Cannabis genetics
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Cannabis genetics is the study of heredity and genetic variation in Cannabis. It covers the organisation of the genome and the inheritance of traits such as sex and chemotype. It also covers how variation is distributed among hemp, drug-type, feral and landrace populations and how domestication and breeding have changed it.
Cannabis is diploid, with ten pairs of chromosomes (2n = 20): nine pairs of autosomes and a pair of sex chromosomes, XX in females and XY in males.[1][2] It is wind-pollinated and in most forms dioecious, so plants are highly heterozygous. Many drug-type strains are propagated as clones to keep their genetic identity.[3] Laws against growing the plant, which reached even research plantings, slowed its genetic study compared with that of other major crops and held back the building of breeding programmes and germplasm collections.[2][4][5]
Genome surveys separate hemp from drug-type cannabis across the whole genome. Below that division, much of the variation follows geography.[3][6] The arrangement of that variation is the subject of genetic diversity; the evolutionary relationships behind it are reconstructed in the phylogenetics of the genus.
The genome
The first draft genome, published in 2011, came from a female plant of the drug-type cultivar Purple Kush. Built from short sequencing reads, it comprised a draft sequence of 534 megabases (Mb) and a transcriptome of about 30,000 genes. THCA synthase occurred in the Purple Kush transcriptome, while the hemp cultivar Finola carried CBDA synthase in its place.[2] The assembly fell into some 136,000 scaffolds, too fragmented to show how the two synthase genes are arranged on the chromosomes.[7]
Long-read sequencing anchored to genetic maps later produced chromosome-scale assemblies.[7][8] A map of a cross between Purple Kush and Finola, published in 2019, found genes and recombination concentrated near the ends of the chromosomes, with long, gene-poor and repeat-rich central blocks in which crossing over is rare; its authors compared the arrangement with that of wheat and other grains. The THCA and CBDA synthase genes lie in large stretches rich in retrotransposons that differ almost entirely between the drug and hemp parents, embedded in about 40 Mb of DNA that barely recombines.[7] A 2021 assembly of CBDRx, a cultivar high in cannabidiol, resolved nine autosomes and the X chromosome. Its 13 cannabinoid synthase sequences, all but two of them pseudogenes, lie near the centromere of one chromosome, most of them in tandem arrays.[8]
A pangenome published in 2025 brought together 193 genomes from 144 plants, male and female. Wide regions of the genome proved highly variable for a single species, in sequence and in structure, while the cannabinoid synthase genes carried very little diversity. About 79 per cent of the haploid genome of some 750 Mb consists of transposable elements. The study attributed the evolution of the genome to their activity and to hybridisation, not to whole-genome duplication.[5]
Inheritance of traits
Sex follows the X and Y chromosomes.[1] The mechanism and the monoecious hemp cultivars that depart from it are the subject of Sex determination in cannabis. The expression of sex can still be shifted. Silver nitrate or silver thiosulfate applied to female plants induces male flowers whose pollen sets seed that gives rise only to female plants (feminised seeds).[9]
When Etienne de Meijer and colleagues crossed pure-THC with pure-CBD plants in 2003, every F1 plant had a mixed chemotype and the F2 generations segregated into pure-CBD, mixed and pure-THC plants in a 1:2:1 ratio. They proposed one locus, B, with two codominant alleles.[10] The genome assemblies revised the model. THCA synthase and CBDA synthase sit at separate loci, and the Finola genome held no THCA synthase gene, active or inactive. The close physical linkage of the two genes in a region of suppressed recombination explains why chemotype segregates as if a single gene controlled it.[7][8]
In a cross between the hemp cultivars Carmagnola and USO31, whole-genome mapping found 69 quantitative trait loci for agronomic and biochemical traits, plant height and cannabinoid content among them. Most of the loci co-localised, which the authors took to mean that a small number of regions control much of the difference between the two parents. In cannabis, biochemical traits are more heritable than agronomic ones.[11] Total cannabinoid content is inherited apart from chemotype. In a cross between the drug cultivar Skunk No. 1 and the hemp cultivar Carmen, a single locus explained more than 90 per cent of the variance in the ratio of THC to CBD, while none of six loci for total cannabinoid content lay at the synthase arrays.[8]
