In 2015, a Canadian team ran the DNA of 81 drug-type cannabis samples and 43 hemp samples through the same genotyping test. A sample sold as Jamaican Lambs Bread, a classic “sativa”, came out almost identical to an “indica” from Afghanistan, and across the set the names on the jars had only a loose relationship to what was in the plants.[1] That is the cannabis genome problem in one result: a crop bred for fifty years in secret, named by its sellers, and only now being read.
Genetics and genomics are two ways into the same question. Genetics asks how traits and variation are inherited: whether a seedling will be male, whether a plant can make THC. Genomics asks the same questions across the whole sequence at once: how it is built, where the genes sit, how one plant’s copy differs from another’s. Cannabis has had the first for decades, from breeders working by eye. It has had the second since 2011.
What is the cannabis genome?
A genome is a plant’s complete DNA sequence: its genes, and the long stretches between them. Cannabis carries that sequence on 20 chromosomes in ten pairs, one of each pair from each parent. Nine pairs are ordinary; the tenth is the sex pair, and females are typically XX and males XY.[2] When a paper gives a genome size, about 830 million bases for cannabis, it means one set of ten chromosomes, not all the DNA in a cell.[3, 2] The 2025 pangenome assemblies carried about 35,000 predicted genes each.[4]
Most of the sequence is not genes. It is repetitive DNA, much of it transposable elements that copy themselves around the genome, and that is why the early assemblies were so incomplete: a short sequencing read cannot tell one copy of a repeat from another. Long reads can, and the modern assemblies date from them.
Two more terms carry the rest of this article. A reference genome is one plant’s sequence, assembled as completely as possible, for other plants to be compared against. A pangenome is a collection of such genomes from many plants, built to capture a crop’s variation rather than one example of it.[4]
What decides whether a plant makes THC or CBD?
Two genes, which encode the enzymes THCA synthase and CBDA synthase. The genes sit side by side in one region of DNA on one chromosome (a locus, in the genetics term), and the enzymes they make compete for the same starting material. A plant with a working copy of only the first gene is THC-dominant; only the second, CBD-dominant; both, a mixed Type II plant.[5, 6]
In Cornell field trials, 217 hemp plants at two New York sites were genotyped and tested, and the THC each plant made tracked which synthase genes it carried, not where or how it was grown. In one variety sold as stable CBD hemp, as many as two-thirds of the plants grown from its seed made THC above the legal limit.[7] Seeds from one variety are siblings, not copies, which is the practical difference between growing from seeds and growing from clones. In those populations, hemp that “goes hot” was a matter of which genes it carried rather than how it was grown, and the same chemotype markers are what a genetic test reads in a seedling.
The two enzymes act on the same precursor, CBGA, which our page on the acidic cannabinoids covers. The surprise of the genome work was the neighborhood. A 2019 genetic map found both genes sitting in a large, repetitive, structurally tangled region that rarely recombines, so the drug-type and hemp versions are inherited as a block and are hard to assemble.[5] The 2021 reference genome confirmed the structure and found the working synthases surrounded by broken copies of themselves.[8]
What the synthase locus does not explain is how much cannabinoid a plant makes in total. In the 2021 mapping population, overall potency was linked to other chromosomes altogether.[8] The ratio is one locus; the yield is many. That matters for hemp: a CBD-type plant makes a little THC alongside its CBD, so a very CBD-rich crop can test over the legal limit with no THC gene at all, as our hemp vs cannabis page explains.
Where did cannabis come from?
East Asia, by the best current genomic evidence, with a single domestication in early Neolithic times. A 2021 study sequenced 110 plants from around the world, feral and cultivated, hemp and drug type, and found four genetic groups. The most basal group was made up of landraces and feral plants from China, and everything grown today, hemp or drug, descended from that pool.[2]
Not everyone accepts the date or the single origin. The 12,000-year figure is a divergence time modelled from the DNA, with a wide range around it, which the authors then matched to cord-marked pottery of about that age from South China and Taiwan.[2] The taxonomist John McPartland has argued that the sampling missed Russia and Afghanistan and that the mutation rate behind the clock was never cross-checked.[9] The 2025 pangenome, 193 assemblies from 144 plants, drew a related conclusion from different data: an ancient wild relative of cannabis probably still exists somewhere in Asia.[4] Our page on landrace varieties covers the regional lines that history produced.
