Triticeae Genomics for Sustainable Agriculture

Lead Research Organisation: Earlham Institute
Department Name: Directorate Office

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.

Publications

10 25 50
 
Title Circos plot: Chinese Spring Genome 
Description Circos plot displaying features of the TGACv1 CS42 genome assembly. 
Type Of Art Image 
Year Produced 2017 
Impact This design inspired a line of (unfortunately non-dishwasher safe) collectors plates and the Circolution Collage exhibited in Office 208, Earlham Institute, Norwich, UK. 
URL https://github.com/krasileva-group/tgacv1-circos
 
Title Collage: Circolution 
Description This artwork conveys and reminds of the pain and suffering that is the basis of wheat genomics. It shows the various stages from draft to final product, with additional detours. It is exhibited in office 208, Earlham Institute, Norwich Research Park, Norwich, NR4 7UZ. Unfortunately, it is off limits to the general public. 
Type Of Art Artwork 
Year Produced 2017 
Impact This piece serves as a source of inspiration during the long days and nights of wheat genomics research. 
URL https://github.com/cschu/circolution/blob/master/circolution.jpg
 
Description We have made considerable progress in achieving objective 1. In November 2015 we released a new draft genome sequence of the bread wheat reference cultivar: Chinese Spring 42 . This assembly is ~40% more complete, and contains 40 times longer sequences than previous assemblies. This data is publicly available on the EI and ENSEMBL websites, for BLAST searching, browsing gene models and to download. To build this assembly we wrote a new scaffolder to integrating additional data types e.g. longer range mate pairs (~20kb) and fosmid libraries in vectors that are compatible with Illumina sequencing of fosmid ends (FosIlls) for scaffolding in the 40kb range. A manuscript has been submitted to BioRxiv (http://biorxiv.org/content/early/2016/10/13/080796) describing this work, and subsequently published in Genome Research journal in May 2017 (Clavijo, Venturini et al. 2017). To this Chinese Spring reference assembly we have now added another 4 hexaploid and one tetraploid assemblies which are publicly available http://opendata.earlham.ac.uk/Triticum_aestivum/EI/v1/

For objective 2 we have annotated genes within the genome using new data generated as part of this project which includes full length transcripts sequences using PacBio long read technology and strand specific Illumina-compatible RNA-seq libraries with long (250bp on Illumina) reads. See Clavijo, Venturini et al. 2017.

For objective 3 we released our genome assembly assigning scaffolds to chromosome arms using flow sorted data that we published in 2014. We have now integrated PopSeq genetic markers, which allows us to identify known and novel translocations: see Clavijo, Venturini et al. 2017. We made a high-coverage 40kb "jumping" library of fosill clones for assessing the long range integrity of different wheat genome assemblies. This showed that the TGAC V1 assembly is as accurate as the subsequent NR Gene (IWGSC RefSeq v1) wheat assembly, although more fragmentary. Fosill paired-end reads were used to scaffold the TGAC V1, leading to three-fold increase in contiguity (BioRxiv bioRxiv 219352; doi: https://doi.org/10.1101/219352 ).

For objective 4 as discussed in the mid term review, we have developed a high throughput, low cost BAC sequencing pipeline to prepare and sequence the samples in a rapid, cost-effective manner. We have parallelised processes to sequence at first 384 samples (BACs) at once then increased this 6-fold to processing 2304 samples at once, and most recently 9,216 samples. We have also decreased the cost and increased the throughput to the extent that it is possible to sequence the whole bread wheat genome using randomly generated BACs at low cost. This would achieve further cost savings as creating a Minimum Tiling Path (MTP) is time consuming and costly. We have integrated these random BACs with those of the already sequenced 3DL MTP - a useful test case for the whole genome. BACs from chromosome 3DL have been integrated with PacBio long reads from the Triticum V3 wheat assembly to generate large scaffolds of 2.8 Mb N50. These are being used for detailed comparison with chromosome 3L from Aegilops tauschii. We have also used these BACs for quality control of our TGACv1 assembly (Clavijo, Venturini et al. Genome Research 2017) and supplied them to the IWGSC.

For objective 5 we have tested Moleculo synthetic long range data, 10x Genomics, plus in vitro (Dovetail) and in vivo Hi-C data for longer range scaffolding especially in areas of poor recombination.

For objective 6, the re-sequencing of genes of mutagenised populations and genes of diverse Triticeae genomes relevant to wheat pre-breeding research, we have developed an automated exome resequencing pipeline starting with leaf tissue and progressing to identify EMS induced SNPs in the coding regions of the majority of wheat genes. This pipeline is useful for wheat and numerous other crops and was used to identify over six million EMS-induced mutations in 1200 lines of cv. Cadenza. The data is available for public searches on the www.wheat-tiling.com website, where users can also request seed for lines of interest. This work is now published in Krasileva et al. PNAS 2017. We have recently sought to complement the TILLING resources using an orthogonal mutagenesis technique (X-ray induced deletions) with different biases, and so capture remaining gene function. Here we combine the ultra-cheap library approach (developed here for sequencing BACs) to shallow sequence ~1000 Paragon deletion lines, and use the optimised alignment pipeline (developed here for scaffolding contigs) to map reads with very high discrimination and call induced deletions.

