Using Genetics to Differentiate Cannabis Cultivars: A Conversation with Philippe Henry of Egret Bioscience

The growing list of cannabis plant names is augmented with each new legalized market as cultivators put their own spins on their hybrids. Here in Pennsylvania, for example, we have regional names like Keystone Kush or Punxsutawney Punch that may not mean much to consumers in other geographies. While these cultivar names provide growers with an opportunity to brand their novel genetics with a personal label, consumers may struggle to understand the differences between one name or another.

Add in conversations of sativa and indica, and the picture gets fuzzier.

How product cultivators, manufacturers, and media sources educate consumers is vital in this burgeoning industry. The complexity of cannabis is vast enough already without complicating the situation into obscurity. A fundamental characteristic of any cannabis plant is its chemovar (the chemistry of the variety) and the molecular differences amongst terpenes and minor cannabinoids has been shown to best differentiate the plants. I recently spoke with Philippe Henry, Ph.D., CEO and director of Egret Bioscience, a company focused on developing novel analytical and genetic testing for psychedelics and cannabis to learn more about his past research into terpenes, and how they best distinguish different cannabis cultivars.


JSL: What’s wrong with the current vernacular of educating cannabis users with terms like sativa or indica? What system do you think would make more sense?

PH: I think this is more of a historical artifact than anything else. There’s nothing wrong with indica/sativa if you are to equate them with drug type temperate vs equatorial varieties. The current situation in North American cannabis is much more complex and involves years of crossbreeding, yielding a mix-matched germplasm with intermediate forms (poly-hybrids).

A better system would be to use neutral genetic markers couched in a well curated germplasm collection (that does not yet exist) to have objective delineation of cannabis groups. Examples of neutral genetic markers include microsatellites (repeat regions in the genome with no known functions) as well as single nucleotide polymorphisms (SNPs) that fall outside of gene region and regulatory elements.  Chemotyping is a temporary solution where we can group cannabis accessions in a limited number of groups with shared characteristics, yet the possibility of generating similar chemical profiles from diverse origins is highly probable.


JSL: You’ve published data on the chemical classification of hundreds of cannabis cultivars, pointing to specific dominant terpene classes. [1,2] What were the central findings?

PH: Since most of the cannabis accession we had access to had high (to very high) THC, we initially looked at other metabolites such as terpenes to group cannabis accessions. We found that a limited number of terpenes could tease groups apart, in particular limonene, myrcene, and terpinolene. Additional research with more varied samples yielded interesting data on the ability of cannabinoids, terpenoids, flavonoids, to differentiate cannabis accessions, while sterols and triterpenoids had no discriminatory power.


JSL: Can you briefly explain how genetic sequencing and understanding SNPs works, and why this approach was selected for better classifying cannabis cultivars?

PH: Sequencing enables us to read the genomes of species. Parts of the genome that have different letters at a particular location (locus) are known as single nucleotide polymorphisms (SNPs) if only a single base pair differs between accessions. These are the most abundant variations in any species’ genome.

Genetic markers can be typed in an irrefutable manner and in all types of samples such as seeds, stems, leaves, flowers, kief, etc. Some genetic markers can be neutral and as such be inherited without the effect of selection (breeding). These markers are particularly useful to resolve complex phylogenies and provide a signal of the evolutionary history of each variety without the muddling effect of crossbreeding. This results in hybrid genotypes between the parents and repeated and multiple breeding events introduce random variation that swamps the phylogenetic signal one would hope to have access to through DNA sequencing. [3]


JSL: What terpenes or groups of terpenes have you found to best differentiate different cannabis cultivars?

PH: Terpinolene or terpinolene/limonene best differentiate between the equatorial hazes (alternatively “sativa”) and other varieties classically considered to be of “indica” descent, which would typically have myrcene/pinene or myrcene/limonene as their dominant terpenes.


JSL: What other molecules have you found to differentiate cannabis plants?

PH: CBD-dominant cultivars had higher amounts of cannabidivarin (CBDV), cannabichromene (CBC), α-pinene, β-myrcene, (-)-guaiol, β-eudesmol, α-eudesmol, α-bisabolol, orientin, vitexin, and isovitexin.

THC dominant cultivars had higher total tetrahydrocannabivarin (THCV), total cannabigerol (CBG), camphene, limonene, ocimene, sabinene hydrate, terpinolene, linalool, fenchol, α-terpineol, β-caryophyllene, trans-β-farnesene, α-humulene, trans-nerolidol, quercetin, and kaempferol.

Compound levels in intermediate varieties were generally equal to or in between those in CBD dominant and THC dominant plants overall, with higher amounts of β-myrcene, (-)-guaiol, β-eudesmol, α-eudesmol, and α-bisabolol. [4]

The most recent unpublished work on an independent dataset has hinted to terpinolene, geraniol, menthol, myrcene, humulene, α- and β-pinene, and cannflavin A as discriminatory chemical markers in high THC accessions.


JSL: With the ability to use genetic analyses to take a deeper dive into what truly differentiates one cannabis plant from another, how could this body of work change the way that we educate consumers about cannabis?

PH: Having access to large genomic assays for cannabis (www.lighthousegenomics.com and www.kannapedia.net) now enables one to compare individual cannabis plants and determine their level of relatedness to each other. As such, one can identify identical clones, siblings, parents, etc. This information can be distilled into a singular barcode that would be unique for each variety and provide information on the expected chemotype of the variety to be consumed. For example, the popular OG Kush line typically expresses a myrcene/limonene/caryophyllene chemotype.

While it is also possible for plants with a diverse lineage to have similar chemotypes, a genetic barcode would irrefutably identify a cultivar, and as such, reduce mislabeling, substitutions, and adulterations as is commonly seen in this emerging marker (e.g. Blue Dream and Pink Kush examples sold by Canadian Licensed producers).



[1] Henry P, Hilyard A, Johnson S, Orser C. Predicting chemovar cluster and variety verification in vegetative cannabis accessions using targeted single nucleotide polymorphisms. PeerJ Preprints. 2018;6:e27442v1. [journal impact factor = N/A; times cited = 4]


[2] Henry P, Khatodia S, Kapoor K, Gonzales B, Middleton A, et al. 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. J Cannabis Res. 2020;2:26. [journal impact factor = N/A; times cited = 4]


[3] Jin D, Henry P, Shan J, Chen J. Classification of cannabis strains in the Canadian market with discriminant analysis of principal components using genome-wide single nucleotide polymorphisms. PLoS One. 2021 Jun 28;16(6):e0253387. [journal impact factor = 3.24; times cited = 1]


[4] Jin D, Henry P, Shan J, Chen J. Identification of chemotypic markers in three chemotype categories of Cannabis using secondary metabolites profiled in inflorescences, leaves, stem bark, and roots. Front Plant Sci. 2021 Jul 1;12:699530. [journal impact factor = 5.753; times cited = 2]

About the author

Philippe Henry, Ph.D., Egret Bioscience, and Florentin Coppey, M.Sc., NIRLab

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