Tag Archives: DNA

By Khyrrah-Cymone Shepard

Genome sequencing has made remarkable strides since the initiation of “The Human Genome Project” in 1990. Still, there are many challenges that must be overcome before this methodology can reach its fullest potential and be useful in serving as a method of Cannabis sativa genetics verification and tracking throughout the cannabis supply chain. Several major milestones that must be realized include end-to-end haploid type (single, unpaired set of chromosomes instead of complete paired set or “diploid”), long read, resolved genome sequences at a reasonable cost within a reasonable timeframe and with confidence in accuracy (Mostovoy et al.). These genomes are typically generated as shorter reads that are then scaffolded (Fig 1.) or matched to reference genomes in order to build a longer continuous read. While shorter sequencing reads indeed lower the cost barrier for producing more genomic data, it has created another issue as a result of this short-read technology.

Figure 1: Four sets of sequencing data (long-read WGS, Hi-C, optical mapping, and short-read WGS) were produced to generate the goat reference genome. A tiered scaffolding approach using optical mapping data followed by Hi-C proximity-guided assembly produced the highest-quality genome assembly. (Bickhart et al.)

There are two main issues with the more affordable short read sequencing methodology, the first being that sequential variants are typically not detected, especially if they involve a ton of repeats/inverted repeats, due to the limitation of the current referenced Cannabis genomes and the mapping process of the short-read sequences. This is especially unfortunate because larger variants can have up to a 13% variance within a diploid multichromosomal genome, such as Cannabis sativa, and this variance is thought to largely contribute to disease in various species, or maybe terpene profile in Cannabis sativa. Not being able to detect these variances with more affordable sequencing methodologies is particularly problematic and reference genomes produced with short read sequences are typically highly fragmented. The second limitation is the inherent errors, gaps and other ambiguities associated with taking tons of short read sequences and combining them all, like a jigsaw puzzle, in order to draft the larger genomic picture. While there is software with algorithms to assist in deciphering raw sequences, there is still much more work to be done on this challenge, considering that cannabis genome sequencing is new genomics territory. Unfortunately, as researchers seek higher and higher levels of data quality, shortcomings of this type of sequencing technology begin to become apparent. This sort of sequencing methodology relies heavily on reference sequences. This isn’t much of an issue with microbial genomes, which tend to be rather short and typically have one chromosome, however, when seeking to analyze much longer genomes with multiple diploid chromosomes and tons of mono and dinucleotide repeats, problems arise (English et al.).

Figure 2: Blockchain Digital Stamping Certificate which publicly documents the date and time of the completion of this work. (Mckernan – Crypto Funded Public Genomics)

The other category of sequencing is long read sequencing. Long read sequencing is as it sounds, the deciphering of much longer DNA strands. Of course, the technology is limited by the quality of the DNA captured, therefore, special high molecular weight DNA extraction protocols must be deployed in order to obtain the proper DNA quality (Fig. 3). Once this initial limitation is overcome there is the stark cost of long read sequencing technology. PacBio without a doubt makes one of the highest quality long read sequence generating instruments that has ever graced the field of biotechnology, but due to the steep price tag of the machine, progress in this field has been stifled simply because it just isn’t affordable and the read depth for mammalian and plant genomes is currently almost completely prohibitive until read lengths double in length for this instrumentation. In order to produce what is considered to be a “validated genome” both short read and long read sequencing methodologies are combined. Long read sequencing data is used to produce the reference contigs because they are much easier to assemble, then short read sequencing is scaffolded against the reference contigs as a sort of “consensus validation” of the long read contigs.

