Tag Archives: genomics

December 23, 2020

Smart Plants: A Q&A with Jonathan Vaught, CEO and Co-Founder of Front Range Biosciences

By Aaron Green

Plant genetics are an important consideration for cultivators planning to grow cannabis crops. Genetics can affect how well a plant grows in a particular environment under various conditions and have a major impact on the production of cannabinoids, terpenes as well as other molecules and traits expressed by the plant.

Front Range Biosciences is a hemp and cannabis genetics platform company, leveraging proprietary next generation breeding and Clean Stock® tissue culture nursery technologies to develop new varieties for a broad range of product applications in the hemp and cannabis industries. FRB has global reach through facilities in Colorado, California and Wisconsin, and a partnership with the Center for Research in Agricultural Genomics in Barcelona, Spain. FRB is headquartered in Lafayette, Colorado.

We spoke with Jonathan Vaught, Ph.D., CEO and co-founder of Front Range Biosciences. Jonathan co-founded Front Range in 2015 after a successful career in the diagnostics and food testing industries.

Aaron Green: Jon, thank you for taking the time today. I saw in the news you recently sent tissue cultures to the International Space Station? I’d love to learn more about that!

Hemp tissue culture samples like these sat in an incubator aboard the ISS

Jonathan Vaught: This was a collaborative project between the BioServe group at the University of Colorado Boulder, which is a part of their aerospace engineering program. They do research on the International Space Station, and they have for quite some time. We partnered with them and another company, Space Technology Holdings, a group that’s working on applications of space travel and space research. We teamed up to send tissue culture samples to the space station and let them sit in zero gravity at the space station for about a month, and then go through the reentry process and come back to Earth. We brought them back in the lab to perform some genomic analyses and try to understand if there’s any underlying genetic changes in terms of the plants being in that environment. We wanted to know if there was anything interesting that we could learn by putting these plant stem cells and tissue cultures in an extreme environment to look for stress response, and some other possible changes that might occur to the plants by going through those conditions.

Aaron: That’s an interesting project! Are there any trends that you’re following in the industry?

Jon: We’re excited to see ongoing legalization efforts around the world. We’ve seen continued progress here in the United States. We still have a long way to go, but we’re excited to see the additional markets coming onboard and regulations moving in the right direction. Also, we’re excited to see some of the restorative justice programs that have come out.

Aaron: How did you get involved at Front Range Biosciences?

Jon: It really starts with my background and what I was doing before Front Range Biosciences. I’ve spent more than 15 years developing commercializing technologies in human diagnostics, food safety and now agriculture.

I started my career during graduate school in biotech at the University of Colorado at Boulder, where I helped develop some of the core technology for a human diagnostic startup company called Somalogic here in Colorado. I went to work for them after finishing my dissertation work and spent about six years there helping them grow that company. We ended up building the world’s largest protein biomarker discovery platform primarily serving pharmaceutical companies, hospitals and doctors, with personalized medicine and lab tests for things like early detection of chronic illness, cancer, heart disease and inflammation.

I then went to another startup company called Beacon Biotech, that was interested in food safety. There I helped develop some similar technologies for detecting food-borne illness — things like salmonella, listeria and E. coli. That was my introduction to big food and big agriculture. From there, I went to help start another company called Velocity Science that was also in the human diagnostic space.

Along the way, I started a 501(c)3 nonprofit called Mountain Flower Goat Dairy, a dairy and educational non-profit that had a community milk-share, which included summer camps and workshops for people to learn about local and sustainable agriculture. I became more and more interested in agriculture and decided to take my career in that path and that’s really what set me up to start Front Range Biosciences.

Aaron: Do you have any co-founders?

Jon: I have two other co-founders. They both played various roles over the last four years. One was another scientist, Chris Zalewski, PhD. He currently works in the R&D department and helps oversee several different parts of the company including pathology and product development. My other co-founder, Nick Hofmeister served as chief strategic officer for the last few years, and has helped raise the majority of our funding. We’ve raised over $45 million dollars, and he played a big role in that.

Aaron: What makes you different from other cannabis seed companies?

