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'.

Publications

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Burridge AJ (2017) High-Density SNP Genotyping Array for Hexaploid Wheat and Its Relatives. in Methods in molecular biology (Clifton, N.J.)

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Hawkesford MJ (2019) Exploiting genetic variation in nitrogen use efficiency for cereal crop improvement. in Current opinion in plant biology

 
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.
Exploitation Route More efficient breeding for developing worl agriculture. New candidate traits/QTL for the DFW Breeders Toolkit.
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.
First Year Of Impact 2014
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
 
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 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 Germplasm exchange for 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 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 Meeting with service providers for genotyping 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