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
- URGI webpage: https://wheat-urgi.versailles.inra.fr/Seq-Repository/Assemblies
- Must register for account to get access to the BLAST database and download the assembly: http://www.wheatgenome.org/user/register
- 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
- expVIP 16 studies with both TGAC and IWGSC CSS gene models
- WheatExp 6 studies with IWGSC CSS gene models
- Cereals DB: Particularly good for SNP databases, for marker data i.e. KASP assays. Hosted by the University of Bristol.
- Grain genes: Database of molecular and phenotypic information 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”
- VURV Pedigree information database Pedigree information database from the Crop Research Institute, Czech Republic containing 74,527 wheat accessions from 2006 and earlier
- JIC GRU pedigree information database Pedigree information database from the John Innes Centre Germplasm Resources Unit containing wheat, barley and oat varieties from 2012 and earlier
- AHDB pocketbook Pedigree information is available for the latest UK varieties of wheat, barley, oats and oilseed rape in the AHDB pocketbook
General Plant Genomics Tools and Databases
- EnsemblPlants: Genome-based portal for various plant species. Training available at Ensembl Training
- Gramene: Has different data to EnsemblPlants, but also uses its infrastructure; aimed at comparative functional genomics in crop and model species
- Phytozome: Different data to EnsemblPlants 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
- 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)