Do Cannabis Clones Change Over Time? What Sequencing Says About Mother Plants and Tissue Culture
Growers have said it for years: a cultivar "isn't what it used to be." Vigor fades, potency slips, and the clone you're running today doesn't seem to match the one you started with. Is that real, or just memory playing tricks? Over the past few years, a group of Canadian researchers has started putting numbers to the question. Here are three of their studies, and what they mean together.
A note on terms
The changes in these studies build up inside a single clonal line, as cells divide in a mother plant or in tissue culture. Scientists call DNA changes that arise this way somatic mutations. Genetic or epigenetic changes that arise during tissue culture are called somaclonal variation. Growers usually notice the end result as clonal decline: a line that seems to lose vigor or potency over time.
Study 1: one mother plant, many genomes
In a 2022 study in The Plant Genome, Kristian Adamek, Andrew Maxwell Phineas Jones (University of Guelph) and colleagues deep-sequenced a single 'Honey Banana' mother plant. The plant was about a year and a half old and 2.4 m tall. They took stem samples from the bottom, middle and top.
Every cell in a plant is supposed to carry the same DNA. Instead, the team found that each part of the plant had its own set of variants. The top of the plant stood out: nearly 600,000 variants were unique to the top sample, compared with about 148,000 unique to the bottom and about 77,000 unique to the middle. Genetic diversity was elevated in or near four genes in the cannabinoid and terpene pathways, including CBDAS, though none of those genes carried high-impact mutations.
This was one plant with no replicates, so it can't tell us how common this is. But it shows that a mother plant is not one genome. It's a mosaic, and cuttings from different parts of it may not be identical.
Study 2: mutations add up with every subculture
In 2024, Adamek, Jones and Davoud Torkamaneh (Université Laval) asked the same question about tissue culture. They genotyped 70 clones that had been through 6 to 11 subcultures and found 9,405 polymorphic variants.
The key finding: mutations increased with the number of subcultures, even though all the clones were the same age. In other words, it's not time in culture that matters most, it's how many times a line has been divided and transferred. Most variants were low-impact, but 14 high-impact variants turned up in genes important for plant development, and 6 were in genes linked to cannabinoid and terpene synthesis.
The authors point to banana as a model. Commercial banana propagators typically limit cultures to about five subcultures before restarting from fresh stock, to keep off-types in check.
Study 3: methylation marks travel with the clone
Not all change is in the DNA sequence. Epigenetic marks, like DNA methylation, help switch genes up or down. In a 2024 study in Frontiers in Plant Science, Justin Boissinot, Torkamaneh and colleagues developed a fast, low-cost method called CREAM to read methylation patterns, and used it on 78 cannabis clones in tissue culture.
They found 2,272 methylated regions that varied among the clones. But the patterns were preserved across subcultures, so consistently that the team could tell apart two subsets of clonal lines by their methylation alone. In this system, tissue culture carried a line's epigenetic signature forward rather than scrambling it.
How this fits with the 60-week study
We recently wrote about a 2026 study that followed three cultivars for 60 weeks in culture. It found most new mutations appeared at initiation and in the first five subcultures, then leveled off. That sounds different from the 2024 finding that mutations keep adding up with each subculture. The studies used different cultivars, protocols and time frames, so they don't have to contradict each other. Together they point to the same two pressure points: the initiation step, and the number of times a line is subcultured.
What this means for growers
Mother plants change too. Somatic mutations build up in long-lived mothers, and different branches can carry different variants. Tissue culture isn't the only source of change.
Count subcultures, not just months. The number of transfers appears to matter more than calendar age.
Keep a reference. Store the original material and plan when to return to it, rather than propagating indefinitely from copies of copies.
Epigenetic marks can persist. Moving a line into tissue culture doesn't automatically wipe its history.
How we approach it at Zennetix
So far we haven't seen signs of instability in our lines, and we keep watching for it. If a line ever needs a fresh start, we can re-initiate it through meristem culture. We're also building a long-term reference library using cold storage and cryopreservation, so the original genetics are always there to come back to.
Caveats
The 2022 study looked at a single plant. The 2024 studies used genotyping and methylation methods that sample part of the genome rather than all of it. None of the three measured whether these changes affected yield, potency or plant structure. That's the next question the field needs to answer.
Sources
Adamek, K., Jones, A.M.P., Torkamaneh, D. (2022). Accumulation of somatic mutations leads to genetic mosaicism in cannabis. The Plant Genome. https://doi.org/10.1002/tpg2.20169
Adamek, K., Jones, A.M.P., Torkamaneh, D. (2024). Somatic mutation accumulations in micropropagated cannabis are proportional to the number of subcultures. Plants, 13(14), 1910. https://doi.org/10.3390/plants13141910
Boissinot, J., Adamek, K., Jones, A.M.P., Normandeau, E., Boyle, B., Torkamaneh, D. (2024). Comparative restriction enzyme analysis of methylation (CREAM) reveals methylome variability within a clonal in vitro cannabis population. Frontiers in Plant Science, 15. https://doi.org/10.3389/fpls.2024.1381154
Questions about keeping your genetics true to type? Email us at sales@zennetix.com.
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