Intra-plant genetic diversity in cannabis: Clone not a clone? | The Plant Genome Webinar

Adamek et al. (2021) discovered genetic diversity within a single cannabis mother plant by deep sequencing the whole genome of samples from the top, middle and bottom.

The cultivation of cannabis plants for medicinal or recreational applications is primarily achieved using clonal cuttings from elite stock plants, better known as mother plants. Bananas, potatoes, grapes, hops, and many other plant species are also cultivated using vegetative propagation to ensure that desirable and consistent phenotypes are passed onto the clones for mass production. In theory, clones are identical to the parent stock. However, there have been numerous anecdotal reports from cannabis growers that have described a decay over time in the quality of clones and often observe reduced plant vigor and secondary metabolites levels. These observations have led to concerns with consistency and the potential loss of major genetic characteristics. While this has not been formally evaluated in cannabis, it has been observed in other plant species that are vegetatively propagated and is thought to be related to the accumulation of deleterious somatic mutations, as referred to as Muller’s Ratchet. Hence, our research set out to investigate if somatic mutations accumulate within cannabis and, thereby, provide a plausible explanation for the observed decline in quality over time.
Whole-genome sequencing was conducted at three locations of a single mother plant, representing the bottom, middle and top regions. Utilizing bioinformatics, millions of variants were detected by aligning the samples’ genomes to a reference genome. Furthermore, the reference genome functioned as an outgroup that revealed the samples’ shared and distinct allelic states. The sequences of the samples were compared to one another and identified that nearly 600,000 (34%) variants were unique to the top while the bottom only contained 148,000 (12%), and middle with 77,000 (9%) unique variants. These results identified genetic mosaicism within an individual cannabis mother plant and revealed the concern of mother plants accumulating mutations over time and passing them onto clonal cuttings. Eventually, the quality will be negatively impacted as mutations are more prone to damaging gene function than improve it. However, this is not always the case as somatic mutations can be beneficial too and are responsible for numerous new cultivars from bud sports for plant species such as citrus trees, apple trees, and grapevines. Clones were thought to be genetically identical to the mother plants, but this does not appear to be the case as each branch has the potential to accumulate its own set of unique mutations.
Additionally, a bioinformatics-based approach was used to identify mutations located at or near critical genes for both cannabinoid and terpene pathways. While none were found to have a high-impact effect (i.e. disrupting gene function), four genes were discovered with more than double genetic variation compared to the average for the whole genome. These comparisons suggest that mutations may not be entirely random and that there are mutationally prone regions within the genome, also known as mutational hotspots. As a result, mutations could accumulate and exist within specific pathways. However, future research with various cultivars and generational data will be necessary to uncover a complete understanding. Overall, our study displayed various amounts of intra-plant mutations and revealed the substantial genetic diversity within a single cannabis mother plant.

Featured Article and Transcripts
“Accumulation of somatic mutations leads to genetic mosaicism in cannabis” published in The Plant Genome: https://doi.org/10.1002/tpg2.20169

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The Plant Genome: https://acsess.onlinelibrary.wiley.com/journal/19403372
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Soil Science Society of America (SSSA): https://www.soils.org/

Resources
CSA News Article – https://acsess.onlinelibrary.wiley.com/doi/epdf/10.1002/csan.20640
Dr. Max Jones lab: https://www.plant.uoguelph.ca/amjones
Dr. Davoud Torkamaneh: https://www.ibis.ulaval.ca/en/research/davoud-torkamaneh/

Shout Outs and Disclaimers
This webinar is Copyrighted by the American Society of Agronomy, Crop Science Society of America, and Soil Science Society of America.

Opinions and conclusions expressed by authors are their own and are not considered as those of the American Society of Agronomy, Crop Science Society of America, Soil Science Society of America, its staff, its members, or its advertisers.

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