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Genome-specific primer design with PolyMarker

Genome-specific primer design with PolyMarker

On 28 October 2020, the IWGSC organized a webinar entitled "Genome-specific primer design with PolyMarker" presented by Ricardo Ramirez-Gonzalez (John Innes Centre, UK)

Click on the image to watch a recording of the webinar (YouTube external link)


The design of genetic markers is of particular relevance in wheat breeding programs. Traditional primer design tools, such as primer3, are designed to test the viability of a primer on a target sequence. However, in polyploids with repetitive regions an extra step of validation is required to ensure the specificity of the primers. To ensure uniqueness across the three genomes in Hexaploid wheat, PolyMarker is a pipeline that first, finds the homoeolog regions to the target sequence; then, it produces a local alignment and selects the a genome-specific primer pair; and finally it validates the viability of the primer candidates. The online version of PolyMarker ( PolyMarker.info ) is focused on SNP markers for the KASP protocol. However, the command line version has options to design primers of different sizes for different applications. This webinar (i) explains the principles of primer design in polyploids; (ii) explores applications of PolyMarker, including SNP markers, validation of deletions and PCR markers of an arbitrary size; and (iii) discuss genotyping on the context.


Ricardo H. Ramirez-Gonzalez, Postdoctoral Scientist, John Innes Centre, UK


Ramirez-Gonzalez, R. H., Uauy, C., & Caccamo, M. (2015). PolyMarker: A fast polyploid primer design pipeline. Bioinformatics, 2–3. doi:10.1093/bioinformatics/btv069