Figure 3: Depiction of various DNA high molecular weight DNA quality captured during cannabis genome submission project. (Mckernan – Crypto Funded Public Genomics)

Despite the shortcoming of utilizing short read sequencing technology for analysis of the cannabis genome, it is still useful especially when combined with other longer read sequencing technologies or optical mapping technologies. Kevin McKernan, chief scientific officer of Medicinal Genomics, has been working feverishly to bridge the information gap between the cannabis genome and other widely studied plant genomes. As a scientist that worked on the Human Genome Project in 2001, McKernan has a demonstrated history of brilliance in the field of genomics. This paved the way for him to coordinate the first crypto funded and blockchain notarized sequencing project (DASH DAO funded) (Fig. 2), which was completed in 60 days, and surprisingly showed that the cannabis genome is over 1 billion bases long which is 30% larger than any cannabis genome submitted prior to his work. By reaching the standard of 500kb N50 set forth by the Human Genome Project, Kevin McKernan was able to see new aspects of the cannabis genome that were not visible due to the fragmented genomic data previously generated. Information such as a possible linkage of THCA synthase and CBDA synthase genes is crucial when seeking to use the cannabis genome for verification and tracking purposes. This is because special linkages can be considered a type of “genetic marker” that may be used to differentiate cannabis cultivars and lineages. There are many types of genetic markers, including SNP (single nucleotide polymorphisms), VNTR (variable number tandem repeats) and even patterns of gene expression. Funding and recording of cannabis genomics must be further developed in order for potential markers to be identified and validated via larger scale genome-wide association studies.

These technologies, when combined, often reduce the number of scaffolds while increasing the percent of resolved genome by filling in gaps within the drafted genome. Nanopore sequencing is an especially interesting and innovative sequencing technology that is useful in many ways. One of the most powerful uses of this technology is its ability to upgrade the quality of draft and pushed genomes by resolving poorly organized genomes and genomic structure for a fraction of the time and cost of other long read sequencing platforms (Jian et al.), making it an excellent candidate for solving cost and time constraints. Nanopore’s portability and convenience makes it a real-time solution to solving genetics-based problems and questions. A notable use of this technology is recorded during an epidemiological outbreak in Africa, its proof of concept in pathogen detection in space, and its ability to detect base modifications during sequencing process. Even still there are more uses to this exciting technology and it has the potential to elevate cannabis genomics and the field of genomics entirely, while remaining portable and expeditious. A shortcoming of the Nanopore sequencing platform is its low sequencing coverage, which makes this platform inefficient for applications like haplotype phasing and single nucleotide variant detection due to the number of variants to be detected being smaller than the published variant-detection error rates of algorithms using MinION data. Single nucleotide variants can be considered to be genetic markers, especially markers for disease, so this is what inhibits Nanopore from resolving our cannabis genome sequencing problems, as of today.

There are genetic markers to discover, molecular biology protocols to optimize, and industry wide potential for exciting collaborationMany algorithmic problems seem to occur due to input data quality. Typical input data quality suffers as the reads get longer and the sequencing depth gets shorter, resulting in not enough data being generated by the sequencing to provide confidence in the genome assembly. To mitigate this, scientists may decide to fractionate a genome, sequence it, or they may clone a difficult to sequence region with highly repetitive regions in order to produce reads with greater depth and thus resolve the region. They can then perform single molecule sequencing to resolve genome structure then determine and confirm the place of the cloned region. Thus, it seems that the best solution to the limitation of algorithms is to be aware of sequencing platform limitations and compensate for these limitations by using more than one sequencing platform to obtain enough pertinent data to confidently produce authentic, “validated” genome assemblies (Huddleston et al.). With input data being critical in producing accurate sequencing data, standardization of DNA isolation protocols, extraction reagents and any enzymes utilized may be deemed necessary.

To conclude, the field of cannabis genomics is teeming with opportunities. There are genetic markers to discover, molecular biology protocols to optimize, and industry wide potential for exciting collaboration. More states will need to take into account the lack of federal government research grant availability and begin to think of creative ways to get cannabis science funds to continue the development of this industry. Specifically speaking, developing a feasible method for genetic tracking of cannabis plants will require improvements within the availability of sequencing technology, improvements in deploying the resources to these projects in order for them to be completed expeditiously, and standardization/validation of methods and SOPs used in order to increase confidence in the accuracy of the data generated.

