Wheat 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 (both elite lines and landrace accessions), diploid and tetraploid progenitors 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 wheati. Details of the 820K Array can be found in the article High-density SNP genotyping array for hexaploid wheat and its secondary and tertiary gene pool.
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 data
The Axiom 35k Breeders' Array has been used to screen 6,144 lines. Download options:
- Extract genotypes for a particular variety on the 35K breeders array.
- 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.
Axiom® Wheat Relatives Array data
- Extract genotypes for a particular variety on the 35K wheat relatives array.
- Axiom® Wheat relatives array probe set. Details of array content, including probes and sequences.
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.
- C) To extract data for individual varieties on the 820K array click here.
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 For convenience, all of marker data sets are scored AA, AB or BB. These designations do not necessarily represent the two homozygote and one heterozygote states; they simply represent the position of the clusters along the X and Y axes defined by the software packages provided by the various manufacturers. For further information we recommended that you contact illumina (iSelect), LGC (KASP) or Affymetrix (Axiom).
VCF file download
A VCF file for the axiom 820K SNPs can be downloaded here.
Maintained by Mark Winfield.