PolyMarker

Polymarker (often capitalized PolyMarker) is a web-based design tool used in genomics to create SNP-based genetic markers, with emphasis on polyploid species. The program automates the design of allele-specific PCR primers for SNP genotyping, commonly aligning with platforms such as KASP. It takes as input a reference genome, a list of SNPs (for example in VCF format), and optional gene annotations, and produces primer sequences along with associated metadata, such as target coordinates, predicted amplicon size, and recommended assay configuration.

To account for polyploid complexity, Polymarker evaluates primer specificity against the reference genome, flagging potential cross-amplification from homoeologous or paralogous sequences. The output is suited for downstream genotyping workflows and high-throughput marker development.

Applications include plant genetics and breeding, where researchers design SNP markers to track traits in polyploid crops (for example, bread wheat, canola, and other Brassica species). The tool aims to streamline marker design and reduce the trial-and-error work involved in primer selection, enabling rapid expansion of genotyping panels.

Limitations include dependence on the quality and completeness of the reference genome, possible challenges with very similar sequences, and the necessity of experimental validation to confirm primer performance on real samples. Polymarker is typically accessed via a web interface hosted by a participating institution and may require registration or local installation for large-scale use.