Let’s get to know your plants at their most fundamental level. Understanding cannabis genetics isn’t just for scientists in lab coats - it’s essential knowledge for any serious breeder trying to create the next exceptional cultivar.

The Basics: Cannabis Has 10 Chromosome Pairs

Cannabis carries its genetic information in 10 pairs of chromosomes (20 total). Nine of these pairs are autosomes - regular chromosomes that aren’t involved in sex determination. The 10th pair? Those are the sex chromosomes, and they play by their own rules.

Think of chromosomes like instruction manuals - they carry all the genes that tell your plant how to develop, from the thickness of its stems to the aroma of its flowers.

Recent Genomic Breakthroughs

Cannabis genomics has advanced rapidly in recent years. Several high-quality reference genomes are now available to researchers and breeders, including:

• The CBDRx genome (2020) with approximately 876 million base pairs
• The Cannbio-2 genome (2022), considered one of the most complete at ~900 million base pairs
• Multiple chromosome-scale assemblies for both drug and fiber-type varieties

These reference genomes reveal that cannabis contains approximately 30,000 genes - a complex genetic landscape that explains the remarkable diversity we see across cultivars.

The Sex Chromosome Story

Unlike most plants, cannabis has a proper XY sex determination system similar to humans. Males carry XY, females carry XX. This is why your female plants will always give you female seeds if you reverse them with silver thiosulfate - they can only pass on X chromosomes, never Y.

To make things even more fun - the Y chromosome in cannabis is unusually large and carries genes that do more than just determine sex. This is why male and female plants often show different growth patterns and stress responses.

Sex Determination Genetics

The sex chromosomes in cannabis (typically labeled as chromosome 10 in modern genome assemblies) have undergone significant evolutionary changes. Recent research has identified over 500 sex-linked genes in cannabis, with many concentrated on the Y chromosome. These genes influence:

• Pollen development in males
• Floral development in females
• Secondary metabolite production differences between sexes
• Growth vigor variations between males and females

Key Genes Every Breeder Should Know

The Cannabinoid Biosynthesis Pathway

Cannabis produces cannabinoids through a complex biochemical pathway involving multiple genes. Here’s a simplified version:

1. Precursor Formation: Geranyl pyrophosphate (GPP) and olivetolic acid (OA) are synthesized

   • Key genes: GPP synthase and olivetolic acid cyclase (OAC)

2. CBGA Production: GPP and OA combine to form cannabigerolic acid (CBGA)

   • Key gene: CBGA synthase

3. Conversion to Major Cannabinoids: CBGA is converted to THCA, CBDA, or CBCA

   • Key genes: THCA synthase, CBDA synthase, and CBCA synthase

The CBDA/THCA Synthase Gene

This is the big one - it determines whether your plant makes CBD or THC. There are three main variants (alleles):

• BT (active THCA synthase)
• BD (active CBDA synthase)
• B0 (inactive form)

The combination of these alleles determines your plant’s chemotype (Type I, II, or III).

Modern genomic research has revealed that THCA and CBDA synthase genes are particularly complex. They exist in multiple copies across the genome, with numerous sequence variations that influence enzyme activity. The region containing these genes shows evidence of significant genomic rearrangements during cannabis evolution, which explains some of the variability we see in cannabinoid profiles.

The AUTO Gene

Controls whether your plant flowers based on age (autoflowering) or day length (photoperiod). It’s recessive, which means you need two copies to get autoflowering traits. Originally, this gene came from Cannabis Ruderalis, evolving due to the very short growing seasons at high latitudes.

The autoflowering trait is controlled by a single gene locus with multiple regulatory regions that interact with plant hormone pathways, particularly those involving gibberellins and flowering-time regulatory proteins.

Terpene Synthase Genes

Multiple genes control terpene production. They’re spread across different chromosomes and interact in complex ways - this is why getting consistent terpene profiles can be challenging.

The cannabis genome contains a remarkable diversity of terpene synthase (TPS) genes - at least 30 functional TPS genes have been identified, organized into several distinct gene families:

• TPS-a subfamily: Primarily responsible for sesquiterpene production (β-caryophyllene, α-humulene)
• TPS-b subfamily: Primarily responsible for monoterpene production (limonene, myrcene, pinenes)
• TPS-c subfamily: Involved in diterpene biosynthesis

These genes show tremendous variation between cannabis varieties, explaining the diverse aromas found across different cultivars. Key terpene synthase genes that have been functionally characterized include:

• CsTPS1 (β-myrcene synthase)
• CsTPS2 (limonene synthase)
• CsTPS3 (α/β-pinene synthase)
• CsTPS5 (β-caryophyllene/α-humulene synthase)
• CsTPS9 (nerolidol/linalool synthase)

Glandular Trichome Development Genes

The specialized glandular trichomes that produce and store cannabinoids and terpenes develop through a complex genetic program. Key gene families involved include:

• Trichome initiation factors: Controlling when and where trichomes form
• Secretory cell development genes: Driving the formation of the specialized cells that synthesize resins
• Metabolic pathway regulators: Coordinating the expression of cannabinoid and terpene biosynthesis genes

Modern Breeding Tools

We now have access to the cannabis genome sequence - think of it as a complete parts catalog for the plant. The CBDRx genome has about 876 million base pairs and contains roughly 30,000 genes. That’s a lot of potential for variation!

