15-IWYP. A genetic diversity toolkit to maximise harvest index by controlling the duration of developmental phases
Lead Research Organisation:
John Innes Centre
Department Name: Crop Genetics
Abstract
The project will identify new genes in bread wheat that will alter the timing of developmental well known landmarks in the wheat crop such as heading date and the crop maturity, but also more subtle changes, invisible in everyday observation of the wheat crop. These include stages in the very earliest days of the development of the wheat spike, which are crucial in determining the number of grains finally produced to build the foundations of new high yielding wheat varieties. The project is a collaboration between scientists in the UK, Argentina, Spain, Australia and the Centre for Improvement of Wheat and Maize (CIMMYT) based in Mexico. These partners will target an increase in yield potential in CIMMYT wheat, which reaches countries for which these improvements can do most to improve global food security.
Technical Summary
Together with rice and maize, wheat forms the staple of the human diet (Braun et al. 2010). It is the most widely grown crop, and a vital component of the agricultural system on every continent except for Antarctica. As well as providing starch calories it is also the main source of plant protein for the global poor. Rates of genetic gain in wheat breeding are not sufficient to meet the demand for wheat (Rosegrant et al., 2013). Failure to address this problem will be catastrophic. An exciting proposition that could increase the rate of genetic gain for wheat is the efficient channeling of basic understanding of biological mechanisms controlling inflorescence development into a programme of breeding for grain yield by developing improved trait combinations delivering benefit in breeders' plots and farm fields. None of the traits that contribute to yield are better understood at the genetic level than flowering time and phenology (by which we mean here, the timing, duration, and environmental interactions of developmental phases of wheat inflorescence development). The work proposed here will further that understanding through the application of genetics, physiology and simulation modeling and will implement breeding interventions at several levels that can be used to maximise harvest index (HI) and yield in wheat.
Planned Impact
The overarching IWYP goal is a 50% yield increase over 20 years. Therefore we have interpreted short, medium, and long term aspects as 5, 10, and 20 years respectively. We propose that, currently, the Harvest Index (HI) is ~40% globally in high potential environments with low levels of stress. In this diagram immediate project outputs are shown as orange arrows. Theyrepresent high biomass germplasm in which HI is increased using tools and knowledge (purple boxes with green text) generated here. This knowledge will be built upon and our approach will be extended in breeding to more efficient varietal improvement with our most tangible project outcomes such as new varieties shown in blue boxes. These will emerge first from CIMMYT and this will be a very direct consequence of mechanisms put in place here. The approach will be easily transferable to other spring wheat programmes and then, with further support and focus, in winter wheat. Commercial support and interaction will expedite this extension. The blue box outcomes will also be new ways of breeding so that the physiological and genetic dissection of phenology described here can be replayed in a synthesis step by which best trait combinations can be predicted and built afresh for new environments and within diverse pools of germplasm. The research direction established in this work and fully integrated into IWYP will accelerate scientific understanding of phenology and floral organogenesis relevant to wheat breeding because of their role in building sink strength, which in turn drives HI, so that mean global HI has increased to 50% after 10 years. The unique interaction between molecular, genetic, physiological, modelling, and breeding approaches causing the boundaries between these disciplines to blur, shown in green. Because all of the tools and resources, including germplasm and markers, will be made freely available to IWYP partners upon discovery/development the impact will be amplified. In twenty years the most striking outcome will be that the approaches established, now experimental, will be considered a routine element of wheat breeding essential to achieve IWYPs ambition and ingrained in breeding as almost tacit knowledge. The new understanding of yield per se applied to high potential environments for IWYP will be applicable under heat and drought, because the genetic and physiological basis of breeding progress made under IWYP will be understood, this transfer will be efficient. Together, these outputs will result in a mean global HI in drought free environments of 60% in 20 years.
The teams involved in the consortium have exceptional track records (see CVs) and deliver state of the art research and breeding in these areas. Much of the progress in phenology research of the last twenty years has been achieved by these groups. They are supported by excellent existing infrastructure, services, and management systems in host institutions so that all can engage fully in achieving the above goals with no infrastructural investment necessary from IWYP. Resources in germplasm, genomics, specialised methodologies, field experimentation platforms, skilled staff base, database structures are brought to the table from projects like ADAPTAWHEAT, WISP, WHEAT CRP, BBSRC GRO, CSIRO, and MasAgro. For these reasons the proposed work presents exceptional value for money, many of the concepts and methodologies employed are free from ongoing projects, so all involved can 'hit the ground running'.