A special thank you to all of my cannabis industry mentors that have molded and elevated my understanding of current needs and applied technologies within the cannabis industry, without you there would be no career within this industry for me. You are immensely appreciated.

Citations

Bickhart, D. M., Rosen, B. D., Koren, S., Sayre, B. L., Hastie, A. R., Chan, S., . . . Smith, T. P. (2017). Single-molecule sequencing and chromatin conformation capture enable de novo reference assembly of the domestic goat genome. Nature Genetics,49(4), 643-650. doi:10.1038/ng.3802

English, A. C., Salerno, W. J., Hampton, O. A., Gonzaga-Jauregui, C., Ambreth, S., Ritter, D. I., . . . Gibbs, R. A. (2015). Assessing structural variation in a personal genome—towards a human reference diploid genome. BMC Genomics,16(1). doi:10.1186/s12864-015-1479-3

Huddleston, J., Ranade, S., Malig, M., Antonacci, F., Chaisson, M., Hon, L., . . . Eichler, E. E. (2014). Reconstructing complex regions of genomes using long-read sequencing technology. Genome Research,24(4), 688-696. doi:10.1101/gr.168450.113

Jain, M., Olsen, H. E., Paten, B., & Akeson, M. (2016). The Oxford Nanopore MinION: Delivery of nanopore sequencing to the genomics community. Genome Biology,17(1). doi:10.1186/s13059-016-1103-0

Mostovoy, Y., Levy-Sakin, M., Lam, J., Lam, E. T., Hastie, A. R., Marks, P., . . . Kwok, P. (2016). A hybrid approach for de novo human genome sequence assembly and phasing. Nature Methods,13(7), 587-590. doi:10.1038/nmeth.3865

March 1, 2018

Colorado vs. California: Two Different Approaches to Mold Testing in Cannabis

By Swetha Kaul, PhD

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Across the country, there is a patchwork of regulatory requirements that vary from state to state. Regulations focus on limiting microbial impurities (such as mold) present in cannabis in order for consumers to receive a safe product. When cultivators in Colorado and Nevada submit their cannabis product to laboratories for testing, they are striving to meet total yeast and mold count (TYMC) requirements.In a nascent industry, it is prudent for state regulators to reference specific testing methodologies so that an industry standard can be established.

TYMC refers to the number of colony forming units present per gram (CFU/g) of cannabis material tested. CFU is a method of quantifying and reporting the amount of live yeast or mold present in the cannabis material being tested. This number is determined by plating the sample, which involves spreading the sample evenly in a container like a petri dish, followed by an incubation period, which provides the ideal conditions for yeast and mold to grow and multiply. If the yeast and mold cells are efficiently distributed on a plate, it is assumed that each live cell will give rise to a single colony. Each colony produces a visible spot on the plate and this represents a single CFU. Counting the numbers of CFU gives an accurate estimate on the number of viable cells in the sample.

The plate count methodology for TYMC is standardized and widely accepted in a variety of industries including the food, cosmetic and pharmaceutical industries. The FDA has published guidelines that specify limits on total yeast and mold counts ranging from 10 to 100,000 CFU/g. In cannabis testing, a TYMC count of 10,000 is commonly used. TYMC is also approved by the AOAC for testing a variety of products, such as food and cosmetics, for yeast and mold. It is a fairly easy technique to perform requiring minimal training, and the overall cost tends to be relatively low. It can be utilized to differentiate between dead and live cells, since only viable living cells produce colonies.

Petri dish containing the fungus Aspergillus flavus.
Photo courtesy of USDA ARS & Peggy Greb.

There is a 24 to 48-hour incubation period associated with TYMC and this impedes speed of testing. Depending on the microbial levels in a sample, additional dilution of a cannabis sample being tested may be required in order to count the cells accurately. TYMC is not species-specific, allowing this method to cover a broad range of yeast and molds, including those that are not considered harmful. Studies conducted on cannabis products have identified several harmful species of yeast and mold, including Cryptococcus, Mucor, Aspergillus, Penicillium and Botrytis Cinerea. Non-pathogenic molds have also been shown to be a source of allergic hypersensitivity reactions.The ability of TYMC to detect only viable living cells from such a broad range of yeast and mold species may be considered an advantage in the newly emerging cannabis industry.

