PolyMarker is an automated bioinformatics pipeline for SNP assay development which increases the probability of generating homoeologue-specific assays for polyploid wheat. PolyMarker generates a multiple alignment between the target SNP sequence and the IWGSC chromosome survey sequences (IWGSC, 2014 ) for each of the three wheat genomes. It then generates a mask with informative positions which are highlighted with respect to the target genome.
We have designed primers for the iSelect 90K chip and the Axiom 820k chip.
PolyMarker is the implementation of the pipeline described in:
Ramirez-Gonzalez R.H., Segovia V., Bird N., Fenwick P., Holdgate S., Berry S., Jack P., Caccamo M. and Uauy C. (2014) RNA-Seq bulked segregant analysis enables the identification of high-resolution genetic markers for breeding in hexaploid wheat. Plant Biotechnol. J., doi: 10.1111/pbi.12281
Ramirez-Gonzalez, R.H., Uauy, C. and Caccamo, M. (2015) PolyMarker: A fast polyploid primer design pipeline. Bioinformatics. In press. doi:10.1093/bioinformatics/btv069
See http://polymarker.tgac.ac.uk/ for more details.