The teams involved in the consortium have exceptional track records (see CVs) and deliver state of the art research and breeding in these areas. Much of the progress in phenology research of the last twenty years has been achieved by these groups. They are supported by excellent existing infrastructure, services, and management systems in host institutions so that all can engage fully in achieving the above goals with no infrastructural investment necessary from IWYP. Resources in germplasm, genomics, specialised methodologies, field experimentation platforms, skilled staff base, database structures are brought to the table from projects like ADAPTAWHEAT, WISP, WHEAT CRP, BBSRC GRO, CSIRO, and MasAgro. For these reasons the proposed work presents exceptional value for money, many of the concepts and methodologies employed are free from ongoing projects, so all involved can 'hit the ground running'.
Publications
Foulkes M
(2022)
Wheat Improvement - Food Security in a Changing Climate
Dixon LE
(2018)
TEOSINTE BRANCHED1 Regulates Inflorescence Architecture and Development in Bread Wheat (Triticum aestivum).
in The Plant cell
Basavaraddi PA
(2021)
Interactions between two QTLs for time to anthesis on spike development and fertility in wheat.
in Scientific reports
Coulton A
(2020)
Segregation distortion: Utilizing simulated genotyping data to evaluate statistical methods.
in PloS one
Basavaraddi PA
(2021)
Phenology and Floret Development as Affected by the Interaction between Eps-7D and Ppd-D1.
in Plants (Basel, Switzerland)
Basavaraddi PA
(2021)
Wheat Developmental Traits as Affected by the Interaction between Eps-7D and Temperature under Contrasting Photoperiods with Insensitive Ppd-D1 Background.
in Plants (Basel, Switzerland)
Dixon LE
(2018)
Developmental responses of bread wheat to changes in ambient temperature following deletion of a locus that includes FLOWERING LOCUS T1.
in Plant, cell & environment
Description | CIMMYT were understood to use a very few versions of key genes to tune wheat varieties for global adaptation. We have added three more genes to that short list and provided molecular markers for deployment in CIMMYT marker assisted selection programme supporting the development of new wheat varieties for developing world agriculture. We have developed a CIMMYT NAM population for gene discovery and a conceptual 'wiring diagram' to guide trait and gene deployment for increased yield potential. We have shown that phenology gene markers are associated with harvest index and yield in wheat. Several gene based markers from the project are now used routinely in wheat breeding programmes. |
Exploitation Route | More efficient breeding for developing and developed world agriculture. New candidate traits/QTL for the DFW Breeders Toolkit. New understanding of the role pf phenology genes in crop fertility. |
Sectors | Agriculture Food and Drink |
URL | https://data.cimmyt.org/dataset.xhtml?persistentId=hdl:11529/10996 |
Description | The genetic maps produced for CIMMYT material are presented on the IWYP dataverse platform and provide a unique tool for valicdation of breeding approaches. Simon Griffiths' linkages with CIMMYT led to the whole genome sequencing of CIMMYT varieties Weebill and Baj by UK consortia for the international wheat PanGenome project. We have contributed to a new conceptual framework, 'the wheat yield wiring diagram'. Our QTL have been entered into the DFW Breeders Toolkit. Now markers identified in IWYP are being used by CIMMYT for the improvement of their germplasm and positive association with Harvest Index have been identified. |
First Year Of Impact | 2019 |
Sector | Agriculture, Food and Drink |
Impact Types | Economic Policy & public services |
Description | Problems caused by introgessions |
Geographic Reach | Multiple continents/international |
Policy Influence Type | Influenced training of practitioners or researchers |
Impact | Wheat breeding companies were made aware about the effect that introgressions have on recombination and why this may lead to difficulties in the future, this has caused some companies to re-examine their breeding strategies |
Description | BBSRC Flexible Talent Mobility Award (FTMA) |
Amount | £25,000 (GGP) |
Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
Sector | Public |
Country | United Kingdom |
Start | 07/2019 |
End | 12/2019 |
Description | International workshops |
Amount | £10,000 (GBP) |
Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
Sector | Public |
Country | United Kingdom |
Start | 06/2019 |
End | 08/2019 |
Title | Breeders tool kit meeting |
Description | Novel wheat lines and novel wheat molecular markers to be transferred to the commercial sector |
Type Of Material | Biological samples |
Year Produced | 2018 |
Provided To Others? | No |
