Tag Archives: phenotype

The First Map of the Cannabis Genome

By Aaron G. Biros
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Sunrise Genetics, Inc., the parent company for Hempgene and Marigene, announced last week they have successfully mapped the cannabis genome. The genome map was presented at the 26th Annual Plant and Animal Genome Conference in San Diego, CA during the panel “Cannabis Genomics: Advances and Applications.”

According to CJ Schwartz, chief executive officer of Sunrise Genetics, the full genome map will allow breeders to develop strains using DNA sequence information to complement phenotyping. “In this way a breeding program can be guided by the breeder versus blindly as it is for just pheno-hunting,” says Schwartz. “At the DNA level, we can identify what version of a set of genes a plant contains, and make predictions as to the phenotype, without ever growing the plant. As we make more and more gene markers, we have more genes to track, and breeding becomes more rapid, efficient and precise.” Schwartz says this is essential for breeding stable, repeatable plants. “A commercial strain will be grown in different environments, with solid genetics, the phenotype will mostly stay true, a term we call Genetic Penetrance.”

Ancestry-painted chromosomes for marijuana Image: Chris Grassa / Sunrise Genetics

Determining a plant’s DNA can be extremely valuable and completing the map of the genome now makes this more precise. It can serve as a point of proof, according to Schwartz, providing evidence of lineage in a breeding project and confirming the uniqueness and identity of a strain. The genome map can also allow breeders to select specific genes to develop custom strains. And in addition to all that, it provides legal protection. “Knowing your plants DNA code is the first step to being able take action so no one else can protect it,” says Schwartz. “Well documented evidence in the development of a customized strains is essential to maintaining control of your plant and keeping those you distrust (big pharma) away, many of which have minimal interest in the whole plant anyhow.”

CJ Schwartz, chief executive officer of Sunrise Genetics

Schwartz says this project took them roughly 18 months to wrap up. “One of the biggest problems was just finding the right plants to grow,” says Schwartz. “In addition we used some emerging technologies and those had some challenges of their own.” According to Schwartz, a key aspect in all this was finding the right collaborators. They ended up working with CBDRx and the plant biology department at the University of Minnesota, where a DEA-licensed lab has been researching cannabis since 2002. “George Weiblen’s group at UM has been working on Cannabis for over a decade,” says Schwartz. “During that time they did repeated selfing to make highly inbred marijuana and hemp lines. The lines were instrumental in deterring the physical order of the genes.”

Ancestry-painted chromosomes for hemp Image: Chris Grassa / Sunrise Genetics

After finishing up some experiments, they expect to get the genome map published on public domain in less than a year, opening up their research to the general public and allowing breeders and growers to use their data. “This will be a very significant publication,” says Schwartz. “The genome assembly allows for the assimilation of all the currently incompatible Cannabis genome sequence datasets from academia and private companies,” says Schwartz. “Joining datasets from 1000s of strains, and from every continent, will generate an essential public resource for cannabis researchers and aficionados alike.” With a tool like this, we can discover the genes that help produce desirable traits. “This project is a major accomplishment for cannabis, bringing it on par with other important crops, providing a scientific tool to unravel the secrets of this incredibly versatile plant,” says Schwartz.

Sunrise Genetics is assisting cannabis businesses in evaluating strains and developing breeding programs, working with a number of customers currently to develop strains for many different specific traits. “We have the expertise to help select parental strains and guide the selection process at each generation using genotype and phenotype information,” says Schwartz. “Essentially we are bringing all the tools any modern plant breeder would use for improving strawberries to cannabis.”

An Introduction to Cannabis Genetics, Part III

By Dr. CJ Schwartz
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Polyploidy in Cannabis

Polyploidy is defined as containing more than two homologous sets of chromosomes. Most species are diploid (all animals) and chromosomal duplications are usually lethal, even partial duplications have devastating effects (Down’s syndrome). Plants are unique as in being able to somewhat “tolerate” chromosomal duplications. We often observe hybrid vigor in the F1, while the progeny of the F1 (F2) will produce mostly sickly or dead plants, as the chromosomes are unable to cleanly segregate.

polyploidy
Polyploids are generated when chromosomes fail to separate (non-disjunction) during pollen and egg generation. The chromosomes normally exist in pairs, thus having only one, or three, interferes in pairing in subsequent generations.

