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The Wheat Genetic Improvement Network (WGIN) - Improving the environmental footprint of farming through crop genetics and targeted traits analysis - IF0146

Description
The UK government is committed to a more sustainable agriculture. Wheat is grown on a larger area and is more valuable than any other arable crop in the UK. The overall aim of this project is to generate pre-breeding material carrying novel traits to the UK breeding companies and to deliver accessible technologies thereby ensuring the means are available to produce new, improved varieties. An integrated scientific 'core' which combines underpinning molecular markers, genetic and genomic research, together with novel trait identification, are being pursued to achieve this goal.

The generation and improving of specific resources and tools will include
- Production of Near Isogenic lines (NILs) to permit detailed analysis of the physiological and molecular basis of key traits within a fixed genetic background
- Further development of the Avalon x Cadenza mapping population to map new traits of interest
- Detailed characterisation of the Paragon gamma and EMS mutagenised populations to associate chromosome regions and / or gene sequences to specific traits
- Exploring specific traits of interest using the newly available AE Watkins collection as well as the Gediflux collection of historically important NW European wheats
- Creating a new mapping population to assist the water use efficiency study and two further mapping populations to align the WGIN core project with the international wheat genome sequencing effort

Targeted traits
- Crop adaptation for climate proofing with special reference to determining the vernalisation requirements of elite genotype
- Nitrogen use efficiency (NUE)
- Characterisation of Quality QTLs linked to NUE which occur independent of total protein content in the harvested grain
- A detailed exploration of the mechanisms underlying genotype variation drought tolerance and crop water use efficiency
- Identification of wheat germplasm which confers either tissue based resistance to Take-all disease and/or ability to restrict soil inoculum build up in 1st wheat situations
- Introgression of extreme resistance to Septoria leaf blotch from Triticum monococcum into hexaploid wheat
- Exploring the Interconnections between the three soil based traits
- Archiving of grain at low temperature from the main trait experiments over the 5 years to permit others to investigate key traits

The procurement of one or more sub-contractor projects to enrich the research done within the network

The project will be managed by a team including representatives of the key UK research groups and breeders. They ensure the project and its outputs are communicated to the wider scientific and end user communities, via a web site, a newsletter, a stakeholder forum, focused meetings and peer reviewed publications. The WGIN will collaborate with equivalent operations overseas to ensure the programme is internationally competitive.
Objective
The wheat genetic improvement network (WGIN) core project will have three activities. Firstly, a closely interactive and tightly knit group that will comprise the WGIN Management Team. This team will meet together 3 times per year and will be responsible for strategic direction and all operational activities. Secondly, the core structural scientific activities of the network to be undertaken, initially by the consortium members (RRes, JIC and UoN) and later through the involvement of appointed sub-contractors. Thirdly, liaison and communication activities by various methods to unite the wheat genetic improvement network (WGIN). The collaborative ‘Stakeholders Forum’ will continue thereby maintaining a wider 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 the activities are closely managed and well integrated with the needs of both the commercial sector and funding agencies (including defra, BBSRC and HGCA).

The responsibilities and objectives of the management team are as follows:

Objective 1.1 Organise 3 management meetings during each project year, produce approved minutes and visit one the WGIN field trials at one site
Objective 1.2 To establish the scientific strategic and research programme for the core project activities
Objective 1.3 To ensure that all the UK wheat research communuity is aware of the resources emerging from the core programme
Objective 1.4 To provide a central focus for wider studies of wheat genetic improvement in the UK, funded by BBSRC and other bodies
Objective 1.5 To facilitate liason between public sector research on the wheat genetic improvement and stakeholders’ in the plant breeding and food industries.
Objective 1.6 To represent UK research on wheat genetic improvement in the wider international arena.
Objective 1.7 Responsible budget management
Objective 1.8 To further develop a process for ensuring the acknowledgement of all the core project resources by other researchers(both national and international) and to ensure appropriate recognition of efforts is made in their publications.
Objective 1.9 To provide secretarial and administrative support to the core project. Include in the core project budget is a salary to provide sixteen hours of secretarial /administrative support each week.

