Wheat Pan-Genomics

Lead Research Organisation: Earlham Institute
Department Name: Research Faculty

Abstract

Bread wheat (Triticum aestivum L.) is the UK's most important crop and the world's most widely cultivated cereal. Understanding the genetic make up of crops is essential for achieving increases in sustainable yield, disease resistance and adaptation to changing growing conditions. However this understanding has been lacking in wheat because it has a exceptionally complex genetic make-up. But recently BBSRC scientists have made a breakthrough in analysing the complete genetic make up of wheat. In this project we aim to build on the UK success by accessing the genetic make up of several key wheat varieties important for global agriculture, and to analyse this data to help identify useful genetic variation. This work will be carried out in an international framework that will maximise the benefit of UK research for this globally important crop.

Technical Summary

This project integrates recent BBSRC-funded innovation in bread wheat genome re-sequencing/analysis capabilities at TGAC/JIC, with the 8-founder MAGIC population developed at NIAB, to address timely questions regarding the composition of the wheat 'pan-genome', and the ways in which this knowledge can be used for wheat genetic improvement.
Specifically, this project will:
-Produce and annotate high-quality reference sequences for the 8 MAGIC founders.
-Produce and annotate high-quality reference sequences for two internationally important CIMMYT wheat lines.
-Survey sequence of 94 maximally diverse wheat landraces from the Watkins collection to access a wide range of useful genetic variation.
-Catalogue millions of sequence variants, including a systematic identification and characterisation of many types wheat structural variants, including chromosome rearrangements, CNV, PAV and InDels, in both genes and repeats.
-Generate GbS data for 1,000 F9 MAGIC individuals, for identification of cross-over locations, haplotype characterisation, and construction of a POPSEQ genetic map for genome sequence scaffold anchoring and QTL analysis.
-Via analysis of MAGIC phenotypic datasets (18 traits over 28 trials), delineate gene and genetic variant content within QTL intervals at unprecedented detail.
-Characterise the effects of SV on genetic recombination rates and segregation distortion.
-Deliver open-access MAGIC datasets, analysis tools, knowledge and training to the wheat R&D community and to industry.

This project will deliver world-class knowledge, resources and training, and help maintain the UK's global position in wheat genetics and genomics, within a coordinated international framework.

Planned Impact

This project aims to develop resources and analytical tools for understanding and exploiting when genome sequence assemblies. These have the potential to radically alter both wheat breeding and crop improvement, and also facilitate new areas of research that will lead to improved crops by understanding the contributions of genetic variation and gene function to traits.
We aim to achieve the following objectives that will ensure that the proposed work achieves its maximal impact.
- To contribute to developing an international strategy for coordinating future work in wheat pan-genomics;
- To establish a network of collaborators and partners for applying outcomes of the research to genomics-led wheat improvement and promoting their uptake by breeders;
- To work with technology providers to develop new services and products to support genetic analyses of wheat based on multiple wheat genome assemblies;
- To demonstrate and promote the benefits of open access to technologies for generating wheat genomic assemblies, and genetic and genomic data;
- To train researchers from industry in the analysis and application of wheat genomics for breeding and technology development;
- To engage with the public about the excitement, power and societal impacts of genomics, enabling them to understand how it it applied for crop improvement, and to continue dialog about changes in how crops are produced.
- To encourage career development in plant science and genomics by hosting school visits and laboratory placements for school children.

We will maintain/develop key partnerships
Impacts of International Coordination
We will work with the Wheat Initiative to ensure this project achieves maximum synergies with related international activities, and that BBSRC achieves the best value for money and maximises its contributions to global wheat research.
Impacts for plant breeders and biotechnology companies
We will continue in-depth engagement and training of crop breeders in new genomics technologies, and prioritise the development of new tools that will facilitate improved breeding
Impacts for Growers and the Public
We will engage with growers and the general public to establish a dialog about the potential impacts of genomics on crop production, how it might influence farming, consumers and the environment.
Impacts for technology development companies and services
We work with Illumina and other genomics companies to help develop technologies and services for cheaper, faster and better genetics and genomics analyses for large and complex crop genomes