Impact | Novel materials and markers to be supplied to the wheat breeding community |
Title | New markers and new genotyping platform for wheat breeding |
Description | New Axiom markers for use in wheat breeding |
Type Of Material | Technology assay or reagent |
Year Produced | 2017 |
Provided To Others? | Yes |
Impact | New markers and new GbyS genotyping platform for screening and genotyping wheat |
Title | CerealsDB |
Description | The CerealsDB web-site was created by members of the Functional Genomics Group at the University of Bristol. The site provides a range of facilities for the study of the wheat genome. The site has been designed with breeders in mind, and we hope that is will be easy and straightforward to use. |
Type Of Material | Database/Collection of data |
Year Produced | 2017 |
Provided To Others? | Yes |
Impact | There have been over 1,528,817 unique visits to the websites and our various datasets have been downloaded 48,295 times (35K Wheat breeders Array: 45,445 downloads and 820K High Density Wheat Array; 2,850 downloads). The trend of increased numbers of researchers visiting our web site shows no sign of slowing down; running as it is at greater than 50,000 unique visits per month. |
URL | http://www.cerealsdb.uk.net/ |
Title | Dataverse repository of nested association mapping populations including high density genotyping and genetic maps aligned to wheat genome |
Description | Segregating populations made with key CIMMYT parents and linking to UK wheat programme parents. |
Type Of Material | Database/Collection of data |
Year Produced | 2017 |
Provided To Others? | Yes |
Impact | This is the first CIMMYT NAM population. Over 250 downloads. Does not use DOIs but 'handles' see hdl:11529/10996 |
URL | https://data.cimmyt.org/dataverse/iwypdvn |
Title | Introgression plotter added to Cerealsdb |
Description | Software to allow users to screen wheat germplasm for potential introgressions from wheat relative |
Type Of Material | Data analysis technique |
Year Produced | 2019 |
Provided To Others? | Yes |
Impact | At the request of the wheat breeding companies we have made this tool available via Cerealsdb so that breeders can check on the presence of possible introgressed regions in the bread wheat genome |
Title | QTL database |
Description | Upload of QTL database to Cerealsdb |
Type Of Material | Data analysis technique |
Year Produced | 2019 |
Provided To Others? | Yes |
Impact | Breeders and academics are now able to download/examine various QTL-based datasets |
Title | Upgrade to cerealsdb (cerealsdb3) |
Description | We have carried out a significant upgrade of cerealsdb to include new analytical tools and a much larger data set |
Type Of Material | Database/Collection of data |
Year Produced | 2019 |
Provided To Others? | Yes |
Impact | Increased level of data downloads and use of tools to detect introgressions in wheat |
URL | http://www.cerealsdb.uk.net/cerealgenomics/CerealsDB/indexNEW.php |
Description | A Genetic Diversity Toolkit to Maximize Harvest Index by Controlling the Duration of Developmental Phases a three month vist to CIMMYT headquarters |
Organisation | International Centre for Maize and Wheat Improvement (CIMMYT) |
Country | Mexico |
Sector | Charity/Non Profit |
PI Contribution | I worked with CIMMYT staff to develop ideas and approaches for future research. |
Collaborator Contribution | They showed me how the CIMMYT physiology and breeding programmes operate. |
Impact | Submission of a grant application to the International wheat yield partnership (IWYP). |
Start Year | 2017 |
Description | A meeting between CIMMYT and DFW funded by BMGF to discuss collaboration projects |
Organisation | International Centre for Maize and Wheat Improvement (CIMMYT) |
Country | Mexico |
Sector | Charity/Non Profit |
PI Contribution | I organised a meeting funded by Bill and Melinda Gates Foundation brought together members of the BBSRC's coordinated wheat programme (Designing Future Wheat) with members of CIMMYT (who breed wheat for the resource poor in the developing world), discuss potential opportunities for interaction. These opportunities are taken forward by writing proposals for Newton , GCRF or IWYP funding calls |
Collaborator Contribution | See above |
Impact | This interaction is still ongoing between members of BBSRC's coordinated wheat programme (Designing Future Wheat) and researchers within CIMMYT with proposals being written for IWYP and Newton calls |
Start Year | 2018 |
Description | Collaboartion with Syngenta to exchnage knowledge on trasformation and double haploid production |
Organisation | Syngenta International AG |
Department | Syngenta Ltd (Bracknell) |
Country | United Kingdom |
Sector | Private |
PI Contribution | exchange of personal to improve our technology in double haploid production |
Collaborator Contribution | Spent time at Syngenta providing input into transformation technolgy |