John: We’ve built the first true cannabis genetics platform. What I mean by that is we built a platform that allows us to develop and produce new plant varieties that support both the hemp and the cannabis markets. To us, it’s all cannabis. Hemp and cannabis are scientifically the same plant. They just have different regulatory environments, different products and different markets, but we stay focused on the plant. Our platform is built on several different pillars. Genetics are one of the core pieces, and by genetics I mean, everything from molecular based breeding to marker assisted breeding to large germplasm collections. We collect different varieties of germplasm, or seed, from all over the world and use those to mix and match and breed for specific traits. We also have large nursery programs. Another one of our pillars of the platform includes greenhouse nursery production — everything from flowering cannabis plants to producing cannabis seeds to cloning and producing mother plants and rooted cuttings or clones.

Then tissue culture is another part of the platform, it’s basically the laboratory version of a greenhouse nursery. It’s housed in a sterile environment and allows us to produce plants that are clean and healthy. It’s a much more effective, modern way to manage the nursery. It’s part of our clean stock program, where we start clean, stay clean, and you can finish clean. It’s really built on all of those different pieces.

We also have capabilities in analytical chemistry and pathology, that allow us to better understand what drives performance and the plants, and both different regions as well as different cannabinoid products or terpene products. All of the science and capabilities of the platform are what allow us to create new varieties faster, better, stronger.

Aaron: It sounds like you’re vertically integrated on the front-end of cannabis cultivation.

Jon: Absolutely, that’s a great way to think about it.

The last piece I’d say is that we have areas of research and development that cover the full span of multiple product lines. We think about it from an ingredient perspective. Cannabinoids and terpenes are certainly what drive a large part of the cannabis market in terms of edibles, smokable flower, vapes and extracts and the different effects and flavors that you get. We also are looking at other ingredients, like plant-based protein and hemp as a viable protein source and the ability for hemp to produce valuable fiber for textiles, as well as industrial building materials and applications.

Lastly, there are additional small molecules that we’re working on as well from a food ingredients perspective. There are all kinds of interesting compounds. Everybody talks about the cannabinoids and terpenes, but there are also things like flavonoids, and some other very interesting chemistries that we’re working on as well.

Aaron: What geographies are you currently in?

Jon: Colorado and California primarily and we have a small R&D partnership in Barcelona.

Hemp clones and seeds is a big part of the Front Range Biosciences business

Aaron: Do you have plans for expansion beyond that?

Jon: Our current headquarters are out of Colorado, and most of our Colorado operations right now are all hemp. Our hemp business is national and international.

We work with a licensed cannabis nursery partner in California which is our primary focus for that market, but we will be expanding the cannabis genetics and nursery program into Colorado next year. From a regulated cannabis perspective, that’s the first move. Beyond that, we’re in conversations with some of the multi-state operators and cannabis brands that are emerging to talk about how to leverage our technology and our genetics platform across some of the other markets.

Aaron: How do you think about genetics in your products?

Jon: Genetics means a lot of things to different folks depending on your vantage point and where you sit in the supply chain. Our business model is based on selling plants and seeds. At the end of the day, we don’t develop oils, extracts and products specifically, but we develop the genetics behind those products.

For us, it’s not only about developing genetics that have the unique qualities or ingredients that a product company might want like CBD, or other minor cannabinoids like THCV for example, but also about making sure that those plants can be produced efficiently and effectively. The first step is to introduce the ingredient to the product. Then the second step is to make sure that growers can grow and produce the plant. That way they can stabilize their supply chain for their product line. Whether it’s for a smokable flower product, or a vape product, or an edible product, it’s really important to make sure that they can reproduce it. That’s really how we think about genetics.

Aaron: What is a smart plant? That’s something I saw on your website.

Jon: It’s really about plants that perform under specific growing regions, or growing conditions. For example, in hemp, it’s one thing to produce CBD or CBG. It’s another thing to be able to produce it efficiently in five different microclimates around the U.S. Growing hemp in Florida or Alabama down on the Gulf Coast versus growing on the Pacific Northwest coast of Washington, or Oregon are two very different growing conditions that require smart plants. Meaning they can grow and thrive in each of those conditions and still produce the intended product. Generally, the different regions don’t overlap. The genetics that you would grow in Pacific Northwest are not going to do as well as some better selected varieties for the South East.

