Triticeae Genomics for Sustainable Agriculture

Lead Research Organisation: Rothamsted Research
Department Name: Plant Biology & Crop Science

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 neay 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.
 
Description We are close to completing the optimisation of the exome capture technology required to achieve the targets in this grant. Data on mutations within our wheat populations will arrive soon, and will be made available on the Ensemble wheat genomic database.
Update: a total of 1209 mutagenised lines of wheat have been processed, identifying ~6 million mutations in genes. These are being exploited by many projects in wheat functional genomics and breeding, creating novel variation in important traits.
Update: a web portal giving access to the mutations identified has been developed. This also allows users to request seed for mutants of interest. Update: see deatiled report from LOLA project team.
Exploitation Route The millions of novel mutations in the wheat genome identified in this project will be invaluable for those investigating wheat biology or developing new varieties. The technology developed can also be used in other important crops.
Sectors Agriculture, Food and Drink,Manufacturing, including Industrial Biotechology

URL http://www.wheat-tilling.com
 
Description The project has so far identified over six million mutations in 1209 mutagenised lines of wheat. These are increasingly being exploited by wheat breeders to modify important traits eg. disease resistance, yield and quality. See detailed report from the whole LOLA project.
First Year Of Impact 2016
Sector Agriculture, Food and Drink
Impact Types Economic

 
Description BBSRC Follow-on Fund: Low viscosity wheat for improved properties for fermentation and animal feed
Amount £144,811 (GBP)
Funding ID BB/K010824/1 
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 02/2013 
End 08/2014
 
Description BBSRC Responsive mode: Proanthocyanidins in Cereals and Brassicaceae: A Cross-Species Approach on their Roles for Seed-Coat Biophysical Properties, Dormancy and Germination
Amount £475,175 (GBP)
Funding ID BB/M001075/1 
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 02/2015 
End 01/2018
 
Description RoSy collaboration
Amount £495,510 (GBP)
Organisation Syngenta International AG 
Department Syngenta Seeds
Sector Private
Country Switzerland
Start 01/2015 
End 01/2018
 
Title TILLING by sequencing 
Description Identification of mutations in wheat genes by exome capture and mapping to a genomic reference. Data for 1209 mutagenized lines of wheat have been uploaded to a website where mutations in specific genes can be searched by name or by similarity to probes. Seeds for the lines can be obtained on completion of an MTA. 
Type Of Material Biological samples 
Year Produced 2015 
Provided To Others? Yes  
Impact Huge interest from academic and commercial wheat researchers and breeders. Many lines already requested. 
URL http://www.wheat-tilling.com
 
Description Identification of GA genes in durum wheat 
Organisation University of California, Davis
Country United States 
Sector Academic/University 
PI Contribution Provided bread wheat sequences for screening a durum wheat sequence database.
Collaborator Contribution Identified durum wheat sequences. Carried out qRT-PCR to confirm expression patterns
Impact Sequences for genes of the GA pathway in durum wheat. Published in BMC Plant Biology: Pearce, S., Huttly, A.K., Prosser, I.M., Li, Y.D., Vaughan, S.P., Gallova, B., Patil, A., Coghill, J.A., Dubcovsky, J., Hedden, P., and Phillips, A.L. (2015). Heterologous expression and transcript analysis of gibberellin biosynthetic genes of grasses reveals novel functionality in the GA3ox family. Bmc Plant Biology 15.
Start Year 2012
 
Description TILLING for disease resistance 
Organisation RWTH Aachen University
Country Germany 
Sector Academic/University 
PI Contribution Hosted a visitor who screened the wheat TILLING population for mutations in Mlo genes. Also subsequently provided information derived by TILLING-by-sequencing by custom analysis of exome captures.
Collaborator Contribution Crossed mutations in A B and D copies of MloI to obtain mildew-resistant wheat lines.
Impact Mildew-resistant lines of wheat (non-GM)
Start Year 2012
 
Description TILLING for novel architectural traits 
Organisation University College Dublin
Country Ireland 
Sector Academic/University 
PI Contribution Provided sequence information for wheat BRI1 genes and information on mutations within a Cadenza-EMS population using exome capture
Collaborator Contribution Taking the mutant lines forward for analysis.
Impact Mutant lines of wheat with lesions in brassinosteroid signalling
Start Year 2012
 
Description TILLING in durum wheat 
Organisation John Innes Centre
Country United Kingdom 
Sector Charity/Non Profit 
PI Contribution Provided a protocol for detection of deletions in EMS-mutagenised populations of wheat
Collaborator Contribution Carried out exome capture of an EMS_mutagenised population of bread wheat and analysed for
Impact Deletion data on durum wheat EMS population. Will be published shortly.
Start Year 2012
 
Description TILLING in durum wheat 
Organisation University of California, Davis
Country United States 
Sector Academic/University 
PI Contribution Provided a protocol for detection of deletions in EMS-mutagenised populations of wheat
Collaborator Contribution Carried out exome capture of an EMS_mutagenised population of bread wheat and analysed for
Impact Deletion data on durum wheat EMS population. Will be published shortly.
Start Year 2012
 
Title Development of a web portal for identification of tilling mutants in wheat 
Description Exon capture and sequencing of 1200 EMS-mutagenized lines within the project identified over 5 million mutations in coding regions of genes. These are publicly accessible via a web portal (www.wheat-tilling.com) and users can identify mutants and request seeds. Commercial wheat breeders pay a one-off licensing fee for freedom-to-operate. So far 270 lines have been licensed for commercial development. 
IP Reference  
Protection Protection not required
Year Protection Granted
Licensed Yes
Impact In addition to commercial users, many hundreds of lines have been supplied to academic wheat biologists world-wide.
 
Description Cereals 
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 Exhibits at the Cereals event for farmers and breeders.
Year(s) Of Engagement Activity 2012,2013,2014