For objective 7 to maximize the impact of the research through training and outreach we provided annual training workshop in using the wheat genomic resources for breeders, and were excited to hear about the breeders work as well as their positive feedback on our progress and to hear what data or tools they would like us to prioritise to serve the community. These meetings were also used to establish a priority list of UK wheat genomes for sequencing.
Exploitation Route Developing new genotyping platforms, identify tightly linked markers and clone genes underlying key traits. Sequenced EMS lines of cv. Cadenza are being used for wheat functional genomics, hypothesis testing and crop improvement, by both academic labs and commercial wheat breeders.
Sectors Agriculture, Food and Drink

URL http://www.wheatgenome.org.uk/
 
Description In three of the 5 years of the project we held a Wheat breeders workshop to update them on the latest tools and data available. Shortly after this we released a new greatly improved genome assembly for the reference Wheat cultivar which is available from http://www.wheatgenome.org.uk/ and now via as a pre-site from ENSEMBL with the genes and markers transferred from the earlier assembly http://pre.plants.ensembl.org/Triticum_aestivum/Info/Index. Already 56 publications cite our wheat genome paper (Clavijo et al 2017), and we are aware of a new exome capture reagent set that has been designed based on our work. This assembly is now available for use by UK and worldwide wheat breeders including the ability to download the assembly for their use, and helping them breed better wheat cultivars. The exome sequencing of EMS-mutagenised lines of cv. Cadenza has provided a valuable resource for wheat breeders. Many commercial and public sector breeders have identified mutations of interest and requested seed, including one major seed company that obtained seed for all 1200 lines. The mutations have been integrated into Plant Ensembl and are also available at project dedicated website. Already 43 publications cite our exome sequencing (Krasileva et al 2017) paper.
First Year Of Impact 2015
Sector Agriculture, Food and Drink
Impact Types Economic

 
Description Bioinformatics Community of Practice (Eight-month training at BecA)
Geographic Reach Africa 
Policy Influence Type Influenced training of practitioners or researchers
Impact Bioinformatics Community of Practice (Eight-month training at BecA)
URL https://acaciaafrica.org/bioinformatics-community-practice/
 
Description Bioinformatics Training Workshop pre-Monogram
Geographic Reach Multiple continents/international 
Policy Influence Type Influenced training of practitioners or researchers
Impact Bioinformatics Traning Workshop pre-Monogram
 
Description Bioinformatics for Plant Biology Course 2018
Geographic Reach Multiple continents/international 
Policy Influence Type Influenced training of practitioners or researchers
Impact Bioinformatics for Plant Biology Course 2018
 
Description Genomic Selection meeting at CGIAR
Geographic Reach Multiple continents/international 
Policy Influence Type Implementation circular/rapid advice/letter to e.g. Ministry of Health
Impact This was an international meeting at CGIAR headquarters covering multiple aspects of the advatages and challenges of genomic selection (GS). A document is currently being drafted for Nature Genetics on the findings form this meeting e.g. "Genomic selection directly addresses three of the four factors that affect the rate of genetic gain in animal and plant breeding (Meuwissen 2003): (i) time - through the ability to select individuals before obtaining their phenotypes, some of which can only be measured after the animal can reproduce or plant reaches maturity; (ii) selection intensity - as the cost of genotyping an individual or line is lower than the cost of phenotyping more candidates for selection can be handled; (iii) and accuracy - because genetic estimates of breeding value (GEBV) can, in some circumstances, be more accurate than conventional estimated breeding values. Additionally, genomic selection can catalyze a unification of breeding methods, tools, and technologies across several plant and animal species, which in turn can provide a push toward the modernization of other aspects of breeding programs. These could include the widespread adoption of clearly defined breeding goals, economic selection indices, objective quantification of genetic gains, and new trial design and analysis."
 
Description PhD lecture on Wheat genomics to Catholic University in Chile
Geographic Reach South America 
Policy Influence Type Influenced training of practitioners or researchers
Impact PhD lecture on Wheat genomics
 
Description Three modules in Cambridge Plant Science undergraduate course
Geographic Reach National 
Policy Influence Type Influenced training of practitioners or researchers
Impact Three modules in Cambridge Plant Science undergraduate course
 
Description UK Future Wheat meeting
Geographic Reach National 
Policy Influence Type Participation in a advisory committee
Impact Formulating a plan for future wheat research in the UK including effective collaboration between experts in JIC, Rothamsted, TGAC, NIAB, Universities of Bristol and Nottingham.
 
Description UK Global Food Security Science Advisory Board
Geographic Reach Multiple continents/international 
Policy Influence Type Participation in a advisory committee
URL https://www.foodsecurity.ac.uk/
 
Description Undergraduate course UEA MSc
Geographic Reach National 
Policy Influence Type Influenced training of practitioners or researchers
Impact Undergraduate course UEA MSc
 
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.
 
Description Workshop on Soft Skills, BGRI Meeting
Geographic Reach Multiple continents/international 
Policy Influence Type Influenced training of practitioners or researchers
Impact Workshop on Soft Skills, BGRI Meeting
 
Description BBSRC responsive mode
Amount £1,504,558 (GBP)
Funding ID BB/P010768/1 
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 04/2017 
End 03/2020
 
Description Federating access to wheat data services for efficient genome-specific marker design
Amount £119,193 (GBP)
Funding ID BB/N023420/1 
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 08/2016 
End 07/2017
 
Description Follow On Fund - Utilising Illumina sequencing for high throughput genotyping of wheat
Amount £147,471 (GBP)
Funding ID BB/P004857/1 
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 01/2017 
End 06/2018
 
Description International Wheat Yield Partnership
Amount £1,500,000 (GBP)
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 06/2018 
End 05/2021
 
Description NRP PhD Studentship - Next generation genomics tools for sustainable bread wheat production
Amount £91,432 (GBP)
Organisation Norwich Research Park 
Sector Private
Country United Kingdom
Start 10/2012 
End 09/2016
 
Description New Investigator Award: Rapid identification of genes and pathways that increase resistance to yellow rust disease of wheat
Amount £297,772 (GBP)
Funding ID BB/N016106/1 
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 09/2016 
End 08/2019
 
Description sLoLa - Triticeae Genomics for Sustainable Agriculture (additional funds)
Amount £749,867 (GBP)
Funding ID BBS/E/T/000GP034 
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 01/2015 
End 01/2017
 
Title Tools to anchor wheat genomic assembly on genetic map 
Description Bioinformatics tools to anchor wheat genomic assemblies 
Type Of Material Technology assay or reagent 
Year Produced 2016 
Provided To Others? Yes  
Impact N/A 
URL https://github.com/krasileva-group/tgac-map
 
Title tandem 
Description Software to find head-to-head gene pairs in a genome 
Type Of Material Technology assay or reagent 
Year Produced 2017 
Provided To Others? Yes  
Impact This tool allowed to elucidate the role of head-to-head gene pairs in the formation of integrated domain fusions (cf. Bailey et al, 2018 Genome Biology) 
URL https://github.com/krasileva-group/tandem
 