After California voted to legalize recreational marijuana, state regulatory agencies began exploring different cannabis testing methods to implement in order to ensure clean cannabis for the large influx of consumers.

Unlike Colorado, California is considering a different route and the recently released emergency regulations require testing for specific species of Aspergillus mold (A. fumigatus, A. flavus, A. niger and A. terreus). While Aspergillus can also be cultured and plated, it is difficult to differentiate morphological characteristics of each species on a plate and the risk of misidentification is high. Therefore, positive identification would require the use of DNA-based methods such as polymerase chain reaction testing, also known as PCR. PCR is a molecular biology technique that can detect species-specific strains of mold that are considered harmful through the amplification and analysis of DNA sequences present in cannabis. The standard PCR testing method can be divided into four steps:

The double stranded DNA in the cannabis sample is denatured by heat. This refers to splitting the double strand into single strands.
Primers, which are short single-stranded DNA sequences, are added to align with the corresponding section of the DNA. These primers can be directly or indirectly labeled with fluorescence.
DNA polymerase is introduced to extend the sequence, which results in two copies of the original double stranded DNA. DNA polymerases are enzymes that create DNA molecules by assembling nucleotides, the building blocks of DNA.
Once the double stranded DNA is created, the intensity of the resulting fluorescence signal can uncover the presence of specific species of harmful Aspergillus mold, such as fumigatus.

These steps can be repeated several times to amplify a very small amount of DNA in a sample. The primers will only bind to the corresponding sequence of DNA that matches that primer and this allows PCR to be very specific.

PCR testing is used in a wide variety of applications
Photo courtesy of USDA ARS & Peggy Greb.

PCR is a very sensitive and selective method with many applications. However, the instrumentation utilized can be very expensive, which would increase the overall cost of a compliance test. The high sensitivity of the method for the target DNA means that there are possibilities for a false positive. This has implications in the cannabis industry where samples that test positive for yeast and mold may need to go through a remediation process to kill the microbial impurities. These remediated samples may still fail a PCR-based microbial test due to the presence of the DNA. Another issue with the high selectivity of this method is that other species of potentially harmful yeast and mold would not even be detected. PCR is a technique that requires skill and training to perform and this, in turn, adds to the high overall cost of the test.

Both TYMC and PCR have associated advantages and disadvantages and it is important to take into account the cost, speed, selectivity, and sensitivity of each method. The differences between the two methodologies would lead to a large disparity in testing standards amongst labs in different states. In a nascent industry, it is prudent for state regulators to reference specific testing methodologies so that an industry standard can be established.

February 20, 2018

An Insider’s View: How Labs Conduct Cannabis Mold Testing

By Swetha Kaul, PhD

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As both recreational and medical cannabis legalization continues to progress across the country, each state is tasked with developing regulatory requirements to ensure that customers and patients receive clean cannabis for consumption. This requires cannabis to undergo laboratory testing that analyzes the presence of microbial impurities including yeast and mold.

Some states, such as Colorado, Nevada, Maine, Illinois and Massachusetts use total yeast and mold count testing (TYMC) and set a maximum yeast and mold count threshold that cultivators must fall below. Other states, such as California, require the detection of species-specific strains of Aspergillus mold (A. fumigatus, A. flavus, A. niger and A. terreus), which requires analyzing the DNA of a cannabis sample through polymerase chain reaction testing, also known as PCR.

Differences in state regulations can lead to different microbiological techniques implemented for testing.Before diving in further, it is important to understand the scientific approach. Laboratory testing requirements for cannabis can be separated into two categories: analytical chemistry methods and microbiological methods.

