Genotyping vs sequencing: Which approach should
you choose?

Genotyping and sequencing are complementary technologies that address different objectives within breeding and research programmes. Genotyping focuses on analysing known genetic markers at specific loci, making it suitable for marker-assisted selection, genomic selection, quality control and parentage testing. Sequencing is commonly used for genotyping, SNP discovery, genome characterisation and marker identification, depending on programme objectives. Many breeding programmes use sequencing for marker discovery before transitioning validated markers into routine SNP genotyping workflows. Organisations evaluating genomic analysis strategies can explore both NGS for Agrigenomics and PCR for Agrigenomics solutions to identify the most suitable approach.

SNP genotyping explained

SNP genotyping is one of the most widely used approaches for analysing genetic variation in breeding and genomics programmes. By examining single nucleotide polymorphisms (SNPs), researchers can identify alleles associated with traits of interest and apply this information to marker-assisted selection, genomic prediction, trait mapping and parentage analysis. SNP markers are abundant throughout plant and animal genomes and can be incorporated into scalable screening programmes supporting both research and commercial breeding objectives.

Common genetic marker types

Genotyping methods comparison

Selecting the appropriate genotyping platform depends on marker density requirements, sample volumes, application objectives and programme scale. LGC Biosearch Technologies supports multiple approaches ranging from targeted SNP genotyping to genome-wide discovery workflows, enabling organisations to choose technologies aligned with their research and breeding goals.

KASP™ genotyping technology

KASP™ is an allele-specific PCR genotyping chemistry used for targeted SNP genotyping across plant, animal and research applications. The technology supports marker-assisted selection, marker-assisted backcrossing, parentage testing and quality assurance workflows. KASP genotyping enables flexible assay deployment and scalable SNP screening capabilities for breeding programmes operating across different throughput requirements. Users interested in implementing KASP workflows can also explore complementary PCR for Agrigenomics and Automation Instruments solutions.

Applications of KASP™ genotyping include:

• Marker-assisted selection (MAS)
• Marker-assisted backcrossing (MABC)
• Parentage testing
• Quality control screening
• Genomic breeding programmes
• Trait validation studies

From marker discovery to validated assays

Genotyping programmes often begin with marker discovery and progress towards routine assay deployment. Sequencing technologies can identify candidate variants associated with traits of interest, after which validated markers can be incorporated into targeted genotyping assays for large-scale screening. This workflow enables breeding programmes to move from discovery research to practical implementation while maintaining continuity across genomic workflows. High-quality sample preparation is fundamental to success, making Plant and Animal DNA Extraction an important first step in many programmes.

Typical workflow includes:

• DNA extraction
• Genome characterisation or SNP discovery
• Marker validation
• Panel validation
• Routine SNP genotyping

• Marker-assisted breeding decisions

Marker-assisted selection in plant and animal breeding

Marker-assisted selection (MAS) uses genetic markers to track the inheritance of target alleles and support breeding decisions. By identifying favourable genetic profiles before phenotypic evaluation is complete, breeders can focus resources on promising candidates and streamline breeding programmes. MAS is frequently deployed alongside genomic selection, trait mapping and marker-assisted backcrossing strategies to support crop and animal improvement programmes.

Common applications include:

• Wheat breeding
• Poultry genomics
• Parentage analysis
• Quality assurance testing
• Genomic selection programmes

Choosing the right genotyping approach

1. Genotyping for large breeding programmes: The most appropriate genotyping approach depends on sample numbers, marker density requirements and programme objectives. Targeted SNP genotyping methods such as KASP™ are commonly used for routine screening, while sequencing-based workflows support higher marker density and marker discovery applications.
2. Genotyping for genomic selection: Genotyping plays an important role in genomic breeding programmes by enabling the analysis of genetic markers associated with traits of interest. Both PCR-based and sequencing-based technologies can support genomic selection strategies depending on programme goals and data requirements.
3. DNA quality considerations: DNA requirements vary according to the technology used. KASP™ genotyping workflows can support lower-quality or crude DNA samples, while targeted sequencing and whole genome sequencing applications generally require medium- to high-quality purified DNA. Organisations seeking to optimise sample preparation can explore Plant and Animal DNA Extraction solutions.
4. Factors that influence genotyping workflow selection: Workflow selection is influenced by sample volume, marker density, DNA quality requirements, assay requirements and programme objectives. These factors help determine whether targeted SNP genotyping or sequencing-based approaches are the most appropriate solution.
5. Scaling genotyping programmes: As breeding programmes grow, requirements for throughput, efficiency and standardisation often increase. Integrating genotyping technologies with Automation Instruments can help laboratories support higher sample volumes and streamline workflow management.