SeqSNP™ is the targeted genotyping by sequencing service that accelerates plant and animal breeding programmes. Screen hundreds to 10,000+ markers while still being cost-effective on an industrial scale. We’ve worked together with partners in the plant, livestock and aquaculture industries to ensure SeqSNP meets cost, time, and flexibility requirements to work in real world breeding programmes. We offer SeqSNP as part of an all-inclusive package which includes a BioArk sampling kit for plants and aquaculture, DNA extraction, and targeted sequencing with SeqSNP.
SeqSNP is highly suited to the following key breeding applications:
- Genomic selection/genomic prediction
- Marker assisted selection / breeding (MAS/MAB)
- Marker assisted back crossing (MABC)
- QTL screening
- Trait mapping
SeqSNP explained: A massively parallel marker screening approach for high-throughput genomic selection.
SeqSNP advantages
- Faster turnaround times. Ship your samples to our US or Europe sites.
- Targeted genotyping by sequencing of thousands of markers. Optimal for 100’s up to 10,000+ markers. Broad range allows standardisation of different species on the same technology for data comparability.
- Cost reduction. Efficient laboratory processes and enrichment chemistry ensure low processing costs.
- Minimal setup costs. Allows a low and transparent all-inclusive cost per sample model.
- Flexible marker sets. Allows batches of samples to be genotyped on variable marker sets, with the freedom to add additional assays even at late stages of the project.
- Convert to high-throughput assays. Easy conversion of markers to KASP™ or BHQ™ dual-labelled probe assays, both compatible for high-throughput processes.
- De-novo variant detection in target SNP region.*
* Please discuss the options with your project manager prior to the start of your project.
The right kind of collaboration brings you long-term success.
Included in your SeqSNP service
SeqSNP does not require the high setup costs associated with, for example, array genotyping. Pricing includes all the services listed in the table below and full project quotations are available on request.
Pricing and conditions may vary depending on the technical requirements for specific organisms. Please enquire for a free-of-charge consultation with our sequencing specialists.
| Service | Specification |
|---|---|
| Dedicated project management support | |
| BioArk Sample Collection Kit | Included (for leaf, seeds and fish) |
| DNA extraction from human, animal or plant samples | Extraction from non-plant samples is included at a competitive fixed fee per sample |
| Probe design and probe library generation (bioinformatics and laboratory) | Assay design using customer-provided SNP sequence information |
| Library preparation and next generation sequencing (laboratory) | Sample processing and Illumina NGS run |
| Analysis of NGS reads (bioinformatics) | Scored genotyping data provided as standard, raw sequence data (FASTQ format) available on request |
Not included in the service
- Statistics or breeding consultancy
Key considerations
SeqSNP is available for all species. Sample types and formats that are accepted are described in the guidance notes, other sample types can usually be accepted but additional costs may apply. Any sample number can be processed but a minimum of 192 samples is charged.
SNP markers can be individually selected at the start of the project, with the flexibility to add additional markers during the project, please note that this will have time and cost implications. Please inform us at the earliest possibility if you may want to add markers or re-use oligo libraries in the future.
For higher sample number projects, turnaround time and availability of additional services may vary. We would be happy to discuss your requirements and deliver a bespoke solution to meet your needs.
Terms additional to our standard terms and conditions apply. Please see the guidance notes for more details.
Don't just take our word for it
“We worked with LGC to dissect the genetic diversity and population structure of our newly developed tropical extra-early quality protein maize (QPM) inbred lines for enhanced heterosis of grain yield and other traits under low-soil nitrogen condition in Africa. The SeqSNP genotyping platform also enabled us to identify 15 SNP markers that had significant association with low-soil nitrogen traits, which would be further validated for Marker-assisted selection (MAS) breeding in the West Africa Centre for Crop Improvement (WACCI) maize breeding program. We used the SeqSNP service to develop 2500 SNPs for 160 inbred lines for maize breeding at WACCI. The services were cost-effective and provided us with high quality data which was delivered to us within six weeks. The SeqSNP project had a remarkable impact on our breeding program because it accelerated the selection of inbred lines for high heterosis in hybrid development for low soil nitrogen stress in Africa. ”
-Dr. Pearl Abu, West Africa Centre for Crop Improvement (WACCI) University of Ghana, West Africa