Title PolyMarker 
Description Update on Primer design for polyploid species 
Type Of Material Computer model/algorithm 
Year Produced 2019 
Provided To Others? Yes  
Impact New biology 
URL http://bar.utoronto.ca/efp_wheat/cgi-bin/efpWeb.cgi
 
Title Wheat Expression 
Description The majority of RNA-seq expression studies in plants remain underutilised and inaccessible due to the use of disparate transcriptome references and the lack of skills and resources to analyse and visualise this data. We have developed expVIP, an expression Visualisation and Integration Platform, which allows easy analysis of RNA-seq data combined with an intuitive and interactive interface. Users can analyse public and user-specified datasets with minimal bioinformatics knowledge using the expVIP virtual machine. This generates a custom web browser to visualise, sort and filter the RNA-seq data and provides outputs for differential gene expression analysis. We demonstrate expVIP's suitability for polyploid crops and evaluate its performance across a range of biologically-relevant scenarios. To exemplify its use in crop research we developed a flexible wheat expression browser (www.wheat-expression.com) which can be expanded with user-generated data in a local virtual machine environment. The open-access expVIP platform will facilitate the analysis of gene expression data from a wide variety of species by enabling the easy integration, visualisation and comparison of RNA-seq data across experiments. 
Type Of Material Computer model/algorithm 
Year Produced 2016 
Provided To Others? Yes  
Impact This database provides open access to over 400 RNAseq studies in wheat and the underlying algorithms are all available to adapt to any species with a reference genome. Over 11,000 sessions from >5,000 and >50,000 pageviews 
URL http://www.wheat-expression.com
 
Title Wheat TILLING 
Description Database with data from exome captured wheat mutants 
Type Of Material Database/Collection of data 
Year Produced 2017 
Provided To Others? Yes  
Impact Over 2,000 unique users across >5,000 sessions. 
URL http://www.wheat-tilling.com
 
Title Wheat TILLING 
Description This resource consists of TILLING populations developed in tetraploid durum wheat cv 'Kronos' and hexaploid bread wheat cv 'Cadenza' as part of a joint project between the University of California Davis, Rothamsted Research, The Earlham Institute, and John Innes Centre. We have re-sequenced the exome of 1,535 Kronos and 1,200 Cadenza mutants using Illumina next-generation sequencing, aligned this raw data to the IWGSC Chinese Spring chromosome arm survey sequence, identified mutations, and predicted their effects based on the protein annotation available at Ensembl Plants. 
Type Of Material Database/Collection of data 
Year Produced 2016 
Provided To Others? Yes  
Impact Over 5000 access 
URL http://www.wheat-tilling.com/
 
Title Wheat TILLING in EnsemblPlants 
Description Update of sequenced mutants and coordination with ensemblPlants 
Type Of Material Database/Collection of data 
Year Produced 2018 
Provided To Others? Yes  
Impact over 7000 mutants distributed from over 300 orders 
URL http://plants.ensembl.org/Triticum_aestivum/Info/Index
 
Title Wheat Training 
Description This website provides background information and practical resources to help both budding wheat scientists as well as researchers looking to expand their work into wheat. There is a need to improve crops to feed the world's growing population with the backdrop of climate change. Translation of fundamental plant biology research (e.g. from Arabidopsis thaliana) into crops such as wheat provides a potential route to deal with this challenge. However learning even simple tasks such as growing and crossing wheat plants requires time and effort, while material and methods sections in published articles are often short and cannot substitute teaching aids. This is also true for more complex topics such as the genomics aspect of wheat. 
Type Of Material Database/Collection of data 
Year Produced 2016 
Provided To Others? Yes  
Impact >4,500 sessions from >2,700 users 
URL http://www.wheat-training.com/
 
Title Wheat Training 
Description Wheat Training website to help new researchers engage with wheat 
Type Of Material Database/Collection of data 
Year Produced 2018 
Provided To Others? Yes  
Impact http://www.wheat-training.com/ 
URL http://www.wheat-training.com/
 
Title Wheat reTILLING 
Description Rebuild of the Wheat TILLING resource using novel technologies (DRAGEN BioIT Processor + custom software) based on the new wheat reference genome (RefSeq 1.0) and TGAC/Earlham Institute cultivar-specific genome references. This is a collaboration between Earlham Institute, Rothamsted Research, John Innes Centre and UC Davis. 
Type Of Material Database/Collection of data 
Year Produced 2018 
Provided To Others? No  
Impact When the output will be available (within 2018), then it will replace the original Wheat TILLING data and continue to be of use for researchers and breeders. Variant annotation will be hosted by EnsEMBL Plants. 
 
Title eFP expression browser 
Description Expression browser for wheat data 
Type Of Material Database/Collection of data 
Year Produced 2018 
Provided To Others? Yes  
Impact New biology 
URL http://bar.utoronto.ca/efp_wheat/cgi-bin/efpWeb.cgi
 
Description 10 Pangenome Project 
Organisation University of Saskatchewan
Country Canada 
Sector Academic/University 
PI Contribution Collaboration for 10 pangenome project
Collaborator Contribution Collaboration for 10 pangenome project
Impact Sequencing of 10 wheat varieties
Start Year 2017
 
Description A meeting between CIMMYT and DFW funded by BMGF to discuss collaboration projects 
Organisation International Centre for Maize and Wheat Improvement (CIMMYT)
Country Mexico 
Sector Charity/Non Profit 
PI Contribution I organised a meeting funded by Bill and Melinda Gates Foundation brought together members of the BBSRC's coordinated wheat programme (Designing Future Wheat) with members of CIMMYT (who breed wheat for the resource poor in the developing world), discuss potential opportunities for interaction. These opportunities are taken forward by writing proposals for Newton , GCRF or IWYP funding calls
Collaborator Contribution See above
Impact This interaction is still ongoing between members of BBSRC's coordinated wheat programme (Designing Future Wheat) and researchers within CIMMYT with proposals being written for IWYP and Newton calls
Start Year 2018
 
