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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.

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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