Agrigenomics
Genome-wide genotyping, beyond the chip.
Low-pass whole-genome sequencing with imputation gives breeders and researchers a genome-wide marker set at array-like cost — but without a fixed panel, locked to one species or one vendor. One workflow, any species with a reference.
How it works
Sparse sequencing, dense genotypes
We sequence each animal or plant at low coverage — typically 0.5–2× — then statistically impute genotypes against a reference panel. The result is a dataset equivalent to, and often richer than, a SNP array: millions of genotyped positions, including rare and breed-specific variants that fixed chips never see.
With an adequate reference panel, imputation accuracy for common variants is comparable to a high-density chip — and the same NGS workflow adapts to a new breed or a new species without redesigning hardware.
Comparison
Low-pass WGS vs SNP arrays
Arrays were a breakthrough — but a fixed panel is, by definition, blind to anything not on it. Here is the honest trade-off.
| Criterion | SNP chip | Low-pass WGS |
|---|---|---|
| Genomic coverage | Fixed: 50K–800K predefined SNPs | Genome-wide after imputation |
| Novel / rare variants | Not on the panel → invisible | Detected |
| Copy-number & structural | Limited | Genome-wide |
| New breed / population | Custom array redesign | Reference-panel update only |
| Cross-species | One chip per species | One workflow, any reference |
| Runs of homozygosity (ROH) | Panel-limited | Genome-wide |
| Vendor lock-in | Tied to array catalogue | Vendor-agnostic short read |
| Re-analysis | Static dataset | Raw reads re-analysable later |
| Imputation accuracy (common variants) | Reference ~0.97 vs HD | ~0.95–0.98 with a good panel |
Service portfolio
What we deliver for breeding & research
Genomic breeding values
Genome-wide SNP data for GEBV estimation in cattle, sheep, pig and poultry, with integration into national or international reference populations.
Parentage & pedigree
Definitive parentage and pedigree reconstruction from genome-wide markers, including where existing chip data is missing or insufficient.
Inbreeding & ROH
Genome-wide runs-of-homozygosity mapping for inbreeding management in closed breeding populations.
Trait & disease GWAS
Association studies for producer-defined phenotypes — identifying protective or risk alleles directly from sequence.
Population genomics
Genetic-diversity indices, admixture and conservation genomics for rare breeds and biodiversity programmes.
Crop genomics
Genotyping-by-sequencing and low-pass WGS for marker-assisted selection in wheat, maize, soybean and specialty crops.
Species
Where it works
Any species with a reference genome. Aquaculture and non-reference breeds — under-served by commercial chips — often benefit most.
Deliverables
What you receive
- Imputed genotype matrix (VCF / breeder-friendly formats).
- GEBV, parentage, ROH or GWAS outputs, as commissioned.
- Per-sample QC and imputation-quality metrics.
- Reference panel and pipeline versions documented.
- Archived raw reads, re-analysable as panels improve.
Questions
Agrigenomics FAQ
Is imputed low-pass data accurate enough for breeding values?
For common variants, lpWGS at around 1× with a well-constructed reference panel reaches accuracy comparable to high-density chips, and additionally captures low-frequency variants that chips miss. Accuracy depends on panel quality and species — we will be specific for yours.
Can you work with my existing chip data or reference population?
Yes. We can integrate with national or international reference populations and bridge to prior array datasets where appropriate.
What does it cost per sample?
Cost falls with scale and is competitive with array genotyping at volume. Send your species and expected sample numbers and we will quote precisely.
What if there is no good reference panel for my population?
We will tell you honestly. In some cases building or extending a panel is the right first step; in others an array may still be the pragmatic choice for now.
Genotyping a herd, flock or breeding line?
Tell us the species, sample numbers and what you need to estimate. We will propose coverage, reference strategy, deliverables and price.