Wheat 820K and 35K Axiom® Arrays
The Wheat Improvement Strategic Programme (WISP) is pleased to release the information associated with both the 820K and 35K Axiom® arrays.
The Axiom® wheat HD Genotyping Array (Affymetrix product IDs 550491 and 550492 for the two component arrays; axiom_wheat_hd_genotyping_array_datasheet.pdf ) is a high-density array containing 819 571 exome-captured SNP sequences derived from hexaploid wheat accessions, including both elite and landrace accessions, diploid and tetraploid progenitor accessions and wheat relatives. The Axiom® wheat HD Genotyping Array is designed to characterise a range of wheat-related species, and in particular to identify and track introgressions in hexaploid wheat.
High-density SNP genotyping array for hexaploid wheat and its secondary and tertiary gene pool. Plant Biotechnology Journal. Click here to download .pdf file.
The Breeders' 35K Axiom® array (Affymetrix product ID 550524) contains 35,143 SNPs selected to be informative across a wide range of hexaploid wheat accessions. This 384-sample format array is a cost effective and efficient system for screening large numbers of lines. The array has been used to screen a large global collection of elite and landrace varieties including hexaploid and tetraploid accessions and the publicly available dataset (below) is regularly updated.
Characterisation of a Wheat Breeders’ Array suitable for high throughput SNP genotyping of global accessions of hexaploid bread wheat (Triticum aestivium). Plant Biotechnology Journal. Click here to download .pdf file.
35K Axiom® Array dataLast updated 31/10/2016 - the Axiom 35k Breeders' Array has now been used to screen 2119 lines including the WISP Breeders' diversity toolkit lines from the WISP landrace pillar and the WISP Synthetics pillar.
- Axiom® 35k Breeders' array probe set. Details of array content including overlap with KASP and iSelect assays.
- Breeders' 35K Axiom® genotyping data. Genotype scoring was performed in Affymetrix Genotyping Console using recommended QC metrics (0.82 DQC, 97 QC call rate).
- List of lines screened
- Genetic mapping data from five populations, including a consensus genetic map.
820K Axiom® Array data
Please note that the 820K data set is very large and cannot easily be opened and handled in Microsoft Excel format. Thus we are making the data available in two different formats:
- A) For those with bioinformatics support, the whole file may be obtained as a single zipped tab separated txt file; it is best not to try to open this in Excel! Please click here to download.
- B) Alternatively, the file has been divided into five equal sized chunks (files A - E), each containing 164,000 markers. These 'chunks' have also been saved as zipped tab separated txt files and may be opened from within Excel. Please click the each file, A - E, in turn File A, File B, File C, File D, File E to download.
To open/download the 820K wheat Axiom® array probe set, please click here.
genotype calls were assigned as follows:
0 = AA, 1 = AB, 2 = BB, -1 = No call
Scoring on both arrays
Where two samples from different sources share the same name, they are distinguished by the addition of the supplier's initials as a suffix.
Please note that for convenience all of our marker data sets are scored as AA, AB or AB, however, due to the nature of the three different genotyping platforms and the polyploidy nature of the wheat genome, these designations do not necessarily represent the two homozygote and the one heterozygote states, instead they simply represent the position of the clusters against the X and Y axis defined by the software packages. For further information we recommended that you contact either illumina (iSelect), LGC (KASP) or Affymetrix (Axiom).
Finally, one last plea, like all of our previous data, WISP is making its data public so that it can get into the hands of those who can use it best; the breeders and researchers. If you are one of the groups which have made use of WISP data, including BS and BA markers, please do acknowledge the source of the probes when you present your results at conferences or in manuscripts.
VCF file download
A VCF file for the axiom 820K SNPs can be downloaded from here.
Maintained by Mark Winfield.