Impact | Better transformation and double haploid technology available to Bristol |
Start Year | 2019 |
Description | Academic visitor from the University of Salamanca 3/9/2018 |
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 | Academic visit from Javier Bobo Pinilla of the University of Salamanca. Visit was for training, data sharing and discussion of future collaboration opportunities |
Year(s) Of Engagement Activity | 2018 |
Description | Bristol Plant Science Workshop, 2018-10-17 |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | Regional |
Primary Audience | Postgraduate students |
Results and Impact | Amanda Burridge attended the Bristol Plant Science Workshop and presented 'Using Ancient Grains to Improve Modern Bread Wheat' |
Year(s) Of Engagement Activity | 2018 |
Description | CIMMYT visit to IWYP material Field Trials |
Form Of Engagement Activity | Participation in an open day or visit at my research institution |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | Amanda Burridge visited the Obregon CIMMYT site, specifically field sites used for IWYP projects. |
Year(s) Of Engagement Activity | 2017 |
Description | Engagement with industry |
Form Of Engagement Activity | A formal working group, expert panel or dialogue |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Industry/Business |
Results and Impact | Discussion with breeder regarding marker development for tracking introgressions |
Year(s) Of Engagement Activity | 2017 |
Description | Engagement with industry |
Form Of Engagement Activity | A formal working group, expert panel or dialogue |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Industry/Business |
Results and Impact | Discussion with technology provider regarding optimisation of new technology for wheat |
Year(s) Of Engagement Activity | 2018 |
Description | Engagement with industry |
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 | Meeting with technology provider regarding a new genotyping platform and its application |
Year(s) Of Engagement Activity | 2017 |
Description | Engagement with industry |
Form Of Engagement Activity | A formal working group, expert panel or dialogue |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Industry/Business |
Results and Impact | Transfer of markers to technology provider to aid the development of a new genotyping platform |
Year(s) Of Engagement Activity | 2017 |
Description | Engagement with industry |
Form Of Engagement Activity | A formal working group, expert panel or dialogue |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Industry/Business |
Results and Impact | Meeting with service providers for genotyping technical development |
Year(s) Of Engagement Activity | 2017 |
Description | Engagement with industry |
Form Of Engagement Activity | A formal working group, expert panel or dialogue |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Industry/Business |
Results and Impact | Germplasm exchange for technical development |
Year(s) Of Engagement Activity | 2017 |
Description | From Seed to Pasta III, Bologna, Italy, 2018-09-19 |
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 | Amanda Burridge attended and met delegates from From Seed to Pasta III, a conference that focused on durum wheat breeding and processing. |
Year(s) Of Engagement Activity | 2018 |
Description | Invited speaker University of Reading |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | National |
Primary Audience | Professional Practitioners |
Results and Impact | Presentation on the genetics of adaptation in wheat |
Year(s) Of Engagement Activity | 2017 |
Description | Invited speaker at PlantGen2017 |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | Presentation on genetics of adaptation in bread wheat |
Year(s) Of Engagement Activity | 2017 |
URL | https://www.google.co.uk/search?dcr=0&ei=a4WmWpCDJ6GUgAaRpKLwDg&q=plantgen+2017&oq=plantgen+2017&gs_... |
Description | JIC Breeders Day |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | No |
Geographic Reach | National |
Primary Audience | Industry/Business |
Results and Impact | Tours of JICs experimental farm (Church Farm) with presentations by project leaders to show how their research can be applied in plant breeding. |
Year(s) Of Engagement Activity | 2017 |
Description | Keynote presentation at 2019 Monogram |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | Keynote, plenary lecture at Monogram 2019 |
Year(s) Of Engagement Activity | 2019 |
Description | Life Sciences Symposium 2018-02-02 |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | Regional |
Primary Audience | Professional Practitioners |
Results and Impact | Amanda Burridge presented work by the Bristol Cereal Genomics team. |
Year(s) Of Engagement Activity | 2018 |
