MAGIC Yield: Deploying MAGIC Populations for Rapid Development of Genetic Markers for Yield Improvement in Elite UK Winter Wheat

Lead Research Organisation: National Inst of Agricultural Botany
Department Name: Centre for Research

Abstract

Context:
Wheat is the UK's major crop, covering 1.6 million hectares. Maintaining wheat yield is a critical component towards achieving economically and environmentally sustainable food security. To meet growing demand, wheat yields must increase; in the UK, this needs to take place against a background of unpredictable climate and reduced inputs. Delivering 'sustainable intensification' requires breeders to improve both yield and yield stability, in the face of unpredictable future environments. After a post-war period of sustained on-farm UK wheat yield increases, a result of both genetic and agronomic improvement, there has been no increasing trend in yield over the last fifteen years. Improved methods to increase the rate of genetic improvement represent a critical component of the solution.

For the first time in UK wheat research, this project utilises a powerful combination of newly available approaches and resources, allowing detection of the genetic determinants of yield at high-precision, thus enabling rapid deployment of project outcomes within the six participating industrial partners. Central is the use of our unique Multiparent Advanced Generation Inter-Cross (MAGIC) population, which combines high genetic diversity (originating from eight UK wheat varieties), and high levels of genetic reshuffling ('genetic recombination', captured via multiple rounds of intercrossing, and the generation of the resulting 1,000 progeny lines).

Project objectives: MAGIC Yield targets the genetic improvement of grain yield, the principle target for both breeders and farmers. It exploits the powerful union of high-density genetic marker coverage with a MAGIC population that captures high levels of genetic recombination and diversity, to:
(1) Identify and characterise the genetic regions in wheat controlling yield, yield components and yield stability, at high precision.
(2) Provide a molecular tool-kit with which wheat breeders can use in their breeding programs to deploy and track the regions of the wheat genome found to confer beneficial yield and yield stability.
(3) Provide the participating breeders with analysis pipelines and resources with which they can independently carry out analysis of MAGIC datasets, both within and after project duration.
(4) Use the novel molecular breeding methodology, Genomic Selection, to allow selection for yield and yield stability in the MAGIC lines, based on molecular data alone.
(5) Provide resources centered around the MAGIC population, from which future studies targeting additional components of sustainable wheat production can be undertaken.
(6) Develop and enhance interaction between the academic and industrial wheat R&D communities to ensure results and resources are effectively disseminated for the benefit of UK agriculture.

Applications and benefits:
The ability to apply modern molecular breeding approaches to precisely determine the determinants of yield and yield stability will lead to the development of new wheat varieties with improved performance. Such varieties would be of major benefit to the UK agronomy sector, helping increase wheat yields and protect against current and future threats to production from a changing climate. Promoting the UK's wheat R&D sector will help ensure the competitiveness of the agricultural sector, and support UK-based crop research and innovation. Ultimately, promoting stable and sustainable UK wheat production benefits the consumer in terms of food prices, and minimising the environmental impact of food production.

Technical Summary

For the first time in UK wheat research, and in partnership with six industrial partners, MAGIC Yield combines recently available MAGIC biological resources (the eight parent MAGIC wheat population) and genomic platforms (high-density SNP arrays) to dissect the genetics of wheat grain yield, yield components and yield stability. This will be achieved by building upon previous BBSRC investment in the innovative UK Elite MAGIC biological resource (eight founders, three rounds of inter-mating, 1,000 progeny), and subsequent NIAB investment (90k SNP genotyping, generation of three years of yield data). These resources will be combined with emerging genomics and statistical genetic approaches, to deliver the tools and methodological approaches to precisely manipulate yield in UK wheat.

Specific objectives

(1) Genotype all 1,000 MAGIC lines using high-density genetic marker platforms.

(2) Create a high-resolution MAGIC genetic map.

(3) Collate five years of MAGIC yield and yield component phenotypic data.

(4) Undertake high-precision QTL mapping of yield, yield components and yield stability.

(5) Deliver a molecular tool-box and QTL pyramiding models for efficient deployment of beneficial yield loci.

(6) Use Genomic Prediction and Selection to develop models and markers for simultaneous selection of multiple yield phenotypes over successive generations.

(8) Provide MAGIC genetics, genomics and germplasm resources to the wider wheat R&D community.

