# Linkage

> Linkage is the tendency of genes that sit close together on the same chromosome to be inherited together, rather than independently.

- Canonical: https://genetixbay.com/knowledge/glossary/linkage.html
- Also written: genetic linkage, linked genes, linkage drag, linked traits
- 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"

Linkage is the tendency of [genes](https://genetixbay.com/knowledge/glossary/gene.md) that are close together on a [chromosome](https://genetixbay.com/knowledge/glossary/chromosome.md) to be inherited as a unit. They break apart only when crossing over (recombination) happens between them during meiosis, and the closer they are, the rarer that is.

## In practice

Linkage helps and hurts. It helps [marker-assisted selection](https://genetixbay.com/knowledge/glossary/marker-assisted-selection.md): a DNA marker tightly linked to a trait gene predicts the trait in seedlings. It hurts when an unwanted trait rides along with a wanted one. Breeders call that linkage drag: you backcross a trait into a line and a chunk of the donor chromosome comes with it, sometimes carrying poorer vigour or an off aroma.

In cannabis the region around the [THCA](https://genetixbay.com/knowledge/glossary/thca.md) and [CBDA synthase](https://genetixbay.com/knowledge/glossary/cbda-synthase.md) genes is a well-studied case. It is a [stretch](https://genetixbay.com/knowledge/glossary/stretch.md) of repeats and duplicated synthase copies with little recombination, so it tends to move as a block (Laverty et al. 2019; Grassa et al. 2021).

## Units and formula

Distance is measured in centimorgans (cM): 1 cM ≈ 1% recombination per generation between two loci.

## Don't confuse with

- **Independent assortment**: the default for genes on different chromosomes.
- **Sex linkage**: genes on the X or Y chromosome, inherited with sex.
- **Pleiotropy**: one gene affecting several traits; linkage is two genes travelling together.

## Related terms

[Independent assortment](https://genetixbay.com/knowledge/glossary/independent-assortment.md), [Locus](https://genetixbay.com/knowledge/glossary/locus.md), [Chromosome](https://genetixbay.com/knowledge/glossary/chromosome.md), [QTL](https://genetixbay.com/knowledge/glossary/qtl.md), [Marker-assisted selection](https://genetixbay.com/knowledge/glossary/marker-assisted-selection.md), [Introgression](https://genetixbay.com/knowledge/glossary/introgression.md)

## Read more

- [Backcrossing, IBLs and stabilisation](https://genetixbay.com/knowledge/breeding/backcrossing-ibl-stabilisation.md)

## Sources

1. Laverty KU, Stout JM, Sullivan MJ, et al. 2019. A physical and genetic map of Cannabis sativa identifies extensive rearrangements at the THC/CBD acid synthase loci. Genome Research 29(1):146-156. https://doi.org/10.1101/gr.242594.118
2. Grassa CJ, Weiblen GD, Wenger JP, et al. 2021. A new Cannabis genome assembly associates elevated cannabidiol (CBD) with hemp introgressed into marijuana. New Phytologist 230(4):1665-1679. https://doi.org/10.1111/nph.17243
3. Acquaah G. 2012. Principles of Plant Genetics and Breeding, 2nd edition. Wiley-Blackwell. https://doi.org/10.1002/9781118313718