Part 2 Core research activities (JIC, RREs, UoN and sub-contractors)

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 and knowledge on genetic variation in key traits that can be exploited by breeders to achieve improvements in traits influencing crop inputs and performance. The collective aim is to provide a flexible research platform that will permit scientists to focus on improving crop traits that will mitigate the effects of climate change, reduce greenhouse gases, lower energy use, improve water and air quality and thereby reduce the overall footprint of the UK wheat crop.

A. Generating and improving specific resources and tools

Objective 2 To produce a series of Near Isogenic lines (NILs) for key traits (JIC)
Overall objective 2.1 The purpose of this work is to produce precise germplasm stocks (NILs) which differ only for one region of interest, allowing the genetic and physiological dissection of single gene (Mendelian) effects rather that QTL. This will be achieved by marker assisted backcrossing of regions identified as containing important QTL outputs from WGIN 1 and other relevant projects.
Objective 2.1 Crossing programme advanced as far as BC 1 for yield, height, and heading date NIL development
Objective 2.2 Fixed homozygotes produced for yield, height, and heading date BC2 derived NILs.
Objective 2.3 Crossing programme advanced to BC1 for Watkins allele mining NILs,and NUE QTL.
Objective 2.4 Bulk up homozygous BC2 derived NIL material for yield heading date and height.
Objective 2.5 Crossing programme advanced to BC2 for mutant alleles identified in mutant Paragon F2- BSA screen.
Objective 2.6 Crosssing programme advanced to BC2 for Watkins allele mining and NUE QTL. Field trials sown for bulked up BC2 derived NILs
Objective 2.7 Field phenotypes collected for yield, height and heading date NILs.
Objective 2.8 Homozygous BC2 NIL material complete for all traits.

Objective 3 Maintenance of the availability of the Avalon x Cadenza Mapping population

Overall objective 3.1 Continue the maintenance and availablility of authetic seed stocks of the Avalon x Cadenza population.

Objective 4 Fixation of lines harbouring extremes of traits of from the gamma and EMS mutagenised populations (JIC)

Overall objective 4.1 This work will progress the genetic description of potentially useful mutant phenotypes, for example alternative dwarfing genes and senescence effects, which were outputs of WGIN 1. To achieve this traits will be shown to be single gene effects and genetically mapped using bulked segregant analysis (BSA).
Objective 4.1 Twenty Paragon mutant x BIRST spring wheat F2s grown in the field.
Objective 4.2 Fifteen lines representing phenotypic extremes selected for BSA- DNA extracted.
Objective 4.3 DNA of selected lines subjected to DArT genotyping.
Objective 4.4 Genetic location of mutant genes identified.

Objective 5 AE Watkins and Gediflux collections (JIC)
Overall objective 5.1 To provide a high density of new molecular information for both collections, to identify a core collection and to provide fixed lines for the identified drought tolerant germplasm.

Objective 5.1 AE Watkins and Gediflux subjected to DArT genotyping, Genotypic data used to produce establish genetic relationship of accessions and define a reduced (core) germplasm collection. AE Watkins crosses made for the production of genetically fixed populations by single seed descent (SSD).

Objective 5.2 Watkins x Paragon SSD populations progressed up to F3, Watkins or Gediflux x Paragon crosses made for drought traits.
Objective 5.3 Watkins x Paragon SSD populations self fertilised up to to F4
Objective 5.4 Watkins x Paragon self fertilised up to F6, Watkins or Gediflux x Paragon drought traits doubled haploid (DH) populations developed.

Objective 6 To develop new mapping populations which will align WGIN 2 with the International wheat genome sequencing effort.

Objective 6.1 Paragon x Chinese Spring and Paragon x JIC Synthetic SSD populations self fertilised up to F4
Objective 6.2 Paragon x Chinese Spring and Paragon x JIC Synthetic SSD populations self fertilised up to F8. DNA extracted for mapping of new molecular markers.

