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Variations

  • 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

  Origin Improvement status Growth habit Region Large region
RAC875 Australia cultivar Spring Australia Australia
Opata Mexico cultivar Spring North and Central America The Americas
W7984 Mexico synthetic Spring North and Central America The Americas
PBW343 India cultivar spring South-central Asia Asia
Clear White USA cultivar Spring North and Central America The Americas
Vorobey Mexico cultivar Spring North and Central America The Americas
Klein Chamaco Argentina cultivar Spring South America The Americas
Pavon Mexico cultivar Spring North and Central America The Americas
acc2 USA Breeding line Spring North and Central America The Americas
acc3 USA Breeding line Spring North and Central America The Americas
acc4 USA Breeding line Spring North and Central America The Americas
acc1 USA Breeding line Spring North and Central America The Americas
acc5 USA Breeding line Spring North and Central America The Americas
PI366716 Afghanistan landrace Spring South-central Asia Asia
PI406517 Nepal landrace spring South-central Asia Asia
PI349512 Switzerland landrace spring Western and Northern Europe Europe
PI481923 Sudan landrace spring Northern Africa Africa
PI481718 Bhutan landrace spring South-central Asia Asia
PI382150 Japan landrace spring Eastern Asia Asia
PI366905 Afghanistan landrace spring South-central Asia Asia
PI470817 Algeria landrace spring Northern Africa Africa
PI445736 Nepal landrace spring South-central Asia Asia
Hidhab Algeria cultivar spring Northern Africa Africa
PI477870 Peru landrace spring South America The Americas
Dharwar Dry India cultivar spring South-central Asia Asia
Cham 6 Syria/Lebanon cultivar spring Western Asia Asia
Chakwal 86 Pakistan cultivar spring South-central Asia Asia
Berkut Mexico cultivar spring North and Central America The Americas
PI262611 Turkmenistan landrace spring South-central Asia Asia
PI222669 Iran landrace spring Western Asia Asia
PI278297 Greece landrace spring Southern Europe Europe
PI210945 Cyprus landrace spring Western Asia Asia
PI192569 Sweden landrace spring Western and Northern Europe Europe
PI192147 Ethiopia landrace spring South and East Africa Africa
PI8813 Iraq landrace spring Western Asia Asia
PI565213 Bolivia landrace spring South America The Americas
PI82469 North Korea landrace spring Eastern Asia Asia
PI185715 Portugal landrace spring Southern Europe Europe
PI245368 Guatemala landrace spring North and Central America The Americas
PI166333 Turkey landrace spring Western Asia Asia
PI166180 India landrace spring South-central Asia The Americas
PI177943 Turkey landrace spring Western Asia Asia
PI192001 Angola landrace spring South and East Africa Africa
PI153785 Brazil landrace spring South America The Americas
Marquis Canada cultivar spring North and Central America The Americas
Neepawa Canada cultivar spring North and Central America The Americas
AC Barrie Canada cultivar spring North and Central America The Americas
Chinese Spring China cultivar spring Eastern Asia Asia
Utmost Canada cultivar spring North and Central America The Americas
Rialto United Kingdom cultivar winter Western and Northern Europe Europe
Truman USA cultivar winter North and Central America The Americas
49-2914 H1096 Argentina Breeding line facultative South America The Americas
102 Chile cultivar facultative South America The Americas
93 Bulgaria cultivar facultative Western and Northern Europe Europe
Estacao Portugal cultivar winter Southern Europe Europe
Taxi United Kingdom cultivar winter Western and Northern Europe Europe
PR267 United States cultivar winter North and Central America The Americas
Alabasskaja Kazakhstan cultivar winter   Asia
Roemer Winter Germany cultivar winter Western and Northern Europe Europe
407-IV/60 Bosnia and Herzegovina cultivar facultative Western and Northern Europe Europe
403 Chile cultivar winter South America The Americas
Avalon United Kingdom cultivar winter Western and Northern Europe Europe
Update: 12 Jul 2018
Creation date: 27 Feb 2015