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 CSS

TGACv1

IWGSC RefSeqv1.0

 

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 16 studies with both TGAC and IWGSC CSS gene models
  • WheatExp 6 studies with IWGSC CSS 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

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

 

BBSRCLogojohn-innes-logoiwyp-Logo