Part B Targeted traits

Objective 7 To explore whether the differential response of hexaploid wheats to two different cereal aphid species has a simple genetic basis. (RRes)

Objective 7.1 To determine the differential susceptibility to cereal aphids of selected lines from a Spark x Rialto mapping population

Objective 8 To explore Nitrogen use efficiency (NUE) and Quality QTLs linked to NUE in UK adapted germplasm (RRes)

Overall objective 8.1 To dissect the NUE trait and quality QTLs linked to NUE using linked field and non-field experimentation
Objective 8.1 To complete field experimentation on Av x Cad at low N inputs (3rd replicate data set)
Objective 8.2 To complete field experimentation on Av x Cad at standard N inputs (2nd replicate data set)
Objective 8.3 To complete field experimentation on Av x Cad at standard N inputs (3rd replicate data set)
Objective 8.4 To analyse N uptake in glasshouse expt in Av x Cad lines
Objective 8.5 To assess NUE and yield assessments on 24 lines at 4 N levels for selected germplasm (year 1 selection)
Objective 8.6 To assess NUE and yield assessments on 24 lines at 4 N levels for selected germplasm (year 2 selection)
Objective 8.7 To assess NUE and yield assessments on 24 lines at 4 N levels for selected germplasm (year 3 selection)
Objective 8.8 To assess NUE and yield assessments on 24 lines at 4 N levels for selected germplasm (year 4 selection)
Objective 8.9 To assess NUE and yield assessments on 24 lines at 4 N levels for selected germplasm (year 5 selection)
Objective 8.10 To analyse grain functionality in NIL lines in response to varying N (1st replicate year)
Objective 8.11 To analyse grain functionality in NIL lines in response to varying N (2nd replicate year)
Objective 8.12 To explore the Breakdown of tissue N partitioning amongst 12 germplasm lines at 4 N inputs
Objective 8.13 To collate all data sets, publications and final dissemination.

Objective 9 To explore drought tolerance in under UK conditions (UoN)

Overall Objective 9.1 To identify traits and genetic markers for water-use efficiency and drought-tolerance traits in wheat through linkage and association mapping that breeders can use as selection criteria for variety production, and to create wheat germplasm resources, comprising one doubled-haploid population and one diverse germplasm collection, to be used by researchers and breeders to improve water-use efficiency and drought tolerance.

Objective 9.1 To identify the physiological traits explaining improved
water-use efficiency and drought tolerance in elite winter wheat varieties.
Objective 9.2. To identify robust QTLs for water-use efficiency and
drought-tolerance traits using one existing DH population in an elite background.
Objective 9.3 To develop one new DH population in an elite modern background segregating for drought-tolerance traits.
Objective 9.4 To identify through association genetics analysis novel genes and alleles controlling water-use efficiency and drought tolerance.
Objective 9.5 To collate a diverse germplasm collection (cultivars, advanced
lines) from worldwide drought-tolerance wheat breeding programmes as a resource for future association genetics studies.

Objective 10 To explore resistance in wheat to take-all inoculum build up in the soil as well as tissue based resistance (RRes)

Overall objective 10.1 To identify the best germplasm for each take-all reducing trait that can subsequently be used in commercial breeding programmes.

Objective 10.1 To screen the AE Watkins Collection and an ‘improved’ Gediflux Collection to identify potential additional sources of resistance to the take-all fungus under field conditions - year 1
Objective 10.2 To screen the AE Watkins Collection and an ‘improved’ Gediflux Collection to identify potential additional sources of resistance to the take-all fungus under field conditions - year 2
Objective 10.3 To screen the AE Watkins Collection and an ‘improved’ Gediflux Collection to identify potential additional sources of resistance to the take-all fungus under field conditions - year 3
Objective 10.4 To screen the AE Watkins Collection and an ‘improved’ Gediflux Collection to identify potential additional sources of resistance to the take-all fungus under field conditions - year 4
Objective 10.5 To screen the available DH population between one hexaploid source of resistance to take-all and a suitable susceptible parent over 2 years of field trials
Objective 10.6 To screen the three available F3 T. monococcum mapping population and Fi plants for resistance to take all in pot tests and to relate the results to the combined SSR and DArt marker map available
Objective 10.7 To introgress resistance from non-hexaploid and T. monococcum sources into hexaploid wheat using the same strategy developed in activity 11 for Septoria resistance to the BCF1:2 stage
Objective 10.8 To identify and characterise hexaploid wheat germplasm which reduce take-all inoculum build up (TAB) in soil, this will involve scoring the genotypes in the anaual diversity trial as well as in a separate TAB trial and selected hexaploid genotypes based on pedigree analyses - in total 5 years of trials
Objective 10.9 To explore the genetic basis of take-all inoculum build up using the Avalon x Cadenza mapping population - in total 3 years of trials using the full population and after 2 years of trials using a sub-set of the population containing and lacking the identified major QTLs.