Chromosomal duplications, either one chromosome or the whole genome, happen frequently in nature, and actually serves as a mechanism for evolution. However the vast majority (>99.99%) results in lethality.

Thus there is polyploidy in Cannabis, and a few examples are supported by scientific evidence. The initial hybrid may show superior phenotypes and can be propagated through cloning, but there may be little potential for successful breeding with these plants.

Epigenetics and Phenotypic Consistency in Clones

One mechanism of turning off genes is by the DNA becoming physically inaccessible due to a structure resembling a ball. In addition, making molecules similar to DNA (RNA) that prevents expression of a gene can turn off certain genes. Both mechanisms are generally termed epigenetics.

These mice are all genetically identical yet they manifest different phenotypes for fur color.
These mice are genetically identical, yet their coat color phenotype is variable. Something above or beyond (epi) the gene (genetic) is controlling the phenotype.

Epigenetic regulation is often dependent on concentrations of certain proteins. Through the repeated process of cloning, it is possible that some of these proteins may be diluted, due to so many total cell divisions and epigenetic control of gene expression can be attenuated and results in phenotypic variability.

Sexual reproduction, and possibly tissue culture propagation, may re-establish complete epigenetic gene regulation, however the science is lacking. Epigenetic gene regulation is one of the hottest scientific topics and is being heavily investigated in many species including humans.

Hermaphrodites and Sex Determination

Cannabis is an extremely interesting genus (species?) for researching sex determination. Plants are usually either monoecious (both male and female organs on a single plant), or dioecious, separate sexes. Sex determination has evolved many times in many species. Comparing the mechanisms of sex determination in different organisms provides valuable opportunities to contrast and compare, thereby developing techniques to control sex determinations.

The sex organs on a Cannabis plant identified.
The sex organs on a Cannabis plant identified.

Cannabis is considered a male if it contains a Y-chromosome. Females have two X chromosomes. Even though female Cannabis plants do not have the “male” chromosome, they are capable of producing viable pollen (hermaphrodite) that is the source of feminized seeds. Therefore, the genes required to make pollen are NOT on the Y-chromosome, but are located throughout the remainder of the Cannabis genome. However, DNA based tests are available to identify Male Associated Sequence (MAS) that can be used as a test for the Y-chromosome in seedlings/plants.

Natural hermaphrodites may have resulted from Polyploidization (XXXY), or spontaneous hermaphrodites could be a result of epigenetic effects, which may be sensitive to the environment and specific chemical treatments.

Feminized seeds will still have genes segregating, thus they are not genetically identical. This shouldn’t lead to a necessary decrease in health, but could. A clone does not have this problem.

The other issue is that “inbreeding depression” is a common biological phenomenon, where if you are too inbred, it is bad…like humans. Feminized seeds are truly inbred. Each generation will decrease Heterozygosity, but some seeds (lines) may be unhealthy and thus are not ideal plants for a grower.

GMO– The Future of Cannabis?

Is there GMO (genetically modified organism) Cannabis? Probably, but it is likely in a lab somewhere…deep underground! Companies will make GMO Cannabis. One huge advantage to doing so is that you create patentable material…it is unique and it has been created.

The definition of a GMO is…well, undefined. New techniques exist whereby a single nucleotide can be changed out of 820 million and no “foreign” DNA remains in the plant. If this nucleotide change already exists in the Cannabis gene pool, it could happen naturally and may not be considered a GMO. This debate will continue for years or decades.

Proponents of GMO plants cite the substantial increase in productivity and yield, which is supported by science. What remains to be determined, and is being studied, are the long-term effects on the environment, ecosystem and individual species, in both plants and animals. Science-based opponent arguments follow the logic that each species has evolved within itself a homeostasis and messing with its genes can cause drastic changes in how this GMO acts in the environment/ecosystem (Frankenstein effect). Similarly, introducing an altered organism into a balanced ecosystem can lead to drastic changes in the dynamics of the species occupying those ecological niches. As in most things in life, it is not black and white; what is required is a solid understanding of the risks of each GMO, and for science to prove or disprove the benefits and risks of GMO crops.