P. Henry, D. Caplan et al
Sep 11, 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
Cannabis Genetics and Chemotypes
This study looked at the genetics of over 400 cannabis samples from North America using a set of 23 genetic markers. The goal? To better understand how cannabis varieties differ—not just by appearance or marketing labels like “indica” or “sativa,” but based on actual DNA and chemical traits.
The results showed five major genetic groups that matched up with key differences in cannabinoid and terpene profiles. It also uncovered frequent mislabeling and surprising overlap between varieties that were thought to be distinct. Some clusters were clearly high-THC types, others were CBD-rich or industrial hemp.
What makes this research important is that it offers a more reliable way to track and classify cannabis strains, improve consistency, and support better breeding. For growers, breeders, and regulators, this kind of genetic insight can help make sense of a very messy and often mislabeled market.
Background
Cannabis (Cannabis sativa L.) is cultivated for fiber, seed, medicinal, and recreational use. Legal restrictions have historically limited large-scale genetic research, especially in North America. With legalization expanding, reliable tools are needed to assess genetic diversity, authenticate cultivars, and link plant genetics to traits like cannabinoid and terpenoid content. SNP (single nucleotide polymorphism) genotyping offers a cost-effective way to capture this genetic variation.
Study Goals
The authors aimed to:
Develop a practical SNP genotyping assay for cannabis.
Apply it to a broad set of North American cultivars.
Describe population structure and diversity.
Identify SNPs linked to traits of commercial and regulatory interest.
Methods
Samples: 420 accessions from Canada (Saskatchewan, Manitoba, British Columbia) and Nevada, USA, covering hemp, grain, and THC-rich resin types.
SNP Selection: 23 markers chosen for informativeness, reproducibility, and functional links to cannabinoid and terpene biosynthesis.
Platform: Kompetitive Allele Specific PCR (KASP).
Analysis: STRUCTURE and Principal Coordinate Analysis (PCoA) to detect clusters; AMOVA to partition variation; association tests for SNP–trait links.
Findings
Genetic Clusters: Five main groups emerged:
Hemp varieties (low THC, higher CBD).
Two distinct THC-rich resin groups with different terpenoid dominance (e.g., myrcene vs. limonene/terpinolene).
A mixed/intermediate chemotype group.
Grain/fiber types with unique allelic patterns. These generally matched cultivation purpose and chemical profile, though overlap existed due to hybridization.
Diversity Patterns: Significant variation occurred both within and among clusters, reflecting diverse breeding histories and germplasm exchange.
Trait Associations: SNPs near THCAS (THC synthase) and CBDAS (CBD synthase) genes linked to THC/CBD ratios. Others tied to terpene synthase genes influencing aroma and flavor.
Assay Utility: The 23-SNP panel could differentiate cultivars, assign unknown samples to clusters, detect relatedness for breeding, and support traceability in regulatory settings.
Implications
The assay provides a cost-effective, reproducible tool for:
Breeders: Protecting cultivar identity and tracking inheritance.
Regulators: Verifying compliance and preventing mislabeling.
Producers: Ensuring chemical consistency for branding.
Researchers: Studying domestication and diversification.
Limitations
Only 23 SNPs, so fine-scale variation and rare alleles may be missed.
Sampling focused on Canada and Nevada, limiting broader representativeness.
Hybridization blurs genetic boundaries.
Environment and epigenetics also influence cannabinoid and terpenoid profiles.
Conclusion
A targeted 23-SNP assay can capture genetic diversity, structure, and functional variation in cultivated North American cannabis. While not a substitute for broader genomic tools, it offers a practical base for breeding, regulation, and research, especially when paired with chemical profiling.