Designing Future Wheat Resources

TILLING Project

This resource consists of TILLING 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.

The exomes of 1,535 Kronos and 1,203 Cadenza EMS-mutagenized M2 plants were sequenced using Illumina next-generation sequencing as described in Krasileva et al (2017, Proc Natl Acad Sci USA 114, E913-E921). As part of DFW (work package 2), we mapped the sequences to the IWGSC RefSeq v1.0 assembly, identified mutations and predicted their effects based on the RefSeqv1.0 protein annotation. In addition, unmapped reads were mapped to the Kronos and Cadenza genome assemblies available at grassroots wheatis.tgac.ac.uk/grassroots-portal/blast .

The SNP calls can be found on www.wheat-tilling.com/ and from the browser in Ensembl plants. The bam files can be accessed directly via grassroots and subsets can be retrieved by region using the below.

Methods:
  • Raw sequencing data: European Read Archive (ENA study PRJEB11524).
  • Cadenza and Kronos mapped reference: IWGSC refseq v1.0 Chinese Spring parts file.
  • Unmapped Cadenza reads reference: Cadenza v1.1.
  • Unmapped Kronos reads reference: Kronos v1.1.

Reads were trimmed using sickle/scythe (v1.33) then mapped with BWA and marked with picard tools within the Dragen system (v01.011.222.02.04.04.36875). Unmapped reads from mapping to IWGSC refseq v1.0 reference were extracted using samtools (v0.1.18) and converted to fastq using bedtools bamToFastq (v2.17.0). All SNPs were called using GATK within the Dragen system.

SNP filtering was done using python scripts found at https://github.com/cschu/royal_dragen.