All the resources

Resources are manually added and edited by our contributors.




This online database contains information from a project at the SCRI to mine wheat and barley genes for SNPs which were mapped in barley crosses.
http://bioinf.scri.ac.uk/barley_snpdb/

Results of search for all markers in BarleyDB
http://ukcrop.net/perl/ace/search/BarleyDB?class=Marker

These are the largest and most authoritative cereal collections in the UK comprising 9513 wheat, 10838 barley and 2613 oat accessions. All material is sent out under the Standard Material Transfer Agreement of the International Treaty for Plant Genetic Resources for Food and Agriculture.
http://www.jic.ac.uk/germplasm/

Provide an efficient transformation capability for the main UK crops, while facilitating further improvements in transformation technology and delivery to the UK research community.
http://www.bract.org/

As part of a BBSRC funded program to discover useful sequence polymorphisms in bread wheat we have sequenced the wheat variety Chinese Spring using Roche 454 technology. The draft assembly of the gene-rich regions of the genome, or the raw sequence reads can be searched using the BLAST form below. This project is a collaboration between the Universities of Bristol and Liverpool together with the John Innes centre in Norwich.
http://www.cerealsdb.uk.net/CerealsDB/Documents/DOC_search_reads.php

BrachyBase displays the JGI 4X draft genome assemblies with FGENESH gene predictions, rice cDNAs, grass transcript assemblies, and grass ESTs aligned
http://www.brachybase.org/

Brachypodium distachyon is a promising model system for temperate grasses structural and functional genomics because of its physical, genetic and genome attributes. The sequencing of the inbred line Bd21 (www.brachypodium.org) started in 2007. However, a transformation method remains to be developed for the community standard line Bd21. Here we describe a facile, efficient and rapid transformation system for Bd21 using Agrobacterium-mediated transformation of compact embryogenic calli (CEC) derived from immature embryos.
http://www.brachytag.org/collection.htm

The Cereal Pathogen Resistance Allele Database (CPRAD) catalogues information on the pathogen resistance alleles reported to be found in genotypes of barley and in future wheat and oats. It is fully searchable on a range of criteria and initial query results are displayed in a table.
http://cprad.scri.ac.uk/

Results of a survey (conducted during summer 2008) of the current status of cereal transformation in Europe. - 32 separate institutions in 13 different countries. The Survey is editable.
http://www.monogram.ac.uk/CTL.php

The CerealsDB (Cereals Data Base) web-site is created and maintained by members of the Functional Genomics Group at the University of Bristol. The site provides a range of facilities for the study of the wheat genome.
http://www.cerealsdb.uk.net/CerealsDB/Documents/DOC_CerealsDB.php

Bristol Kansas and Healthgrain
http://www.cerealsdb.uk.net/cgi-bin/dart_form.pl

Protocol for growing Brachypodium plants , Brachypodium tissue culture , Brachypodium T-DNA plant production , Brachypodium FST retrieval , Brachypodium FST analysis
http://www.brachytag.org/science.htm

The electronic Rothamsted Archive (e-RA) provides a permanent managed database for secure storage of Rothamsted's long term experimental data. Together with the accompanying meteorological records, associated documentation and sample archive, it is an unique historical record of experiments that have been measured continuously for over 150 years. Users have easy access to experimental data and specialist background information on the effects of agricultural practices on soils, crops and associated ecosystems
http://www.era.rothamsted.ac.uk/

FoggDB is a database funded by the BBSRC UK CropNet project, for the storage of genetic mapping data pertaining to the temperate forage grasses, Lolium Perenne, Lolium multiflorum and Festuca Pratensis.
http://ukcrop.net/perl/ace/search/FoggDB

Temperate forage grasses with the emphasis on wild and semi-natural populations of those species which are of importance to UK agriculture i.e. Lolium, Festuca and Dactylis. Also includes old cultivars and landraces used in UK agriculture. Select UK National Plant Inventory, then search for specific genera or species.
http://grfa.org.uk/search/plants/index.html

Probes, primes and genes with links to mapped locations.
http://wheat.pw.usda.gov/cgi-bin/graingenes/browse.cgi?class=marker

HGCA Recommended Lists (RL) provide information on yield and quality performance, agronomic features and market options for recommended varieties to assist growers with variety selection. Here you can find the latest Recommended Lists for wheat, oilseed, barley and oats as well as harvest results and trials information.
http://www.hgca.com/content.template/23/0/Varieties/Varieties/Varieties%20Home%20Page.mspx

