Seq Repository

• Projection of 2.8M SNPs from IWGSC RefSeq v1.0 onto v2.1 (A. Vasudevan, S. Cloutier)

Related publication and dataset to download .
VCF file of 2,799,166 single nucleotide polymorphism (SNP) markers positioned onto the Chinese Spring reference assembly RefSeq v2.1 developed by the International Wheat Genome Sequence Consortium (IWGSC; Zhu et al., 2021). These SNPs were lifted from the 1,000 wheat exome project, originally positioned onto RefSeq v1.0 (He et al., 2019). The SNP projection from RefSeq v1.0 onto RefSeq v2.1 was accomplished using LiftOff (Shumate and Salzberg, 2021).

• 1000 wheat exomes (E. Akhunov) 

Data are available to download and browse .

Genome-level DNA sequence variation map is required to establish links between causal variants and phenotypes as well as to understand the role of environmental, demographic and human-driven factors in shaping the genomic diversity of modern wheat. Here, we used a reference wheat genome IWGSC RefSeq v1.0 to generate a haplotype map based on the targeted re-sequencing of more than 1,000 diverse wheat landraces and cultivars, and tetraploid wild and domesticated relatives.

Web page

1000 wheat exomes project data is described in He et al., Nature Genetics, 2019   pdf

• Varietal SNPs (J. Dubcovsky, E. Akhunov) 

Varietal SNPs generated (capture plus sequencing) and called by the Akhunov lab and aligned to the IWGSC RefSeq v1.0 by the Dubcovsky lab are available to download and browse .

This dataset is under Toronto agreement , so analysis cannot be published before the data generators' publications.

All requests should be adressed to E. Akhunov and J. Dubcovsky .

• IWGSC SNPs (E. Paux) 

List of 3,289,847 intervarietal SNPs with fraction (ISBP or low-copy sequence), chromosomal origin, corresponding IWGSC contig, and context sequence.

Download the table .

Read the publication .

• Variations discovered by GBS and WEC (E. Akhunov)

Download the VCF files.

A sample of 62 diverse wheat lines was re-sequenced using the whole exome capture (WEC) and genotyping-by-sequencing (GBS) approaches.

Please see more details in the paper :
Author:   Katherine W. Jordan, Shichen Wang, Yanni Lun, Laura-Jayne Gardiner, Ron MacLachlan, Pierre Hucl, Krysta Wiebe, Debbie Wong, Kerrie L. Forrest, IWGSC, Andrew G. Sharpe, Christine H. D. Sidebottom, Neil Hall, Christopher Toomajian, Timothy Close, Jorge Dubcovsky, Alina Akhunova, Luther Talbert, Urmil K. Bansal, Harbans S. Bariana, Matthew J. Hayden, Curtis Pozniak, Jeffrey A. Jeddeloh, Anthony Hall, Eduard Akhunov
Title:      A Haplotype Map of the Allohexaploid Wheat Genome Reveals Distinct Patterns of Selection on Duplicated Homoeologous Genes
Journal:  Genome Biology
Year:      2015

1. Variations discovered by GBS:
    1.1 GBS_filtered_Indels.vcf 
    1.2 GBS_filtered_SNPs.vcf
2. Variations discovered by WEC:
    2.1 WEC_filtered_Indels.vcf 
    2.2 WEC_filtered_SNPs.vcf

Details on Wheat Hapmap data .

 Wheat lines