Analytical chemistry is the science of qualitatively and quantitatively determining the chemical components of a substance, and usually consists of some kind of separation followed by detection. Analytical methods are used to uncover the potency of cannabis, analyze the terpene profile and to detect the presence of pesticides, chemical residues, residuals solvents, heavy metals and mycotoxins. Analytical testing methods are performed first before proceeding to microbiological methods.

Microbiological methods dive deeper into cannabis at a cellular level to uncover microbial impurities such as yeast, mold and bacteria. The techniques utilized in microbiological methods are very different from traditional analytical chemistry methods in both the way they are performed and target of the analysis. Differences in state regulations can lead to different microbiological techniques implemented for testing. There are a variety of cell and molecular biology techniques that can be used for detecting microbial impurities, but most can be separated into two categories:

Methods to determine total microbial cell numbers, which typically utilizes cell culture, which involves growing cells in favorable conditions and plating, spreading the sample evenly in a container like a petri dish. The total yeast and mold count (TYMC) test follows this method.
Molecular methods intended to detect specific species of mold, such as harmful aspergillus mold strains, which typically involves testing for the presence of unique DNA sequences such as Polymerase Chain Reaction (PCR).

Among states that have legalized some form of cannabis use and put forth regulations, there appears to be a broad consensus that the laboratories should test for potency (cannabinoids concentration), pesticides (or chemical residues) and residual solvents at a minimum. On the other hand, microbial testing requirements, particularly for mold, appear to vary greatly from state to state. Oregon requires random testing for mold and mildew without any details on test type. In Colorado, Nevada, Maine, Illinois and Massachusetts, regulations explicitly state the use of TYMC for the detection of mold. In California, the recently released emergency regulations require testing for specific species of Aspergillus mold (A. fumigatus, A. flavus, A. niger and A. terreus), which are difficult to differentiate on a plate and would require a DNA-based approach. Since there are differences in costs associated and data produced by these methods, this issue will impact product costs for cultivators, which will affect cannabis prices for consumers.

January 24, 2018

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.”

January 11, 2018

Sunrise Genetics Partners With RPC, Begins Genetic Testing in Canada

By Aaron G. Biros

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Sunrise Genetics, Inc., the parent company of Marigene and Hempgene, announced their partnership with New Brunswick Research & Productivity Council (RPC) this week, according to a press release. The company has been working in the United States for a few years now doing genomic sequencing and genetic research with headquarters based in Fort Collins, CO. This new partnership, compliant with Health Canada sample submission requirements, allows Canadian growers to submit plants for DNA extraction and genomic sequencing.

Sunrise Genetics researches different cannabis cultivars in the areas of target improvement of desired traits, accelerated breeding and expanding the knowledge base of cannabis genetics. One area they have been working on is genetic plant identification, which uses the plant’s DNA and modern genomics to create authentic, reproducible, commercial-ready strains.

Matt Gibbs, president of Sunrise Genetics, says he is very excited to get working on cannabis DNA testing in Canada. “RPC has a long track record of leadership in analytical services, especially as it relates to DNA and forensic work, giving Canadian growers their first real option to submit their plant samples for DNA extraction through proper legal channels,” says Gibbs. “The option to pursue genomic research on cannabis is now at Canadian cultivator’s fingertips.”

Canada’s massive new cannabis industry, which now has legal recreational and medical use, sales and cultivation, previously has not had many options for genetic testing. Using their genetic testing capabilities, they hope this partnership will better help Canadian cultivators easily apply genomic testing for improved plant development. “I’m looking forward to working with more Canadian cultivators and breeders; the opportunity to apply genomics to plant improvement is a win-win for customers seeking transparency about their Cannabis product and producers seeking customer retention through ‘best-in-class’ cannabis and protectable plant varieties,” says Gibbs. The partnership also ensures samples will follow the required submission process for analytical testing, but adding the service option of genetic testing so growers can find out more about their plants beyond the regular gamut of tests.