Description Bayer 
Organisation Bayer
Department Bayer CropScience Ltd
Country United Kingdom 
Sector Private 
PI Contribution Wheat genetics and genomics
Collaborator Contribution Wheat breeding and molecular knowledge
Impact joint projects
Start Year 2012
 
Description KWS 
Organisation KWS UK
Country United Kingdom 
Sector Private 
PI Contribution Genetics and genomics
Collaborator Contribution Breeder know how and germplasm
Impact joint projects
Start Year 2009
 
Description Limagrain 
Organisation Limagrain
Country France 
Sector Private 
PI Contribution Genetics and genomics
Collaborator Contribution Germplasm and breeder know-how
Impact Phd Studentship, field trails, among others
Start Year 2009
 
Description New marker technologies for wheat using Illumina sequencing 
Organisation Earlham Institute
Country United Kingdom 
Sector Academic/University 
PI Contribution The overall aim of the partnership with EI is to develop a new set of sequencing technologies for high-throughput genotyping of wheat using the power of Illumina sequencing. JIC is providing ideas and concepts and wheat DNA samples for analyses and coordinates the project; UPDATE: NIAB is providing access to populations for genotyping
Collaborator Contribution The EI provides sequencing and analyses and interpretation in the partnership. NIAB provide lines for testing genotyping and assistance with analysis of data.
Impact It is too early for any outputs of the project. We have done extensive computational analyses of 10 sequenced and assembled wheat varieties and identified vast numbers of variety-specific polymorphisms. These have been mapped to the reference assembly. A set of 1000 polymorphic regions mapped to each Mb of group 3 chromosomes was identified and gene capture probes designed. DNA from a wide variety of testing lines has been made. In the coming months this DNA will be genotyped to test the method. Future goals are to refine the method to make it cost effective for application in pedigree breeding
Start Year 2017
 
Description New marker technologies for wheat using Illumina sequencing 
Organisation National Institute Of Agricultural Botany
Country United Kingdom 
Sector Private 
PI Contribution The overall aim of the partnership with EI is to develop a new set of sequencing technologies for high-throughput genotyping of wheat using the power of Illumina sequencing. JIC is providing ideas and concepts and wheat DNA samples for analyses and coordinates the project; UPDATE: NIAB is providing access to populations for genotyping
Collaborator Contribution The EI provides sequencing and analyses and interpretation in the partnership. NIAB provide lines for testing genotyping and assistance with analysis of data.
Impact It is too early for any outputs of the project. We have done extensive computational analyses of 10 sequenced and assembled wheat varieties and identified vast numbers of variety-specific polymorphisms. These have been mapped to the reference assembly. A set of 1000 polymorphic regions mapped to each Mb of group 3 chromosomes was identified and gene capture probes designed. DNA from a wide variety of testing lines has been made. In the coming months this DNA will be genotyped to test the method. Future goals are to refine the method to make it cost effective for application in pedigree breeding
Start Year 2017
 
Description New marker technologies for wheat using Illumina sequencing 
Organisation Natural History Museum
Country United Kingdom 
Sector Public 
PI Contribution The overall aim of the partnership with EI is to develop a new set of sequencing technologies for high-throughput genotyping of wheat using the power of Illumina sequencing. JIC is providing ideas and concepts and wheat DNA samples for analyses and coordinates the project; UPDATE: NIAB is providing access to populations for genotyping
Collaborator Contribution The EI provides sequencing and analyses and interpretation in the partnership. NIAB provide lines for testing genotyping and assistance with analysis of data.
Impact It is too early for any outputs of the project. We have done extensive computational analyses of 10 sequenced and assembled wheat varieties and identified vast numbers of variety-specific polymorphisms. These have been mapped to the reference assembly. A set of 1000 polymorphic regions mapped to each Mb of group 3 chromosomes was identified and gene capture probes designed. DNA from a wide variety of testing lines has been made. In the coming months this DNA will be genotyped to test the method. Future goals are to refine the method to make it cost effective for application in pedigree breeding
Start Year 2017
 
Description Punjab Agricultural University 
Organisation Punjab Aricultural University
Country India 
Sector Academic/University 
PI Contribution Know how on wheat genomics and genetics, training.
Collaborator Contribution Gernplasm, local knowledge
Impact Have helped partners implement marker technology.
Start Year 2011
 
Description RAGT 
Organisation RAGT Seeds
Country United Kingdom 
Sector Learned Society 
PI Contribution Genetics and genomics
Collaborator Contribution Wheat germplasm and know how
Impact Shared projects
Start Year 2009
 
Description Syngenta 
Organisation Syngenta International AG
Country Global 
Sector Public 
PI Contribution Have shared germplasm for use in their breeding programmes.
Collaborator Contribution Have taken up JIC IP to use in their breeding operations.
Impact This has just started.
Start Year 2017
 
Title EMBER - GlutenSeq Pipeline 
Description Pipeline for processing of GlutenSeq data. 
Type Of Technology Software 
Year Produced 2017 
Open Source License? Yes  
Impact This pipeline allows the analysis and downstream processing of sequencing data obtained via targeted Gluten gene captures. 
 
Title Expression Browser in wheat 
Description Expression browser for wheat gene expression data 
Type Of Technology Webtool/Application 
Year Produced 2018 
Open Source License? Yes  
Impact New biology 
URL http://www.wheat-expression.com/
 
Title Galaxy id_fusion pipeline 
Description Galaxy implementation of integrated domain fusion detection pipeline (cf. Sarris et al, 2016 BMC Biology) 
Type Of Technology Software 
Year Produced 2016 
Open Source License? Yes  
Impact Tool available for use on Galaxy platforms. 
URL https://github.com/krasileva-group/id_fusion
 
Title Royal Dragen 
Description Royal dragen is a software developed by Dr. Rob King (Rothamsted Research) and Dr. Christian Schudoma (Earlham Institute). The software allows to perform variant filtering on Dragen-generated variant calls. The software was designed to mimic the behaviour of MAPS in wheat tilling experiments (cf. Krasileva et al., PNAS 2017). 
Type Of Technology Software 
Year Produced 2017 
Open Source License? Yes  
Impact The software, together with the Dragen BioIT processor allows to significantly speed up tilling analyses on wheat exome capture data. 
URL https://github.com/cschu/royal_dragen
 
