level of assistance will ensure that the scientists are focused on delivering the science objectives and are not involved in administrative tasks or the organisation and preparations for the various management/stakeholder meetings envisaged.

Part 2 Core research activities (JIC, RRes and sub-contractor)
At the core of the WGIN will be a platform of genetic and genomic resources, technology, knowledge and data that will provide the long-term foundation for continued investment in wheat genetic improvement activities. The WGIN will specifically develop resources and tools for the identification, utilisation and deployment of valuable allelic variation that can be exploited by breeders to achieve improvements in traits influencing crop inputs and performance.

Objective 2 Plant genetic resources (JIC)
Overall objective 2.1 To characterise at the phenotypic and molecular levels, and make available, the national wheat varietal and specialist genetic lines collection held at JIC.

Objective 2.1 To identify and evaluate genetic resources of utility to the core research platform, satellite projects and LINK projects.

Objective 2.2 To maintain appropriate levels of seed stocks and to provide them to partners who require them.

Objective 3 Genetic mapping and marker development (JIC)
Overall objectives To populate current maps with genic markers based on EST sequences, and to link the genetic map to a physical one based on BACs. To drive discovery towards informative, function-related and high throughput ‘genotyping- compatible’ markers.

Objective 3.1 Early decision by the management team on two wheat mapping populations to be developed that have the greatest diversity (marker polymorphism) and utility (differential traits).

Objective 3.2 To enrich the reference wheat mapping population [Opata x Synthetic] with genic SSR and SNP markers, thereby linking WGIN activities to those of the international wheat mapping community.

Objective 3.3 To identify BACs harbouring ESTs allocated to deletion bins.
Objective 3.4 To develop more effective and efficient markers systems in wheat whilst at the same time ensuring applicability to UK wheat breeding.
Objective 3.5 To link key sustainability traits to specific molecular markers

Objective 4 Hexaploid diversity screen (JIC) To establish an open-ended (initially largely genotypically-based) database of wheat germplasm relevant to the UK gene pool, for the monitoring of temporal and geographical trends in diversity, and as a resource for future association studies.

Objective 5 Trait identification (RRes, JIC and appointed sub-contactor)To generate quantitative information on important traits for sustainable agriculture and to provide this knowledge in an accessible database.

Objective 5.1 To identify traits with the potential to deliver sustainable wheat production.

Objective 5.2 Establish and maintain a traits database

Objective 5.3 Traits to assist the satellite Defra projects

Objective 5.4 Grain quality traits

Objective 5.5 Assemble of materials required for the main hexaploid diversity trial

Objective 5.6 Identification and employment of sub-contractor to conduct the traits trial in year1

Objective 5.7 The appointed sub-contractor to conduct the main trails trial years 2-5

Objective 5.8 Data entry into traits database and data analyses

Objective 5.9 Specific trait characterisation within the available mapping populations

Objective 5.10 Linking specific traits to specific molecular markers

Objective 6 Exploiting T. monococcum as a model for detection of traits, genes and variant alleles and for identifying phenotype: genotype relationships (RRes)
To exploit a diploid wheat as a model for the more rapid detection and characterisation of novel genes and variant loci that confer resistance to various fungal and viral diseases of importance in the UK. To establish phenotype: genotype relationships by testing variant alleles of specific genes known to be functional importance to defence in model species. To provide genic markers for specific allelic variants that confer specific traits in hexaploid wheat.

Objective 6.1 Screen 100 diploid wheat accessions for disease resistance traits.

Objective 6.2 Undertake a genotype diversity screen.

Objective 6.3 Create mutagenised populations for 1-2 accessions of high interest.

Objective 6.4 Use PCR TILLING to survey the diploid accessions and mutagenised populations for sequence variants linked to specific plant defence traits in model species.

Objective 6.5 Test specific lines with a range of variant alleles for disease resistance/ susceptibility.

Objective 6.6 Generate appropriate F2 segregating populations and test to confirm variant allele-trait associations.

Objective 6.7 Use PCR TILLING to identify the corresponding functionally important alleles in hexaploid sources. Relate sequence variants to trait expression.

Objective 6.8 Deliver genic based markers for specific allelic variants that confer specific traits in hexaploid wheat.

Objective 6.9 If correct variant allele fails to confer the expected trait in hexaploid wheat, attempt to restore trait expression by crossing the donor hexaploid line to different gene diversity pools and assess the progeny for gain of function. A similar approach was used to restore the function of the Leaf rust resistance gene Lr34 (Kerber and Aung T (1999) Phytopathol. 89: 518-521).

Objective 7 Mutagenesis (JIC/RRes)
To generate and make available knock-out and change of function mutants as a resource for gene discovery and the identification of novel allelic variants.

Objective 8 Wheat Crosses ( Wheat breeders)
An annual deposit into the JIC stock centre of elite parent and F1 seed from most of the UK wheat breeders. This important resource will reduce the lead in times required for new research projects, because the growing of the first two plant generations will be saved. The F1 seed will be used in future research projects to generate specific segregating F2 populations and / or DH mapping populations.

