Genetic diversity
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Genetic diversity in Cannabis is the range of alleles and genotypes carried within the species, among its populations, and within an individual plant. It spans the deep division between fibre-and-seed hemp and drug-type cannabis, the differentiation among regional landraces, and the variation in chemical profile from one population to the next.[1]
Genetic diversity is the raw material of adaptation and breeding: it underlies the crop's spread across latitudes and the range of chemotypes and fibre, seed and drug forms selected from it. Its loss is a central concern of cannabis conservation, because the displacement of many locally adapted landraces by a few widely grown modern cultivars, together with gene flow from those cultivars into surviving traditional populations, narrows the pool of variation that future selection can draw on.
Diversity in cannabis is organised mainly by use-type and geography rather than by the familiar "sativa" and "indica" labels of commerce, which correspond poorly to genetic identity.[1] It is quantified with the standard measures of population structure — allelic richness, heterozygosity, nucleotide diversity and fixation indices — applied to molecular markers ranging from a handful of microsatellites to genome-wide SNP datasets.
Measuring genetic diversity
Genetic diversity in a cannabis population is summarised by the proportion of loci that vary, the number of alleles they carry (allelic richness), and heterozygosity — the fraction of loci at which an average individual carries two different alleles. Differentiation between populations is measured by fixation indices such as FST, which rises from zero (identical allele frequencies) towards one (populations fixed for different alleles). Partitioning the total variation into within- and among-population components, by analysis of molecular variance, shows where diversity resides.[2]
The markers used have changed with sequencing technology. Early forensic and breeding studies typed a dozen or so microsatellite loci;[3] most current work uses thousands to millions of SNPs recovered by genotyping-by-sequencing or whole-genome resequencing, the same platforms that produced the reference assemblies.[1][2][4]
Gene pools and population structure
The deepest genetic split in the species is between drug-type cannabis and fibre-and-seed hemp. Genotyping 81 drug-type and 43 hemp samples at some 14,000 SNPs, one genome-wide survey found the two significantly differentiated across the genome, with an average FST of about 0.16 — comparable to the differentiation between human continental groups — and recovered them as two clusters whose membership tracked the first principal component almost exactly. The distinction is not confined to the genes controlling cannabinoid production but runs genome-wide.[1] A larger microsatellite survey of 1,324 plants from 48 varieties likewise separated fibre from drug types cleanly and assigned essentially every plant to the correct type.[3]
The two pools differ in how their diversity is arranged. Hemp carries the broader base: it is significantly more heterozygous than drug-type cannabis and less subdivided among varieties.[1][3] Drug-type cannabis holds less variation within any one lineage — many named clones are highly homozygous, the signature of repeated selfing and vegetative propagation — yet the lineages are strongly differentiated from one another, so that among-variety FST in the drug pool (about 0.39) far exceeds that among hemp varieties (about 0.15).[3] The commercial "strain" is a weak guide to this structure: in one comparison a third of samples were genetically closer to differently named plants than to plants sharing their own name, and reported sativa/indica ancestry explained little of the genetic variance.[1][3]
Traditional landraces show the pattern expected of an outbreeding crop: most variation sits within each population rather than between populations. In a genome-wide study of Iranian drug-type landraces, roughly 93–96% of the variation lay within populations and only about 1% among them; the material formed a distinct lineage of drug-type cannabis and a reservoir of alleles not represented elsewhere.[2]
Geographic and landrace variation
Across its range cannabis is structured by geography, and traditional landraces are the units in which much of that regional diversity is held. A survey of 645 plants from 52 Chinese and international accessions, using chloroplast sequence, recovered three latitudinal lineages — low-, mid- and high-latitude — with genetic distance increasing with geographic and latitudinal distance and most variation partitioned among the three groups (FST ≈ 0.70).[5] The lineages differ in the traits that matter for growing at a given latitude — flowering time, height, stem thickness and branching all change with latitude — pointing to local adaptation shaped largely by photoperiod.[5]
This geographic structure means that landrace populations from different regions carry different, locally adapted variation, so that the diversity of the species is distributed across many places at once. The Iranian landraces sampled above formed a genetic pool distinct from European hemp and from Western drug cultivars, and their maintainers grew them with no formal breeding programme.[2] Documented landrace variation of this kind — collected and described region by region — is the empirical core of cannabis diversity.[6]
Origins and domestication
The present-day arrangement of cannabis diversity is the legacy of a long domestication. Whole-genome resequencing of a broad worldwide sample places the origin of the domesticated crop in East Asia, with a basal group made up of feral plants and Chinese landraces and the separation of hemp and drug-type lineages estimated at several thousand years ago; the study concluded that pure wild progenitors are probably extinct, so that plants growing wild today descend from cultivated ancestors.[7] Domestication thus channelled the crop's variation into the use-type lineages seen today, a process traced in more detail in the phylogenetics of the genus.