Objective 11 Introgression of extreme resistance to Septoria leaf blotch from Triticum monococcum into hexaploid wheat (RRes)

Overall objective 11.1 To introgress the TmStb1 resistance locus which confers an extremely high level of field resistance to Septoria tritici into hexaploid wheat

Objective 11.1 To convert the two closest linked DArT markers to the TmStb1 locus to PCR based markers
Objective 11.2 To complete the backcrossing of F1 plants to a range of hexaploid wheats.
Objective 11.3 To complete the selfing of the 1st set of BC1F1 plants to a range of hexaploid wheats and then genotype the F2 progeny to identify BCF1:2 recombinants containing the TmStb1 region.
Objective 11.4 To complete the seed bulking up procedure for the selected BCF1:2 recombinants containing the TmStb1 region and complete the phenotyping using a range of Septoria isolates.
Objective 11.5 To complete the selfing of the 2nd set of BC1F1 plants to a range of hexaploid wheats and then genotype the F2 progeny to identify BCF1:2 recombinants containing the TmStb1 region.
Objective 11.6 To screen about 300 T. monococcum accessions in the RRes collection assembled during WGIN1 for variation in TmStb1 region.
Objective 11.7 To complete the seed bulking up procedure for the selected BCF1:2 recombinants containing the TmStb1 region in different hexaploid wheat backgrounds complete the phenotyping using a range of Septoria isolates.
Objective 11.8 To provide BCF1:2 seed to the wheat breeders with marker information and efficacy results.
Objective 11.9 To screen accessions with variant alleles for resistance to differential isolates of M. graminicola.
Objective 11.10 To undertake the 1st year of field trials of the most advanced introgressed lines in different hexaploid wheat backgrounds and with the most appropriate control genotypes.
Objective 11.11 To undertake the 2nd year of field trials of the most advanced introgressed lines in different hexaploid wheat backgrounds and with the most appropriate control genotypes.
Objective 11.12 To exploration of the use of selected amphiploids Chinese spring chromosome 1A, 3A and 5A substituted by T. monococcum 1Am, 3Am and 5Am for the introgression of additional Septoria resistance loci.

Objective 12 To explore the interconnections between the three soil based traits (RRes, JIC, UoN)

Overall objective 12. To identify what similarities and differences exist between germplasm with good NUE, good drought tolerance and / or take-all resistance.

Objective 12.1 To interconnect the NUE and WUE a selection of genotypes will be included in at least 2 years of trialling.
Objective 12.2 To cross compare the physiological traits specifically associated with NUE, drought or take-all resistance. This may reveal new common themes to how plants cope with abiotic and biotic stress.
Objective 12.3 To identify QTLs which confer either enhanced N uptake or reduced take-all inoculum build-up in the Avalon x Cadenza mapping population will be compared. This may reveal either common or unlinked root processed.
Objective 12.4 To explore the performance of the best drought tolerance and take-all resistant germplasm in the NUE diversity trial at the 4 N rates in project years 4 and 5.

Objective 13 To archive grain samples from the main WGIN NUE trials (linked to objective 8) RRes

Main objective 13.1 To provide a grain storage facility, for the storage for up to 1 year of threshed grain (10kg) from each plot of the two field trial and to store a 1kg threshed grain sample from each plot of both field trials at -20C indefinitely.

