1. Introduction and General overview

This in silico TILLING resource consists of two EMS-mutagenised populations developed in tetraploid durum wheat cv 'Kronos' and hexaploid bread wheat cv 'Cadenza' as part of a joint project between the University of California Davis, Rothamsted Research, The Earlham Institute, and John Innes Centre.

We have re-sequenced the exome of 1,535 Kronos and 1,200 Cadenza mutants using Illumina next-generation sequencing, aligned this raw data to the IWGSC Chinese Spring chromosome arm survey sequence, identified mutations, and predicted their effects based on the protein annotation available at Ensembl Plants.

To facilitate the use of this resource we have included additional documentation which is outlined below. We have also developed a Wheat training website to aid reserachers new to wheat get started in this fascinating crop species. We hope you enjoy!

##Identifying TILLING mutants in the database

• Searching TILLING database with known gene or scaffold
• Using BLAST to identify mutations

Selecting TILLING mutants

• Interpreting the output file
• Mutation categories
• Considerations when selecting a mutant line
• [Ordering seeds] (https://github.com/homonecloco/bioruby-wheat-db/wiki/6.-Ordering-seeds)

Additional information

• What to do next after recieving seeds
• [What to do if you have an incomplete gene model] (https://github.com/homonecloco/bioruby-wheat-db/wiki/8.-What-to-do-if-you-have-an-incomplete-gene-model)
• JBrowse visualization at UC Davis

Capture design sequences

• Capture Design Reference (FASTA)
• UCW Kronos Contigs from unmapped reads and contigs from IWGSC v1 genomes A and B (FASTA)
• TGAC Cadenza Contigs from unmapped reads (FASTA)

Summary Tables

• GeneAnnotationTableSummary_Kronos_main_set for Kronos (Excel)
• GeneAnnotationTableSummary_Cadenza_main_set for Cadenza (Excel)