Introgression
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Introgression is the incorporation of genes from one lineage into the genome of another through hybridisation followed by repeated backcrossing of the hybrids to one of the parental lineages. Typically a small part of the donor's genome is transferred.[1] The botanist Edgar Anderson coined the term, which his studies of hybridisation in spiderworts exemplified.[1] His 1949 monograph Introgressive Hybridization laid out much of the early thinking on how genes pass from one species to another.[2]
Introgression is one outcome of gene flow. Gene flow is any movement of alleles into a population; introgression is the incorporation of alleles from one taxon into another in the generations after hybridisation, whether between species or between distinct populations of one species.[2][1] Hemp and drug-type Cannabis cross readily and their hybrids are fertile,[3][4] so introgression in cannabis runs between lineages that descend from one ancestral gene pool and have been selected for different uses.[5] The cases studied include segments of hemp genome bred into drug-type cultivars for their cannabidiol and the traits of imported hybrid cultivars in the traditional kif plant of Morocco.[4][3] Drug-type alleles in feral hemp populations may be another case, though their origin is debated.[6]
From hybrid to introgressed lineage
A first-generation hybrid carries one set of chromosomes from each parent. When the hybrid and its descendants are crossed back, generation after generation, to the same parent, each backcross halves on average the share of the genome that comes from the other, donor parent. The expected share of the recurrent parent after t backcrosses is 1 − (½)t+1: 75% after one backcross and 87.5% after two. Breeders moving a gene into an established variety usually need five to eight generations of backcrossing.[7]
The donor genome does not shrink evenly. A donor gene kept by selection carries its chromosomal neighbours along. Unwanted donor genes linked to it stay in the recipient, a load breeders call linkage drag.[7] Recombination cuts the donor's chromosomes into shorter pieces over the generations, but many backcrosses are needed to shorten the donor segment around a selected gene.[7] The length of an introgressed segment therefore depends on the time since hybridisation. Introgressed blocks are also generally longer than segments two lineages share only by common descent.[1]
Which donor segments survive depends on chance and on selection. Introgression is called adaptive when natural selection maintains the introgressed alleles in the recipient.[1] In breeding the selection is the breeder's: each backcross generation is screened for plants that carry the donor's allele at the target gene, while the rest of the donor genome is bred out.[7]
Tracing introgression in genomes
Clustering of genome-wide markers estimates what share of each plant's ancestry comes from each of a set of reference populations. In one analysis of 367 cannabis accessions, the cannabidiol-rich cultivar CBDRx drew 89% of its ancestry from drug-type cannabis and 11% from hemp; the drug-type cultivar Skunk#1 drew 78% from drug-type cannabis and 22% from naturalised populations, plants established outside cultivation; the fibre cultivar Carmen drew 94% from hemp.[4]
Ancestry can also be assigned segment by segment along each chromosome, with statistical models that treat the source of each marker as a hidden state and so locate the introgressed blocks.[1] Applied to CBDRx, segment-by-segment assignment placed much of its hemp ancestry on chromosome 7. The model assumed a single influx of hemp into drug-type stock eight generations earlier, a figure taken from the breeders.[4] A third approach fits models of population history with and without migration between groups and compares how well they explain the data, the method by which feral and landrace contributions to the cannabis crops were detected.[5]
The case for adaptive introgression needs signs that selection has acted on the segment and an association between the segment and a trait. It also needs a measured effect of the segment on fitness in the recipient. Suarez-Gonzalez and colleagues call the fitness measurement the most critical of these steps and find it often inadequately addressed.[1]
Introgression in cannabis
Cannabidiol-rich drug-type cultivars
THCA synthase and CBDA synthase compete for the same precursor. Which of the two a plant expresses largely determines its ratio of THC to cannabidiol. Weiblen and colleagues argued that breeding of drug-type cannabis favoured plants without a functional CBDA synthase and found evidence of selection for non-functional forms of the gene. Grassa and colleagues proposed that once highly potent drug-type cultivars existed, crossing them with hemp allowed CBD-dominant plants with drug-type quantities of cannabinoids to be selected.[4]
The genome of CBDRx is mostly of drug-type ancestry, with much of its hemp ancestry on chromosome 7, around the position of CBDA synthase. In a cross between the drug-type cultivar Skunk#1 and the hemp Carmen, the only quantitative trait locus for the THC to CBD ratio mapped to that position and accounted for 92% of the variation in the ratio in the second generation. A scan for selection found signs of recent positive selection nearby.[4] The authors concluded that introgression followed by artificial selection had produced cannabis with combinations of traits not seen before, as it has in other crops. They suggested that breeders had answered demand for cannabidiol with targeted introgression.[4] A pangenome of 193 genomes found such lines in both of its drug-type groups; they are thought to be largely of drug-type ancestry, with a recent history of breeding to introgress CBDA synthase.[8]
Feral populations
The feral cannabis of the Midwestern United States descends from hemp, yet most of its populations include some plants above the legal limit of 0.3% THC. These plants carry the non-functional CBDA synthase allele typical of drug-type cannabis, which the populations hold at low frequency.[6] Two explanations have been offered. The hemp brought to the region may never have been pure, since the chemistry of THC and CBD was worked out only decades after the crop arrived; or THC-type alleles may have entered feral stands more recently, by introgression from clandestine drug cultivation.[9][6]
Wenger and colleagues saw two arguments for historical impurity in Minnesota: hemp growers had no way of testing for THC when the crop was introduced; drug-type pollen is unlikely to be common in the landscape, because drug growers raise female plants and remove the males.[9] In a wider survey, Aina and colleagues suggest that populations at or near Hardy–Weinberg equilibrium reflect local drift, with little immigration of THC-type alleles. Several populations held an excess of intermediate or THC-type plants, which they suggest may be the result of introgression from more recent drug cultivation. They propose genotyping herbarium specimens to see whether the cannabinoid genetics of the populations have changed over time.[6]
Introgression also runs from feral plants into crops. A model of the crop's history fitted to 110 genomes worked best with continuing introgression after domestication into both hemp and drug-type cannabis from a basal group made up mostly of Chinese feral plants and landraces.[5] The feral populations themselves are treated under Feral and ruderal Cannabis.
