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.
See About to know how to prepare your input.
We have designed primers for the iSelect 90K chip and the Axiom 820k chip.
PolyMarker is the implementation of the pipeline described in:
Ricardo H. Ramirez-Gonzalez, Cristobal Uauy, Mario Caccamo; PolyMarker: A fast polyploid primer design pipeline, Bioinformatics, Volume 31, Issue 12, 15 June 2015, Pages 2038–2039. doi:10.1093/bioinformatics/btv069
Ramirez-Gonzalez, R. H., Segovia, V., Bird, N., Fenwick, P., Holdgate, S., Berry, S., Jack, P., Caccamo, M. and Uauy, C. (2015), RNA-Seq bulked segregant analysis enables the identification of high-resolution genetic markers for breeding in hexaploid wheat. Plant Biotechnol J, 13: 613–624. doi: 10.1111/pbi.12281