Variation among populations
In a 2015 survey of 81 drug-type and 43 hemp samples at 14,031 single-nucleotide polymorphisms, the two groups differed across the whole genome and not only at the genes for THC production, with an average FST of 0.156. No marker was fixed for different alleles in the two, which still share most of a common pool of variation.[3] Named drug-type strains are a weak guide to this population structure. In 6 of the 17 comparisons that study made, plants were genetically closer to differently named plants than to plants of the same name.[3]
Below the use-type division, cannabis is structured by geography. Chloroplast sequence from 645 plants of 52 wild and domesticated accessions fell into three lineages distributed by latitude, high, middle and low. Genetic distance rose with geographic distance. Of 20 climatic factors tested, day length was the most important, and the authors read the pattern as local adaptation to the climates of different latitudes.[6] Within a region, landraces hold most of their variation inside each population. In Iranian drug-type landraces, 93 to 96 per cent of the molecular variance lay within populations and about 1 per cent among them, a pattern the authors related to the plant being dioecious.[12]
Domestication, selection and breeding
A 2021 study by Guangpeng Ren and colleagues, which resequenced the genomes of 110 accessions, concluded that cannabis was first domesticated in East Asia in the early Neolithic and that today's hemp and drug cultivars derive from an ancestral gene pool now represented by feral plants and landraces in China. On its evidence the feral plants it sampled, Central Asian ones among them, were historical escapes from cultivation. The study dated the split of the early domesticated lineages from that basal group to about 12,000 years ago and the divergence of hemp and drug types to about 4,000 years ago.[4] The authors of the 2025 pangenome study judged that wild relatives probably still exist in Asia and wrote that refining the history of domestication will need broader sampling and a careful separation of wild from feral plants.[5]
Ren and colleagues found selective sweeps at genes that differ between the two use types: in hemp, genes that inhibit branching and genes of cellulose synthesis; in drug-type plants, genes that promote branching; in both, genes of flowering time and lignin synthesis. Complete THCA synthase sequences were largely missing from hemp cultivars and complete CBDA synthase sequences from drug cultivars. The authors read this as artificial selection for loss-of-function mutations, one in each direction.[4]
Hemp and drug cultivars have been bred largely apart, with little gene flow between them,[4] but modern breeding has crossed them. CBDRx is mostly of drug-type ancestry, with a segment of hemp chromosome carrying CBDA synthase introgressed into it; the authors of its assembly concluded that breeders had used targeted introgression to meet demand for cannabidiol.[8] Crossing also reaches traditional populations. John McPartland and Ernest Small wrote in 2020 that Central and South Asian landraces face extinction through introgressive hybridisation and named four taxa as critically endangered reservoirs of the germplasm from which modern drug strains came.[13]
Conservation
Public collections of hemp germplasm are few and drug-type strains survive mainly in a patchwork of private collections. Cannabis seed also loses viability in long storage. The authors of the 2015 survey warned that the genomic variation it described was in danger of being lost.[3] The authors of the 2025 pangenome study wrote that the gene pool of the species remains only partly characterised.[5] In a small population, alleles are lost by chance through genetic drift, at a rate set by the effective population size: the number of individuals in an idealised population that would show the same amount of drift. Conservation genetics uses such measures, with molecular tools, to understand and protect endangered species.[14]
See also
References
- ↑ 1.0 1.1 Divashuk, M.G.; Alexandrov, O.S.; Razumova, O.V.; Kirov, I.V.; Karlov, G.I. (2014). "Molecular cytogenetic characterization of the dioecious Cannabis sativa with an XY chromosome sex determination system". PLoS ONE. 9 (1) e85118. doi:10.1371/journal.pone.0085118.
- ↑ 2.0 2.1 2.2 van Bakel, H.; Stout, J.M.; Cote, A.G.; Tallon, C.M.; Sharpe, A.G.; Hughes, T.R.; Page, J.E. (2011). "The draft genome and transcriptome of Cannabis sativa". Genome Biology. 12 (10) R102. doi:10.1186/gb-2011-12-10-r102.