What the genome does not support is the indica and sativa split as most people use it. The 2015 study found only a moderate match between a strain’s reported ancestry and its genetics, and hemp closer to the “indica” drug types than to the “sativa” ones.[1] A 2016 study of 340 varieties found three broad groups: hemp, and two drug-type groups that follow leaf shape better than the names do.[10] Our page on strains and cultivars takes the naming problem further.
None of this makes the words useless; it makes them labels for leaf shape and growth habit rather than for lineage, which is where our two-part look at the indica–sativa question ends up.
What can genetics do for growers?
Sex and chemotype tests
A grower can now test a seedling for sex and for chemotype, weeks before either shows. The sex test rests on the chromosomes themselves: cannabis has true X and Y chromosomes, the Y has lost many of its ancestral genes, and a 2020 study of a family of parents and offspring mapped more than 500 genes that travel with sex.[11] A cheap marker assay for sex was published alongside the Cornell chemotype markers.[7] The other route to all-female crops, feminized seed, works by chemistry rather than genetics: silver thiosulfate sprays induce male flowers on female plants, whose pollen carries only X.[12] Our page on reversing the sex of cannabis plants covers the method.
Cultivar identification
Because names are unreliable, a genetic fingerprint is the only way to show that two cuttings are the same plant, or that a licensed cultivar has not been copied. Geneticist Philippe Henry describes the work in our conversation with him.
Breeding possibilities
This is where the genome matters most and has delivered least so far. Cannabinoid and terpene synthases share early steps, and a 2019 study of nine cultivars tied the gene activity in glandular trichomes to the resin each one made.[13] A 2021 review of the field, the one this article originally summarized, put the obstacles plainly: the genetics are poorly understood, clandestine breeding since the 1970s narrowed the gene pool, and cultivars are routinely misclassified.[14]
In our view the 2025 pangenome changes the terms of that debate. With 193 genomes in one framework, a breeder can see which version of a region a plant inherited from which parent, and the synthase genes show unusually low diversity inside a very variable genome.[4] The plant has been bred hard for two compounds, and a great deal of its diversity is still there to work with. Whether it ends up in open breeding programs or in patents is the question the next decade of cannabis genetics will answer.
How was the cannabis genome sequenced?
The first read, in 2011, used short-read machines on the drug-type clone Purple Kush and came back well short of the whole, in many fragments.[3] The milestones since:
| Assembly | Year | Plant | Why it mattered |
|---|---|---|---|
| Purple Kush draft[3] | 2011 | THC-dominant clone | The first cannabis genome, partial and fragmented; showed that this plant used the THC gene where hemp used the CBD gene |
| Purple Kush and Finola maps[5] | 2019 | Drug-type clone and a hemp cultivar | The first map of where genes sit on the chromosomes; found the THC and CBD genes in a repetitive region that is inherited as a block |
| Jamaican Lion family[6] | 2020, preprint | Type II cultivar, both parents and offspring | The first assembly of a plant carrying working THC and CBD genes together; compared gene copies across 40 more cultivars |
| CBDRx, “cs10”[8] | 2021 | High-CBD cultivar | The first genome resolved into whole chromosomes, adopted as the public reference |
| Salk pangenome[4] | 2025 | 144 plants, 193 assemblies | The first view across the whole crop, with both parental chromosome sets separated where the plant allowed it, sex chromosomes included |
| Seed hemp “Yushe”[15] | 2026 | A male hemp plant | A hemp Y chromosome assembled separately from its X |
Assemblies number their chromosomes differently, so a gene “on chromosome 7” in the current reference is not a contradiction of an older paper that puts it elsewhere. The Jamaican Lion work is a preprint, posted in 2020 and not peer-reviewed.
References
- Sawler J, Stout JM, Gardner KM, Hudson D, Vidmar J, Butler L, Page JE, Myles S. The genetic structure of marijuana and hemp. PLoS One. 2015;10(8):e0133292.