Title scvep - super cereal variant effect predictor 
Description This software allows effect prediction of single nucleotide polymorphisms without a reference annotation. 
Type Of Technology Software 
Year Produced 2017 
Open Source License? Yes  
Impact This software was used to filter wheat candidate lines for (virus?) resistance in a collaboration with IPK Gatersleben, Germany. 
URL https://github.com/krasileva-group/scvep
 
Title tandem 
Description Software to detect (head-to-head) gene pairs (tandems) in a genome. 
Type Of Technology Software 
Year Produced 2017 
Impact This software allowed to analyse whether gene tandems might play a role in the formation of integrated domain fusions (cf. Bailey et al, 2018, Genome Biology) 
 
Description ABC (Spain) 
Form Of Engagement Activity A magazine, newsletter or online publication
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Media (as a channel to the public)
Results and Impact Descifrado el genoma del trigo, el cereal más cultivado del planeta
Year(s) Of Engagement Activity 2018
URL http://abci-descifrado-genoma-trigo-cereal-mas-cultivado-planeta-201808162031_noticia.html
 
Description Agricultural Industries Confederation 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Industry/Business
Results and Impact Agribusiness Meeting: A step change in plant breeding to achieve a UK competitive advantage
Year(s) Of Engagement Activity 2016
 
Description Australian, UK scientists solve 30-year wheat rust genetics puzzle 
Form Of Engagement Activity A press release, press conference or response to a media enquiry/interview
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Media (as a channel to the public)
Results and Impact Australian, UK scientists solve 30-year wheat rust genetics puzzle
Year(s) Of Engagement Activity 2018
URL https://www.eurekalert.org/pub_releases/2018-08/uos-aus082418.php
 
Description BBC News 
Form Of Engagement Activity A magazine, newsletter or online publication
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Media (as a channel to the public)
Results and Impact Wheat gene map to help feed the world
Year(s) Of Engagement Activity 2018
URL https://www.bbc.co.uk/news/science-environment-45173968
 
Description BBC World 
Form Of Engagement Activity A broadcast e.g. TV/radio/film/podcast (other than news/press)
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Media (as a channel to the public)
Results and Impact BBC World: wheat genome (Pallab Ghosh)
Year(s) Of Engagement Activity 2018
 
Description BBSRC Food Priming Partnership Workshop 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact BBSRC Food Priming Partnership Workshop
Year(s) Of Engagement Activity 2018
 
Description Borlaug Dialogue 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Supporters
Results and Impact Bolaug Dialogue
Year(s) Of Engagement Activity 2017
 
Description 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 One day training workshop on wheat genomics for breeders, which resulted in incresed use of generated tools and resources
Year(s) Of Engagement Activity 2015
 
Description CPM Magazine 
Form Of Engagement Activity A magazine, newsletter or online publication
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Media (as a channel to the public)
Results and Impact CPM Magazine interview on wheat genome and genetics
Year(s) Of Engagement Activity 2018
URL http://www.cpm-magazine.co.uk/2018/08/21/genetics-hope-future-wheat/#
 
Description Cibus 2018, Salone internazionale dell'alimentazione 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Policymakers/politicians
Results and Impact Cibus 2018, Salone internazionale dell'alimentazione
Year(s) Of Engagement Activity 2018
 
Description Conference talk at Galaxy Community Conference 2016, Indiana University, Bloomington, IN, USA 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Presented Galaxy implementation of Integrated Domain Fusion pipeline to Galaxy community.
Year(s) Of Engagement Activity 2016
 
Description DBT-BBSRC Smart Agriculture Conclave 
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 DBT-BBSRC Smart Agriculture Conclave
Year(s) Of Engagement Activity 2017
 
Description Daily Mail Online 
Form Of Engagement Activity A magazine, newsletter or online publication
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Media (as a channel to the public)
Results and Impact Genetic make-up of wheat has been decoded for the first time: Scientists say it could lead to low allergy varieties and crops that need less water
Year(s) Of Engagement Activity 2018
URL https://www.dailymail.co.uk/sciencetech/article-6068177/Genetic-make-wheat-decoded-time.html
 
Description Discussion Norman Lamb, MP 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Policymakers/politicians
Results and Impact Discussion Norman Lamb, MP
Year(s) Of Engagement Activity 2017
 
Description Discussion with Gov Office Science 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Policymakers/politicians
Results and Impact Discussion with Gov Office Science
Year(s) Of Engagement Activity 2017
 
Description Discussions with Syngenta 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Industry/Business
Results and Impact Discussions on collaborations
Year(s) Of Engagement Activity 2018
 
Description Eastern Daily Press 
Form Of Engagement Activity A magazine, newsletter or online publication
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Media (as a channel to the public)
Results and Impact How Norwich scientists' wheat DNA breakthrough could help feed the world
Year(s) Of Engagement Activity 2018
URL http://www.edp24.co.uk/business/farming/john-innes-centre-norwich-wheat-genome-1-5655948
 
Description El Confidencial (Spain) 
Form Of Engagement Activity A magazine, newsletter or online publication
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Media (as a channel to the public)
Results and Impact El pan del futuro ya está aquí: científicos secuencian los 107.891 genes del trigo
Year(s) Of Engagement Activity 2018
URL https://www.elconfidencial.com/tecnologia/ciencia/2018-08-16/secuencian-genoma-trigo-pan-futuro_1604...
 
