Wheat and barley Legacy for Breeding Improvement

Lead Research Organisation: Earlham Institute
Department Name: UNLISTED

Abstract

To satisfy the demand of an expanding population, agriculture faces the challenge of delivering safer, high-quality, and health-promoting food and feed in an economic, environmentally sensitive, and sustainable manner. While partially achievable by entering marginal lands into agricultural production, a sustained effort is required to generate crops with higher and more stable yields across diverse and changing environments. Wheat and barley are key renewable resources and among the most important crops worldwide. The wild relatives and old cultivars or populations of wheat and barley represent a reservoir of untapped and potentially important genes for crop improvement that have been left behind during the processes of domestication, cultivation, range extension and breeding.

WHEALBI will develop and implement tools, methods and procedures to facilitate the characterisation of wild relatives and local varieties of wheat and barley as sources of genes for use in crop improvement. It will explore the application of modern molecular, computational and analytical tools to provide understanding of the evolutionary processes that have shaped the current diversity in the genepool and to predict exploitable value from unadapted germplasm. It will develop innovative methods to optimise the use of these resources in pre-breeding and breeding programmes.

Within the work package dedicated to identifying the nature and extent of gene sequence diversity in the wheat and barley genepool, TGAC will sequence exomes of >500 diverse wheat accessions. Robust pipelines for identifying and calling true sequence variations will be established. Variants identified will be used downstream for genome wide analyses focussed on functional and adaptive variation and partitioning between different genepools; allele and pathway mining for adaptive traits and grain quality; and in genome-assisted pre-breeding and breeding methods.

Publications

10 25 50
 
Description EI processed the Wheat Accessions and carried out analysis on 506 of the 512 samples/varieties with 6 omissions due to library construction and/or sequencing problems. All data was passed through a dedicated QC pipeline, including adapter trimming, mapping to the reference and calculations of % reads on target. Additional analyses of 'freebayes' SNP calling bioinformatics pipeline was performed.

We applied significant efforts to integrate all the data in a consistent and accurate manner, i.e. pull together all the samples (and any duplicate samples) from multiple sequencing runs, and check any duplicated samples to decide whether it was safer to merge duplicates, or discard the outliers.

After the data was QC'd, all files were packaged and delivered to appropriate project members and WP leaders via Aspera server. EI has successfully achieved its contribution to deliverable D2.1 providing raw sequence data for 506 wheat accessions to grant partners.

EI has also contributed to the barley exome captures. We have received 64 additional barley accessions from project partners and sequencing of these is ongoing.

This the project we have now built a second promoter exon capture platform this is now published, we have also engaged with the 10+plus wheat genome project aiming to de novo sequence and assemble an international set of 16 genome.
Exploitation Route Our data on >500 wheat accessions has been available to the WHEALBI partners and already led to identification of a total of 6,800,653 natural variants in 43,932 wheat genes across all lines. This resource has been available to all 18 international WHEALBI partner institutes/companies, including 4 institutes in UK, and 2 seed companies. This is an incredible resource for the improvement of wheat that is helping to map new traits in wheat diversity collections and provides genetic markers for improving elite varieties.

The new capture platform is being used by CIMMYT, the US CAPs programme and Design future wheat.
Sectors Agriculture, Food and Drink

URL http://www.whealbi.eu/
 
Description The WHEALBI consortium includes seed companies, including KWS,RAGT and Elsoms in the UK. The findings have been available to them and have directly contributed to wheat improvement and marker development. The new capture design is actively being used in the UK and across the world.
First Year Of Impact 2017
Sector Agriculture, Food and Drink
Impact Types Economic

 
Title promoter exon capture data 
Description The data contain the design space for the promoter and exon used in our capture 
Type Of Material Database/Collection of data 
Year Produced 2018 
Provided To Others? Yes  
Impact Whole genome shotgun re-sequencing of wheat is expensive because of its large, repetitive genome. Moreover, sequence data can fail to map uniquely to the reference genome making it difficult to unambiguously assign variation. Re-sequencing using target capture enables sequencing of large numbers of individuals at high coverage to reliably identify variants associated with important agronomic traits. We present two gold standard capture probe sets for hexaploid bread wheat, a gene and a promoter capture, which are designed using recently developed genome sequence and annotation resources. The captures can be combined or used independently. The capture probe sets effectively enrich the high confidence genes and promoters that were identified in the genome alongside a large proportion of the low confidence genes and promoters. We use a capture design employing an 'island strategy' to enable analysis of the large gene/promoter space of wheat with only 2x160 Mb NimbelGen probe sets. Furthermore, these assays extend the regions of the wheat genome that are amenable to analyses beyond its exome, providing tools for detailed characterization of these regulatory regions in large populations. Here, we release the targeted sequence of the capture probe sets on the wheat RefSeqv1, the design space that was used to tile our capture probes across and finally the positions of the probes themselves across this design space for both the gene and promoter capture probe sets. 
URL https://opendata.earlham.ac.uk/wheat/under_license/toronto/Gardiner_2018-07-04_Wheat-gene-promoter-c...
 
