Assay design file including SNPs and the sequences of genotyping probes can downloaded here: 9K Assay design file
The 9K genotyping assay design was described in the following paper:
Cavanagh, C.R., Chao, S., Wang, S., Huang, B.E., Stephen, S., Kiani, S., Forrest, K., Saintenac, C., Brown-Guedira, G.L., Akhunova, A., See, D., Bai, G., Pumphrey, M., Tomar, L., Wong, D., Kong, S., Reynolds, M., da Silva, M.L., Bockelman, H., Talbert, L., et al. (2013). Genome-wide comparative diversity uncovers multiple targets of selection for improvement in hexaploid wheat landraces and cultivars. Proc. Natl. Acad. Sci. U. S. A. 110: 8057-62.
Assay design file including SNPs and the sequences of genotyping probes can downloaded here: 90K Assay design file
Table for conversion of genotype calls in AB format to nucleotide bases: AB_to_nucleotides
Genotype calling was performed using the GenomeStudio Polyploid Clustering Module v1.0 Software developed in collaboration with Illumina, Inc.
The design of the wheat 90K iSelect genotyping assay, the development of clustering algorithms and consensus map are described in the following paper:
About 23K SNP were aligned to the IWGSC reference version 1 genome. The coordinates can be found here.
S. Wang, D. Wong, K. Forrest, A. Allen, S. Chao, E. Huang, M. Maccaferri, S. Salvi, S. Milner, L. Cattivelli, A. M. Mastrangelo, A. Whan, S. Stephen, G. Barker, R. Wieseke, J. Plieske, IWGSC, M. Lillemo, D. Mather, R. Appels, R. Dolferus, G. Brown-Guedira, A. Korol, A. R. Akhunova, C. Feuillet, J. Salse, M. Morgante, C. Pozniak, M. Luo, J. Dvorak, M. Morell, J. Dubcovsky, M. Ganal, R. Tuberosa, C. Lawley, I. Mikoulitch, C. Cavanagh, K. J. Edwards, M. Hayden, E. Akhunov (2014). Characterization of polyploid wheat genomic diversity using a high-density 90,000 SNP array. Plant Biotechnology Journal 2014 Mar 20. doi: 10.1111/pbi.12183. [Epub ahead of print]
For more details, please contact Eduard Akhunov (eakhunov at k-state.edu) or Matt Hayden (matthew.hayden at depi.vic.gov.au).