Participation of industry ensures project aims effectively target breeder requirements, thus facilitating rapid technology transfer. The nature of the resource means that over time, layering of additional phenotypic datasets will permit genetic analysis of multiple phenotype complexes, allowing models to be built for marker-assisted selection based on 'whole-plant' agronomic performance.

Planned Impact

As the UK's major crop, wheat produces an annual grain yield of 13 million tonnes, with a pre-processed value of ~£2 billion. This project will deliver the genetic platforms, know-how and tools to improve yield and yield stability in UK wheat. This addresses a key component of sustainable UK food production, and is positioned at the interface between crop research and its practical translation.

Ultimately, project outcomes will lead to the development of new varieties with increased genetic potential for yield, yield components and yield stability, benefiting growers and downstream users. As an indication project impact on growers, we estimate the benefit of fixing one QTL of minor effect (controlling 1% genetic variation) to be £26 million nationwide. However, project outcomes will impact upon multiple sectors:

1. Private sector wheat R&D and breeding
MAGIC Yield will underpin competitive UK-relevant wheat breeding by helping breeders develop varieties with higher yield potential and yield stability, thus enhancing their performance and marketability. Breeding a new variety requires ~7 years, and a further 2-3 years of National List trials before reaching the market. Project outcomes have the potential to be integrated into breeding programs at the end of year 2, with release of National List accredited varieties ~9 years later. By supporting the alignment of UK biosciences with industry and agriculture, MAGIC Yield will help maximise the productivity and international competitiveness of these sectors.

2. UK farmers and agriculture
UK growers will benefit from the availability of new wheat varieties with improved genetic potential for yield and yield stability (ie the ability to achieve higher and more stable yields), and the associated benefits that go with increased grain yield per unit area (ie reduced input costs, increased land use efficiency). This will help maximise resource-use efficiency and support the sustainability and competitiveness of the UK arable industry.

3. UK biosciences
MAGIC Yield deploys innovative tools and approaches to provide practical solutions to the challenges facing sustainable UK crop production. Timely release of project outcomes will prime further research using MAGIC to further dissect the genetics of wheat yield, yield protection and grain quality. Involving rapidly advancing areas of crop genetic research, this project will provide training and skills relevant to modern crop science, and help raise the international profile and impact of UK biosciences. Collectively, project resources and outputs provide a powerful community resource for the investigation of wheat genetics in UK relevant germplasm.

4. Wider UK public and policy makers
The introduction of new wheat varieties with higher yield per unit input will have downstream effects on consumers and society in general. All parties will benefit from a more stabilised marketplace resulting from greater buffering of UK wheat production against price fluctuations. The project will therefore contribute to increased food security under increasingly volatile and unpredictable economic and environmental conditions. By demonstrating the ability of scientific R&D to provide solutions to national and international policy, goals and legislation, project outcomes will help inform current and future government decision making processes on food security and biosciences.
 
Description We have:

(1) Successfully undertaken wheat yield trials over two seasons, with five sites per season.

(2) Developed protocols to genetically analyse the phenotypic data emerging from the five wheat trial sites.

(3) Identified marker-trait associations, identifying genetic variants linked to regions of the wheat genome controlling target traits.

(4) Converted linked genetic variants to the KASP genetic marker platform, for use by our industrial partners.

(5) Within selected chromosomal regions found to control our traits of interest, identified candidate genes that may control these traits, and have started developing germplasm resources, (i)induced mutations and (ii) Near isogenic lines, to explore the function of these genes.
Exploitation Route Wheat genetic markers linked to traits investigated are available for use by the five breeding companies involved in this BBSRC LINK project.
Sectors Agriculture, Food and Drink

 
Description The wheat genetic analyses undertaken from trial seasons 1 and 2 have identified SNPs linked to traits investigated. Many of these have been converted to KASP markers. The five breeding companies involved in this BSBRC LINK project have access to these resources, for potential use in their breeding and pre-breeding activities.
First Year Of Impact 2015
Sector Agriculture, Food and Drink
Impact Types Economic

 
Description Teaching material for NIAB QMPB course
Geographic Reach Multiple continents/international 
Policy Influence Type Influenced training of practitioners or researchers
Impact Course materials developed for the NIAB Quantitative Methods in Plant Breeding course, which teaches quantitative approaches to academic and industrial plant researchers and breeders
 
Description AHDB postgraduate student bursary
Amount £10,000 (GBP)
Organisation Agricultural and Horticulture Development Board 
Sector Charity/Non Profit
Country United Kingdom
Start 08/2016 
End 02/2017
 
