High Times Magazine recently released an article How Genomics is Shaping the Future of Cannabis Genetics by Oaksterdam’s Director of Academics, Angela Bacca. We conducted many in-depth interviews with experts on cannabis genomics and genetics, which are fascinating reads in their own right that we wanted to share. Below is a Q&A with Alisha Holloway, PhD, Chief Scientific Officer at Phylos Bioscience, about their groundbreaking cannabis genomic research and how it is shaping the industry today.
The Phylos Galaxy displayed the relationship between individual genetically sequenced cannabis cultivars (represented by the stars) and the relationships between them (represented by the constellations). PHOTO SOURCE: Friendly Aussie Buds
Angela Bacca (AB): The Phylos Galaxy used genetic sequencing to visually demonstrate the relationship between cannabis cultivars and really changed the industry’s understanding of the relationship between them, as well as the notion that cultivar names correlated with plant genetics. What were some of the other major discoveries you made with the Phylos Galaxy?
Alisha Holloway (AH): One of the most important discoveries was that the Galaxy gave cultivators a way to verify the uniqueness of their cultivars and understand their pedigrees. It provided clarity in a market where names and lineages were often confusing, and that transparency helped people protect and celebrate what they had.
Another powerful insight was just how much genetic diversity had been preserved, even through decades of Prohibition. That was only possible because growers around the world worked hard, and often at real personal risk, to maintain their collections. Thanks to their stewardship, access to a huge pool of traits is possible; new cannabinoids and other compounds, unique aromas, and disease resistance can continue to shape the future of cannabis.
I also think it is important to clear up one common misconception about the Galaxy. Since there was no trait data linked to the DNA data of those samples, it was not possible to identify genetic markers or use them directly for breeding. The Galaxy was a diversity map, not a breeding engine. To build our breeding program, we had to do the hard work ourselves: growing tens of thousands of plants in our own facility, genotyping them, and carefully measuring every trait of interest. Only by combining DNA data with full trait datasets of the plants we grew were we able to begin identifying markers and using them in breeding.
AB: One of the big differences between 23andMe and Ancestry.com is the DNA samples in their databases. Ancestry’s database skews pretty heavily to Northwest European samples (although this has shifted recently), while 23andMe has a more diverse database that includes DNA from ancient humans from archaeological digs. In this context, how did Phylos’s Galaxy compare, and how did it enable major discovery?
AH: The Phylos Galaxy started with a very diverse set of samples, which provided a broad view of cannabis genetics. Over time, the picture that emerged was shaped by what people were actually growing and selling, so commercial varieties were heavily represented. We also worked hard to include landrace accessions, because those lines carry unique diversity and traits that commercial plants often lack. Landrace varieties may hold resistance to disease, or entirely different chemical profiles, and including them meant the Galaxy showed a more complete picture of diversity, even if we didn’t know what traits that diversity represented
That dynamic led to one of the Galaxy’s most important insights. Cannabis varieties that survived in the market were the ones that met two conditions. They had to create a great experience for consumers, and they had to work economically for cultivators. Without agronomic traits like yield, vigor, or pest resistance, no variety could succeed at scale no matter how amazing the effects were. The sales price doesn’t always scale with the effort to grow a cultivar. Those high-cost-to-grow plants usually stayed in personal head stashes instead of being grown commercially.
By making this visible, the Galaxy showed how market forces shape genetic diversity. It helped explain why certain varieties took over, why others disappeared, and how the industry was filtering plants to balance consumer demand with grower profitability. At the same time, it revealed how untapped diversity could be harnessed to create new possibilities for the future.
“By making this visible, the Galaxy showed how market forces shape genetic diversity. It helped explain why certain varieties took over, why others disappeared, and how the industry was filtering plants to balance consumer demand with grower profitability. At the same time, it revealed how untapped diversity could be harnessed to create new possibilities for the future.”
With the permission of sample submitters, we also released the underlying data to the National Center for Biotechnology Information, making it available to university and independent researchers worldwide. That open access had a real impact. Those data were used for several publications and added to other databases of cannabis genetic variation. Additionally, according to Humboldt Seed Company, this data was critical in successfully challenging an overly broad patent claim, protecting the community’s shared genetic resources.
The Galaxy also gave breeders a way to understand the genetic background of the plants they were working with. Sometimes crossing very different backgrounds produces novel phenotypes and the Galaxy let people see those opportunities before making breeding decisions. By making the results public, we not only supported research and defended against patents, we also gave breeders a way to connect, share knowledge, and collaborate more effectively.
AB: The industry has long been associating specific effects with specific cultivars. Many thought this would happen through genetic sequencing, and it still hasn’t. Can we ever really define a cultivar’s effects by genotype?
It is possible to find genetic markers for specific compounds, like THCV, and then make some predictions about the effects a variety might have. The bigger issue is that we still have not fully mapped which combinations of compounds in cannabis are responsible for which effects. Cannabinoids are only part of the picture. There are hundreds of other molecules at play, and their interactions matter. THCV, for example, often produces an energizing, motivating effect, but just knowing that a plant has the genetic potential for THCV does not tell you how it will interact with other compounds to produce different effects. We are also just beginning to understand why some people have very different experiences with the same products, which remains one of the deeper mysteries of cannabis.
Complicating things further, in many cases, the assays to test for these minor compounds are not widely available. Sometimes demand is low, other times the compounds occur only in very small amounts in most varieties, so testing has not been prioritized. That gap makes it even harder to link chemistry to effects in a systematic way.
So while genetics can provide clues about the expression of cannabinoids and other compounds, we still have a long way to go to understand the complex combinations that bring about all the different effects and uses for cannabis.
The molecular structure of tetrahydrocannabinol (THCV).
AB: What are some of the traits Phylos is researching and breeding for now? How will they change the industry?
AH: Right now, we are focused on traits that allow cultivators to grow at scale efficiently while also creating a reliable consumer experience. The consumer experience always has to be incredible, but growers also need plants that perform. That means high yields, strong potency, complex and interesting aromas, rare cannabinoids, distinctive color variations, clone-like uniformity, and stress tolerance. All of our research funnels into varieties where these traits are not just present but fixed and reliable.
One example is our work with THCV. By using genetic markers that we discovered, we were able to upregulate THCV from about 4 percent to as much as 20 percent, which was an early demonstration of how targeted breeding can create real breakthroughs. This type of work allows growers to bring plants with unique effects to market, which brings profit to the growers and provides consumers with new options.
We are also reinventing autoflower varieties. Traditionally, they had a poor reputation because they had low potency, poor flower quality, and tasted like cooking oil. We committed years of breeding to autoflower because they have amazing advantages—no need for light deprivation, and can be very low touch with a high ratio of flower to other biomass. This is long-term work, generation after generation. Our autoflower lines now deliver what the market never expected from them: high potency, great aromas and tastes, large yields, bud structure with bag appeal, a broader range of effects, and consistency that growers can count on.
This changes the economics of cultivation. Autoflower short cycles open up outdoor production in more regions and allow greater flexibility in crop planning. Overall, seed-based production reduces labor and infrastructure costs indoors, which can be transformative for margins and scale. Organigram has published work showing they were able to reduce costs by 54 percent when shifting to seed-based autoflower production, a clear example of how powerful the impact can be.
Want to learn more about cannabis genetics, genomics, and breeding? Check out our new Cannabis Breeding with James Loud certification program, which includes seven self-paced modules with course videos and an extensive collection of supplemental resources. There is also another opportunity to join live classes in April 2026!