Objective 9 Identification of gene sequence variants with biological relevance by the PCR TILLING technique (RRes)
The high throughput TILLING technique will be established as a core platform technique to explore the diversity that naturally resides at specific loci or which has been generated through mutagenesis. The technique will be applied only to wheat genes of know biological significance. Two projects are initially proposed which each have easily scorable phenotypes. Subsequently, PCR TILLING will be used to evaluation of other key sustainability genes. PCR TILLING has recently been demonstrated to work for rice, maize and diploid and hexaploid wheat, (pers. comm.. Luca Comai and Steven Henikoff, Seattle, USA). In hexaploid bread wheat many novel traits and alleles variants have been produced in the 20Th century by reverse genetics despite concerns over the problem of gene copies residing on homoeologous chromosomes (reviewed by Maluszynski et al., 2001, Chapter 36 in ‘ The World Wheat Book. A History of Wheat Breeding’ eds. Bonjean AP and Angus WJ, Lavosier Publishing ISBN 1-898298-72-6).

Objective 9.1 Candidate genes rht, GA20ox, GA3ox and GA2ox to reduce plant height/ influence pre-harvest sprouting. Candidate genes rht, GA20ox, GA3ox and GA2ox to reduce plant height/ influence pre-harvest sprouting. Seed of the variety Mercia harbouring the extreme dwarf Rht3 allele will be mutagenised with EMS and the M1 and M2 generation grown in the field or polytunnels. PCR TILLING will then be undertaken on DNA pools from the M2 plants to identify variant alleles at the rht3 locus, that is known to control plant height through conferring insensitivity to endogenous GAs. PCR TILLING will also be carried out on M2 pools from the taller Paragon variety (Objective 7) to identify novel alleles at the GA20ox, GA3ox and GA2ox loci that are involved in GA biosynthesis and thus control both plant elongation growth and, potentially, pre-harvest sprouting. Specific phenotype:genotype relationships will then be investigated.

Objective 9.2 Candidate genes, RAR1, SGT1 and NPR1 proposed as global regulators of broad spectrum disease resistance (Shirasu and Schultze-Lefert (2003) Trends Plant Sci. 8: 252-258, ref 10). Pools of seed (n=100) from the diploid and hexaploid mutagenised populations will be screened by PCR TILLING and individual lines subsequently identified that harbour variant alleles of RAR1, SGT1 and NPR1. This pool of mutant genotypes will then be assessed for novel disease resistance phenotypes and specific phenotype:genotype relationships established.

Objective 9.3. The management team to consult the user community through the stakeholders’ forum to identify other target genes for evaluation by TILLING and thereby identify novel allele variant-trait associations for commercial exploitation.

Objective 10 Analysis of rice-wheat synteny (RRes)
For important traits, advantage will be taken of the micro-synteny between rice, barley, maize and wheat using specific bioinformatic analyses.

Objective 10.1 To identify tightly linked markers and candidate gene sequence for novel commercially important traits.

Objective 11 Grain archiving (linked to objective 2.4) (RRes)

Objective 11.1 To provide a grain storing facility, for the storage for up to one year of threshed grain (10 Kg) from each plot of the annual traits field experiment (Objective 2.4).

Objective 11.2 To store a 1 Kg threshed grain sample from each plot of the annual traits field experiment, at -15C indefinitely.

Objective 11.3 To identify how this grain can be accessed by the wider UK research community.

Part 3 Liaison and Communication Activities (JIC, RRes)
The group will establish liaison and exchanges of information between publicly funded research scientist and end users/stakeholders’ via the following mechanisms.

Objective 12 A WGIN Website.
A searchable website with be established and maintained at RRes. It will contain information on each of the core platform research workpackages objectives and progress to date. Each topic will be reviewed at least once every 3 months and updated were appropriate. Copies of the electronic newsletter will be available from the website. In year 2 the WGIN Web-site will be inter-linked with other appropriate cereal genetic and genomic databases and resources worldwide.

Objective 13 Electronic NewsletterThis will be prepared every six months and will include.
§ Progress reports on the WGIN and other relevant Defra-funded research.
§ Reports of the WGIN Management Team Meetings.
§ Other relevant information on wheat improvement including a brief literature survey and information on forthcoming and recent scientific meetings.

Objective 14 Annual Meeting
An annual “Stakeholders’ Forum” will be held to facilitate liaison between the UK wheat research and end user communities.

Objective 14.1 An early activity of the Management Team will be to decide on the composition and activities of the “Stakeholders’ Forum”.

Objective 14.2 The first meeting will aim to introduce the WGIN and current Defra-funded research and to invite comments on the objectives and approaches.

Objective 14.3 Subsequent meetings will be focused on more specific aspects of wheat improvement, based on the views expressed during the first meeting.
Objective 15 To foster strong collaboration between UK wheat researchers

Objective 16 To foster LINK research projects

Objective 17 To establish and maintain international collaborations
Time-Scale and Cost
From: 2003

To: 2008

Cost: £1,850,539
Contractor / Funded Organisations
Rothamsted Research (BBSRC)
Keywords
Arable Farming              
Biotech-non GM              
Cereals              
Crop Diseases              
Crop Improvement              
Farming              
Genetics              
Genomics              
Natural Resource Use              
Plant Genetic Resources              
Sustainable Farming and Food              
Sustainable Production              
Wheat              
Wheat Production              
Fields of Study
Arable Crops