Kif in Morocco
The drug-type cannabis of Morocco may itself carry hemp genes. Robert Clarke and Mark Merlin took the local narrow-leaflet drug plant to be a hybrid between narrow-leaflet drug cannabis and European hemp. Hemp was grown in Morocco before the 10th century, cannabis pollen is carried far and crosses between hemp and the drug-type plant are fully fertile, so Bachir and colleagues see a considerable chance that European hemp genes entered the Moroccan landrace.[3]
Broad-leaflet genetics from Central Asia were brought into the local crop deliberately in 1980. By 2013 Moroccan farmers had about ten hybrid cultivars. Bachir and colleagues write that the local varieties have acquired the traits of the imported ones. In their account the pure narrow-leaflet landrace is rare and faces extinction through introgressive hybridisation.[3] Studies published in 2015 and 2016 sequenced the THCA synthase gene of Moroccan material. One of them found a single-nucleotide variant shared only by a Moroccan landrace and two accessions of Afghan origin among those compared. Bachir and colleagues propose sampling older populations, above all from herbaria, to work out the plant's history.[3] The displacement of kif and its consequences are covered under Cannabis in Morocco and genetic contamination.
Adaptive and deliberate introgression
Introgression supplies new variation alongside mutation and the variation already standing in a population. It is adaptive when selection keeps the introgressed alleles.[1] The maize landraces of the central Mexican highlands are an example. They carry segments introgressed from the wild highland subspecies Zea mays subsp. mexicana, which grows beside them. Two traits thought to suit maize to high elevation, anthocyanin content and microhairs on the leaves, were associated with the highly introgressed regions. Little adaptive gene flow ran the other way, from maize to mexicana.[2]
In cannabis the cannabidiol cultivars are introgression directed by breeders' selection for a hemp allele.[4] Studies of cannabis genetic resources propose more of it: crossing parents from beyond the northern European gene pool used for hemp seed oil to obtain new lipid profiles[8] and bringing variation from regionally adapted feral populations into new hemp cultivars.[6]
Introgression into a rare or endangered population can also harm it. Alleles from a common relative can swamp the rare population's own. Crosses between well-differentiated populations can yield offspring of lower fitness, known as outbreeding depression. The known plant examples of swamping mostly involve crops mating with close wild relatives.[2] For cannabis landraces this threat is treated under genetic contamination.
See also
References
- ↑ 1.0 1.1 1.2 1.3 1.4 1.5 1.6 1.7 Suarez-Gonzalez, A.; Lexer, C.; Cronk, Q.C.B. (2018). "Adaptive introgression: a plant perspective". Biology Letters. 14 (3) 20170688. doi:10.1098/rsbl.2017.0688. PMC 5897607.
- ↑ 2.0 2.1 2.2 2.3 Ellstrand, N.C. (2014). "Is gene flow the most important evolutionary force in plants?". American Journal of Botany. 101 (5): 737–753. doi:10.3732/ajb.1400024.
- ↑ 3.0 3.1 3.2 3.3 3.4 Bachir, Fatima; Eddouks, Mohamed; Arahou, Mohamed; Fekhaoui, Mohammed (2022). "Origin, Early History, Cultivation, and Characteristics of the Traditional Varieties of Moroccan Cannabis sativa L.". Cannabis and Cannabinoid Research. 7 (5): 603–615. doi:10.1089/can.2021.0020.
- ↑ 4.0 4.1 4.2 4.3 4.4 4.5 4.6 4.7 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.
- ↑ 5.0 5.1 5.2 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.
- ↑ 6.0 6.1 6.2 6.3 6.4 Aina, Ademola; Wenger, Jonathan P.; Stanton, Eliot; Majumdar, Chandrani Gon; ElSohly, Mahmoud; Weiblen, George D.; Ellison, Shelby (1 July 2025). "Genetic diversity, population structure, and cannabinoid variation in feral Cannabis sativa germplasm from the United States". Scientific Reports. 15 (1) 20423. doi:10.1038/s41598-025-07912-8. PMC 12215616.
- ↑ 7.0 7.1 7.2 7.3 Lübberstedt, T.; Beavis, W.; Suza, W. (2023). "Marker Assisted Backcrossing". In Suza, W.; Lamkey, K. (eds.). Molecular Plant Breeding. Iowa State University Digital Press. doi:10.31274/isudp.2023.133.
- ↑ 8.0 8.1 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.
- ↑ 9.0 9.1 Wenger, J.P.; Dabney, C.J.; ElSohly, M.A.; Chandra, S.; Radwan, M.M.; Majumdar, C.G.; Weiblen, G.D. (2020). "Validating a predictive model of cannabinoid inheritance with feral, clinical, and industrial Cannabis sativa". American Journal of Botany. 107 (10): 1423–1432. doi:10.1002/ajb2.1550. PMC 7702092.