- ↑ 3.0 3.1 3.2 3.3 3.4 Sawler, J.; Stout, J.M.; Gardner, K.M.; Hudson, D.; Vidmar, J.; Butler, L.; Page, J.E.; Myles, S. (2015). "The genetic structure of marijuana and hemp". PLoS ONE. 10 (8) e0133292. doi:10.1371/journal.pone.0133292.
- ↑ 4.0 4.1 4.2 4.3 Ren, G.; Zhang, X.; Li, Y.; Ridout, K.; Serrano-Serrano, M.L.; Yang, Y.; Liu, A.; Ravikanth, G.; Nawaz, M.A.; Mumtaz, A.S.; Salamin, N.; Fumagalli, L. (2021). "Large-scale whole-genome resequencing unravels the domestication history of Cannabis sativa". Science Advances. 7 (29) eabg2286. doi:10.1126/sciadv.abg2286.
- ↑ 5.0 5.1 5.2 5.3 Lynch, R.C.; Padgitt-Cobb, L.K.; Garfinkel, A.R.; Knaus, B.J.; Hartwick, N.T.; et al. (2025). "Domesticated cannabinoid synthases amid a wild mosaic cannabis pangenome". Nature. 643 (8073): 1001–1010. doi:10.1038/s41586-025-09065-0. PMC 12286863.
- ↑ 6.0 6.1 Zhang, Q.; Chen, X.; Guo, H.; Trindade, L.M.; Salentijn, E.M.J.; Guo, R.; Guo, M.; Xu, Y.; Yang, M. (2018). "Latitudinal adaptation and genetic insights into the origins of Cannabis sativa L." Frontiers in Plant Science. 9 1876. doi:10.3389/fpls.2018.01876.
- ↑ 7.0 7.1 7.2 7.3 Laverty, K.U.; Stout, J.M.; Sullivan, M.J.; Shah, H.; Gill, N.; Holbrook, L.; Deikus, G.; Sebra, R.; Hughes, T.R.; Page, J.E.; van Bakel, H. (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. doi:10.1101/gr.242594.118. PMC 6314170.
- ↑ 8.0 8.1 8.2 8.3 8.4 Grassa, C.J.; Weiblen, G.D.; Wenger, J.P.; Dabney, C.; et al. (2021). "A new Cannabis genome assembly associates elevated cannabidiol (CBD) with hemp introgressed into marijuana". New Phytologist. 230 (4): 1665–1679. doi:10.1111/nph.17243. PMC 8248131.
- ↑ Mohan Ram, H.Y.; Sett, R. (1982). "Induction of fertile male flowers in genetically female Cannabis sativa plants by silver nitrate and silver thiosulphate anionic complex". Theoretical and Applied Genetics. 62 (4): 369–375. doi:10.1007/BF00275107.
- ↑ de Meijer, E.P.M.; Bagatta, M.; Carboni, A.; Crucitti, P.; Moliterni, V.M.C.; Ranalli, P.; Mandolino, G. (2003). "The inheritance of chemical phenotype in Cannabis sativa L.". Genetics. 163 (1): 335–346. doi:10.1093/genetics/163.1.335.
- ↑ Woods, P.; Campbell, B.J.; Nicodemus, T.J.; Cahoon, E.B.; Mullen, J.L.; McKay, J.K. (2021). "Quantitative trait loci controlling agronomic and biochemical traits in Cannabis sativa". Genetics. 219 (2) iyab099. doi:10.1093/genetics/iyab099.
- ↑ Soorni, A.; Fatahi, R.; Haak, D.C.; Salami, S.A.; Bombarely, A. (2017). "Assessment of genetic diversity and population structure in Iranian Cannabis germplasm". Scientific Reports. 7 (1) 15668. doi:10.1038/s41598-017-15816-5.
- ↑ McPartland, J.M.; Small, E. (2020). "A classification of endangered high-THC cannabis (Cannabis sativa subsp. indica) domesticates and their wild relatives". PhytoKeys. 144: 81–112. doi:10.3897/phytokeys.144.46700.
- ↑ Davinack, D. (2024). Molecular Ecology & Evolution: An Introduction. Norton, Massachusetts: Wheaton College. pp. 4, 111.