Useful wheat links

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

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

SNP variation

  • 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 elements

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
  • 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
  • Barlex: The Comprehensive Barley database
  • RGAP: The Comprehensive Rice database (MSU)
  • funRiceGenes: Rice gene function database
  • MaizeGDB: The Comprehensive Maize database
  • TAIR: The Comprehensive A. thaliana database
  • Brachy: The Comprehensive Brachypodium database

 

Germplasm Resources

 

Workshops and Tutorials
  • GARNet September 2016: An introductory workshop covering genomic resources, finding wheat orthologues, wheat expression browsers and in silico TILLING
  • Ensembl Plants: Slides explaning how to use EnsemblPlants

 

Genomic data
  • 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)

 

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