Here we’ve provided a by-no-means exhaustive list of links that we’ve found useful when working on wheat genetics.
Wheat Genome Sequences
IWGSC RefSeqv1.0 (current assembly)
- Genome browser hosted by Ensembl Plants current site
- Download sequence
TGACv1 (previous assembly)
- Genome browser hosted by Ensembl Plants archive Oct 2017 site
- Download sequence
IWGSC CSS (previous assembly)
- Genome browser hosted by Ensembl Plants archive Mar 2016 site
- Download sequence
Wheat pangenome (10+ Genomes Project)
- BLAST server for global wheat varieties
- BLAST server for UK wheat varieties and Kronos
- Wheat Big Picture: A wide range of resources ranging from wheat evolution to developmental stages to SNP markers
- T3 database: A large collection of phenotype and genotype data as well as tools for GWAS and genomic selection
- Recommended Rules for Gene Symbolization in Wheat: PDF of Catalogue of Gene Symbols for Wheat agreed at the 12th international Wheat Genetics Symposium 2013
- Catalogue of Gene Symbols for Wheat: Resource of accepted gene and QTL names, mapping and germplasm information, and laboratory designations for markers. The Catalogue is published in whole periodically with yearly supplements by a committee of experts in wheat research.
- expVIP >30 studies with RefSeq v1.0 and v1.1 gene models (TGAC and IWGSC CSS gene models also available for backwards compatibility)
- Wheat eFP browser Pictographic expression browser with 70 developmental tissue/timepoints with RefSeq v1.0 gene models
- TILLING mutants on Ensembl Plants TILLING mutants mapped to RefSeqv1.0 (add as an extra track or through BioMart)
- TILLING mutant database TILLING mutants mapped to IWGSC CSS
- Cereals DB: Particularly good for SNP databases, for marker data i.e. KASP assays. Hosted by the University of Bristol.
- GrainGenes: Database of genetic markers and maps, QTLs, and genomic sequences specific to Triticeae and Avena.
- MAS wheat: Markers and protocols for marker assisted selection
- Repetitive element database (TREP): “A collection of repetitive DNA sequences from different Triticeae species”
- GRIS Pedigree information database from the Genetic Resources Information System for Wheat and Triticale based at the N. I. Vavilov Research Institute and CIMMYT. GRIS contains pedigree information for over 171,000 wheat and triticale accessions.
- AHDB pocketbook Pedigree information is available for the latest UK varieties of wheat, barley, oats and oilseed rape in the AHDB pocketbook
- Pedigree of UK wheat Recommended List for visualisation in Helium (download) Pedigrees were obtained from UK Recommended List information and from GRIS. For more information on Helium and nomenclature please see Shaw et al 2014 and visit the wiki at Github
General Plant Genomics Tools and Databases
- Ensembl Plants: Genome-based portal for various plant species. Training available at Ensembl Training
- Gramene: Has different data to Ensembl Plants, but also uses its infrastructure; aimed at comparative functional genomics in crop and model species
- Phytozome: Different data to Ensembl Plants and Gramene; use Firefox or Chrome browser with it; also comparative plant genomics
- EBI: Lots of useful web-tools and also data (molecular databases, networks, etc.)
- The Plant List: A working list of all plant species
Other Plant Species' Databases
- JIC Germplasm Resources Unit: curators and distributors of the BBSRC Small Grains Cereal Collection, also crop wild relatives, wheat aneuploids, and wheat/alien chromosomal addition and substitution lines.
- USDA-ARS Germplasm Resources Information Network: curators and distributors of a diverse collection of small grain cereal germplasm from around the world.
Workshops and Tutorials
- GARNet September 2016: An introductory workshop covering genomic resources, finding wheat orthologs, wheat expression browsers and in silico TILLING
- Ensembl Plants: Slides explaning how to use Ensembl Plants
- Genomic data against RefSeqv1.0
- Read_me.txt: Description of the provided files and contact details
- 90k_vs_WGAV1.0_best_alignment.tsv: Best alignment of each SNP marker from the 90k iSelect chip to RefSeqv1.0 with gmap. Provided by Ricardo Ramirez-Gonzalez (John Innes Centre)
- axiom__vs_WGAV1.0_best_alignment.tsv: Best alignment of each SNP marker from the 820k and 35k Axiom chips to RefSeqv1.0 with gmap. Provided by Ricardo Ramirez-Gonzalez (John Innes Centre)
- TGACv1.cds.fa-vs-NRGene_v1.0.95id100cov.amended.gff3.gz: Alignment of the TGACv1 gene models to RefSeqv1.0 using gmap. Provided by Gemy Kaithakottil and David Swarbreck (Earlham Institute)
- Gene-only_TGACv1.cds.fa-vs-NRGene_v1.0.95id100cov.amended.gff3.gz: Subset of the previous file where only the “gene” field has been extracted to reduce the size (can be opened with Notepad++/excel).
- JIC_iSelect_RefSeq_positions_WINGEN.xlsx: iSelect SNPs positions on RefSeqv1.0 (BLAST). Provided by Luzie Wingen (John Innes Centre)