Cannabis has been a worldwide harvest for millennia. While it is better known today as marijuana for its ThC psychoactive cannabinoid (tetrahydrocannabinol), historically, cannabis has been a cornerstone of human civilization, providing seed oil, textiles and food for more than 10,000 years. Today, cannabis remains a substitute and underutilized resource, but the legislation of the United States approved in 2014 and 2018 has revitalized the development of cannabis crops for medicinal, grain and fiber applications.
Researchers from the Salk Institute have created the most comprehensive, high quality and detailed cannabis Atlas of Cannabis to date. The team analyzed 193 different cannabis genomes (complete sets of genetic information), revealing a diversity, complexity and unprecedented without exploiting opportunities within this fundamental agricultural species. This historical achievement was the result of a collaboration of several years with Oregon CBD, Oregon State University and the Hudsonalpha Biotechnology Institute.
The findings, published in Nature On May 28, 2025, he prepared the stage for transformative advances in agriculture, medicine and cannabis -based industry.
“Cannabis is one of the most extraordinary plants on Earth. Despite its global importance as a source of medicine, food, seed oil and fiber for at least the last 10,000 years, it remains one of the least developed main crops of modern times, largely due to a century of legal restrictions,” says Todd Michael, senior author of the study and research teacher in Salk. “Our team constructed the Most Complete Genetic Map, or Pangenome, of the plant to date by Analyzing Nearly 200 Diverse Cannabis Genomes, Showing That We Are Just Starting to see the full potential of this Amazing Plant. Those Same Legal Restrictions Spurred An Underground Breeding Revolution, Revealing Cannabis’s Power As a Chemical Factory.
Background: cannabis as a chemical power
Cannabis sativaAlso known as hemp, it is a native flowering plant in Asia. Cannabis has many unique characteristics that have made it a prominent crop in the course of human history, such as its ability to produce strong fibers for textiles or its medicinal qualities derived from being one of the few plants to make large amounts of cannabinoids. Today’s innovators suggest that cannabis oil could rival canola or soybeans with correct reproduction, or that cannabis derivatives could even be used as a sustainable alternative to aircraft fuel.
Cannabis is a chemical power. It can produce more than 30% by dry weight such as terpenes and cannabinoids, small chemicals that the plant makes to protect against predators, but humans take advantage of for purposes that alter mood. The terpenes create the exquisite aromas that attract us to fruits and flowers, while cannabinoids interact with the human body to provide many therapeutic properties. A cannabinoid, non -psychedelic cannabidiol (CBD), expanded the cannabis public vision when the “Charlotte” website was used to treat epileptic seizures. The CBD, the tetrahydrocannabinol (THC) and more than 100 poorly studied cannabinoids have been used to treat a variety of ailments, such as pain, arthritis, nausea, asthma, depression and anxiety.
It is important to note that the impact that this selective reproduction has had on the genomic diversity of cannabis has remained a mystery. Solving this mystery has been difficult since cannabis has a complicated genome. First, cannabis is among the least 5% of plants that have sexes other than women and men in separate plants. Secondly, cannabis genomes contain many transpononable elements, which are repetitive sections of DNA that can “jump” around the genome and, therefore, are difficult to track.
Key discoveries: new and surprisingly diverse genetic patterns
Scientists use a technology called sequencing to determine nucleic acid patterns, which are connected through the double propeller of DNA to form base pairs, along the DNA threads. Traditional short reading sequencing methods cut the DNA to investigate it, piece by piece, only a few hundred base pairs at the same time. New long -term reading sequencing techniques can capture thousands of base pairs at the same time.
“There are limits for what you can discover with short-reading sequencing technologies, since these short genetic extracts are impossible to unite significantly when you are looking for complex genome regions, especially repetitive DNA sequences,” says the co-direct author Lillian Padgitt-Cobb, a postdoctoral researcher in Michael’s laboratory. “We are among the first to take advantage of this long -term reading technology on scale in the context of the pygenoma, and with that all these ideas about the structural variation and the order of genes that can inform the decisions of the final game on the breeding of favorable features in cannabis plants come.”