Publications

10 25 50

Related Projects

Project Reference Relationship Related To Start End Award Value
BB/P010768/1 15/05/2017 30/06/2018 £1,084,628
BB/P010768/2 Transfer BB/P010768/1 01/10/2018 10/10/2021 £955,196
 
Description We have generated sequences for genomic assembly of Rialto, Soissons, Xi19, Hereford, Alchemy and Brompton. These lines represent 80% of diversity of UK wheat and have been used to make an intercrossed population of MAGIC lines. We have also undertaken to sequence the CIMMYT lines Baj and Weebil, sources of key variation for yield stability. Skim sequencing of the MAGIC population of ca 1000 lines is planned, and the Watkins collection of landraces has been skim sequenced to identify sequence variation.
We have developed new tools for assembly of these sequences to improve haplotype reconstruction assembly is now underway.
Exploitation Route All sequence data and assemblies will be placed in public repositories. Working relationships with UK breeders established in the Triticeae LOLA project will ensure genomics information and technologies will be developed to support UK wheat breeders
Sectors Agriculture, Food and Drink,Energy

 
Description The predicted impacts will arise from a deeper understanding of wheat genomic diversity, how this is shaped by breeding, and how the genetic diversity of MAGIC progenitor lines contributes to agronomic traits. The project is linked to and makes a large contribution to the international wheat pan-genome project. This amplifies the impacts
First Year Of Impact 2017
Sector Agriculture, Food and Drink
Impact Types Economic

 
Description Meeting with Professor Lionel Clark (Chair of the Synthetic Biology Leadership Council) to discuss synbio strategy in Agrifood sector
Geographic Reach National 
Policy Influence Type Participation in a advisory committee
 
Description Outcomes of plans to analyse Chinese and European wheat varieties using common standards
Geographic Reach Asia 
Policy Influence Type Influenced training of practitioners or researchers
Impact The objectives of this collaboration have yet to be realised due to difficulties in sharing Chinese marker details, DNA samples and germplasm. This mens the proposed collaboration will not work
 
Title Sequencing and assembly of Claire, Paragon, Robigus, Cadenza and Weebil hexaploid wheat lines 
Description Sequencing and assembly of 4 UK elites Claire, Paragon, Robigus, Cadenza and 1 Mexican (CIMMYT) Weebil hexaploid wheat cultivars 
Type Of Material Database/Collection of data 
Year Produced 2019 
Provided To Others? Yes  
Impact large dataset covering >50% UK genetic diversity, 1st Mexican (heat and drought tolerant line) made publicly available 
URL https://www.ebi.ac.uk/ena/browser/view/PRJEB35709
 
Title BSG 
Description BSG allows is a framework to analyse sequence graphs such as those generated by various genome assemblers. It provides a workspace that can contains a graph and datastores for paired, linked and long reads. These reads can be mapped to the graph, and can be used to untangle or scaffold the graph. A SWIG API enables BSG to be used as a Python module, and there is experimental Julia and R support. 
Type Of Technology Software 
Year Produced 2018 
Open Source License? Yes  
Impact We are currently producing genome assemblies of: multiple wheat cultivars, multiple strawberry cultivars, and more. 
 
Description Feature article on genomics in the Easton Daily Press 
Form Of Engagement Activity A magazine, newsletter or online publication
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Public/other audiences
Results and Impact The Article was to cover the research activity at the Earlham Institute and at the Norwich Research park and how it would impact the general public
Year(s) Of Engagement Activity 2019
 
Description Illumina users group meeting 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact Presentation: "Plant genomics - assembling genomies and understanding haplotypes"
Year(s) Of Engagement Activity 2018
 
Description Meetings of the Wheat 10 Genome Project on pangenomics 
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 I attended a meeting on Wheat Pan-genomics connected to the Wheat Initiative meeting in Munich Germany. The International 10 Genome Project outlined their plans and progress, I updated them on the progress and plans of our project. The 10GP covers USA, Canada, China, Japan, India, Australia, Germany, France, Switzerland and UK - but each of these is studying Elite varieties from developed countries who an afford to join this project. Our grant includes the sequencing of 2 CIMMYT varieties (Weebil and Baj), which are from a for-public-good breeding program targeting the developing world. There was much interest in comparing to these lines, and so we have joined the International 10GP by committing to add these genomes to the project.
Year(s) Of Engagement Activity 2018
URL http://www.10wheatgenomes.com/
 