The IWGSC was established by a group of plant scientists, breeders, and growers dedicated to sequencing the wheat genome. By gaining increased understanding of the biology of agronomically important traits and deploying state-of-the-art molecular tools, plant scientists and breeders will be able to accelerate wheat improvement to meet the challenges of the 21st century. The Consortium is committed to ensuring that the sequence of the wheat genome and the resulting DNA-based tools are available for all to use without restriction.
http://www.wheatgenome.org/

Videos on practical methods related to germplasm collections
http://www.youtube.com/user/JICGermplasm/videos?view=0

The RBG Kew DNA Bank contains approximately 40,000 samples of plant genomic DNA (as at the beginning of year 2010), all stored at -80°C. DNA samples can be ordered from Kew using this site. The fees assessed do not imply that DNA samples are being purchased, but rather this fee is meant to offset the cost of producing the sample and maintaining and shipping it. RBG Kew standard terms of supply (see MTA form) restrict commercial use of the DNA supplied.
http://apps.kew.org/dnabank/homepage.html

The list of genes provided below has been obtained by BLAST search routine against sequences available in online databases (e.g. GenBank, EMBL). T1 seeds are available from all T-DNA insertion lines (genotype Bd21). Validation and T2 seed production is ongoing. T1 and/or T2 seeds are available from the John Innes Centre and can be requested online.
http://www.brachytag.org/known-genes.htm

NIAB online repository for marker-assisted selection assays
http://www.niab.com/mas/

The MOsDB is a resource for publicly available sequences of the rice (Oryza sativa L.) genome. Rice is an experimental model for the cereal crops research and an agriculturally important plant, providing food for more than half of the world population.
http://mips.gsf.de/proj/plant/jsf/rice/index.jsp

As part of IGER’s interest in energy crops, DEFRA is funding a Miscanthus genetic improvement programme.
http://www.miscanthusbreeding.org/

Comparative Genomics using the model grass Brachipodium distachyon
http://www.modelcrop.org/

List of talks on Barley at the PAG XIII conference
https://pag.confex.com/pag/xxi/webprogram/Session1487.html

PHI-base is a web-accessible database that catalogues experimentally verified pathogenicity, virulence and effector genes from fungal, Oomycete and bacterial pathogens, which infect animal, plant, fungal and insect hosts. PHI-base is therfore an invaluable resource in the discovery of genes in medically and agronomically important pathogens, which may be potential targets for chemical intervention. In collaboration with the FRAC team, PHI-base also includes antifungal compounds and their target genes. Each entry in PHI-base is curated by domain experts and is supported by strong experimental evidence (gene disruption experiments, STM etc), as well as literature references in which the original experiments are described. Each gene in PHI-base is presented with its nucleotide and deduced amino acid sequence, as well as a detailed description of the predicted protein\'s function during the host infection process.
http://www.phi-base.org

PLEXdb (Plant Expression Database) is a unified public resource for gene expression for plants and plant pathogens. PLEXdb serves as a bridge to integrate new and rapidly expanding gene expression profile data sets with traditional structural genomics and phenotypic data. The integrated tools of PLEXdb allow investigators to use commonalities in plant biology for a comparative approach to functional genomics through use of large-scale expression profiling data sets.
http://www.plexdb.org/index.php

PpETS (Polyploid Estimated Transcript Server) is a resource which aims to help biologists working on polyploid plant species to get the best estimate of transcript sequences so that they can design specific primers to these.
http://www.rothamsted.ac.uk/ppets/modperl/index.pl

Comparing a partial amino acid sequence for a protein with an organism\'s genome sequence immediately enables recognition of both the corresponding gene and the protein\'s complete amino acid sequence.
http://www.jic.ac.uk/corporate/services-and-products/proteomics.htm

QUOATS - This five year (14 September 2009 - 13 September 2014) research project (LK09124) will develop and apply state-of-the-art genomic and metabolomic tools for oat genetic improvement. Focus is on the understanding and manipulation of key traits that will enhance the value of oats in human health improvement, capitalise on the value of oats as a low input cereal, increase the environmental and economic sustainability of cereal based rotations, realise the potential of oats as a high value animal feed and develop new opportunities for using oats through advanced fractionation.
http://www.quoats.org/

SCRI’s state-of-the-art facilities provide a comprehensive resource for plant transformation in Scotland. Our team of researchers aim to provide the highest quality of service using methods that have been developed by leading scientists throughout the world.
http://www.FunGen.co.uk/

The facility provides access for all SCRI staff and external collaborating groups to high-throughput genomics technologies and expertise.
http://www.scri.ac.uk/research/genetics/genesanddevelopment/sequencingandmicroarray