Description | Meeting with South African deligation to discuss meiosis, genotyping and wheat breeding |
Form Of Engagement Activity | A formal working group, expert panel or dialogue |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Industry/Business |
Results and Impact | Meeting with British Council lead South African delegation to discuss wheat breeding and possible further links |
Year(s) Of Engagement Activity | 2018 |
Description | Meeting with international experts in wheat breeding and recombination |
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 | Meeting of international experts in wheat breeding and recombination/marker development to consider future prospects |
Year(s) Of Engagement Activity | 2018 |
Description | Monogram 2018 - John Innes Centre |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | Amanda Burridge presented 'Rapid and Affordable Genotyping by Sequencing Optimised for Hexaploid Wheat' at Monogram 2018 |
Year(s) Of Engagement Activity | 2018 |
Description | Plant Development and Evolution International Workshop 2018-02-22 |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Postgraduate students |
Results and Impact | Amanda Burridge attended the Plant Development and Evolution International Workshop in Zurich with the presentation 'Improving Wheat Photosynthesis using Wild Relatives' |
Year(s) Of Engagement Activity | 2018 |
Description | Plant and Animal Genomes (PAG) XXVI |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Industry/Business |
Results and Impact | Amanda Burridge attended Plant and Animal Genomes (PAG) XXVI and presented 'CerealsDB Version 4.0: A Review of Tools and Data for Wheat Breeders and Research Scientists' |
Year(s) Of Engagement Activity | 2018 |
Description | Presentation at Plant and Animal Genome Meeting |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | Presentation was W257 Developmental and Physiological Dissection of QTLs in Wheat NAM Populations Stefano Bencivenga, Luzie U. Wingen, Scott Boden and Simon Griffiths, John Innes Centre, Norwich, United Kingdom |
Year(s) Of Engagement Activity | 2018 |
URL | https://pag.confex.com/pag/xxvi/meetingapp.cgi/Person/49737 |
Description | Public dialog and debate |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | Regional |
Primary Audience | Public/other audiences |
Results and Impact | A pint of science debate on the price of bread and wheat breeding |
Year(s) Of Engagement Activity | 2017 |
Description | Radio broadcast Farming today |
Form Of Engagement Activity | A press release, press conference or response to a media enquiry/interview |
Part Of Official Scheme? | No |
Geographic Reach | National |
Primary Audience | Industry/Business |
Results and Impact | Interview for farming today on wheat breeding and its importance; 14th July 2017 |
Year(s) Of Engagement Activity | 2017 |
Description | Rank Prize acceptance speech |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | National |
Primary Audience | Professional Practitioners |
Results and Impact | Rank prize (2018) acceptance speech |
Year(s) Of Engagement Activity | 2017 |
URL | http://www.rankprize.org/index.php/prizes/prizes-2018 |
Description | Rank Symposium on "The shape of wheat to come" |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Study participants or study members |
Results and Impact | The Rank Symposium of "The shape of wheat to come" was a four day event organised by Edwards and Higgins to promote the area of recombination to a wide range of international scientists ranging from PhD students to retired professors |
Year(s) Of Engagement Activity | 2018 |
Description | Stakeholder Workshop: Social Responsibility and Wheat Research 13/9/18 |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | No |
Geographic Reach | National |
Primary Audience | Policymakers/politicians |
Results and Impact | Stakeholders talked about their own interests (and/or those of their community) in relation to the many uses of wheat. The event also considered stakeholder responses as the basis for a report on social responsibility and wheat research targeted at policy audiences |
Year(s) Of Engagement Activity | 2018 |
Description | Visitors from the University of Florence 2-6 July 2018 |
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 | Academic visit from Alberto Masoni and Massimo Gori of the University of Florence. Visit was for training, data sharing and discussion of future collaboration opportunities |
Year(s) Of Engagement Activity | 2018 |
Description | Wheats and Women International Conference, National Research Council, Rome, 2018-06-14 |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Policymakers/politicians |
Results and Impact | Amanda Burridge attended and presented at the first Women in Wheat (Carlotta Award) conference in Rome. |
Year(s) Of Engagement Activity | 2018 |