Data

OzWheat V1.0 SNP data assets

Commonwealth Scientific and Industrial Research Organisation
Dillon, Shannon ; Marquardt, Annelie ; Andrew, Sam ; Gock, Andrew ; Ramm, Kerrie ; Rathjen, Tina ; Forrest, Kerrie ; Hunt, James ; Suchecki, Rad ; Trevaskis, Ben ; McNeil, Meredith ; Hyles, Jessica
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ctx_ver=Z39.88-2004&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Adc&rfr_id=info%3Asid%2FANDS&rft_id=info:doi10.25919/8mqs-h972&rft.title=OzWheat V1.0 SNP data assets&rft.identifier=https://doi.org/10.25919/8mqs-h972&rft.publisher=Commonwealth Scientific and Industrial Research Organisation&rft.description=Single nucleotide polymorphism genotypes for ~300 varieties from the OzWheat diversity panel generated with alternative platforms combined in a single matrix. Original platform source files are also provided. Transcript SNPs:63,222 SNP loci. 298 wheat lines. File=OzWheat_Transsnp_filtered_CS1.0_231130.hmp.txt90K Illumina SNP array:23362 SNP loci. 286 wheat lines from OzWheat panel 1 and 300 lines from OzWheat panel 2. File=V1_V2_commonSNP_merged.hmp40K Illumina SNP array:10670 SNP loci. 286 wheat lines. File=OW1_40K_filtered.hmp.txtDARTseq:56467 SNP loci. 282 wheat lines. File=Report_DW21-6152_SNP_mapping_2.csvCombined platform SNP - joins SNPs called from transcriptome data, 90K and 40K array and DARTseq. 115,260 SNP loci. 296 wheat lines. File=OzWheat_Transsnp40k90kDArT_filtered_CS1.0_alleleinfo_240102.hmp.txtKeeble-Gagnère G, Pasam R, Forrest KL, et al. Novel Design of Imputation-Enabled SNP Arrays for Breeding and Research Applications Supporting Multi-Species Hybridization. Front Plant Sci. 2021;12:756877. Published 2021 Dec 22. doi:10.3389/fpls.2021.756877Lineage: Transcript SNPs were generated in strategic investment projects OD-107742, OD-211556, OD-220968DARTseq SNPs were generated as part of Jess Hyles PhD project and funded by The University of Sydney40 and 90K data was generated in collaboration with AgVic under the GRDC DAV00127 project, and through OD-105738, OD-107742 and OD-209560.&rft.creator=Dillon, Shannon &rft.creator=Marquardt, Annelie &rft.creator=Andrew, Sam &rft.creator=Gock, Andrew &rft.creator=Ramm, Kerrie &rft.creator=Rathjen, Tina &rft.creator=Forrest, Kerrie &rft.creator=Hunt, James &rft.creator=Suchecki, Rad &rft.creator=Trevaskis, Ben &rft.creator=McNeil, Meredith &rft.creator=Hyles, Jessica &rft.date=2025&rft.edition=v16&rft_rights=Creative Commons Attribution-Noncommercial 4.0 Licence https://creativecommons.org/licenses/by-nc/4.0/&rft_rights=Access to the data is restricted&rft_rights=All Rights (including copyright) CSIRO 2022.&rft_subject=SNP&rft_subject=genotype&rft_subject=OzWheat&rft_subject=wheat&rft_subject=90K&rft_subject=40K&rft_subject=transcriptome&rft_subject=DartSeq&rft_subject=Crop and pasture improvement (incl. selection and breeding)&rft_subject=Crop and pasture production&rft_subject=AGRICULTURAL, VETERINARY AND FOOD SCIENCES&rft.type=dataset&rft.language=English Access the data
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Creative Commons Attribution-Noncommercial 4.0 Licence
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Access to the data is restricted

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Single nucleotide polymorphism genotypes for ~300 varieties from the OzWheat diversity panel generated with alternative platforms combined in a single matrix. Original platform source files are also provided.

Transcript SNPs:
63,222 SNP loci. 298 wheat lines.
File=OzWheat_Transsnp_filtered_CS1.0_231130.hmp.txt

90K Illumina SNP array:
23362 SNP loci. 286 wheat lines from OzWheat panel 1 and 300 lines from OzWheat panel 2.
File=V1_V2_commonSNP_merged.hmp

40K Illumina SNP array:
10670 SNP loci. 286 wheat lines.
File=OW1_40K_filtered.hmp.txt

DARTseq:
56467 SNP loci. 282 wheat lines.
File=Report_DW21-6152_SNP_mapping_2.csv

Combined platform SNP - joins SNPs called from transcriptome data, 90K and 40K array and DARTseq.
115,260 SNP loci. 296 wheat lines.
File=OzWheat_Transsnp40k90kDArT_filtered_CS1.0_alleleinfo_240102.hmp.txt

Keeble-Gagnère G, Pasam R, Forrest KL, et al. Novel Design of Imputation-Enabled SNP Arrays for Breeding and Research Applications Supporting Multi-Species Hybridization. Front Plant Sci. 2021;12:756877. Published 2021 Dec 22. doi:10.3389/fpls.2021.756877
Lineage: Transcript SNPs were generated in strategic investment projects OD-107742, OD-211556, OD-220968

DARTseq SNPs were generated as part of Jess Hyles PhD project and funded by The University of Sydney

40 and 90K data was generated in collaboration with AgVic under the GRDC DAV00127 project, and through OD-105738, OD-107742 and OD-209560.

Available: 2025-11-26

Data time period: 2020-01-01 to 2020-12-31

This dataset is part of a larger collection

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Subjects
40K | 90K | Agricultural, Veterinary and Food Sciences | Crop and Pasture Improvement (Incl. Selection and Breeding) | Crop and Pasture Production | DartSeq | OzWheat | SNP | genotype | transcriptome | wheat |

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Identifiers
ACN 633 798 857