Objective 13.1 To harvest and store grain from NUE diversity trial and A x C DH mapping population - all plots - year 1
Objective 13.2 To harvest and store grain from NUE diversity trial and A x C DH mapping population - all plots - year 2
Objective 13.3 To harvest and store grain from NUE diversity trial and A x C DH mapping population - all plots - year 3
Objective 13.4 To harvest and store grain from NUE diversity trial - all plots - year 4
Objective 13.5 To harvest and store grain from NUE diversity trial - all plots - year 5


Objective 14 The identification and employment of sub-contractors to conduct specific research projects. (The management team)

Objective 14.1 To procure one or more sub-contractor project through a formal application process
Objective 14.2 To develop a contact with each sub-contractor before the research commences
Objective 14.3 For each subcontract to produce both interim and final reports at the indicated time intervals and for these to be placed on the WGIN website

Objective 15 The WGIN Website The searchable website will be maintained at RRes. It will contain information on the WGIN project (2003 – 2008) and the WGIN renewal project (2009-2013) in two separate domains. It will contain information on each of the core platform research objectives and progress to date. Each topic will be reviewed at least one every 3 months and updated where appropriate. Copies of the electronic newsletter will be available from the website as well as information on defra funded link projects involving wheat. The website will continue to be inter-linked with other appropriate cereal genetic and genomic databases and resources worldwide.

Objective 15.1 To maintain the WGIN website and include all results and new information from year 1
Objective 15.2 To include information on all recent past and current Defra link projects involving wheat
Objective 15.3 To better link WGIN website to the MONOGRAM website and upload all relevant publications
Objective 15.4 To prepare a diagram which linking the various objectives within the WGIN 2 project to all existing UK projects funded by the various sponsors
Objective 15.5 To maintain the WGIN website and include all results and new information from year 2
Objective 15.6 To maintain the WGIN website and include all results and new information from year 3
Objective 15.7 To maintain the WGIN website and include all results and new information from year 4
Objective 15.8 To maintain the WGIN website and include all results and new information from year 5


Objective 16 Electronic Newsletter

This will be prepared every six months and will include

- Progress reports on the WGIN and other relevant defra-funded research
- Other relevant information on wheat improvement including a brief literature survey and information on forthcoming and recent scientific meetings

Objective 16.1 To produce and circulate two electronic stakeholder newletters for year 1
Objective 16.2 To produce and circulate two electronic stakeholder newletters for year 2
Objective 16.3 To produce and circulate two electronic stakeholder newletters for year 3
Objective 16.4 To produce and circulate two electronic stakeholder newletters for year 4
Objective 16.5 To produce and circulate two electronic stakeholder newletters for year 5


Objective 17 Annual meeting

An annual ‘Stakeholders’ Forum’ will be held to facilitate liaison between the UK wheat research and end user communities

Objective 17.1 To hold an annual stakeholders meeting in November for year 1
Objective 17.2 To hold an annual stakeholders meeting in November for year 2
Objective 17.3 To hold an annual stakeholders meeting in November for year 3
Objective 17.4 To hold an annual stakeholders meeting in November for year 4
Objective 17.5 To hold an annual stakeholders meeting in November for year 5

Objective 18 Focussed workshops on specific topics

Objective 18.1 To hold an open focussed workshop on the Avalon x Cadenza mapping population
Objective 18.2 To hold an open focussed workshop on the archived samples from the 1st five years of the NUE diversity and A x C field trials and thereby identify existing and new projects which could use this resource.
Objective 18.3 To hold an open discussion with the wheat breeders which is focussed on fulfilling crop vernalisation requirements for UK grown wheats.


Objective 19 To establish and maintain international collaborations

Objective 19.1 To organise joint workshops each year with either CIMMYT, INRA, Adelaide and ICARDA by raising suitable funding from other sources.

Objective 20 To publicise the existence of the project

Objective 20.1 To be achieved on an annual basis through talks, field demonstrations, articles in the popular press and through interviews / discussions with interested NGOs and non-NGOs
Project Documents
• EVID4 - Final project report : Evid4 IF0146 Final Report   (907k)
Time-Scale and Cost
From: 2008

To: 2014

Cost: £1,756,119
Contractor / Funded Organisations
Rothamsted Research (BBSRC), John Innes Centre (BBSRC), University - Nottingham
Keywords
Arable              
Breeding              
Crop Diseases              
Crops              
Genetics              
Integrated Farming Systems              
Resource efficient and resilient food chain              
Sustainable Farming and Food Science              
Sustainable Farming Systems              
Water Use              
Wheat