Wheat Genomics for Sustainable Agriculture

Lead Research Organisation: EMBL - European Bioinformatics Institute
Department Name: Ensembl Genomes

Abstract

Securing food supply on a global scale requires solutions to a complex set of unprecedented problems, including rising demand due to major population increases and social mobility, global climate change, rising energy costs and land, water and nutrient limitations. Finding and implementing these solutions is a top priority for governments and scientists worldwide, and has been articulated as a key BBSRC strategic objective. Opportunities for plant science to contribute to global food security include increasing the yield and quality of crops, combatting diseases, enabling maximal crop productivity in sub-optimal growth conditions, and increasing maximal yield potential. Utilising non- food components of food crops, such as cell wall material and waste products of food production to produce energy and industrial feedstocks, has a major role in reaching sustainability and maximising overall yield of renewable resources from limited land and soils. Grass crops are essential for human existence by directly or indirectly serving as the primary source of human nutrition. Wheat, rice and coarse grains such as maize are the most important crops for human food production, therefore increasing grain production sustainably is a critically important strategic and scientific objective. Wheat is the main arable crop in the UK, planted on 60% of arable land, with an annual farm gate value of ~£2.5b and a processed product value of approximately £150bn. Yield increases in wheat are slowing compared to past gains achieved primarily through improved agronomy and also in relation to other grain crops, notably maize. Genetic and transgenic improvement of wheat is therefore a very high priority in the UK and world- wide, and large international programmes for wheat genetic improvement are underway. A high quality genomics sequence provides a complete, accurate and durable record of genes, predicted proteins and other genomic elements that today are a fundamental foundation for nearly all areas of biological research. This proposal describes a UK component of an international coordinated wheat genome sequencing project that will make decisive and innovative contributions to sequencing the wheat genome and supporting crop improvement through genomics.

Technical Summary

Bread wheat has an exceptionally complex genome comprised of three independently- maintained genomes, each of which is approximately 6 Gb- more that the entire human genome. Wheat genes are found predominantly as small (1-4) clusters, with an average density of between 1 gene/86kb in proximal regions and 1gene/180 kb in distal regions of the chromosome. Genes and gene islands are separated by extensive tracts of nested retrotransposon repeats comprising approximately 85% of the genome. The gene content of diploid grasses is approximately 30-35,000 suggesting bread wheat has approximately three times this number of genes. The scale and complexity of this genome requires a large coordinated effort and the development and application of new technologies. Work in the International Wheat Genome Sequencing Consortium aims to generate accurate sequences of nearly all genes, annotate these and place them in a syntenic framework. Four chromosomes will be sequenced to high quality reference standards using a combination of established methods and novel sequencing technologies. Re-sequencing methods will be developed to access sequence variation in the Triticeae in concert with the pre-breeding programme. Finally, bioinformatics resources for the long- term maintenance and analysis of the sequence will be established.

Planned Impact

The transformative effect of access to high quality genome sequence that is carefully analyzed, and directly and freely available to all users, is well known. Wheat is one of the three major crop plants of global importance, and the predicted impact of a high quality wheat genome resource on crop improvement will be profound, as genomics provides a framework for new breeding methods that are substantially faster and more effective. The wheat genome project will have two immediate impacts on a wide range of new research in wheat by researchers world-wide, and on the application of genomics to breeding and crop improvement by the breeding and agricultural biotechnology industries. Thus plant and crop scientists working in academia and industry are direct beneficiaries of the outcomes of the project. The impact of a genome sequence to these researchers will be profound. Access to and systematic study of all proteins sequence variation in the Triticeae, global gene expression, and the systems-level analysis of biological functions will transform research in crop improvement. Because many agronomic traits in wheat, such as yield and abiotic stress responses, are due to the effects of many genes, such traits will now be accessible to the full range of experimentation possible in modern biology. Consequently progress towards increasing yield stability and sustainable production will be substantially accelerated. The agricultural biotechnology and crop breeding industries, and bioinformatics and computer scientists working on genome assembly and analysis, will benefit from a similar revolutionary effect of genomics seen in rice and maize breeding. A key impact will be the direct and permanent improvements in the rate and scope of wheat breeding, leading to the production of new wheat varieties that can maintain high levels of productivity with reduced inputs. Research funding organizations are also direct beneficiaries of this project by enabling transformative research in wheat improvement, particularly through international collaborations. The impact is a major tangible contribution to meeting important societal goals in food security and sustainable production world-wide. Many indirect beneficiaries of the research can be predicted. Wheat growers will benefit from new varieties that will be more productive and with new end-uses, leading to more stable incomes and diversified production. By addressing the environmental sustainability of crop production through new genomics- lead research in nutrient- and water- use efficiency, the major environmental footprint of wheat production could be reduced, having a beneficial impact on the ecology and sustainability of the agricultural landscape. Other indirect beneficiaries are food processors, who will have access to affordable and a more secure supply of a global staple product. In turn consumers will benefit from more stable prices and access to a staple food.

