How KASP™ genotyping works

KASP™ (Kompetitive Allele Specific PCR) is a PCR-based genotyping technology that enables accurate bi-allelic discrimination of single nucleotide polymorphisms (SNPs) and insertion-deletion (InDel) markers. It is widely used in plant and animal breeding programmes to generate genetic data that supports marker-assisted selection, trait development and breeding decisions.

KASP chemistry uses competitive allele-specific PCR to distinguish between genetic variants. During amplification, allele-specific primers compete to bind to the target DNA sequence. Successful amplification occurs when a primer matches the target sequence, generating a fluorescent signal that identifies the genotype.

A standard KASP workflow includes four key components:

1. Assay mix:

   Contains two allele-specific forward primers and one common reverse primer. Each allele-specific primer contains a unique tail sequence that enables fluorescent signal generation during amplification.

2. Master mix:

   Contains the PCR reagents required for amplification and endpoint fluorescence detection.

3. Competitive amplification:

   Allele-specific primers compete during PCR. The resulting amplification pattern reflects the genetic variant present in the sample.

4. Endpoint detection:

   Fluorescence is measured using a compatible plate reader or qPCR instrument. Samples form clusters that correspond to homozygous and heterozygous genotypes, enabling straightforward visual interpretation of results.

KASP assay development and deployment

Breeding programmes often rely on previously published or proprietary genetic markers to track traits of interest. KASP genotyping assays can be developed from SNP and InDel marker information, enabling rapid deployment within existing breeding workflows.

KASP by Design services provide support throughout assay development, helping researchers convert markers into validated genotyping assays. This approach can reduce development time while helping teams achieve reliable assay performance.

Once developed, assays can be implemented across a range of project sizes, from small-scale research studies to large, high-throughput breeding operations. Flexible workflow options allow breeding programmes to scale genotyping capacity as project requirements evolve.

Key benefits include:

• Conversion of published SNP and InDel markers into genotyping assays
• Development of custom assays for proprietary breeding programmes
• Support for trait screening and marker-assisted selection
• Scalability from low-throughput to high-throughput operations
• Compatibility with manual and automated laboratory workflows

SNP and InDel genotyping for plant and animal breeding

Genetic markers play an important role in modern breeding programmes by helping researchers identify desirable traits more efficiently.

SNP genotyping

Single nucleotide polymorphisms (SNPs) are single base-pair differences within a DNA sequence. They are among the most commonly used genetic markers for trait discovery, parentage analysis and marker-assisted selection.

InDel genotyping

Insertion-deletion (InDel) markers identify small insertions or deletions within a DNA sequence. These markers can provide additional genetic information for breeding and genetic analysis programmes.

KASP technology supports accurate discrimination of:

• SNP markers
• InDel markers
• Homozygous genotypes
• Heterozygous genotypes

The resulting genotype data can help breeders make informed decisions when selecting breeding lines, evaluating germplasm and monitoring trait inheritance across populations

Marker-assisted selection using PCR genotyping

Marker-assisted selection enables breeders to use genetic information to identify desirable traits earlier in the breeding process. Instead of relying solely on observable characteristics, breeders can use genotyping data to screen populations and select individuals carrying target genetic markers.

PCR genotyping technologies such as KASP help accelerate selection decisions by providing reliable genetic information for breeding programmes. This approach can improve efficiency, reduce development timelines and support more informed decision-making.

Common applications include:

• Disease resistance breeding
• Yield improvement programmes
• Quality trait selection
• Germplasm screening
• Parentage verification
• Breeding population management

By integrating genetic data into breeding strategies, organisations can make more effective selections throughout programme development.

High-throughput genotyping workflows

Breeding programmes vary significantly in size, from small research studies to large-scale commercial operations. KASP workflows are designed to support a range of throughput requirements, allowing organisations to choose the most appropriate format for their project.

Supported formats include:

• 96-well plates
• 384-well plates
• 1536-well plates
• Automated genotyping workflows

As sample volumes increase, automated liquid handling and high-throughput platforms can help laboratories improve efficiency, reduce manual intervention and maintain consistent data quality.

The ability to scale genotyping operations allows researchers and breeding organisations to expand projects without changing underlying assay chemistry.

PCR genotyping instrument compatibility

Introducing new genotyping technologies should not require major changes to existing laboratory infrastructure. KASP assays are designed to work with a wide range of fluorescence detection platforms, helping organisations implement genotyping workflows using existing equipment where appropriate.

KASP assays are compatible with:

• Most FRET-capable fluorescence plate readers
• Many qPCR instruments
• IntelliQube™ platforms
• Nexar™ automation systems
• SNPline™ genotyping workflows

This flexibility enables laboratories to integrate PCR-based genotyping into existing operations while supporting future expansion and automation requirements. Breeding programmes can implement genotyping workflows that align with their throughput requirements, budget and operational goals.

Benefits of KASP technology for agrigenomics

KASP technology helps breeding programmes generate reliable genotyping data while scaling workflows from research projects to high-throughput operations. It supports a broad range of plant and animal breeding applications while allowing organisations to deploy only the markers relevant to their programme.

Benefits include:

• Accurate SNP and InDel genotyping
• Flexible marker selection
• Support for marker-assisted selection
• Scalable throughput options
• Cost-effective workflow implementation
• Compatibility with existing laboratory infrastructure
• Support for custom assay development

From trait discovery and germplasm screening to large-scale breeding programmes, KASP enables researchers and breeders to generate the genetic insights needed to advance modern agrigenomics programmes.