What is Genotyping by Sequencing?
Genotyping by Sequencing, also known as GBS, is a powerful genetic screening method for discovering single nucleotide polymorphisms (SNPs). Traditional GBS utilizes restriction enzymes to reduce whole genomes into small fragments which are then amplified by PCR and sequenced on short-read sequencing platforms.
What is Molecular (Plant or Animal) Breeding?
Molecular breeding (e.g. plant or animal breeding) utilizes DNA markers (SNPs) that are tightly linked to phenotypic traits to assist in genomic selection to deliver improved plant and animal species for agricultural use. As major drivers like population growth, urbanization and economic development feed into an ever-complex agricultural landscape, agricultural genomics has taken a central role to offer sustainable solutions for the global food challenge.
Bridging the gap between low-plex PCR SNP assays and high-density arrays
Among the many SNP genotyping platforms, such as low-plex PCR assay and high-density array-based methods, Next-Generation Sequencing (NGS) has proven to be an exceptional tool for the discovery, validation, and assessment of genetic markers. NGS offers high multiplex levels, robust call rates, and an economical approach to genotyping large numbers of SNPs and samples. Targeted genotyping by sequencing (GBS) can focus on thousands of markers to provide a cost-effective, high-throughput genotyping solution that is customizable, flexible, and scalable.
| Low-Plex qPCR | AgriType 2.0 Amplicon Sequencing | High-Density Array | |
|---|---|---|---|
| # of SNPs | Low | Up to 7,000 | 5,000 - 50,000 |
| # of Samples | High | High | Low |
Some of the key genotyping by sequencing plant (plant genotyping) and animal molecular breeding applications and genotyping methods include:
- Marker-assisted selection (MAS)
- Genomic selection (GS)
- Trait mapping
- Quantitative trait locus (QTL) screening
- Marker-assisted backcrossing (MABC)
Learn more about genotyping by sequencing
Cost-Effective Solution to Accelerate Molecular Breeding
The AgriType Targeted Genotyping by Sequencing Solution is designed and developed to address large-scale genotyping projects in agrigenomics (the application of genomics in the field of agriculture). The AgriType solution is powered by an advanced primer design algorithm and an efficient ultra-high multiplex PCR-based target enrichment chemistry. AgriType genotyping by sequencing provides a cost-effective solution to construct NGS libraries to quickly and efficiently screen hundreds to tens of thousands of markers of interest to accelerate genotyping studies in fields such as aquaculture, livestock farming, and seed breeding.
- Scalable High-Throughput Genotyping System. Target thousands of relevant markers in the same assay.
- Fast Turnaround Time. Get custom assays delivered in 4 to 6 weeks. Use AgriType genotyping solution to accelerate your large-scale molecular breeding programs. Our PhD-level expert scientists are here to provide speedy and comprehensive support throughout the design, ordering, and technology adoption process, including excellent after-sales technical support.
- Cost-Effective Solution. Process thousands of samples at a time on Illumina® platform.
- Minimizes consumable consumption. This single-plate workflow reduces consumable cost and loss of material from material transfer.
- Streamlined, Automation-Friendly Workflow. Generate sequencing-ready libraries in just 3 hours using a simple, three-step protocol that can be easily automated.
- High-Quality, Reproducible Results. Prepare high-quality NGS libraries with high marker call rates and efficient use of sequencing reads.
Learn more about molecular breeding
How Does Genotyping by Sequencing Work?
The AgriType 2.0* genotyping by sequencing solution has been optimized to accommodate higher-throughput needs and offers a streamlined workflow that is easily automated in both 96 and 384 well plates. The multiplex PCR-based protocol can be completed in just 3 hours, with very little hands-on-time of 25 minutes via a simple multiplexing PCR followed by an indexing PCR.
DNA Purification and QC
1.Multiplex PCR
2. Dilution Step
3. Indexing PCR
Quality Control
Sequencing
Data Analysis
AgriType 2.0* Target Enrichment and Library Preparation
3-5 hours of total assay time, 20 minutes of hands-on time
*Product in development. Contact your local sales rep to learn more.
High-Quality AgriType NGS Panels for All Panel Sizes
AgriType panels show consistently superior sequencing specifications, accommodating a wide gamut of panel size, to meet all your research needs. AgriType 2.0 offers detection of up to 7000 targets in a single panel.
| Amplicons per reaction | Uniformity (0.2x Mean Coverage) | % Mapping Rate | % On-Target Rate |
|---|---|---|---|
| 15 | 100% | 98.8% | 98.9% |
| 109 | 100% | 96.2% | 99.2% |
| 200 | 99.5% | 97.2% | 96.8% |
| 600 | 99.5% | 99.0% | 97.5% |
| 1500 | 98.8% | 99.7% | 96.4% |
| Panel Size | Uniformity (%) | % Mapping Rate | % On Target Rate |
|---|---|---|---|
| 2550 (Cotton) | 94.57 | 99.87 | 88.47 |
| 436 (Tomato) | 96.75 | 97.60 | 99.38 |
| 6808 (Soybean) | 81.245 | 99.935 | 95.06 |
| 200 (Corn) | 86.67 | 93.67 | 97.60 |
Genotyping By Sequencing: Frequently Asked Questions
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