It’s not only different outdoor growing regions, but it’s different production styles too. When you think about regulated cannabis the difference between outdoor and indoor greenhouse is mixed light production. Even with hydroponic type growing methods, there are lots of different ways to grow and produce this plant and it’s not a one size fits all. It’s really about plants that perform well, whether it’s different regions in the United States in outdoor production or different indoor greenhouses with mixed lights and production methods.

Aaron: You market CBG hemp as a product line. What made you start with CBG? Is that a pull from the market or something you guys see trending?

Jon: So I think it’s a little bit of both. We offer CBD dominant varieties and CBG dominant varieties of hemp. We also now have other cannabinoids in the pipeline that we’ll be putting out in different varieties next year. Things like CBC as well as varins, or propyl cannabinoids. Also things like CBDV, CBCV, or CBGV, which are the propylcannabinoid versions of the more familiar compounds.

There was a lot of market demand for CBG. It was a fairly easy cannabinoid to produce as a single dominant cannabinoid similar to CBD or THC. There’s a lot of up-and-coming demand for some of the other minor cannabinoids. Up until a few years ago, CBD was considered a minor cannabinoid. It wasn’t until Charlotte’s Web in the Sanjay Gupta story that it became a major cannabinoid. So I think we see some level of market pull across the category.

On the flip side of that, we have one of the world’s largest R&D teams and consolidated expertise in terms of cannabis. We see the potential for minor cannabinoids, and even terpenes and other compounds like flavonoids to have wide ranging implications in human health. Everything from wellness products, to active pharmaceutical ingredients, to recreational products. From our perspective, that’s the reason why we’re pushing these ingredients. We believe that there are a lot of good products that come out of this work and the genetics that produce these minor cannabinoids.

Aaron: Okay, great. And then last question, is there anything you’re interested in learning more about?

Jon: I think the most exciting thing for me, given my background in clinical diagnostics and human health, is to see more data around how all of these different compounds of the plant can support improved wellness, health and nutrition. I think we’ve only scratched the tip of the iceberg. This type of research and data collection takes years, even decades, especially to see outcomes over time of people using these products. I’m really excited to see more of that and also hopefully be able to make stronger conclusions about some of the benefits that can be had from this plant.

Aaron: That’s the end of the interview, thanks Jon!

June 9, 2020

New Cannabis Science Course Offered at University of Colorado at Boulder

By Cannabis Industry Journal Staff

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According to a press release, the University of Colorado at Boulder is offering a new course focused on cannabis science through the Continuing Education program at the university during the upcoming Summer and Fall semesters.

The class is called Modern Cannabis Science and will involve a lot of genetic research. The course is sponsored by the Agricultural Genomics Foundation, a non-profit dedicated to scientific research and education in cannabis. In the press release, they describe the course as meant for students who are well informed, but “seek a deeper appreciation of scientific advancements in cannabis genetics.”

Here’s a snapshot of what students can expect to learn from it:

In Modern Cannabis Science, we will explore the range of Cannabis research currently available covering topics such as evolutionary history and global distribution, sex chromosomes, genetic contribution to chemotype, and analyses to aid law enforcement and forensic investigations. We will examine how genetic data allow us to understand relationships between strains and common categories in the Cannabis genus, and why this is important for breeding, policy-making, and medical purposes.

The press release suggests students who enroll can expect to use this knowledge in the cannabis industry. “For example, a budtender will be able to more accurately recommend strains to users,” reads the press release. “Similarly, medical personnel will more fully understand the relationship between strains, the compounds they produce, and how to properly advise Cannabis patients.”

For more information, take a look at the course here.

October 31, 2018

Soapbox

Challenges in Cannabis Genome Sequencing for Genetic Tracking and Traceability

By Khyrrah-Cymone Shepard

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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

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.”