RPC is a New Brunswick provincial research organization (PRO), a research and technology organization (RTO) that offers R&D testing and technical services. With 130 scientists, engineers and technologists, RPC offers a wide variety of testing services, including air quality, analytical chemistry of cannabis, material testing and a large variety of pilot facilities for manufacturing research and development.

They have over 100 accreditations and certifications including an ISO 17025 scope from the Standards Council of Canada (SCC) and is ISO 9001:2008 certified. This genetic testing service for cannabis plants is the latest development in their repertoire of services. “This service builds on RPC’s established genetic strengths and complements the services we are currently offering the cannabis industry,” says Eric Cook, chief executive officer of RPC.

December 20, 2017

Soapbox

Cannabis and the Environment: Navigating the Interplay Between Genetics and Transcriptomics

By Dr. Zacariah Hildenbrand

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It is that time of year where the holidays afford us an opportunity for rest, recuperation and introspection. Becoming a new father to a healthy baby girl and having the privilege to make a living as a scientist, fills me with an immeasurable sense of appreciation and indebtedness. I’ve also been extremely fortunate this year to spend significant time with world-renowned cannabis experts, such as Christian West, Adam Jacques and Elton Prince, whom have shared with me a tremendous wealth of their knowledge about cannabis cultivation and the development of unique cannabis genetics. Neither of these gentlemen have formal scientific training in plant genetics; however, through decades of experimentation, observation and implementation, they’ve very elegantly used alchemy and the principles of Mendelian genetics to push the boundaries of cannabis genetics, ultimately modulating the expression of specific cannabinoids and terpenes. Hearing of their successes (and failures) has triggered significant wonderment and curiosity with respect to what can be done beyond the genetic level to keep pushing the equilibrium in this new frontier of medicine.

Lighting conditions can greatly impact the expression of terpenes (and cannabinoids) in cannabis.Of course genetics are the foundation for the production of premium cannabis. Without the proper genetic code, one cannot expect the cannabis plant to express the target constituents of interest. However, what happens when you have an elite genetic code, the holy grail of cannabis nucleotides if you will, and yet your plant does not produce the therapeutic compounds that you want and/or that are reflective of that elite genetic code? This ‘loss in translation’ can be explained by transcriptomics, and more specifically, epigenetics. In order for the genetic code (DNA) to be expressed as a gene product (RNA), it must be transcribed, a process that is modulated by epigenetic processes like DNA methylation and histone modification. In other words, the methylation of the genetic code can dictate whether or not a particular segment of DNA is transcribed into RNA, and ultimately expressed in the plant. To put this into context, if the DNA code for the enzyme THCA synthase is epigenetically silenced, then no THCA synthase is produced, your cannabis cannot convert CBGA into THCA, and now you have hemp that is devoid of THC.So what is the best lighting technology to enhance the expression of terpenes?

With all of that being said, how do we ensure that our plants thrive under favorable epigenetic conditions? The answer is the environment; and the expression of terpenes is an ideal indicator of favorable environmental conditions. While amazing anti-inflammatories, anti-oxidants and metabolic regulators for humans, terpenes are also extremely powerful anti-microbial agents that act as a robust a line of defense for the plant against bacteria and pests. So, if the threat of microbes can induce the expression of terpenes, then what about other environmental factors? I am of the opinion that the combination of increased exposure to bacteria and natural sunlight enhances the expression of terpenes in outdoor-grown cannabis compared to indoor-grown cannabis. This is strictly my opinion based off of my own qualitative observations, but the point being is that lighting conditions can greatly impact the expression of terpenes (and cannabinoids) in cannabis.

