# Genotyping: what a DNA test can and can't prove

> A DNA test can reliably show whether two samples are the same genotype, rule out a claimed parent (exclusion), support a parent-child relationship when both parents are sampled, predict sex and chemotype class from seedlings, and place a plant on a map of genetic groups. It cannot prove a 40-year-old pedigree from a name, measure THC %, tell you a plant's 'indica percentage', or guarantee how it will grow.

- Canonical: https://genetixbay.com/knowledge/breeding/genotyping-what-tests-prove.html
- Category: Breeding · Level: Breeder
- Evidence: Supported · Status: Draft: awaiting expert review
- Stage: Any stage · Systems: Any system
- Updated: 2026-10-31 · Licence: CC BY-SA 4.0 (https://creativecommons.org/licenses/by-sa/4.0/), attribute "GenetixBay Knowledge Base (genetixbay.com/knowledge)"

## Questions and answers

**Can a DNA test prove my strain's lineage?** A DNA test can support a cannabis strain's lineage only when the claimed mother, the claimed father and several offspring are all sampled, and close relatives are ruled out. Without the parents, DNA can exclude a claimed parent but not confirm one. It cannot prove an old story attached to a name unless there is a documented reference sample to compare.

**Can genetics tests tell if two clones are the same?** Yes, genetic tests can tell whether two cannabis clones are the same [genotype](https://genetixbay.com/knowledge/glossary/genotype.md), provided the lab reads enough markers. Thousands of SNPs give far better resolution than a handful of microsatellites. Expect tiny differences from somatic mutation and genotyping error, and ask the lab for its error rate and replicate data before trusting a match.

**What does a cannabis genotype report show?** A cannabis genotype report shows the plant's readings at many DNA positions (SNPs or microsatellites) and how they compare with other samples, ideally as identity-by-state or kinship values. It can also report validated trait markers for sex, [chemotype](https://genetixbay.com/knowledge/glossary/chemotype.md) class and some flowering genes. A 'match' is only as good as the reference database behind it.

**Can DNA tell me the [THC](https://genetixbay.com/knowledge/glossary/thc.md) percentage?** No, DNA cannot tell you a cannabis plant's THC percentage. Validated markers can usually predict chemotype class, meaning THC-dominant or CBD-dominant, but [total cannabinoid content](https://genetixbay.com/knowledge/glossary/total-cannabinoids.md) is a quantitative, many-gene trait that depends heavily on environment and on the testing lab. DNA also doesn't measure flavour or effect.

**Is a sativa/indica percentage from a DNA test real?** A sativa/indica percentage from a DNA test is not meaningful ancestry. Genome-wide research found samples labelled 'indica' and 'sativa' were genetically indistinct. Such percentages only describe similarity to the lab's reference panel, and reference panels are biased towards commercial material, so '62% sativa' should not be read as a measure of where the plant came from.

**What do I need for an [L4](https://genetixbay.com/knowledge/glossary/evidence-levels-l0-l4.md) lineage confirmation?** An L4 lineage confirmation needs young leaf samples from the claimed female, the claimed male or [reversed female](https://genetixbay.com/knowledge/glossary/sex-reversal.md), and at least 5 offspring, each labelled with [GB-IDs](https://genetixbay.com/knowledge/glossary/gb-id.md) and photographed at sampling. Send them with a chain-of-custody note for parentage or kinship analysis, then attach the report as a GB-DOC for a staff archivist to check.

**Short answer.** DNA is excellent at **identity** (same plant or not), **exclusion** (this can't be the parent) and **trait markers** with proven links (sex, chemotype class, some flowering genes). It is weaker at **inclusion** without both parents sampled, and useless for proving an old story attached to a name. It does not measure potency, flavour or effect.

## What's happening

A genotype test reads many DNA positions (SNPs or microsatellites) in a sample. Comparing those readings across samples answers questions about relatedness. Parentage logic is simple [1]: a child must carry one allele from each parent at every position. One consistent mismatch across many markers (allowing for error) excludes a parent; consistent matches support but don't prove parentage, because relatives of the true parent may also match.

