KASP Assay Search

KASP Assay Search enables researchers to search a database of validated KASP markers and design new markers based on genomic comparisons for rice genotyping applications.

Key Features:

• Validated KASP Marker Database: Users can search 3,366 validated trait-specific KASP markers from a panel of 178 diverse rice varieties.
• Untested Design Database: Users can access more than one million so-far untested KASP designs.
• Multi-Reference Genome Search: Searches can be performed across three reference genomes including Nipponbare MSU7 and R498.
• Microsatellite Proximity Search: The tool includes designs in proximity to previously published microsatellite markers.
• Genomic Context Retrieval: Users retrieve target variations for 129 rice genomes plus their genomic locations with ±25 bp flanking sequences.
• Ambiguous Base Designs: The marker designs incorporate ambiguous (degenerate) bases to broaden applicability across diverse Oryza sativa genotypes.

Scientific Applications:

• Rice Genotyping: The tool supports genotyping applications in Oryza sativa using validated KASP markers.
• Population Structure Analysis: The validated marker panel resolves diversity panels into expected population groups.
• Breeding Program Support: Breeders can search for trait-specific markers at breeder-selected loci for diverse breeding applications.
• Functional Variant Genotyping: The database includes 98,238 predicted functional markers for applications requiring functional variant detection.

Methodology:

A bioinformatics pipeline compared 129 rice genomes from 89 countries with the indica reference genome R498 to generate approximately 1.6 million KASP designs for common variants; up to 5 KASP each for 1,024 breeder-selected loci were assayed in 178 diverse rice varieties to generate validated markers.