A community resource for wheat functional genomics
Lead Research Organisation:
University of Bristol
Department Name: Biological Sciences
Abstract
UK-based resources for wheat research are currently isolated and tailored to 'in-house' needs. As such they are often invisible to or inaccessible by the outside world. With the backing of the wheat community, Monogram (consisting of Rothamsted, IGER, JIC and SCRI), the Wheat Genetic Improvement Network (WGIN) and the Small Grain Cereal Network (SGCN), we propose to initiate a process which brings together these resources under one umbrella namely the existing SGCN and its associated web site. Our approach will organise the UK's wheat tools and resources such that they become accessible to all, while having a 'customer first' approach whereby users of the new SGCN site need to perform single searches regardless of the resources' physical location. With the resources requested the Bristol group will oversee the process whereby both its current biological/bioinformatics' resources and several new resources become available via the SGCN web site. This process will form the initial resource 'modules' of the SGCN web site to which other members of the community will be encouraged to add to over time in line with BBSRC's recently launched data sharing policy. Given the global challenges facing all plant scientists we believe that this proposal represents the best opportunity yet for the UK wheat community to work as one and face the future as an integrated community.
Technical Summary
As part of the BBSRC funded Investigating Gene Function (IGF) programme (IGF12403) the Bristol group, in collaboration with the John Innes Centre and SCRI was charged with developing a basic set of biological and bioinformatics tools for wheat genomics. Several important resources, from all the major centres carrying out wheat research, have been developed since the creation of the IGF resources and these now need to be properly integrated into the available analytical tools. These recently developed resources include a 244K feature wheat array, various TILLING populations, large data sets of cDNA EST microarray and Affymetrix GeneChip experiments and genotyping data generated by various procedures. This proposal is therefore designed to directly address the funding agencies concern that wheat resources are 'plagued by the inability of different providers to co-ordinate properly' and it therefore aims to link all UK wheat resources in a form which can be used by the non-(bioinformatic)-expert and which encourages resource usage among the wider cereal community.
People |
ORCID iD |
Keith Edwards (Principal Investigator) | |
Gary Barker (Co-Investigator) |
Publications
Wilkinson PA
(2012)
CerealsDB 2.0: an integrated resource for plant breeders and scientists.
in BMC bioinformatics
Wilkinson PA
(2016)
CerealsDB 3.0: expansion of resources and data integration.
in BMC bioinformatics
Wang S
(2014)
Characterization of polyploid wheat genomic diversity using a high-density 90 000 single nucleotide polymorphism array
in Plant Biotechnology Journal
Raffan S
(2021)
Wheat with greatly reduced accumulation of free asparagine in the grain, produced by CRISPR/Cas9 editing of asparagine synthetase gene TaASN2
in Plant Biotechnology Journal
Przewieslik-Allen AM
(2018)
Developing a High-Throughput SNP-Based Marker System to Facilitate the Introgression of Traits From Aegilops Species Into Bread Wheat (Triticum aestivum).
in Frontiers in plant science
King J
(2017)
A step change in the transfer of interspecific variation into wheat from Amblyopyrum muticum.
in Plant biotechnology journal
Allen A
(2016)
Characterization of a Wheat Breeders' Array suitable for high-throughput SNP genotyping of global accessions of hexaploid bread wheat ( Triticum aestivum )
in Plant Biotechnology Journal
Description | We have discovered and developed tens of thousands of wheat molecular markers (called SNPs). These SNPs are being used by wheat breeders to breed advanced varieties of wheat. |
Exploitation Route | The SNP markers are currently being used by wheat breeders across the world to developed new varieties via enhanced breeding procedures. |
Sectors | Agriculture Food and Drink |
URL | http://www.cerealsdb.uk.net/ |
Description | The information is being used by the wheat community including the wheat breeders |
First Year Of Impact | 2009 |
Sector | Agriculture, Food and Drink |
Impact Types | Economic |
Description | A pipeline for efficient recombination in wheat |
Amount | £200,364 (GBP) |
Funding ID | BB/W003317/1 |
Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
Sector | Public |
Country | United Kingdom |
Start | 09/2021 |
End | 03/2023 |
Title | Introgression plotter added to Cerealsdb |
Description | Software to allow users to screen wheat germplasm for potential introgressions from wheat relative |
Type Of Material | Data analysis technique |
Year Produced | 2019 |
Provided To Others? | Yes |
Impact | At the request of the wheat breeding companies we have made this tool available via Cerealsdb so that breeders can check on the presence of possible introgressed regions in the bread wheat genome |
Title | QTL database |
Description | Upload of QTL database to Cerealsdb |
Type Of Material | Data analysis technique |
Year Produced | 2019 |
Provided To Others? | Yes |
Impact | Breeders and academics are now able to download/examine various QTL-based datasets |
Title | Upgrade to cerealsdb (cerealsdb3) |
Description | We have carried out a significant upgrade of cerealsdb to include new analytical tools and a much larger data set |
Type Of Material | Database/Collection of data |
Year Produced | 2019 |
Provided To Others? | Yes |
Impact | Increased level of data downloads and use of tools to detect introgressions in wheat |
URL | http://www.cerealsdb.uk.net/cerealgenomics/CerealsDB/indexNEW.php |
Description | Collaboartion with Syngenta to exchnage knowledge on trasformation and double haploid production |
Organisation | Syngenta International AG |
Department | Syngenta Ltd (Bracknell) |
Country | United Kingdom |
Sector | Private |
PI Contribution | exchange of personal to improve our technology in double haploid production |
Collaborator Contribution | Spent time at Syngenta providing input into transformation technolgy |
Impact | Better transformation and double haploid technology available to Bristol |
Start Year | 2019 |