Publications

10 25 50
 
Description Through this award, we have made the wheat genome available through Ensembl Plants. We have mapped other data, including sequence alignments and variant calls, onto the genome and made it available through a single, integrating interface. We have performed comparative genomic analysis between wheat and other related species. We have helped organise the submission of successive versions of the reference wheat genome sequence to the international nucleotide sequence archives. We have extended the Ensembl software suite for genome analysis, storage and dissemination to cover polyploid species. Most recently, we upgraded our reference species to include the new genome assembly and annotation that has been produced by our collaborators on the grant, the Earlham Institute. We have integrated variant and sequence alignment data, and performed comparative analyses to related plant species using DNA and protein sequences. We have also played a role in discussions, coordinated by the Wheat Initiative, to devise a community-wide strategy for the annotation of wheat gene names.
Exploitation Route The information made accessible is of use to plant breeding companies (as well as to plant scientists). Large scale correlation of the reference genome with phenotypic measurements, improvement to the reference genome and its annotation, the compiling of more extensive catalogues of natural variation, and the development of reference-quality genome sequences from other cultivars, are all expected and their integration into a common database framework (on top of the existing reference genome) will increase their subsequent applicability to plant breeding. Improved assemblies incorporated into the resource have significantly increased the accuracy and completeness of the resource and its potential for downstream use.
Sectors Agriculture, Food and Drink,Chemicals,Digital/Communication/Information Technologies (including Software)

URL http://plants.ensembl.org/Triticum_aestivum/Info/Index
 
Description The Ensembl wheat database has been used by plant breeding companies to access genomic information that can inform their breeding programmes.
First Year Of Impact 2013
Sector Agriculture, Food and Drink
Impact Types Economic

 
Description Joint authorship of an opinion paper in response to a call from the ad-hoc Technical Expert Group of the Convention on Biological Diversity
Geographic Reach Multiple continents/international 
Policy Influence Type Participation in a national consultation
URL https://www.cbd.int/abs/DSI-views/DivSeek.pdf
 
Description BBSRC Strategic Programme in Designing Future Wheat (DFW)
Amount £1,395,200 (GBP)
Funding ID BB/P016855/1 
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 03/2017 
End 03/2022
 
Title Wheat genome database 
Description Data from the bread wheat Tritium aestivum and related species have been included in Ensembl Plants, an integrative resource offering access to genome scale data from a variety of plant species. Successive improvements to the genome sequence have been accommodated including polymorphism data important for breeding (increasingly, in collaboration with CerealsDB), and the incorporation of the new TGAC 1.0 genome assembly. The database was developed originally with funding from BB/J00328X/1 and development has continued with funding from BBS/E/J/000PR9782. 
Type Of Material Database/Collection of data 
Year Produced 2012 
Provided To Others? Yes  
Impact The data structure, analysis pipelines and visualisation interfaces have been developed to accommodate polyploid crops in general of which bread wheat is our first example. Ensembl Plants (as a whole) has had 156,037 unique visitors in 2017. 
URL http://plants.ensembl.org/Triticum_aestivum/Info/Index
 
Title Software for viewing polyploid genomes 
Description New functionality added to the Ensembl genome browser and associated software (APIs, pipelines etc.) to support the analysis and discovery of polyploid genomes, including identification of homoeology, determination of evolutionary ancestry, and parallel display of varietal and inter-homoeologous variants. 
Type Of Technology Webtool/Application 
Year Produced 2014 
Impact Provision of informative access to the emerging genome of bread wheat, a critically important polyploid crop species. 
URL http://plants.ensembl.org/Triticum_aestivum/Info/Index
 
Description EU-China expert seminar on identifying potential joint priorities for research and innovation in food, agriculture and biotechnology 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Policymakers/politicians
Results and Impact I participated in an EU-China expert seminar on identifying potential joint priorities for research and innovation in food, agriculture and biotechnology, designed to identify future priorities for joint funding schemes based on the direction of current research.
Year(s) Of Engagement Activity 2016
 
Description Invited Presentation at the de.NBI symposium in Bielefeld, Germany, October 2017 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact An invited presentation was given to the annual symposium of the de.NBI bioinformatics network in Germany.
Year(s) Of Engagement Activity 2017
 
Description Invited presentation in the the C3BI seminar series held at the Institut Pasteur, Paris. 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact An invited presentation was given in the the C3BI seminar series held at the Institut Pasteur, Paris.
Year(s) Of Engagement Activity 2017
URL https://c3bi.pasteur.fr/seminars-tba-non-vertebrate-genomics/
 
Description Invited presentation/workshop at the Sainsbury Laboratory. Cambridge 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Professional Practitioners
Results and Impact Invited presentation/workshop at the Sainsbury Laboratory, Cambridge
Year(s) Of Engagement Activity 2017
 
