# SNP

> A SNP (single nucleotide polymorphism) is a position in the DNA where plants differ by one base letter; thousands of them form the markers used in cannabis genotyping.

- Canonical: https://genetixbay.com/knowledge/glossary/snp.html
- Also written: single nucleotide polymorphism, SNPs, SNP marker, snip
- Glossary category: Genetics and breeding · Evidence: Established
- Status: Draft: awaiting expert review · Updated: 2026-10-31
- Licence: CC BY-SA 4.0 (https://creativecommons.org/licenses/by-sa/4.0/), attribute "GenetixBay cannabis glossary"

A SNP (pronounced "snip") is a single position in the genome where individuals differ by one DNA letter: some plants carry an A there, others a G. Each SNP is a [locus](https://genetixbay.com/knowledge/glossary/locus.md) with, usually, two [alleles](https://genetixbay.com/knowledge/glossary/allele.md). They are abundant, stable and cheap to read in bulk, which makes them the standard marker for modern [genotyping](https://genetixbay.com/knowledge/glossary/genotyping.md).

## In practice

A SNP panel reads hundreds to tens of thousands of positions at once. Comparing two cuts across a large panel gives a confident answer on whether they are the same [genotype](https://genetixbay.com/knowledge/glossary/genotype.md). Studies of North American cannabis used SNP panels to map population structure and show that commercial labels do not match genetic groups well (Henry et al. 2020).

Most SNPs have no known effect on traits; they are markers, not causes. A few sit in or near [genes](https://genetixbay.com/knowledge/glossary/gene.md) that matter, such as the synthase loci, and can be used to predict a trait in [seedlings](https://genetixbay.com/knowledge/glossary/seedling.md).

## Don't confuse with

- **Mutation**: the event that originally created a SNP; a SNP is the resulting variation in the population.
- **Gene**: a SNP is one letter; a gene spans thousands.
- **Microsatellite (SSR)**: an older marker type based on short repeated sequences.

## Related terms

[Genotyping](https://genetixbay.com/knowledge/glossary/genotyping.md), [Marker-assisted selection](https://genetixbay.com/knowledge/glossary/marker-assisted-selection.md), [QTL](https://genetixbay.com/knowledge/glossary/qtl.md), [Locus](https://genetixbay.com/knowledge/glossary/locus.md), [Allele](https://genetixbay.com/knowledge/glossary/allele.md)

## Read more

- [Genotyping: what a DNA test can and can't prove](https://genetixbay.com/knowledge/breeding/genotyping-what-tests-prove.md)

## Sources

1. Henry P, Khatodia S, Kapoor K, 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.
2. Barcaccia G, Palumbo F, Scariolo F, Vannozzi A, Borin M, Bona S. 2020. Potentials and challenges of genomics for breeding cannabis cultivars. Frontiers in Plant Science 11:573299. https://doi.org/10.3389/fpls.2020.573299