CerealsDB: A community resource for wheat genomics

Lead Research Organisation: University of Bristol
Department Name: Biological Sciences

Abstract

CerealsDB ( http://www.cerealsdb.uk.net/) is one of the most highly accessed wheat web sites with over 5,000 unique accesses per month.

The reasons for CerealsDB's success are clear; it provides the community with sequence and single nucleotide polymorphism (SNP)-based information in a form accessible to and understandable by non-experts.

While CerealsDB is successful, to remain of value to its users, it needs to develop in conjunction with the community's expectations. In addition, CerealsDB needs to expand its remit to include further interaction with other web sites such as the internationally based Wheat Initiative. This development is new to this application as in our previous work we developed tools specifically for the UK community rather than the global wheat community. However, although our previous work did focus on the UK community, the easy to use style of CerealsDB has already resulted in the web site becoming international recognised, with many of its users being from non-UK organisations.

In this further development, CerealsDB will continue work with UK users to develop sequence and SNP-based resources; however, it will also extend its horizons to include interactions with international web-based resources and the exploitation of genomics resources such as the wheat reference sequence. This extension to its remit will result in an expanded audience for CerealsDB and more extensive tools and datasets being made available to the community.

Technical Summary

"A community resource for wheat functional genomics" was one of the first projects to be funded by the BBR initiative. The resources enabled Bristol and Rothamsted Research to develop "CerealsDB" and "Monogram". CerealsDB and Monogram are accessed directly or via other web sites such as the Wheat Improvement Strategic Program (WISP), the International Wheat Initiative and GrainGenes. CerealsDB hosts tools and resources to access and analyse sequence and SNP-based datasets for wheat (Triticum aestivum) and related species. CerealsDB assists breeders and academics in exploring the wheat genome and selecting strategies for genotyping and marker assisted selection. CerealsDB includes a database in excess of 100,000 varietal SNPs, of which several thousand have been validated and mapped on one of three mapping populations. CerealsDB also contains information on DArT markers and Expressed Tagged Sequences (ESTs), and was the first site to host the 5x genome sequence for the variety Chinese Spring released in 2010. Since launch, CerealsDB has been updated regularly, with the last update on the 1st May 2013 with the addition of a further ~1,500 mapped SNP markers and a mapping function which assigns unmapped SNPs to putative homoeologous specific chromosome arms.

To ensure that CerealsDB remains on of the most useful wheat-based web sites and to increase the communities awareness of the resources hosted, we intend to develop CerealsDB to included further tools such as an expanded SNP/genotype database, including iSelect and Axiom based datasets along with facilities to identify and characterise functional SNPs. In addition, new releases will include graphic tools to enable breeders and academics to link mapped and non-mapped SNPs/genes across a variety of wheat related species. Finally, although CerealsDB has always been designed to be easy to use, we will provide training across the range of activities included within the web site.

Planned Impact

The BBSRC web site states that "BBSRC is the principal funder of food-related research in the UK and has food security as one of its key strategic drivers." In the UK wheat is, by a significant margin, the most valuable arable crop and therefore not surprisingly the status of the UK wheat crop is a national issue often reported in the press. While BBSRC funds a large number of wheat-related projects, for the most part, it is the translation of this research into wheat varieties with increased yield or improved qualities such as improved bread making qualities that provides the impact required by BBSRC if it is to deliver its strategic objectives. Translation of wheat research in line with BBSRC's strategic priorities, almost always involves either mapping and cloning genes or crossing alleles of interest into elite varieties. In all cases, since its launch, CerealsDB has helped researchers to achieve impact by providing wheat geneticists with unencumbered sequences and SNP-based information which is easy to access and free from IP or MTAs.

The development of CerealsDB has led to strategic changes in the approaches taken by various wheat breeders, for instance many regard the development of CerealsDB as a significant factor in their decision to convert their marker labs to the SNP-based markers.

In accordance with BBSRC strategy to achieving impact, Prof. Edwards has actively engaged with industry, for instance through the CIRC program and via his participation in a BBSRC science interchange programme with Advanta-Nickerson (now Limagrain) Seeds to exchange technologies and ideas. In addition the university base of the Bristol group and the institutional base of TGAC allows each to incorporate its research directly into undergraduate, post-graduate and post doc teaching. This approach has been remarkably successful and has resulted in numerous young researchers being placed within agricultural institutes or companies as PhD students, researchers or employees.

The facilities offered by CerealsDB are unique. We know that this because our users tell us. Although CerealsDB is international recognised as being a primary source of wheat sequences and SNP-based markers, we believe that by adding the facilities described, Bristol will ensure that it increases its international profile and continues to provide a valuable (almost) one stop shop for wheat functional genomics. In so far as we are aware no similar commercially available resources exist, however, it is important to note that our web site is used by both academic and the industrial sectors with several companies relying on it for a substantial part of their business and many of our improvements have been carried out at the suggest of the UK wheat breeding sector.

Publications

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Burridge AJ (2017) High-Density SNP Genotyping Array for Hexaploid Wheat and Its Relatives. in Methods in molecular biology (Clifton, N.J.)

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Wilkinson PA (2016) CerealsDB 3.0: expansion of resources and data integration. in BMC bioinformatics

 
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/cerealgenomics/Index_Home.html
 
Title 10,00 wheat KASP markers 
Description 10,000 wheat KASP markers made available as a commercial product via the company LGC 
Type Of Technology New Material/Compound 
Year Produced 2015 
Impact Cheap, flexible genotyping in wheat now available to the global community; this product is now a significant product in LGC's portfolio 
URL http://www.cerealsdb.uk.net/cerealgenomics/Index_Home.html
 
Title Axiom® Wheat Breeder's Genotyping Array 
Description Axiom® Wheat Breeder's Genotyping Array: Developed in collaboration with Affymetrix for large scale high throughput genotyping of wheat; specifically designed for wheat breeders. Now a commercial product and is currently being used by Uk and European wheat breeders 
Type Of Technology New/Improved Technique/Technology 
Year Produced 2014 
Impact 384 microarray plate design makes it suitable for ultra high throughput genotyping of large numbers of wheat samples. It is currently the only one of its kind. 
URL http://media.affymetrix.com/support/technical/datasheets/axiom_wheat_breeders_genotyping_array_datas...
 
Title Axiom® Wheat HD Genotyping Arrays 
Description Axiom® Wheat HD Genotyping Array: Developed in collaboration with Affymetrix for large scale high throughput genotyping of wheat. Now a commercial product 
Type Of Technology New/Improved Technique/Technology 
Year Produced 2014 
Impact Now makes the large scale genotyping of wheat a possibility 
URL http://www.affymetrix.com/catalog/prod850001/AFFY/Axiom%26%23174%3B-Wheat-Genotyping-Arrays#1_1
 
Description Monogram 2018 - John Innes Centre 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Amanda Burridge presented 'Rapid and Affordable Genotyping by Sequencing Optimised for Hexaploid Wheat' at Monogram 2018
Year(s) Of Engagement Activity 2018
 
Description Plant and Animal Genomes (PAG) XXVI 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Industry/Business
Results and Impact Amanda Burridge attended Plant and Animal Genomes (PAG) XXVI and presented 'CerealsDB Version 4.0: A Review of Tools and Data for Wheat Breeders and Research Scientists'
Year(s) Of Engagement Activity 2018