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Cannabis Genetics: Building a better crop

by Mike May
Published: Jun 01, 2017   
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A spider’s web of lines connects globes of colors that rotate slowly on my screen, showing a three-dimensional map. As I click on one globe, a box emerges on the screen. This box informs me that four cuts of a cannabis strain called “Golden Pineapple Clone Group” have been sequenced, along with who collected the cuts and from where. This is Phylos Galaxy —a population genetics map of cannabis DNA that profiles more than 3,000 strains collected from more than 80 countries. Phylos Galaxy was developed by Alisha Holloway, director of bioinformatics at Phylos Bioscience.

Genotyping cannabis—determining the order of amino acids that make up its DNA—is a blooming business. When I ask Reggie Gaudino—vice president, science, genetics and intellectual property at Steep Hill Labs —why anyone would genotype cannabis, he replies: “Why genotype any plants?” His answer: “To be able to breed any plant, you want to find traits that you find desirable and augment them.” A sequenced genotype reveals elements of DNA, such as single nucleotide polymorphisms (SNPs), that relate to unique and potentially useful traits of a specific strain. “Genotyping gives you many different levels of information that are useful to try to manipulate any crop,” he explains.

For medicinal cannabis, some strains are more effective in treating specific conditions than others. As Jes Kristof, director of research at Phylos Bioscience, says, “Very specific strains address specific medical conditions, and the wrong one can even create an adverse effect.” Genotyping is the only way to guarantee the authenticity of the strain.  

Foiling fraud and getting the best cannabis strain for purpose

Some dispensaries and growers, Kristof says, have sold cannabis products under the incorrect name, just because that name sells better. With genotyping, she says, “consumers can see what they’re buying, growers can confirm what they’re growing and breeders can identify which plants they want to breed with.”

Although cannabis can be genotyped in about the same way as any other organism, Gaudino says that it’s still rare. “Only a few organizations are doing it,” he notes. When cannabis is genotyped, a company typically uses next-generation sequencing (NGS), which handles samples relatively quickly. For example, Steep Hill uses an NGS platform from Pacific Biosciences, and Phylos Bioscience uses one from Illumina .

Every sequencing run at Phylos Bioscience includes about 100 samples, and the Illumina NGS platform provides high coverage—meaning that it explores the genotype thoroughly. “We’re not shaving data to save money,” Kristof says.

Results of DNA sequencing offer advantageous information for growers. Specifically, the speed of the process makes a big difference in breeding and growing. Instead of growing a plant for eight months to see if it has the desired traits, genotype sequencing can reveal the traits of the plant by using DNA from the leaves of plants that have only been grown for one to two months. “If you can decide if you want to breed a plant by the time it’s one foot tall instead of eight, you can do more generations,” Gaudino explains. “We have customers getting four generations a year.”

In short, scientists can test and describe the DNA of cannabis to improve products and ensure that products include the right strain. “The take-home point,” Kristof says, “is that cannabis is a plant, and all of the same real science that goes into the study of any plant can be done on cannabis.” And it should be.


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