Genetic Markers and Breeding Applications

Modern genomics has enabled the development of DNA-based markers tied to important traits:

• Single Nucleotide Polymorphisms (SNPs): Over 100,000 validated SNP markers are available across the cannabis genome
• Simple Sequence Repeats (SSRs): Thousands of microsatellite markers useful for tracking inheritance
• Insertion/Deletion Polymorphisms (InDels): Structural variations that can influence gene function

These markers allow marker-assisted selection (MAS) for:

• Chemotype prediction (THC:CBD ratio)
• Sex determination before flowering
• Disease resistance traits
• Terpene profile tendencies

This knowledge lets us:

• Track specific genes through breeding programs
• Understand how traits are inherited
• Develop molecular markers for selection (if you have fancy-pants lab equipment…)
• Predict breeding outcomes more accurately

What This Means for Your Breeding Program

Understanding the genome helps you make better breeding decisions. For example:

• Want to create all-female seeds? Now you know why XX parents are essential
• Working with autoflowering traits? You understand why both parents need to carry the recessive allele
• Breeding for specific cannabinoid profiles? You can track the inheritance patterns

Chromosome Mapping and Linkage

The cannabis genome is organized into specific regions with clusters of related genes:

• Chromosome 1: Contains many genes related to fiber quality and stem development
• Chromosome 6: Houses many terpene synthase genes
• Chromosome 7: Contains clusters of genes involved in cannabinoid biosynthesis
• Chromosome 10: The sex chromosomes, with many genes showing sex-biased expression

Understanding which traits are linked (meaning they tend to be inherited together) can help you plan crosses more effectively. For instance, certain terpene profiles may be more difficult to separate from specific cannabinoid ratios if their controlling genes are physically close on the same chromosome.

Looking Forward

The cannabis genome still holds many mysteries. We’re discovering new genes all the time that influence everything from frost production to pathogen resistance. As our understanding grows, so do the possibilities for precision breeding.

Emerging Genomic Tools

The cannabis breeding community is beginning to benefit from cutting-edge genomic technologies:

• CRISPR-Cas9 genome editing: The potential to precisely modify specific genes (though regulatory challenges remain)
• High-throughput phenotyping: Associating genetic markers with observable traits at scale
• Whole-genome selection: Using genome-wide marker data to predict breeding value
• Comparative genomics: Learning from related plant species with better-studied genomes

Key Takeaways for Breeders

• Cannabis has 10 chromosome pairs
• Sex determination is genetic (XX/XY)
• Key traits often involve multiple genes
• Modern genomic tools can help guide selection
• The cannabinoid pathway involves a cascade of enzymes, with THCA/CBDA synthase being particularly important
• Terpene production is controlled by diverse gene families with complex regulation
• DNA markers can accelerate traditional breeding approaches

In the next post, we’ll think about how to use this knowledge for practical trait selection. Until then, consider how understanding these genetic fundamentals might change your breeding strategy.

Points to ponder

1. What traits are you most interested in tracking genetically?
2. How has understanding genetics changed your breeding approaches?
3. What genetic mysteries would you most like to see solved?

Remember: Genes are your building blocks. The better you understand them, the better equipped you are to build something extraordinary.

Conclusion

The cannabis genome represents one of the most fascinating areas of plant genetics research today. What was once a black box is now being meticulously mapped, offering breeders unprecedented insight into how cannabis expresses its remarkable diversity. While we’ve covered substantial ground in this article, we’ve barely scratched the surface of what genomics will bring to cannabis cultivation in the coming years.

For the practical breeder, even without access to sophisticated laboratory equipment, understanding these genetic principles provides a framework for more methodical and successful breeding programs. By tracking inheritance patterns, planning crosses with genetic principles in mind, and keeping detailed records of your plant’s phenotypic expressions, you’re participating in the same scientific process that has revolutionized agriculture across human history.

As genomic tools become more accessible and our understanding of cannabis genetics deepens, the boundary between traditional breeding and molecular-assisted approaches will continue to blur – offering exciting possibilities for both small and large-scale breeding operations.

Reading time: 15 minutes (2,700 words at 180 words/minute)

References

1. Grassa, C.J., et al. (2021). A complete Cannabis chromosome assembly and adaptive admixture for elevated cannabidiol (CBD) content. BioRxiv. https://www.biorxiv.org/content/10.1101/458083v4
2. Laverty, K.U., 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://genome.cshlp.org/content/29/1/146.full
3. van Bakel, H., et al. (2011). The draft genome and transcriptome of Cannabis sativa. Genome Biology, 12(10), R102. https://genomebiology.biomedcentral.com/articles/10.1186/gb-2011-12-10-r102
4. Braich, S., et al. (2022). A new and improved genome sequence of Cannabis sativa. GigaScience, 11, giac093. https://doi.org/10.1093/gigascience/giac093
5. Zager, J.J., et al. (2019). Gene Networks Underlying Cannabinoid and Terpenoid Accumulation in Cannabis. Plant Physiology, 180(4), 1877-1897. https://doi.org/10.1104/pp.19.00246
6. Allen, L.N., et al. (2019). Complex Variability within the THCA and CBDA Synthase Genes in Cannabis Species. Journal of Forensic Investigation, 7(1), 1-9.
7. Campbell, L.G., et al. (2020). Cannabinoid inheritance relies on complex genetic architecture. Cannabis and Cannabinoid Research, 5(1), 105-116. https://doi.org/10.1089/can.2018.0015

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[This post assumes legal hemp/cannabis breeding in compliance with all applicable laws and regulations.]