The seed portal is a way to find basic information about the seed samples conserved in the Seed Vault
http://www.nordgen.org/sgsv/

The collection consists mainly of wheat varieties and a few tetraploid and diploid lines. The lines are maintained as grain from bagged ears from glasshouse grown plants. Small seed samples are available under the SMTA of the International Treaty for Plant Genetic Resources for Food and Agriculture.
http://www.jic.ac.uk/germplasm/Bristol%20CrlsDB%20Stocks.html

There are over 6 million samples, or accessions, held in genebanks world wide. Maintaining these accessions in a viable state represents a massive investment of resources over time. However there are concerns that the return on this investment is limited due to poor utilization of the material in breeding programs. Actually finding the accessions most likely to provide the genetic variation required is a major constraint.
http://www.figstraitmine.org/index.php?dpage=14

The Centre is a joint venture of Rothamsted Research and the Biotechnology and Biological Research Council (BBSRC), and is a leading UK facility for research and service activity in plant and microbial metabolomics. It is located in the new Centenary Building on the Rothamsted campus, where state-of-the-art analytical chemistry, bioinformatic, microbiological and molecular biology resources appropriate to the Centre’s needs are housed in a purpose-built laboratory complex.
http://www.metabolomics.bbsrc.ac.uk/index.htm

The Scottish Barley Variety Database contains a comprehensive collection of barley variety descriptions collated and presented by Science and Advice for Scottish Agriculture (SASA) in Edinburgh.
http://barley.agricrops.org/menu.php

RRes maintains and distributes a collection of 50 accessions. Information on these can be searched via the database managed by the Germplasm Resoruces Unit at the JIC. Simply select Triticum in the Genus and monococcum in the species boxes and click search. The records will then appear.
http://data.jic.bbsrc.ac.uk/cgi-bin/germplasm/cereals.asp

Comprises some 1200 selections of landrace wheats collected from around the world in the late 1920s. This provides a unique snapshot of genetic diversity and geographic distribution prior to large scale plant breeding. It is also a source of novel genes for wheat improvement.
http://www.wgin.org.uk/index.php?area=ResearchAct&page=obj2

Transcription factors (TFs) regulate gene expression by interacting with promoters of their target genes and are classified into families based on their DNA-binding domains. Genes coding for TFs have been identified in the sequences of model plant genomes...
http://wwwappli.nantes.inra.fr:8180/wDBFT/

Watkins collection phenotype data from the 2006 JIC field trial - Phenotype data of the EMS mutated Paragon M5 population collected at JIC between March and August 2006- Mapping data for the Avalon x Cadenza DH population - Development and analysis of 146 Conserved Orthologous Sequence (COS) markers in Wheat, Rice and Brachypodium distachyon - Avalon and Cadenza Field Trial 2006
http://www.wgin.org.uk/resources/researchresults.php

The BBSRC wheat breeding programme is divided into 4 pillars (Landraces, Synthetics, Alien Introgression, Elite Wheats) and 2 themes (Phenotyping and Genotyping).
http://www.wheatisp.org/

Principally the site is aimed at those who wish to obtain information about SNP markers; e.g., the sequence upon which they are based, obtain primers used for their identification, identify the haplotypes of common UK varieties. However, there are pages that describe, in simple terms, what SNPs are and how they can be a wonderful tool for the breeder.
http://www.cerealsdb.uk.net/CerealsDB/SNPS/Documents/DOC_snps.php

The objective of the proposed programme is the development of pre-breeding germplasm, characterised for key traits, and the identification of genic markers for selecting these traits, for use both in commercial breeding programmes and for academic research.
http://www.monogram.ac.uk/wg6.php

On the WheatBP (Wheat, the big picture) site we provide background information on all aspects of wheat. We are sure that there is something here for everyone: farmers, millers, brewers, teachers, students, cereal biologists or, indeed, anyone who might be interested in getting to know a little more about one of the world's most important crops.
http://www.wheatbp.net/WheatBP/Documents/DOC_WheatBP.php

(2x, 4x and 6x wheat species, and both wild and cultivated relatives) The collection of around 1350 accessions has been built up over the past 60 years. An extremely diverse source of novel genes for cereal improvement, which is thus additionally important for taxonomic reference studies. All material is sent out under the Standard Material Transfer Agreement of the International Treaty for Plant Genetic Resources for Food and Agriculture.
http://data.jic.bbsrc.ac.uk/cgi-bin/germplasm/triticeae/