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.

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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

Overview of project process

Depending on your requirements, your project may start at different stages of the workflow.

SeqSNP service project workflow

Turnaround time

Standard turnaround time for the service is 2 weeks from start of processing to data delivery. Please note that this does not include probe library design. Probe library design typically takes 4 to 6 weeks; it is therefore advisable to provide SNP sequences as early as possible to prevent delays.

Bespoke turnaround times are available on request. Please contact us to discuss this prior to commencing your project.

Related resources

Guidance notes: SeqSNP service guidance notes

Species list: Plant species list for service projects

Poster: SeqSNP: A massively parallel marker screening approach – high-speed and high-throughput genomic selection for plants and livestock

White paper: SeqSNP tGBS as alternative for array genotyping in routine breeding programs

Publication: Genomic prediction unifies animal and plant breeding programs to form platforms for biological discovery

Comprehensive sample submission guide: Tables summarising DNA or sample submission and related forms

Data sheet: stGBS – simplified, targeted genotyping by sequencing kits and services for high-throughput AgBio applications 

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Related products

Kits for in-house use

Library preparation kits for in-house use are also available.

Kits includes all reagents, buffers, enzymes, adaptors and oligos necessary for DNA fragmentation, multiplex adaptor ligation, probe annealing and extension and PCR amplification of final library.

Please enquire for more information or use the quote request form.


  • Lezzoni AF, McFerson J, Luby J, et al. RosBREED: bridging the chasm between discovery and application to enable DNA-informed breeding in rosaceous crops. Hortic Res 7, 177. Published 2020.
  • Steele K, Tulloch MQ, Burns M, Nader W. Developing KASP Markers for Identification of Basmati Rice Varieties. Food Anal. Methods 14, 663–673. Published 2021.
  • Bokore FE, Cuthbert RD, Hiebert CW, et al. Mapping stem rust resistance loci effective in Kenya in Canadian spring wheat (Triticum aestivum L.) lines ‘AAC Prevail’ and ‘BW961’. Canadian Journal of Plant Pathology 43:sup2, S263-S274, Published 2021.
  • Abu P, Badu-Apraku B, Ifie BE, et al. Genetic diversity and inter-trait relationship of tropical extra-early maturing quality protein maize inbred lines under low soil nitrogen stress. PLoS ONE 16(6): e0252506. Published 2021.