Description El Mundo (Spain) 
Form Of Engagement Activity A magazine, newsletter or online publication
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Media (as a channel to the public)
Results and Impact El genoma del trigo harinero ayudará a crear variedades más resistentes
Year(s) Of Engagement Activity 2018
URL http://www.elmundo.es/ciencia-y-salud/ciencia/2018/08/16/5b75ab13468aeb3d7e8b458b.html
 
Description El Pais (Spain) 
Form Of Engagement Activity A magazine, newsletter or online publication
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Media (as a channel to the public)
Results and Impact El genoma del alimento que da a la humanidad una de cada cinco calorías
Year(s) Of Engagement Activity 2018
URL https://elpais.com/elpais/2018/08/16/ciencia/1534414224_631189.html
 
Description FSOV-Paris 
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 Meeting with French breeders to discuss FSOV activities
Year(s) Of Engagement Activity 2016,2017,2018
 
Description Farmers Weekly 
Form Of Engagement Activity A magazine, newsletter or online publication
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Media (as a channel to the public)
Results and Impact Scientists apply for GM wheat and Crispr brassica field trials
Year(s) Of Engagement Activity 2019
URL https://www.fwi.co.uk/arable/scientists-apply-for-gm-wheat-and-crispr-brassica-field-trials
 
Description Garnet York 2018 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Garnet York 2018
Year(s) Of Engagement Activity 2018
 
Description Gatbsy Plant Science Students 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Schools
Results and Impact Can wheat genomics help alleviate food insecurity?
Year(s) Of Engagement Activity 2017
 
Description Genoma completo del trigo augura mayor rendimiento y seguridad alimentaria al mundo 
Form Of Engagement Activity A magazine, newsletter or online publication
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Media (as a channel to the public)
Results and Impact Genoma completo del trigo augura mayor rendimiento y seguridad alimentaria al mundo
Year(s) Of Engagement Activity 2018
URL http://www.economiaynegocios.cl/noticias/noticias.asp?id=496697
 
Description International Plant Genomics Congress (London) 
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 "Sequencing wheat TILLING populations opens new horizons in functional genomics" at the International Plant Genomics Congress, May 2015 London UK
Year(s) Of Engagement Activity 2015
 
Description International Wheat Genetics Symposium - presentation & workshop 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact A presentation on the progress to date of the sequencing of the wheat genome
Year(s) Of Engagement Activity 2013
URL http://12iwgs.sci.yokohama-cu.ac.jp/img/contents/IWGSC_Workshop_Program.pdf
 
Description International wheat congress (Frankfurt) 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Other audiences
Results and Impact Conference presentation organized by German Federal Office for Agriculture and Food (BLE)
Year(s) Of Engagement Activity 2016
URL http://www.wheatinitiative.org/events/international-wheat-congress
 
Description Invited talk: From tracking Arabidopsis RNAs to exploring the wheat genome - A journey through plant bioinformatics. Evolution Seminars IOE and EEB joint seminar program, University of Haifa, Israel, April 18, 2016. Hosted by Prof. Tzion Fahima 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Postgraduate students
Results and Impact People were introduced into the complex and versatile world of plant bioinformatics, into how methods from other bioinformatics areas can be used for problems in plant-pathogen and crop bioinformatics.
Year(s) Of Engagement Activity 2016
 
Description Italian Society of Genetics (SIGA) and Plant Biology (SIBV) Joint meeting 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Postgraduate students
Results and Impact Keynote at PISA
Year(s) Of Engagement Activity 2017
 
Description JIC Annual Science Meeting 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact JIC Annual Science Meeting
Year(s) Of Engagement Activity 2018
 
Description JIC Open day 
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 JIC Open Day
Year(s) Of Engagement Activity 2018
 
Description JIC Science Innovation Showcase 
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 Industry/Business
Results and Impact Talk at JIC Science Innovation Showcase with over 100 industry representatives
Year(s) Of Engagement Activity 2018
 
Description KWS Wheat network discussions 
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 Discussion with KWS scientist and breeders on wheat networks
Year(s) Of Engagement Activity 2018
 
Description Keynote: Canadian Wheat Symposium 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Canadian Wheat Symposium
Year(s) Of Engagement Activity 2018
 
Description Keynote: From Seed to Pasta III 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact From Seed to Pasta III
Year(s) Of Engagement Activity 2018
 
Description MSc Domestication 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Postgraduate students
Results and Impact MSc course on Domestication
Year(s) Of Engagement Activity 2017
 
Description 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 invited talk "Sequencing wheat TILLING populations brings a revolution to functional analyses of wheat genes" at Monogram, UK based researchers with an active interest in small grain cereal and grass. 2015, Rothamsted, UK
Year(s) Of Engagement Activity 2015
 
Description Monogram 2016 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 Bioinformatics worshop highlighting the resources for wheat improvement which led to increased use of our tools
Year(s) Of Engagement Activity 2016
 
Description Monogram Bioinformatics Workshop 
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 Monogram Bioinformatics Workshop
Year(s) Of Engagement Activity 2017
 
Description Oxford Farming Conference talk 
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 Oxford Farming Conference talk
Year(s) Of Engagement Activity 2019
URL https://www.youtube.com/watch?v=mp0QJDivWgA
 
Description PAG 2015 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Tilling for Disease Resistance Genes" PAG 2015 "Applied Triticeae workshop", Sunday Jan 2015 Invited speaker
Year(s) Of Engagement Activity 2015
 
Description PAG workshop - Strategies For Sequence Improvement Of BAC-Based Wheat Chromosome Arm Assemblies 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Workshop held at Plant and Animal Genome conference to present strategies and discuss with peers
Year(s) Of Engagement Activity 2013
URL https://pag.confex.com/pag/xxi/webprogram/Paper7288.html
 
Description Penny Mordaunt, Secretary of State for International Development. 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Policymakers/politicians
Results and Impact Penny Mordaunt, Secretary of State for International Development.
Year(s) Of Engagement Activity 2018
 
Description Pint of Science 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Public/other audiences
Results and Impact Norwich Science Festival
Year(s) Of Engagement Activity 2016
 
Description Planning meeting for wheat pan-genomics 
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 There have been three meetings to scope out and plan activities in wheat pan-genomics. In Jan 2017 we met at the Plant & Animal Genome Conference to scope out interest, again in Cambridge in June 2017 to review progress, and most recently at PAG in Jan 2018. The value of these coordination meetings is to ensure BBSRC-funded research in wheat synergises with related work elsewhere in the world.
Year(s) Of Engagement Activity 2017
URL http://www.monogram.ac.uk/docs/MN2017/Bioinformatics/3_10%20Genomes%20Project%20-%20Pozniak_Cristoba...
 
