PolyMarker is an automated bioinformatics pipeline for SNP assay development which increases the probability of generating homoeologue-specific assays for polyploid species. PolyMarker generates a multiple alignment between the target SNP sequence and the selected reference genome (from the drop off menu in green below). It then generates a mask with informative polymorphic positions between homoeologs which are highlighted with respect to the target genome.
See About to know how to prepare your input. For wheat, we have designed primers for the iSelect 90K chip and the Axiom 820k chip.
If your request is terminated due a timeout, try with less markers and make sure the SNPs are not in low complexity regions.