Description Meetings of the Wheat 10 Genome Project on pangenomics 
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 I attended a meeting on Wheat Pan-genomics connected to the Wheat Initiative meeting in Bologna Italy. The International 10 Genome Project outlined their plans and progress, I updated them on the progress and plans of our project. The 10GP covers USA, Canada, China, Japan, India, Australia, Germany, France, Switzerland and UK - but each of these is studying Elite varieties from developed countries who an afford to join this project. OUr grant includes the sequencing of 2 CIMMYT varieties (Weebil and Baj), which are from a for-public-good breeding program targeting the developing world. There was much interest in comparing to these lines, and we have now joined the International 10GP by committing to add these genomes to the project.
Year(s) Of Engagement Activity 2017
URL http://www.10wheatgenomes.com/
 
Description Monogram Bioinformatics workshop 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact I presented the breakthroughs in wheat genetics that are coming from our work on 8 of the most important UK elite wheat cultivars. The audience was a mix of researchers, prebreeders, breeders, agronomists and farmers.
Year(s) Of Engagement Activity 2018
 
Description Nature Day at Norwich Science Festival 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Public/other audiences
Results and Impact 7500 members of the general public attended Nature Day at Norwich Science Festival. A number of activities were available to engage the general public with the work of the institute. A number of talks/presentations were scheduled also.
Year(s) Of Engagement Activity 2018
 
Description Presentation at PAG conference San Diego USA 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact I presented our latest data on comparative gene expression between diploid and hexaploid wheat lines
Year(s) Of Engagement Activity 2019
 
Description Public engagement as part of the 1851 Royal Commission even on "Genetic engineering" at the NHM and broadcast on the BBC World Service 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Schools
Results and Impact As part of the reception before the debate on "Genetic Engineering" and broadcast on the BBC, I demonstrated to the public with plant samples how Wheat is a consequence of an historic, and natural, hybridization of three grass species. Furthermore that these events are still occurring and beneficial e.g. Triticale is a hybrid of wheat and rye, and wheat cultivars such as Rialto contain ~250,000,000bp of DNA from rye, which makes them resistant to fungi that otherwise would require extensive use of environmentally damaging pesticides.

With my colleague, Sandra Knapp, we also showed with samples how Solanaceae crop wild relatives can be used to introduce desirable traits controlled by single genes into crops such as potatoes and tomatoes.
Year(s) Of Engagement Activity 2018
URL https://www.bbc.co.uk/mediacentre/proginfo/2018/39/the-weekend-documentary-the-engineers
 
Description Talk at conference in MPI Golm Germany 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Postgraduate students
Results and Impact Attended the "plants and people" conference at MPI Golm, Germany. This conference is organised by the PhD students at the institute who are also presenting. The meeting attracted speakers from across the world and also from across the field of plant science from research, industry, EU regulations, and public engagements. It was very interesting to be able to meet with so many professionals across the field, and with young scientists doing their PhDs.
Year(s) Of Engagement Activity 2019
URL https://plants-and-people.mpg.de/node/7
 
Description Techology Day at Norwich Science Festival 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Public/other audiences
Results and Impact 7500 members of the general public attended Nature Day at Norwich Science Festival. A number of activities were available to engage the general public with the work of the institute. A number of talks/presentations were scheduled also.
Year(s) Of Engagement Activity 2018
 
Description Workshop talk 
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 Presented to "workshop on multi-parental populations", this was held in Cambridge UK, but was attended by international researchers from Europe, plus scientists from ICRISAT and IRRI ( CGIAR breeding institutes). My presentation introduced our work on Wheat and MAGIC populations in my talk "Combining genome technologies with genetics to analyse MAGIC populations". There was a lot of interest in how genomics can be used in breeding, as showed in our work, and the workshop attendees have written a review on "multi-parental populations" for the Hereditary journal.
Year(s) Of Engagement Activity 2019
URL http://mtweb.cs.ucl.ac.uk/mus/www/MAGICdiverse/MAGIC_workshop.htm