Description Plant Genetics and New Breeding Technologies II, Vienna 
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
Year(s) Of Engagement Activity 2016
 
Description Poster Presentation Schudoma C, Clark M, and Krasileva KV. It's a grass, grass, grass - Profiling plant gluten genes with targeted resequencing and bioinformatics, Genome 10K and Genome Science Conference, Earlham Institute, Norwich, UK, August 29-31, 2017 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact People were introduced to the discovery of the "dark glutenome", i.e. non-canonical gluten loci found in hexaploid wheat.
Year(s) Of Engagement Activity 2017
 
Description Poster Presentation Schudoma C, Raats D, Bailey P, Gordon L, Stitt T, and Krasileva KV. Taming the beast - Overcoming the challenges in working with complex plant genomes, ISMB 2016, Orlando, Florida, USA, July 8-12, 2016 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact People were made aware that large plant genomes are a challenge and that this can be tackled by better algorithms, use of unconventional hardware (first use of DRAGEN BioIT processor, which was originally developed for human diagnostics, for plant genomics).
Year(s) Of Engagement Activity 2016
 
Description Poster at Genome Science - A method to simultaneously construct up to 12 different sized Illumina Nextera long mate pair libraries with reduced DNA, time and costs 
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 Poster to the Genome Science Conference - University of Birmingham, UK - September 2015

Opportunity to present and discuss developments with peers and colleagues
Year(s) Of Engagement Activity 2015
 
Description Poster at PAG 2016 Conference - A novel strategy to assemble the hexaploid wheat genome: beyond Chinese Spring and towards a pan-genome 
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 Poster at the Plant and Animal Genomes Conference - 11 January 2016 - San Diego, CA, USA

To discuss with peers across the field
Year(s) Of Engagement Activity 2016
URL https://pag.confex.com/pag/xxiv/webprogram/Paper21578.html
 
Description Poster at PAG 2016 Conference - Wheat Research at TGAC 
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 Poster at Plant and Animal Genome Conference - January 2016 - San Diego, CA, USA

At The Genome Analysis Centre (TGAC), we are focused on decoding wheat genome and understanding how variation within and across genomes affects the plant and its interaction with the environment
Year(s) Of Engagement Activity 2016
URL https://pag.confex.com/pag/xxiv/webprogram/Paper21311.html
 
Description Poster to Genome Science - Back to BACs- A High-Throughput, low cost sequencing pipeline 
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 Poster at Genome Science conference - Oxford, UK - 2 September 2014

Opportunity to present and discuss with colleagues and peers developments in sequencing
Year(s) Of Engagement Activity 2014
 
Description Poster to UK Next Generation Sequencing 2012 - Optimising sequencing strategies for the assembly of large and complex genomes 
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 Poster at the UK Next Generation Sequencing conference - University of Nottingham - 28-30 August 2012

Opportunity to discuss with colleagues and peers the strategies being used within TGAC
Year(s) Of Engagement Activity 2012
 
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 PAG 2013 - Optimizing sequencing strategies for the assembly of large and complex genomes 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Presentation to the Plant and Animal Genome Conference - 15 Jan 2013 - San Diego, CA, USA

Opportunity to present and discuss developments with peers and colleagues
Year(s) Of Engagement Activity 2013
URL https://pag.confex.com/pag/xxi/webprogram/Paper7288.html
 
Description Previously grainy wheat genome comes into focus 
Form Of Engagement Activity A press release, press conference or response to a media enquiry/interview
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Media (as a channel to the public)
Results and Impact Previously grainy wheat genome comes into focus
Year(s) Of Engagement Activity 2018
URL https://www.jic.ac.uk/news-and-events/news/2018/08/wheat-genome-focus/
 
Description Quarterly principle investigators' meeting - Wheat LoLa collaborators' meeting 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact Hosting and contributing to the quarterly wheat LoLa collaborators' meeting with colleagues from the BBSRC and other sister institutes

Discussions on updates and next steps in the project
Year(s) Of Engagement Activity 2013
 
Description Rachel Lambert, Senior Livelihoods Adviser, Agriculture Research DFID 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Policymakers/politicians
Results and Impact Rachel Lambert, Senior Livelihoods Adviser, Agriculture Research DFID
Year(s) Of Engagement Activity 2018
 
Description Radio Cardiff 
Form Of Engagement Activity A press release, press conference or response to a media enquiry/interview
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Media (as a channel to the public)
Results and Impact Radio interview for genome paper: Radio Cardiff
Year(s) Of Engagement Activity 2018
URL https://www.mixcloud.com/pythagoras_trousers/pythagoras-trousers-episode-421-mapping-the-wheat-genom...
 
Description Radio Extramadura (Spain) 
Form Of Engagement Activity A broadcast e.g. TV/radio/film/podcast (other than news/press)
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Media (as a channel to the public)
Results and Impact Interview in spanish regarding wheat genome sequence
Year(s) Of Engagement Activity 2018
URL http://www.canalextremadura.es/alacarta/radio/audios/principio-de-incertidumbre-la-secuenciacion-del...
 
Description Redburn 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Industry/Business
Results and Impact Talk at Redburn investment bank
Year(s) Of Engagement Activity 2017
 
Description Release of 6 wheat genome assemblies 
Form Of Engagement Activity A press release, press conference or response to a media enquiry/interview
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Industry/Business
Results and Impact Coupled to the EI talk at Plant and Animal Genomes in USA "From Zero to Many: Assembling Wheat Genomes with w2rap" we released 6 wheat genome assemblies
Year(s) Of Engagement Activity 2017
URL http://www.earlham.ac.uk/can-we-produce-better-wheat-crop-feed-world-single-multiple-wheat-genomics
 
Description Science 
Form Of Engagement Activity A magazine, newsletter or online publication
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Media (as a channel to the public)
Results and Impact Wheat's complex genome finally deciphered, offering hope for better harvests and nonallergenic varieties
Year(s) Of Engagement Activity 2018
URL http://www.sciencemag.org/news/2018/08/wheat-s-complex-genome-finally-deciphered-offering-hope-bette...
 
