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Abstract
BackgroundThe taxonomic classification of Cannabis genus has been delineated through three main types: sativa (tall and less branched plant with long and narrow leaves), indica (short and highly branched plant with broader leaves) and ruderalis (heirloom type with short stature, less branching and small thick leaves). While still under discussion, particularly whether the genus is polytypic or monotypic, this broad classification reflects putative geographical origins of each group and putative chemotype and pharmacologic effect.MethodsHere we describe a thorough investigation of cannabis accessions using a set of 23 highly informative and polymorphic SNP (Single Nucleotide Polymorphism) markers associated with important traits such as cannabinoid and terpenoid expression as well as fibre and resin production. The assay offers insight into cannabis population structure, phylogenetic relationship, population genetics and correlation to secondary metabolite concentrations. We demonstrate the utility of the assay for rapid, repeatable and cost-efficient genotyping of commercial and industrial cannabis accessions for use in product traceability, breeding programs, regulatory compliance and consumer education.ResultsWe identified 5 clusters in the sample set, including industrial hemp (K5) and resin hemp, which likely underwent a bottleneck to stabilize cannabidiolic acid (CBDA) accumulation (K2, Type II & III). Tetrahydrocannabinolic acid (THCA) resin (Type I) makes up the other three clusters with terpinolene (K4 - colloquial “sativa” or “Narrow Leaflet Drug” (NLD), myrcene/pinene (K1) and myrcene/limonene/linalool (K3 - colloquial “indica”, “Broad Leaflet Drug” (BLD), which also putatively harbour an active version of the cannabichrometic acid Synthase gene (CBCAS).ConclusionThe final chemical compositions of cannabis products have key traits related to their genetic identities. Our analyses in the context of the NCBI Cannabis sativa Annotation Release 100 allows for hypothesis testing with regards to secondary metabolite production. Genetic markers related to secondary metabolite production will be important in many sectors of the cannabis marketplace. For example, markers related to THC production will be important for adaptable and compliant large-scale seed production under the new US Domestic Hemp Production Program.
Highlights
The taxonomic classification of Cannabis genus has been delineated through three main types: sativa, indica and ruderalis
Our analyses in the context of the NCBI Cannabis sativa Annotation Release 100 allows for hypothesis testing with regards to secondary metabolite production
Genetic markers related to secondary metabolite production will be important in many sectors of the cannabis marketplace
Summary
The taxonomic classification of Cannabis genus has been delineated through three main types: sativa (tall and less branched plant with long and narrow leaves), indica (short and highly branched plant with broader leaves) and ruderalis (heirloom type with short stature, less branching and small thick leaves). Despite the large diversity in secondary metabolite profiles across thousands of cultivars, the stratification into drug-type cannabis or fibre-type cannabis hinges on the dry weight concentration of a single cannabinoid, Δ9-tetrahydrocannabinol (THC). This approach which prevails today in the USDA interim regulations, employs a THC concentration of 0.3% as the threshold separating hemp and drug-type cultivars, with concentrations below 0.3% defined as hemp (Dolgin 2019). Despite human cultivation for over 6000 years in varying climates worldwide (Clarke and Merlin 2013), its evolution, taxonomic classification, and phylogenetic connections remain poorly understood These deficiencies stem from limited research, irregular breeding efforts, unorganized selection, ex situ conservation, and government restrictions, which resulted in the high heterozygosity observed within cannabis genomes today These deficiencies stem from limited research, irregular breeding efforts, unorganized selection, ex situ conservation, and government restrictions, which resulted in the high heterozygosity observed within cannabis genomes today (e.g. Rahn et al 2016; McPartland 2018)
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