Description BBSRC DTP PhD
Amount £70,000 (GBP)
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 09/2016 
End 09/2020
 
Title MAGIC seed 
Description Seed of over 1,000 MAGIC wheat lines is available on request for use in either collaborative or independent research projects 
Type Of Material Biological samples 
Year Produced 2015 
Provided To Others? Yes  
Impact Collaboration with new partners in Ireland (teagasc) and France (Arvalis). Research programme (independent) initiated at Reading University. Seed passed to breeders fo use in their research and breeding. Colaborative research with breeders 
URL http://www.niab.com/pages/id/402/NIAB_MAGIC_population_resources
 
Title MAGIC map 
Description The MAGIC SNP Genetic map. More markers mapped with more precision than previously released by anyone 
Type Of Material Database/Collection of data 
Year Produced 2015 
Provided To Others? Yes  
Impact Downloaded by breeders and researchers. 
URL http://www.niab.com/uploads/files/MAGIC_pedigree_tables.xlsx
 
Title MAGIC population raw data 
Description MAGIC wheat population. Raw data available for download 
Type Of Material Database/Collection of data 
Year Produced 2015 
Provided To Others? Yes  
Impact Data downloaded. Requests for more information 
URL http://www.niab.com/pages/id/402/NIAB_MAGIC_population_resources
 
Description NIAB EI JIC partnership 
Organisation Earlham Institute
Country United Kingdom 
Sector Academic/University 
PI Contribution We have met on several occasions to try to establish a route by which we can collaborate to help explore ways in which the NIAB Elite MAGIC population could be exploited to underpin further wheat genettic and genomic advances in the UK. Meetings were followed up with draft outlines of research ideas, and meetings to elaborate on them.
Collaborator Contribution EI and JIC partners contributed to research discussions and were involved in drafting research idea outlines, and elaborating on these.
Impact The collaboration is multidisciplinary (wheat quantitative genetics and genomics), and resulted in a joint grant application to BBSRC RM in 2016. The joint application has been selected for funding by BBSRC, and started in 2017 (NIAB: BB/P010741/1).
Start Year 2016
 
Description NIAB EI JIC partnership 
Organisation John Innes Centre
Country United Kingdom 
Sector Academic/University 
PI Contribution We have met on several occasions to try to establish a route by which we can collaborate to help explore ways in which the NIAB Elite MAGIC population could be exploited to underpin further wheat genettic and genomic advances in the UK. Meetings were followed up with draft outlines of research ideas, and meetings to elaborate on them.
Collaborator Contribution EI and JIC partners contributed to research discussions and were involved in drafting research idea outlines, and elaborating on these.
Impact The collaboration is multidisciplinary (wheat quantitative genetics and genomics), and resulted in a joint grant application to BBSRC RM in 2016. The joint application has been selected for funding by BBSRC, and started in 2017 (NIAB: BB/P010741/1).
Start Year 2016
 
Description Breeders' day presentation 
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 Presentations and discussons with the UK cereal wheat breeding community
Year(s) Of Engagement Activity 2022
 
Description British Science Foundation event: Science Cafe public meeting, 2016 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Public/other audiences
Results and Impact British Science Foundation event: Science Cafe public meeting, 2016
Sparked keen interest and discussion amongst the members of the public present.
Year(s) Of Engagement Activity 2016
 
Description Cereals 2016 
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 Demonstration plots and information boards at Cereals 2016, the major UK farming industry event. Generated discussions with industry.
Year(s) Of Engagement Activity 2016
 
Description Conference abstract and poster submission to Monogram 2017 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Conference abstract and poster submission to Monogram 2017, titled "Using MAGIC to dissect the genetics of below- and above-ground phenotypes in wheat"
Year(s) Of Engagement Activity 2017
 
Description Displat at 2019 Cereals Event 
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 Display as part of NIAB stand at the major UK Arable Event, "Cereals"
Year(s) Of Engagement Activity 2019
 
Description Display at NIAB open day 
Form Of Engagement Activity Participation in an open day or visit at my research institution
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact Displat at NIAB Open Day
Year(s) Of Engagement Activity 2019
 
Description Field plot demonstrations at NIAB open day June 25th 2017 
Form Of Engagement Activity Participation in an open day or visit at my research institution
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Industry/Business
Results and Impact Using field plots of germplasm from MAGIC projects, together with associated posters, to demonstrate applications of research to industry/business at NIAB open day. Engagement with industry and feedback of needs of agricultural industry and farmers.
Year(s) Of Engagement Activity 2017
 