Description Science and Faith 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Public/other audiences
Results and Impact Is it ethical to oppose modern plant breeding technologies
Year(s) Of Engagement Activity 2017
 
Description Scientists on the Loose at The Cut Science Café 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Public/other audiences
Results and Impact Scientists on the Loose at The Cut Science Café was a panel discussion with general public about wheat genomics, new technologies, which led to enthusiastic questions from the audience and further visit of a school student to do one week internship in my group
Year(s) Of Engagement Activity 2016
 
Description Spiegel Online 
Form Of Engagement Activity A magazine, newsletter or online publication
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Media (as a channel to the public)
Results and Impact Researchers crack wheat puzzles - and hope for fewer hunger victims
Year(s) Of Engagement Activity 2018
URL http://www.spiegel.de/wissenschaft/natur/weizen-forscher-entschluesseln-genom-und-wollen-hunger-eind...
 
Description TGAC web and social media figures relating to the wheat genome release 
Form Of Engagement Activity Engagement focused website, blog or social media channel
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Media (as a channel to the public)
Results and Impact http://www.tgac.ac.uk/news/241/15/The-Genome-Analysis-Centre-announces-an-important-milestone-in-wheat-research/
http://www.tgac.ac.uk/news/254/15/Milestone-resource-in-wheat-research-now-available-for-download/

Clippings: 195

Circulation: 1,314,581
AVE: £7,378

EurekAlert - 4,028

Web views: 2,645 from 66 countries

Social media reach: 1m
Year(s) Of Engagement Activity 2015
URL http://www.tgac.ac.uk/news
 
Description TSL summer school 2016 
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 The Sainsbury Laboratory summer school provides training to granduate students and postdocs from all over the world
Year(s) Of Engagement Activity 2016
 
Description Talk Aarhus 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Postgraduate students
Results and Impact Talk at Aarhus University
Year(s) Of Engagement Activity 2017
 
Description The Atlantic 
Form Of Engagement Activity A magazine, newsletter or online publication
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Media (as a channel to the public)
Results and Impact Scientists Finally Crack Wheat's Absurdly Complex Genome
Year(s) Of Engagement Activity 2018
URL https://www.theatlantic.com/science/archive/2018/08/wheat-genome-is-best-thing-since-sliced-bread/56...
 
Description The Economist 
Form Of Engagement Activity A magazine, newsletter or online publication
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Media (as a channel to the public)
Results and Impact Revealing the wheat genome could lead to hypoallergenic bread
Year(s) Of Engagement Activity 2018
URL https://www.economist.com/science-and-technology/2018/08/18/revealing-the-wheat-genome-could-lead-to...
 
Description The Guardian 
Form Of Engagement Activity A magazine, newsletter or online publication
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Media (as a channel to the public)
Results and Impact Scientists sequence wheat genome in breakthrough once thought 'impossible'
Year(s) Of Engagement Activity 2018
URL https://www.theguardian.com/science/2018/aug/16/scientists-sequence-wheat-genome-in-breakthrough-onc...
 
Description Towards a sustainable future for wheat genomics 
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 The second Wheat breeders workshop introduced the latest, freely available wheat genomic resources and the new opportunities these bring for sophisticated analysis, with the potential to accelerate traditional crop improvement methods. The workshop was an opportunity for companies to both learn about the new datasets and to influence the direction of these interfaces.
Year(s) Of Engagement Activity 2015
URL http://www.earlham.ac.uk/case-study-towards-sustainable-future-wheat-genomics
 
Description Training in "Bioinformatics to advance wheat breeding" 
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 Training in "Bioinformatics to advance wheat breeding"
Year(s) Of Engagement Activity 2017
 
Description Wheat Functional Genomics - NIB 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact Presentation to the research community and industry at Wheat Functional Genomics, Rothamsted
Year(s) Of Engagement Activity 2015
 
Description Wheat as a model organism 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Postgraduate students
Results and Impact A one day workshop highlighting most recent tools that enable high impact wheat research
Year(s) Of Engagement Activity 2016
 
Description Wheat breeders' workshop 
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 The second Wheat Breeders' Workshop entitled, "Towards A Sustainable Future for Wheat Genomics" was held at The Genome Analysis Centre (TGAC) on 20-21 October 2015 to show new and upcoming resources to wheat breeders and involve them in future development of the tools they stand to benefit from
Year(s) Of Engagement Activity 2015
URL http://www.tgac.ac.uk/news/240/15/Wheat-breeders-techno-remix/
 
Description Wheat breeders' workshop 
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 The Genome Analysis Centre (TGAC) hosted the workshop "Towards a sustainable future for wheat genomics" that introduces the latest, freely available wheat genomic resources and the new opportunities these bring for sophisticated analysis
Year(s) Of Engagement Activity 2014
URL http://www.tgac.ac.uk/news/103/15/TGAC-takes-the-lead-towards-a-sustainable-future-for-wheat-genomic...
 
Description Wired Magazine 
Form Of Engagement Activity A magazine, newsletter or online publication
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Media (as a channel to the public)
Results and Impact AFTER 13 YEARS, SCIENTISTS FINALLY MAP THE MASSIVE WHEAT GENOME
Year(s) Of Engagement Activity 2018
URL https://www.wired.com/story/after-13-years-scientists-finally-map-the-massive-wheat-genome/
 
Description interview with TV - Anglia News, February 2016 
Form Of Engagement Activity A press release, press conference or response to a media enquiry/interview
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Media (as a channel to the public)
Results and Impact interview with TV - Anglia News, February 2016
Year(s) Of Engagement Activity 2016
 
Description planning wheat genome analyses 
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 An annual meeting to plan multiple aspects of wheat genome and epigenome sequencing
Year(s) Of Engagement Activity 2018
 
Description podcast Wheat Genome 
Form Of Engagement Activity A press release, press conference or response to a media enquiry/interview
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Media (as a channel to the public)
Results and Impact Dewing Grain podcast Wheat Genome
Year(s) Of Engagement Activity 2018
URL http://www.dewinggrain.co.uk/podcast-item/?id=34
 
Description • EPSO-EC Conference at EXPO Milano 
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 EU meeting on new breeding technologies
Year(s) Of Engagement Activity 2015