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.
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
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
Jackson HA
(2022)
Genomic erosion in a demographically recovered bird species during conservation rescue.
in Conservation biology : the journal of the Society for Conservation Biology
Bevan MW
(2017)
Genomic innovation for crop improvement.
in Nature
Lu FH
(2018)
Independent assessment and improvement of wheat genome sequence assemblies using Fosill jumping libraries.
in GigaScience
Scott MF
(2020)
Multi-parent populations in crops: a toolbox integrating genomics and genetic mapping with breeding.
in Heredity
Walkowiak S
(2020)
Multiple wheat genomes reveal global variation in modern breeding.
in Nature
Walkowiak S
(2020)
Multiple wheat genomes reveal global variation in modern breeding.
in Nature
International Wheat Genome Sequencing Consortium (IWGSC)
(2018)
Shifting the limits in wheat research and breeding using a fully annotated reference genome.
in Science (New York, N.Y.)
Description | We assembled genome sequences for all parents of the MAGIC population, plus CIMMYT lines Baj and Weebil, sources of key variation for yield stability. These sequences are being annotated and improved. The MAGIC population, of ca 1000 lines, and the Watkins landraces collection have been skim sequenced to identify sequence variation. We have developed new tools for assembly of these sequences, with further developments to improve haplotype reconstruction underway. Some of these assemblies have been analysed and published as part of the International Wheat PanGenome, which is currently the best global reference for wheat sequence variation and has provided initial insights into wheat global diversity. |
Exploitation Route | All sequence data and assemblies will be placed in public repositories, partial results are already available and being used by the research and breeding communities. 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. |
Sector | Agriculture, Food and Drink |
Impact Types | Economic |
Description | Membership of BBSRC Transformative technology Panel |
Geographic Reach | National |
Policy Influence Type | Membership of a guideline committee |
Impact | The transformative technology strategy advisory panel have influence BBSRC policy on data intensive bioscience and big ideas pipeline |
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 |
Description | Wheat pan-genomics |
Geographic Reach | Multiple continents/international |
Policy Influence Type | Membership of a guideline committee |
Impact | We described the EI technological advances and our plans to use these for improved wheat breeding with interested parties from developed and developing countries to improve their wheat breeding programs by sequencing key accessions from their countries. This has lead to the establishment of a large multi-national collaboration with substantial cross links and obvious synergies. The worry prior to this meeting was that there would be disparate efforts using different technological approaches which would prevent comparison, meta-analysis and lead to a split in wheat genetics/genomics - this has been avoided and we expect great progress to be made in short time frames. |
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 |
Description | Collaboration with IPK for wheat scaffolding |
Organisation | IPK Gatersleben |
Country | Germany |
Sector | Private |
PI Contribution | A collaboration between my team using W2RAP genome assemblies (contigs scaffolded with long mate pair data) with Martin Mascher's group at IPK who developed TRITEX assembler (contigs scaffolded with long mate pair, then 10x genomics linked reads, finally HiC data). TRITEX is similar to NRGene's de novo magic assembler. We supplied our W2RAP assemblies with 10x and HiC datasets for 10 wheat genomes, and worked with the team to apply their longer range scaffolding approach. This also includes us testing the method applying their approach implemented in our code for 10x data. We QC'd their assemblies and paid for a staff member to assemble more genomes. |
Collaborator Contribution | TRITEX is not am easily portable software package, and needs some human QC and tuning according to the genome and datasets. By working with IPK we were able to analyse our data on the pipeline stably installed on their servers, and with a team well used to using it. Martins team tested the approach on two varieties, Robigus and Claire. After QC we were impressed, and because the postdoc was leaving we found another postdoc who could work on the project for some months to scaffold the remaining genomes, leading to 10-100x improvement in scaffolding contiguity. |
Impact | 10 W2RAP+TRITEX genome assemblies with psuedomolecule data. |
Start Year | 2021 |
Description | Genome scaffolding method - small genome test bed |
Organisation | University of East Anglia |
Department | School of Environmental Sciences UEA |
Country | United Kingdom |
Sector | Academic/University |
PI Contribution | We were developing scaffolding approaches using W2RAP and TRITEX assembler methods. However, wheat is a huge complex system in which to test new methods. We decided to test the methods on a smaller bird genome using data from this project. This genome is ~10x smaller than wheat, and bird genomes are well decribed by the B10K project, with very high levels of synteny between avian genomes. We produced psuedomolecules which allowed production of figures showing how inbred individuals were across their chromosomes. |
Collaborator Contribution | Datasets, sanity checks of our data, publishing these results in Jackson et al. Conservation Biology 2022 see https://doi.org/10.1111/cobi.13918 |
Impact | This is a multi-disciplinary collaboration between conservation biologists, genomics experts, and population geneticists. We published this study in Conservation Biology (see URL). |
Start Year | 2021 |
Title | SDG |
Description | SDG 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 SDG 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. |
URL | https://f1000research.com/articles/8-1490 |
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 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 | 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 | 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 | Our Broken Planet - NHM exhibition |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Public/other audiences |
Results and Impact | I worked with the Natural History Museum team to contribute towards the exhibition "Our broken planet: How we got here and ways to fix it" this was open from May to August 2022, but was planned months before this. Specifically I contributed towards the design of a cabinet explaining how modern agriculture is carried out, and how research is working to maximise yields, minimise environmental impacts, specifically around the use of genetics. The cabinet contained different types of wheat, and in a recording I explained how they differ morphologically and genetically, and how we are seeking to breed new varieties of wheat that use less water, pesticides and fungicides by developing better wheat genetics. |
Year(s) Of Engagement Activity | 2022 |
URL | https://www.nhm.ac.uk/visit/our-broken-planet.html |
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 | Presentation to international wheat pan-genome project expert group on our progress in improving UK cultivar scaffolding |
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 | Presentation on bringing UK academically derived assemblies towards the same level as the other international assemblies all produced by a commercial company (NRGene). This sparked discussion on how this would allow better UK cultivar and breeding study, and better comparison between UK and international cultivars. |
Year(s) Of Engagement Activity | 2020 |
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 |