- Ren G, Zhang X, Li Y, Ridout K, Serrano-Serrano ML, Yang Y, Liu A, Ravikanth G, Nawaz MA, Mumtaz AS, Salamin N, Fumagalli L. Large-scale whole-genome resequencing unravels the domestication history of Cannabis sativa. Sci Adv. 2021;7(29):eabg2286.
- van Bakel H, Stout JM, Cote AG, Tallon CM, Sharpe AG, Hughes TR, Page JE. The draft genome and transcriptome of Cannabis sativa. Genome Biol. 2011;12(10):R102.
- Lynch RC, Padgitt-Cobb LK, Garfinkel AR, et al. Domesticated cannabinoid synthases amid a wild mosaic cannabis pangenome. Nature. 2025;643:1001–1010.
- Laverty KU, Stout JM, Sullivan MJ, Shah H, Gill N, Holbrook L, Deikus G, Sebra R, Hughes TR, Page JE, van Bakel H. A physical and genetic map of Cannabis sativa identifies extensive rearrangements at the THC/CBD acid synthase loci. Genome Res. 2019;29(1):146–156.
- McKernan KJ, Helbert Y, Kane LT, Ebling H, Zhang L, Liu B, Eaton Z, McLaughlin S, Kingan S, Baybayan P, Concepcion G, Jordan M, Riva A, Barbazuk W, Harkins T. Sequence and annotation of 42 cannabis genomes reveals extensive copy number variation in cannabinoid synthesis and pathogen resistance genes. bioRxiv. 2020. Preprint, not peer-reviewed.
- Toth JA, Stack GM, Cala AR, Carlson CH, Wilk RL, Crawford JL, Viands DR, Philippe G, Smart CD, Rose JKC, Smart LB. Development and validation of genetic markers for sex and cannabinoid chemotype in Cannabis sativa L. GCB Bioenergy. 2020;12(3):213–222.
- Grassa CJ, Weiblen GD, Wenger JP, Dabney C, Poplawski SG, Motley ST, Michael TP, Schwartz CJ. A new Cannabis genome assembly associates elevated cannabidiol (CBD) with hemp introgressed into marijuana. New Phytol. 2021;230(4):1665–1679.
- McPartland JM. Was cannabis first grown in eastern China? O’Shaughnessy’s (beyondthc.com), 19 July 2021. Commentary, not peer-reviewed.
- Lynch RC, Vergara D, Tittes S, White K, Schwartz CJ, Gibbs MJ, Ruthenburg TC, deCesare K, Land DP, Kane NC. Genomic and chemical diversity in Cannabis. Crit Rev Plant Sci. 2016;35(5–6):349–363.
- Prentout D, Razumova O, Rhoné B, Badouin H, Henri H, Feng C, Käfer J, Karlov G, Marais GAB. An efficient RNA-seq-based segregation analysis identifies the sex chromosomes of Cannabis sativa. Genome Res. 2020;30(2):164–172.
- Lubell JD, Brand MH. Foliar sprays of silver thiosulfate produce male flowers on female hemp plants. HortTechnology. 2018;28(6):743–747.
- Zager JJ, Lange I, Srividya N, Smith A, Lange BM. Gene networks underlying cannabinoid and terpenoid accumulation in Cannabis. Plant Physiol. 2019;180(4):1877–1897.
- Hurgobin B, Tamiru-Oli M, Welling MT, Doblin MS, Bacic A, Whelan J, Lewsey MG. Recent advances in Cannabis sativa genomics research. New Phytol. 2021;230(1):73–89.
- Wei H, Yang Z, Zhuang L, Pan X, Jia H, Jiang S, Li Q, Xu J, Tao A, Fang P, Qi J, Ming R, Zhang L. A haplotype-resolved genome assembly of seed hemp (Cannabis sativa) and analysis of Y chromosome divergence from the X. Hortic Res. 2026;13(1):uhaf268.
Updated November 2026: this article was rewritten by the editors as the hub for our cannabis genetics coverage, drawing in four earlier pieces. Originally published 24 May 2022 by Sabina Pulone as a summary of one review paper.
Image: schematic diagram by Terpenes and Testing.
Scientifically reviewed by Chana Frenkel, Ph.D. · Edited by Nani Frenkel, chief editor.