Description Participation in Triticeae Gene Nomenclature Meeting 
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 Participation in a meeting, convened by the Wheat Initiative, to plan for future action on the nomenclature of Triticeae genes.
Year(s) Of Engagement Activity 2016
 
Description Participation in meeting on Plant genetic resources and SDGs: needs rights and opportunities 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Policymakers/politicians
Results and Impact The sharing of biological data related to plant genetic resources, and ensuring that the benefits from this sharing are equitably distributed throughout the world, are a matter of important societal concern. A meeting of interested parties was convened to advise the DivSeek organisation, which had been asked to prepare a position paper for the secretariat of the International Treaty on Plant Genetic Resources on behalf of a number of organisations involved in the generation, management and usage of such data. Publications aimed at other audiences are also expected to result from this meeting.
Year(s) Of Engagement Activity 2016
URL http://www.divseek.org/news/
 
Description Participation in meeting on Wheat Genomic Resources in the Post-Reference Genome Era 
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 Presentation to a meeting convened by the wheat initiative to identify future priorities for international wheat research.
Year(s) Of Engagement Activity 2016
URL http://www.wheatinitiative.org/events/wheat-genomic-resources-post-reference-sequence-era
 
Description Presentation at ELIXIR Innovation and SME forum, Wageningen, Netherlands 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Industry/Business
Results and Impact Presentation to ELIXIR SME Forum in Wageningen, NL, about presentation of wheat and barley genomes in Ensembl Plants.
Year(s) Of Engagement Activity 2015
URL http://www.elixir-europe.org/events/innovation-and-sme-forum-data-driven-innovation-agri-food-indust...
 
Description Presentation at Monogram Network meeting 2017 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact http://www.monogram.ac.uk/MgNW2017.php
Year(s) Of Engagement Activity 2017
URL http://www.monogram.ac.uk/MgNW2017.php
 
Description Presentation at the Conference "The Future of Science: The Digital Revolution: What is changing for humankind" 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Undergraduate students
Results and Impact A presentation at a conference attended mostly by undergraduate and high-school students, focused on far-reaching changes in scientific practice.
Year(s) Of Engagement Activity 2016
URL http://www.futureofscience.org/press/first-world-conference-on-the-future-of-science-science-and-soc...
 
Description Presentation on to meeting on Wheat as a Model Organism, Norwich, 2016 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Postgraduate students
Results and Impact A presentation on wheat resources in Ensembl Plants was given to an audience of early-career researchers at the workshop on "Wheat as a model organism" held at the Earlham Institute in Norwich, UK.
Year(s) Of Engagement Activity 2016
URL http://www.earlham.ac.uk/wheat-model-organism
 
Description Presentation on wheat genome at Plant and Animal Genomics Meeting, San Diego, 2015 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Postgraduate students
Results and Impact Presentation on representation of wheat genome in Ensembl Plants to a mixed audience of postgraduate researchers, academic scientists and industrial representatives.
Year(s) Of Engagement Activity 2015
 
Description Presentation to EBI industry workshop on Ontologies for Agriculture, Food and Nutrition April 2017 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Industry/Business
Results and Impact I participated in, and gave an invited presentation to, an EBI industry workshop on Ontologies for Agriculture, Food and Nutrition in April 2017. Participants were members of industry working in this domain.
Year(s) Of Engagement Activity 2017
URL https://www.ebi.ac.uk/industry/private/industry-workshop/2017/04/ontologies-agriculture-food-and-nut...
 
Description Talk at Lorenz Centre workshop on computational pan-genomics 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Postgraduate students
Results and Impact Contribution to a 5-day discussion meeting designed to shape thinking about the representation of pan-genomes and the tools that can model them.
Year(s) Of Engagement Activity 2015
URL https://www.lorentzcenter.nl/lc/web/2015/698/info.php3?wsid=698
 
Description Wageningen seminar 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Postgraduate students
Results and Impact Seminar delivered to mixed audience of professional researchers, postgraduate students and industry participants about presentation of wheat and barley genomes in Ensembl Plants.
Year(s) Of Engagement Activity 2014
 
Description Wheat Breeders Workshop 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Industry/Business
Results and Impact A wheat breeders workshop was organised 20th-21st October at TGAC, to present developments that have occurred during the project 'Triticieae Genomics for Sustainable Agriculture' to European wheat breeders.
Year(s) Of Engagement Activity 2015
 
Description Workshop on "Exploring Plant Variation Data" 
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 A workshop was held over 3 days (1st-3rd July 2015), focusing on plant variation data, to student, academic and industrial participants. Ensembl resources on wheat and barley developed with funding from the relevant BBSRC grants were included in the presentations.
Year(s) Of Engagement Activity 2015
URL https://www.ebi.ac.uk/training/events/2015/exploring-plant-variation-data