Useful wheat links – Wheat Training

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)

TGACv1 (previous assembly)

IWGSC CSS (previous assembly)

Wheat pangenome (10+ Genomes Project)

Wheat Databases

General information

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.

Gene expression

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

Mutants

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

SNP variation

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 elements

Repetitive element database (TREP): “A collection of repetitive DNA sequences from different Triticeae species”

Pedigree information

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

Germplasm Resources

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