The geographic centre of that diversity is still debated. The chloroplast study above found its earliest-diverging lineage at low latitude and argued for a southern rather than a Central Asian origin, while noting that wild and domesticated plants within each region shared their commonest sequences.[5] Reconciling these maternally inherited markers with the whole-genome picture remains an open question, taken up in the phylogenetic literature on the genus.
Forces shaping diversity
Several population-genetic processes together set how much diversity cannabis holds and how it is arranged. The first is the mating system. Cannabis is normally dioecious and wind-pollinated, so it is an obligate outcrosser; the resulting gene flow keeps individuals within a population heterozygous and genetically distinct, which is why a traditional landrace holds most of its diversity within the population and cannot be maintained true from a single plant.[2] The details of the sex system that enforces this outcrossing are covered under Sex determination in cannabis.
Against this, genetic drift and bottlenecks remove variation from small or newly founded populations: isolated landraces, and above all the narrow founder base of many modern drug-type lines, lose diversity by chance.[3] Selection adds structure — farmers select for fibre, seed or drug use, and the local climate selects for appropriate flowering time, producing the latitudinal clines already described.[5] Finally, inbreeding through selfing and clonal propagation, standard in modern drug-type breeding, drives within-line diversity down and can expose inbreeding depression; the highly homozygous clones recovered in marker surveys are its clearest mark.[3]
Conservation
The diversity assembled over millennia is eroding quickly. As a small number of high-potency hybrids displace the many landraces once grown for local use, and as introgression carries hybrid alleles into the traditional populations that remain, the cultivated gene pool narrows — a form of genetic erosion. Gene flow between the pools is not hypothetical: cannabidiol-rich hemp ancestry has been detected introgressed into drug-type genomes, showing how readily the two mix once they meet.[8] Where cultivation is illegal the risk is sharper still: the Iranian landraces that carry a unique share of drug-type diversity are maintained informally and under legal pressure, with no programme to conserve them.[2]
Conserving cannabis diversity therefore means capturing it before it is lost and holding it in a way that keeps it intact. Ex situ holdings — seed banks and curated core collections — must sample enough plants per population, and enough populations, to retain rare alleles; because the crop is an outbreeder with separate sexes, a viable accession needs many individuals of both sexes to hold an adequate effective population size, which is the reasoning set out under germplasm sampling and minimum viable population. In situ maintenance of landraces in their home regions preserves not only the alleles but the local adaptation that shaped them. Documenting which populations exist, where, and how distinct they are is the first step, and the purpose this database serves.
See also
References
- ↑ 1.0 1.1 1.2 1.3 1.4 1.5 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.
- ↑ 2.0 2.1 2.2 2.3 2.4 2.5 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.
- ↑ 3.0 3.1 3.2 3.3 3.4 3.5 3.6 Dufresnes, C.; Jan, C.; Bienert, F.; Goudet, J.; Fumagalli, L. (2017). "Broad-scale genetic diversity of Cannabis for forensic applications". PLoS ONE. 12 (1) e0170522. doi:10.1371/journal.pone.0170522.
- ↑ 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.
- ↑ 5.0 5.1 5.2 5.3 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.
- ↑ Clarke, R.C.; Merlin, M.D. (2013). Cannabis: Evolution and Ethnobotany. Berkeley: University of California Press.
- ↑ 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.
- ↑ Grassa, C.J.; Weiblen, G.D.; Wenger, J.P.; Dabney, C.; Poplawski, S.G.; Motley, S.T.; Michael, T.P.; Schwartz, C.J. (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.