Genotyping by sequencing (GBS) is widely used in plant and animal breeding programmes to support single nucleotide polymorphism (SNP) discovery, marker development and genomic analysis. Approaches range from restriction enzyme-based genome complexity reduction methods to hybridization- and amplicon-based targeted genotyping by sequencing that focus sequencing on selected markers relevant to breeding objectives. Based on programme scale, marker density and data requirements, breeding teams can use different sequencing strategies to support genomic selection, trait mapping and population studies.
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Genotyping by sequencing overview
Targeted and genome-wide genotyping approaches for agrigenomics
What is GBS?
Genotyping by sequencing (GBS) combines genome complexity reduction, sequencing and marker identification to generate genotypic information across populations. Restriction enzyme-based methods can analyse many samples simultaneously and are commonly used for SNP discovery and genome-wide marker generation, whereas targeted genotyping by sequencing focuses on predefined markers and panels ranging from hundreds to thousands of targets.
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How GBS works
Genotyping by sequencing workflows typically involve either targeted probe-based amplification or restriction enzyme digestion, sample barcoding, library pooling, sequencing and variant calling. Multiplexing allows many samples to be processed together while maintaining sample identity.
Enzymatic vs targeted
Restriction enzyme-based GBS focuses on genome complexity reduction and marker discovery. Targeted GBS directs sequencing towards defined genomic targets, supporting predictable marker assessment and targeted genotyping applications.
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Amplicon sequencing
Amplicon sequencing approaches such as Amp-Seq One support targeted genotyping applications, while Flex-Seq™ and Capture-Seq provide additional targeted sequencing options for programmes requiring higher marker densities or broader genomic coverage and capability to assess complex genomes.
How LGC helps
From plant breeding programmes focused on accelerating genetic gain in livestock and aquaculture breeding programmes advancing genomic selection and trait improvement.
Who we support
Plant and animal breeding companies and institutes who rely on genomic technologies to improve selection accuracy, accelerate breeding cycles and develop new varieties or populations with desirable traits. These organisations use genotyping and sequencing data to support marker-assisted selection, genomic prediction, diversity analysis and trait discovery across a wide range of species.
How we support
We provide scalable next-generation sequencing (NGS) solutions that generate reliable, actionable genomic data. Our solutions are flexible and support applications ranging from targeted genotyping and genomic selection to marker discovery and population studies, while balancing marker density, throughput, turnaround time and cost-effectiveness.
How agrigenomics connects
Applications
Explore applications where genotyping and sequencing technologies support genomic selection, trait discovery, population analysis and crop improvement.
Technologies
The genotyping and sequencing approaches that support agrigenomics workflows, from targeted marker analysis to genome-wide discovery.
Featured Resources
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Guiding Réunion harrier conservation with population genomics
Human activity is driving sharp reductions in the population sizes of many species worldwide. These anthropogenic bottlenecks erode genetic diversity and are contributing to what many scientists now describe as a mass extinction event. 1
Why breeding programmes choose LGC for genotyping and sequencing
Delivering flexible NGS solutions that support agrigenomics programmes.
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Global impact
37,000+
Customers supported worldwide
Reach
144
Countries served globally
-Dr. Sydney Reese
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Frequently asked questions
What is targeted GBS?
Targeted GBS focuses sequencing on predefined genomic targets, unlike restriction enzyme-based GBS approaches that rely on genome complexity reduction.
Can GBS work without a reference genome?
GBS is commonly used for SNP discovery when a reference genome sequence is unavailable.
When should I use amplicon sequencing?
Amplicon sequencing is suitable for targeted genotyping applications where specific markers are being analysed.
What applications are supported?
Applications include genomic selection, genome-wide association studies (GWAS), marker discovery, haplotyping, parentage testing and marker assisted selection (MAS).
What sample types are accepted for laboratory services?
DNA quality requirements vary by technology, from crude preparations through to purified DNA.
What turnaround times are available?
Service turnaround times vary by technology and project requirements.
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Genotyping experts for breeding programmes
Whether you're evaluating genotyping by sequencing, targeted GBS or amplicon sequencing approaches, our experts can help identify the right strategy for your breeding programme, genomic selection objectives and data requirements.
Genotyping method comparison
Compare genotyping technologies according to programme objectives, marker density and data requirements.
Genotyping method selection table
Method | Primary Use | Marker Density |
|---|---|---|
KASP | Endpoint genotyping | Hundreds |
Amp-Seq One | Amplicon-based tGBS | Thousands |
Flex-Seq™ | Hybridisation-based tGBS | Tens of thousands |
Capture-Seq | Capture-based tGBS | Hundreds of thousands |
Restriction Enzyme GBS | Marker discovery | Tens of thousands |
Whole Genome / Skim Sequencing | Genome exploration | Whole genome |