Description EAGER - Eduard Akhunov 
Organisation Kansas State University
Country United States 
Sector Academic/University 
PI Contribution Joint funding and publications, method development
Collaborator Contribution Access to material and bioinformatics methods
Impact EAGER -BBSRC grant A PATHWAY TO THE EXPLOITATION OF EPIGENETIC VARIATION IN UK, US AND INTERNATIONAL BREEDING PROGRAMMES Gardiner, L.-J., Brabbs, T., Akhunov, A., Jordan, K., Budak, H., Richmond, T., et al. (2019). Integrating genomic resources to present full gene and putative promoter capture probe sets for bread wheat. GigaScience. http://doi.org/10.1093/gigascience/giz018 IWGS Consortium, Jordan, K. W., Wang, S., Lun, Y., Gardiner, L.-J., MacLachlan, R., et al. (2015). A haplotype map of allohexaploid wheat reveals distinct patterns of selection on homoeologous genomes. Genome Biology, 16(1), 680. http://doi.org/10.1186/s13059-015-0606-4
Start Year 2018
 
Description KWS 
Organisation KWS UK
Country United Kingdom 
Sector Private 
PI Contribution Generated double haploid population for the IWYP project and provide material for INTREPID and the BBSRC/EAGER work
Collaborator Contribution Know of the techniques and approaches we are using, early access to the data we generate
Impact Double haploid seed population
Start Year 2017
 
Description RAGT 
Organisation RAGT Seeds
Country United Kingdom 
Sector Learned Society 
PI Contribution Identify key material for our EAGER project and Design future wheat. Support for collaboration with IBM.
Collaborator Contribution Discussion of methods and analysis of material relevant to RAGT.
Impact none yet
Start Year 2018
 
Description 10 plus wheat genome project workshop 
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 The meeting was to provide a consortium update on the 10 plus wheat genome project
Year(s) Of Engagement Activity 2018
URL http://www.10wheatgenomes.com
 
Description Bioinformatics for 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 The practical course featured a collection of methods and bioinformatics tools fundamental for modern breeding, especially for crops. Next generation sequencing (NGS) has made large collections of open-source diversity genomic data possible, such as SNPs, that can be used as molecular markers for breeding. Combined with phenotypes, genome-wide association studies provide breeders with an understanding of the molecular basis of complex traits. Content: SNP calling/discovery and SNPs effects and context; NGS techniques for genotyping; Genetic markers, linkage analysis, and genetic maps; High-throughput phenotyping and image analysis; Association mapping (GWAS); Genome-wide predictions, modelling and simulations; Genomic selection.
Year(s) Of Engagement Activity 2017
URL http://www.earlham.ac.uk/bioinformatics-breeding
 
Description Oral presentation at conference: Training on Durum Wheat Genomics and Breeding, University of Bologna, Italy 
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 Oral presentation at training conference to educate and train breeders, farmers and students in bioinformatic techniques for the analysis of wheat genomics data
Year(s) Of Engagement Activity 2017
URL http://www.wheatinitiative.org/events/durum-ewg-workshop-bioinformatics-advance-wheat-breeding
 
Description Oral presentation at the Wheat and Barley Legacy for breeding improvement annual meeting at the University of Haifa, Israel 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Attended and presented work at the Wheat and Barley Legacy for breeding improvement annual meeting at the University of Haifa, Israel. This built links with researchers in Italy, France and Israel for future collaboration and sparked their interest in epigenetic research.
Year(s) Of Engagement Activity 2017
 
Description Oral presentation: Agilent User group meeting 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Industry/Business
Results and Impact I presented my work analysing the methylation of wheat to many of the users of Agilent technology in the UK since I implemented Agilent technology for the study. Many PI's and postdoctoral researchers were present and were interested in how they could use this methodology for their own analyses.
Year(s) Of Engagement Activity 2018
URL https://www.chem.agilent.com/edm/2017/06/Uk_Seminar_2017/Documents/GenUGM/Agenda_GUGM.pdf
 
Description Scientists on the Loose at The Cut Science CafĂ© 
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 Talk and discussion with Elsoms seeds 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Industry/Business
Results and Impact The talk was to breeders and crop scientist work at Elsoms seed, The aim was to raise awareness of the work that Design future wheat and my group were doing. This lead to a letter of support for our BBSRC grant and a line of communication with their wheat and brassica breeders.
Year(s) Of Engagement Activity 2018
 
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 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