The wheat 9K iSelect assay is available!
Preliminary results from the pilot 9000 SNP iSelect experiment: A pilot 9000 SNP Infinium assay was developed by USA/Australia collaborative project (PIs: Akhunov/Hayden). It includes SNPs discovered in transcriptomes generated from a set of 27 US and Australian lines. The assay is being used for genotyping a diverse set of tetraploid and hexaploid wheat lines and cultivars. Preliminary tests performed by S. Chao and M. Hayden showed that more than 90% of SNPs produce high-quality genotype calls with up to 65-70% being polymorphic in a diverse sample of U.S. and Australian cultivars with a minor allele frequency >0.05. These SNPs now are being placed on the genetic map using 4-way MAGIC (Colin Cavanagh) and SynOp mapping populations. We estimate that in these populations we can map up to 4000 SNPs.
Realizing the utility of this assay for wheat breeding we would like to make it accessible to researchers. If you want to use 9K iSelect for your own research you need to join our consortia by sending a request to E. Akhunov (firstname.lastname@example.org) with indication of the number of lines you have for genotyping. The consortia has one condition: the results obtained using the 9K iSelect assay can be published only after the major manuscript describing 9K assay design and SNP map will be published by the consortia. We are making significant efforts to have this data published in the nearest future.
You will be responsible for arranging the genotyping experiments with facilities that have access to Illumina genotyping platforms capable of processing Infinium assays.
However, before deciding to use this assay you should take into account the fact that the 9K iSelect includes only SNPs discovered in US and Australian cultivars. We are currently testing the distribution of these SNPs in other populations. Our group is using a set of homozygous and heterozygous controls to assess the performance of each SNP. The analysis of this data is underway and will be released as soon as it will become available. We are planning to present the first results during the coming ITMI meeting in Mexico (Mexico City, Mexico, September 5 - 9, 2011).
This work is a contribution to the efforts of the International Wheat SNP Working Group (IWSWG) to deliver advanced SNP genotyping platforms to the wheat research community.
US/Australia iSelect development team: Eduard Akhunov, Matt Hayden, Shiaoman Chao, Gina Brown-Guedira, Mark Sorrells, Deven See, Colin Cavanagh
9K iSelect design and genotyping:
USDA AFRI (E.A.)
Grains Research and Development Corporation (GRDC, Australia) (M.H.)
Pilot genotyping: Triticeae CAP (USDA, USA); Department of Primary Industries Victoria (Australia); CSIRO Food Future Flagship (Australia); From Seed to Pasta (AGER, Italy); KWS Lochow GMBH; DuPont-Pioneer; WestBred – Monsanto; CIMMYT.