The Genetic Structure of Marijuana and Hemp

PLoS One. 2015 Aug 26;10(8):e0133292. doi: 10.1371/journal.pone.0133292. eCollection 2015.


Despite its cultivation as a source of food, fibre and medicine, and its global status as the most used illicit drug, the genus Cannabis has an inconclusive taxonomic organization and evolutionary history. Drug types of Cannabis (marijuana), which contain high amounts of the psychoactive cannabinoid Δ9-tetrahydrocannabinol (THC), are used for medical purposes and as a recreational drug. Hemp types are grown for the production of seed and fibre, and contain low amounts of THC. Two species or gene pools (C. sativa and C. indica) are widely used in describing the pedigree or appearance of cultivated Cannabis plants. Using 14,031 single-nucleotide polymorphisms (SNPs) genotyped in 81 marijuana and 43 hemp samples, we show that marijuana and hemp are significantly differentiated at a genome-wide level, demonstrating that the distinction between these populations is not limited to genes underlying THC production. We find a moderate correlation between the genetic structure of marijuana strains and their reported C. sativa and C. indica ancestry and show that marijuana strain names often do not reflect a meaningful genetic identity. We also provide evidence that hemp is genetically more similar to C. indica type marijuana than to C. sativa strains.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Cannabis / classification
  • Cannabis / genetics*
  • Genotyping Techniques*
  • Phylogeny
  • Polymorphism, Single Nucleotide
  • Species Specificity

Associated data

  • BioProject/PRJNA285813

Grants and funding

SM received funding from the Canada Research Chairs ( in the form of a Tier 2 Chair Award. Anandia Labs provided support in the form of salaries for authors JS and JEP, and The DOC Solutions provided financial support for author DH, but did not have any additional role in the study design, data collection and analysis, decision to publish, or preparation of the manuscript. The specific roles of these authors are articulated in the ‘author contributions’ section. SM received funding from the Natural Sciences and Engineering Research Council of Canada ( in the form of a Discovery Grant. Anandia Labs provided funds for DNA sequencing of cannabis samples via a contract to the SM lab at Dalhousie University.