The study is not the first to use the long -term reading sequence: in fact, Michael himself was the first researcher in generating a cannabis genome at the chromosome level using long reading sequencing in 2018, which revealed a complex genetic architecture where cannabinoids are synthesized and explained the reproduction history behind the antiepileptic charlotte network. Where this new study stands out is its integrity. It contains most of the genomes so far, and is the first to include sexual chromosomes and, in relation to the first to have a haplootype resolution.
Cannabis is a Diploid plant. This means that, as humans, it contains two sets of chromosomes, one inherited from a male plant and the other of a female plant. Although most of the genomes published to date have only been able to decode a chromosome, also known as haplootype resolution, the team was resolved both Cannabis chromosomes sets. When observing both sets of chromosomes, the researchers revealed an unprecedented amount of genetic variation, possibly up to 20 times that of humans.
“With this haplotype resolution,” explains Padgitt-Cobb, “we can see what was inherited from only one of the parent plants and begin to understand the breeding and background of that plant.”
The study of the team collected genomes of 144 different cannabis plants from around the world to gather 193 total genomes, 181 of which had never been cataloged before. The total genome is greater than the total plant due to that haplootype resolution, since each plant that had both sets of investigated chromosomes produced two genome sets. Collectively, these many genomes constitute the pygenoma, which was analyzed to understand the total scope of genetic diversity within cannabis species.
The high quality of the genomes collected allowed researchers to solve previously invisible genetic patterns, including the architecture of the genes responsible for cannabinoid synthesis and, by incorporating sex chromosomes, a first look at cannabis chromosomes and.
His first discovery was that there is unexpected diversity within the species. Throughout the pygenoma, 23% of the genes were found in each genome, 55% nearly Universal (seen in 95% -99% of genomes), 21% were between 5% and 94% of genomes, and less than 1% were completely unique. Some of the most universal genes were those that produce cannabinoids.
While cannabinoid genes were consistent in all genomes, genes related to fatty acid metabolism, growth and defense were not. These variable genes are an unleashed reproduction pool, and their selective reproduction could also make cannabis more robust in the field or improve the nutritional content of hemp oil to be a competitor between existing seed oils. In particular, the research team discovered that the structural variation in the biosynthetic path of fatty acids contributes to the production of tetrahydrocannabivarin (THCV), a rare varine cannabinoid that gives attention to its non -psychoactive and energizing effects.
Looking more closely at cannabinoid genes in the pygenoma, the researchers concluded that two genes, THCA and CBDA are probably under strong selective pressure of humans directed by humans for the content of THC and CBD. It is important to highlight that they discovered that cannabinoid genes are in transpononable elements. Reproduction selectively for genes within these transpononable elements “jumping” has created, in turn, an immense diversity among cannabis plants.
Looking to the future: optimization of plants for health and industry
The researchers also identified interesting objectives for agricultural optimization. First, when observing the differences between European and Asian genomes, they concluded that there is probably an old cannabis relative somewhere in Asia waiting to be discovered. This wild relative will have new genetic adaptations related to its unique environmental history, which makes it a large amount of information for the breeding of cannabis plants that are more resistant crops.
Finally, the novel understanding of sex chromosomes revealed that there are genes only Present in “father” plants that can be used to raise better performance descendants. Modern marijuana breeding takes advantage of “feminization”, where farmers induce a female plant to make male flowers, without completely passing the Y chromosome and. These new findings suggest that reproduction programs may lack valuable genetic diversity and a potential of features encoded in the omitted male genomes. The incorporation of true male plants in reproduction strategies could unlock passed genetic gains and expand opportunities for crop improvement.
“In the last 10 years, breeders have already done a decent job to obtain yields and make cannabis an economically viable harvest,” says Co-First Author Ryan Lynch, postdoctoral researcher in Michael’s laboratory. “Once there is interest in the market there, combined with these new ideas about cannabis genomes that can guide reproduction efforts, I can see the hemp and hemp oils that really rise both in human health and in industry applications.”
In the short term, the team hopes that the Pangenome will serve as a dynamic resource for researchers around the world to be built and use to inform cultivation strategies, helping to perform the unskilled potential from cannabis as a valuable culture of multiple uses cultivated for fiber, seed oil and medicine.
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