A plant in flowering under an LED fixture

So what is the best lighting technology to enhance the expression of terpenes? Do I use full spectrum lighting or specific frequencies? The answer to these questions is that we don’t fully know at this point. Thanks to the McCree curve we have a fundamental understanding of the various frequencies within the visible light spectrum (400-700nm) that are beneficial to plants, also known as Photosynthetically Active Radiation (PAR). However, little-to-no research has been conducted to determine the impacts that the rest of the electromagnetic spectrum (also categorized as ‘light’) may have on plants. As such, we do not know with 100% certainty what frequencies should be applied, and at what times in the growth cycle, to completely optimize terpene concentrations. This is not to disparage the lighting professionals out there that have significant expertise in this field; however, I’m calling for the execution of peer-reviewed experiments that would transcend the boundaries of company white papers and anecdotal claims. In my opinion, this lack of environmental data provides a real opportunity for the cannabis industry to initiate the required collaborations between cannabis geneticists, technology companies and environmental scientists. This is one field of research that I wish to pursue with tenacity and I also welcome other interested parties to join me in this data quest. Together we can better understand the environmental factors, such as lighting, that are acting as the molecular light switches at the interface of genetics and transcriptomics in cannabis.

April 11, 2016

An Introduction to Cannabis Genetics, Part I

By Dr. CJ Schwartz

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What is DNA?

DNA stores information about how to build an organism. Just as a series of 0’s and 1’s represents digital data, DNA data is represented by four letters (A, C, G and T), which inherently allows DNA to store more information per unit (Figure 1).

The amount of DNA required to build a human is mind-boggling. The human genome has 3.2 billion A’s, C’s, G’s, or T’s, (called nucleotides). Cannabis has 820 million nucleotides. This is true for every cell in the organism. The DNA from a single human cell when spread out would stretch six feet long. A cell is not visible to the naked eye, yet it contains a microscopic thread of DNA six feet long! If you put all the DNA molecules in your body end to end, the DNA would reach from the Earth to the Sun.

DNA is common in all living things, and all living things are related through DNA. Humans and plants share 50% of their genes. In humans, 99.9% of the DNA is identical, thus just 0.1% of DNA differences accounts for all of the variation observed in humans. Cannabis, as a species, is more variable with approximately 1% of the DNA being different among strains. DNA is a super efficient and reliable information storage system. However, mistakes (mutations) do occur and while infrequent, these mutations account for all the differences observed within a species and is called natural genetic variation. Variation within the genomes of a species can help the species survive in unfavorable conditions (evolution) and is also the source of differences in traits, which is the material that is required for successful breeding.

Natural Genetic Variation

DNA mutations occur in every generation and these changes will be different in each individual creating natural genetic variation. Mutations (or more accurately referred to as DNA changes) will be inherited by offspring and will persist in the population if the offspring reproduce.

DNA differences maintain diversity in the gene pool, allowing organisms to respond to new environments (migration) or environmental changes (adaptation). The two most commonly described cannabis families are Indicas and Sativas. Indicas, being from cooler temperate regions, have wide leaves allowing the maximum capture of light during the shorter growing season. Sativas, being equatorial, have smaller leaves, which may be an advantage for such things as powdery mildew in a humid environment. Figure 2 shows the enormous amount of natural variation in leaves for one species with a worldwide population (Arabidopsis thaliana).

A DNA change that occurred a long time ago will be more useful to divide people/plants into different groups. For example, there are ancient DNA changes that differentiate humans originating from Europe or Asia. Other newer DNA changes allow us to further divide Europeans into those originating from Northern versus Southern Europe. Thus, different DNA changes have different values for determining relatedness or ancestry, yet every DNA change provides some information for determining heredity.

Family Trees

By comparing DNA changes among different strains, we can measure the relatedness between strains. For example, if strain A has a DNA change indicative of Kush ancestry and strain B has a DNA change indicative of hemp ancestry, we can assign strains to branches of the cannabis family tree comprised of strains that contain similar DNA changes. Figure 3 shows 184 strains that have been characterized for these changes, and the position of each strain is based on its shared DNA with neighboring strains. The two best-defined families of cannabis are hemp (blue) and kush (black). Strains within a family are more closely related. Strains in separate families, such as kush and hemp, are more distantly related.

Editor’s Note: This is the first installment in a series of articles focused on answering common questions regarding cannabis genetics. If you have questions regarding cannabis genetics, or wish to speak more about the topic please post in the comments section below. The next installment will delve into the THC synthase, gene discovery and manipulation and mapping chromosomes.