## Can and can't

| Question | Can a test answer it? | Notes |
|---|---|---|
| Are these two clones the same genotype? | **Yes**, with enough markers | Expect tiny differences from somatic mutation and genotyping error [7] |
| Is plant X a possible parent of [seed lot](https://genetixbay.com/knowledge/glossary/seed-run.md) Y? | **Yes, by exclusion** | Strongest when several offspring are tested |
| Is plant X *the* parent? | **Supported** if both parents and offspring are sampled and close relatives are ruled out | This is the L4 standard |
| Is this the "original" 1990s cut? | Only by comparison with a documented reference sample | Without a reference, no |
| Will this seedling be male? | **Yes** with validated sex markers [3] | |
| Is this seedling THC- or CBD-dominant? | **Usually**, chemotype class markers [3] | Markers can fail in some [germplasm](https://genetixbay.com/knowledge/glossary/germplasm.md) |
| Is this an [autoflower](https://genetixbay.com/knowledge/glossary/autoflower.md)? | **Sometimes** [6] | Markers don't predict all auto sources |
| What THC % will it test? | **No** | Total cannabinoids are quantitative and environment- and lab-dependent |
| What does it taste like / feel like? | **No** | Terpene synthase variants are linked to labels [5], but aroma is multi-gene and environmental |
| What % indica vs sativa is it? | **Not meaningfully** | Genome-wide, "indica" and "sativa" labelled samples were genetically indistinct in [5]; such percentages describe similarity to a reference panel, not ancestry |
| Which landrace is it from? | Only roughly, if the reference panel contains relevant landraces | Reference panels are biased to commercial material [2] |

## What to ask a lab

1. **What markers and how many?** Thousands of SNPs give far better resolution than a few microsatellites. Schwabe and McGlaughlin used 10 microsatellites [4]; Henry et al. used 22 targeted SNPs chosen for ancestry and chemotype across 420 [accessions](https://genetixbay.com/knowledge/glossary/accession.md) [2]. Both are useful research panels; neither is a whole-genome fingerprint.
2. **What reference database?** Matches are only as good as the samples behind them.
3. **Error rate and repeatability?** Ask for replicate data.
4. **How do they report relatedness?** Look for identity-by-state or kinship values, not marketing labels.
5. **Can they run parentage with your own parents and offspring?** This is what L4 needs.
6. **Data ownership:** can you download raw genotypes, and who else can use them?

## Step by step: an L4 parentage test

1. Sample the claimed female, the claimed male (or reversed female) and at least 5 offspring. Use young leaf tissue, labelled with GB-IDs.
2. Record sampling with dated photos showing the label and plant.
3. Send to the lab with a chain-of-custody note.
4. Request a parentage or kinship analysis.
5. Attach the report as a GB-DOC to the LIN claim. A staff archivist checks consistency.

## Common mistakes

- Taking "98% match to Strain X" as identity. Ask: match to what sample, from where?
- Treating "62% sativa" as ancestry.
- Assuming a DNA match means the same flower quality. Health ([HLVd](https://genetixbay.com/knowledge/glossary/hop-latent-viroid.md)), environment and somatic changes still matter.

## Evidence

- Parentage logic and exclusion vs inclusion: *Established* [1].
- Clone identity and population structure from SNP assays: *Supported* [2][4].
- Sex and chemotype markers: *Supported* [3].
- Indica/sativa labels not reflecting genome-wide ancestry: *Supported* [5].
- Autoflower markers: *Supported* in mapped germplasm [6].

## Sources

1. Jones AG, Small CM, Paczolt KA, Ratterman NL. 2010. A practical guide to methods of parentage analysis. Molecular Ecology Resources 10(1):6-30. https://doi.org/10.1111/j.1755-0998.2009.02778.x
2. Henry P, et al. 2020. A single nucleotide polymorphism assay sheds light on the extent and distribution of genetic diversity, population structure and functional basis of key traits in cultivated north American cannabis. Journal of Cannabis Research 2:26. https://doi.org/10.1186/s42238-020-00036-y
3. Toth JA, Stack GM, Cala AR, et al. 2020. Development and validation of genetic markers for sex and cannabinoid chemotype in Cannabis sativa L. GCB Bioenergy 12(3):213-222. https://doi.org/10.1111/gcbb.12667
4. Schwabe AL, McGlaughlin ME. 2019. Genetic tools weed out misconceptions of strain reliability in Cannabis sativa: implications for a budding industry. Journal of Cannabis Research 1:3. https://doi.org/10.1186/s42238-019-0001-1
5. Watts S, McElroy M, Migicovsky Z, et al. 2021. Cannabis labelling is associated with genetic variation in terpene synthase genes. Nature Plants 7:1330-1334. https://doi.org/10.1038/s41477-021-01003-y
6. Toth JA, Stack GM, Carlson CH, Smart LB. 2022. Identification and mapping of major-effect flowering time loci Autoflower1 and Early1 in Cannabis sativa L. Frontiers in Plant Science 13:991680. https://doi.org/10.3389/fpls.2022.991680
7. Adamek K, et al. 2022. Accumulation of somatic mutations leads to genetic mosaicism in cannabis. The Plant Genome 15(1):e20169. https://doi.org/10.1002/tpg2.20169