Description Field plot demonstrations at NIAB open day June 26th 2018 
Form Of Engagement Activity Participation in an open day or visit at my research institution
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Industry/Business
Results and Impact Using field plots of germplasm from MAGIC projects, together with associated posters, to demonstrate applications of research to industry/business at NIAB open day. Engagement with industry and feedback of needs of agricultural industry and farmers.
Year(s) Of Engagement Activity 2018
 
Description Invited speaker Gregor Mendel Institute, Austria 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Invited talk, NIAB MAGIC research
Year(s) Of Engagement Activity 2016
 
Description MAGIC 2019 talk James Cockram 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Talk title: Wheat MAGIC research at NIAB
purpose: disseminate results
outcomes: interactions and disucssions with peers
Year(s) Of Engagement Activity 2019
 
Description MAGIC YIELD article for CPM magazine, 2017 
Form Of Engagement Activity A magazine, newsletter or online publication
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Article for Crop Production Magazine describing the work carried out in the MAGIC YIELD project, and its relevance to industry.
Year(s) Of Engagement Activity 2017
URL http://www.cpm-magazine.co.uk/2017/05/16/theory-field-genes-reveal-secrets/
 
Description MAGIC presentation at Monogram 2015 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact Oral presentation of MAGIC map and other MAGIC results/plan at annual national meeting of UK wheat researchers.
Year(s) Of Engagement Activity 2015
URL http://www.monogram.ac.uk/MgNW2015.php
 
Description NIAB Poster Day 2017 
Form Of Engagement Activity Participation in an open day or visit at my research institution
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Professional Practitioners
Results and Impact Poster and practical demonstrations to disseminate current work
Year(s) Of Engagement Activity 2017
 
Description NIAB Quantitative Genetics COurse teaching 2019,2020 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Course teaching Quantitative Genetics to Plant Breeders and Applied PhD students. Incorporates knowledge and experience from NIAB research projects
Year(s) Of Engagement Activity 2019,2020
 
Description NIAB-EMR talk 
Form Of Engagement Activity Participation in an open day or visit at my research institution
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Professional Practitioners
Results and Impact Talk at NIAB-EMR, March, 2017: overview of my research at NIAB-Cambridge.
Year(s) Of Engagement Activity 2017
 
Description PAG MAGIC YIELD poster 2018 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Poster presentation at the Plant and Animal Genomes conference, San Diego, USA, Jan 2018
Year(s) Of Engagement Activity 2018
 
Description Poster presentation at NIAB Staff day 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Professional Practitioners
Results and Impact Poster at NIAB Staff Day on what MAGIC resources
Year(s) Of Engagement Activity 2016
 
Description Presentation to research group at NIAB 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Professional Practitioners
Results and Impact Presentation of results from Wagtail and MAGIC projects to NIAB research group
Year(s) Of Engagement Activity 2016
 
Description Presenting MAGIC demonstration plots at NIAB Open Day 2015 
Form Of Engagement Activity Participation in an open day or visit at my research institution
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact Presenting MAGIC demonstration plots at NIAB Open Day 2015
Year(s) Of Engagement Activity 2015
 
Description Presenting NIAB MAGIC deomonstration field plots and poster at NIAB Directors Day, 2015 
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 Presenting NIAB MAGIC deomonstration field plots and poster at NIAB Directors Day, 2015
Year(s) Of Engagement Activity 2015
 
Description Talk at Eucarpia Biometrics 2015 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Oral presentation of MAGIC mapping project and other MAGIC research outcomes to professional audience from academia and industry
Year(s) Of Engagement Activity 2015
URL http://www.wageningenur.nl/en/show/EUCARPIA-Biometrics.htm
 
Description Talk on Genetic markers and genetic mapping for the MAX-CROP student seminar series, 2015 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Talk on Genetic markers and genetic mapping for the MAX-CROP student seminar series, 2015
Year(s) Of Engagement Activity 2015
 
Description oral presentation for Nottingham University undergrad student visit 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Undergraduate students
Results and Impact Presentation outlining current NIAB work on MAGIC resources to a visit of ~50 undergrad students from Nottingham University.
Outcomes: questions and discussions from the students
Year(s) Of Engagement Activity 2020