March 7, 2016

Researching Cannabis Genetics: A Q&A with CJ Schwartz, Ph.D.

By Aaron G. Biros

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Studying cannabis genetics is a convoluted issue. Strain classification, medicinal effects and plant breeding are particular areas in the science of cannabis that still require heavy research. Marigene, a company researching cannabis genetics, is currently working with universities and research institutes to help map the cannabis genome and catalog genetic variation.

CJ Schwartz, Ph.D.

According to CJ Schwartz, Ph.D., chief executive officer and founder of Marigene, their mission is to “to classify, certify, and improve cannabis.” After studying genetics and cellular biology at the University of Minnesota, Schwartz received his Ph.D. in biochemistry from the University of Wisconsin. His research in the past decade has focused on genetic variations that control flowering time, discovering the expression of a gene called Flowering Locus T leads to differential flowering time of plants and is dependent on their native locations. We sat down with Schwartz to learn more about his research and collaborative efforts.

Cannabis Industry Journal: Why are you researching mapping the cannabis genome?

CJ Schwartz, Ph.D: We seek to identify the genetic differences among cannabis strains and the genes responsible for these differences. Genetic differences are what cause different strains to have different effects. DNA allows reproducibility, consistency, and transparency for your cannabis strains.

The more information we gather about cannabis genetics, the more tools we have available to create tailored strains. Cannabis is a targeted compound. It interacts with a very specific system in the human body, similar to hormones, such as insulin. Understanding the cannabis genome will help bring legitimacy and integrity to cannabis products, and allow us to better understand how chemicals from cannabis interact with the human brain. Genetic identification can provide a method of certification to more comprehensively describe plant material.

Schwartz doing sample preparation on the lab bench.

CIJ: How did you get involved in cannabis research?

Schwartz: My interest in cannabis guided my research career. Cannabis may not be a cure-all, but it has significant and measurable medicinal effects for many patients.

To allow true development of cannabis products, we need more science! Our genetic analysis is required for normalization and acceptance of cannabis products, but also essential for future breeding efforts to develop better and more useful plants.

Our sister company, Hempgene, is applying all of the same technology and techniques for hemp research. One focus of Hempgene is to manipulate flowering time in select hemp cultivars so that they mature at the appropriate time in different environments.

CIJ: What do you hope to accomplish with your research?

Schwartz: We can develop or stabilize a plant that produces a very specific chemical profile for a specific condition, such as seizures, nausea or pain. By breeding plants tailored to a patient’s specific ailment, a patient can receive exactly the medicine that they need and minimize negative side effects.

The current term describing the interaction of cannabis compounds is called the entourage effect. Interactions among compounds can be additive or synergistic. The entourage effect describes synergistic effects, where small amounts of compound A (e.g. Myrcene) vastly increase the effects of compound B (e.g. THC). Instead of flooding one’s body with an excessive amount of chemicals to get a non-specific effect, cannabis plants can be bred to produce a very specific effect.

A view of some of the work stations inside the laboratory at Marigene.

Currently our goal is to catalog the natural genetic variation of cannabis, and to identify DNA changes that affect a trait of interest. Once superior variants of a gene are identified, those variants can be combined, by marker-assisted breeding, to produce new combinations of genes. How different cannabis chemicals interact to produce a desired effect, and how different human genetics influence the efficacy of those chemicals should be the ultimate goal of medical marijuana research.

We are working closely with academic institutions and chemical testing labs to gather data for establishing correlations between specific cannabis strains and desirable chemical profiles. Our closest collaborator, Dr. Nolan Kane at UC-Boulder, is working to complete the Cannabis genomic sequence and generate the first high- resolution cannabis genetic map.

We are currently accepting samples and we produce a report in roughly two to three months. For one sequencing run, we identify 125 million pieces of DNA that are 100 base pairs long. We get so much information so there is a considerable time commitment.