CANNABIS DNA PROJECT

Cannabis Colleagues,

Greetings from the International Hemp Association in Amsterdam. We are writing to tell you about an exciting research program using modern DNA analysis to build a family tree for Cannabis, and to request your participation.

We are collaborating with a US-based group working on a definitive large-scale phylogenetic study of the evolution of Cannabis. Key researchers include Mowgli Holmes, the chief scientific officer at Phylos Bioscience and Rob DeSalle, a professor of evolutionary biology at Columbia University and curator at the American Museum of Natural History.

Presently, the team is building a high-resolution map of the Cannabis genome, based on a modern hybrid THC/CBD strain, using PacBio long-read Next-Gen Sequencing (NGS). The map will serve as a reference key for analysis of thousands of other accessions using an SNP (Single Nucleotide Polymorphism) NGS protocol called GBS (Genotyping By Sequencing) allowing high-resolution characterization of each accession.

So far, the group has sequenced over 400 drug-type Cannabis samples. DNA extraction equipment is installed in nine Cannabis testing labs in six US states, and we continue to gather modern hybrid drug varieties. In the next month the group will finish collecting and sequencing our first 1000 samples. In order to collect data from ancient seeds the group is modifying protocols used for sequencing fragmented Pleistocene DNA samples, developing protocols to work with single seeds, and adding a Whole Genome Amplification step to increase DNA yield.

In few months months we hope to have a provisional relationship map worked out that we can put on the web and will let us ID modern strains and hopefully at least test theories concerning the evolution of Cannabis.

Within six months or a year we will analyze additional modern cultivars plus traditional landraces and possibly herbarium sheets and archeological materials. From there on we will add to the live database which will continue to grow as more samples are received although the architecture should not change. Genome data will be studied via network theory to address the issues of hybridization and reticulation in the phylogeny.

Cannabis is an incredibly varied genus made up of a myriad of local landrace varieties and modern cultivars as well as their feral and wild relatives. This research will generate a huge amount of sequence data and unique SNPs spread over many thousands of samples, and we feel confident we can resolve the evolution of Cannabis under domestication.

To further our study and create as complete an evolutionary tree as possible we need seeds collected overseas (or reproduced domestically) and have not been interbred with modern drug hybrids. We are interested in ALL Cannabis whether grown for fiber, seed or drug production as well as feral and wild populations. We can now collect sufficient high-quality DNA for analysis from a single seed. And there is no requirement to grow the seeds, so we can also use dead seeds. Many conscious travelers, marijuana users and growers collected seeds that they never got around to sowing, and now years later they are dead. Dead seeds are useless to growers and breeders, but they still contain valuable genetic information that can provide us with deeper insights into Cannabis’s evolution. It is also legal for us to send dead non-viable seeds to our lab in the USA by post. We can also extract the DNA from leaves, live or dead, and legally send just the DNA to the USA for sequencing. In fact leaves are faster, cheaper, easier and maybe better then seeds for DNA.

If you have any seeds/leaves you feel may be of interest (living or dead) and want to contribute to this fascinating research feel free to contact us, just PM SamS at IC. We will provide a Netherlands PO Box for you to send the seed samples to us and we will provide an optional questionnaire about each batch of seeds. Batches can range from just a single to 25+ seeds.

As research progresses we will share data with you about any accessions you provide. Upon completion the results will change how we all look at Cannabis, and we will better understand the heritage of modern Cannabis cultivars. Growers will be able to see how their varieties (as well as traditional landraces sent by contributors) fit into the big picture – to determine the landrace origins of modern hybrids (ex., Jamaican, Mexican, Colombian, etc.) and explore deeper evolutionary relationships. Fascinating, eh?
If you have any questions please feel free to contact us.

Additional info including a FAQ about the DNA project:
https://www.icmag.com/ic/showpost.php?p=6660142&postcount=1

All the best,

Rob Clarke and Sam Skunkman

please satisfy my curiosity.

I believe each seed is a unique individual with genes from each parent participant.

much like individuals of our race. similar yet different, capable of passing phenotypical expression altered or not (hence some mutation).

am I way off or are our plants unique after genetic expression?

good luck with your study and findings.

rider

trichrider said:

please satisfy my curiosity.

I believe each seed is a unique individual with genes from each parent participant.

much like individuals of our race. similar yet different, capable of passing phenotypical expression altered or not (hence some mutation).

am I way off or are our plants unique after genetic expression?

good luck with your study and findings.

rider

Click to expand...

Close but I don't think every seed will be as unique as people, much more like most plants, some variation but less than humans.

GodsCronik said:

Close but I don't think every seed will be as unique as people, much more like most plants, some variation but less than humans.

Click to expand...

why would you think that?

do all pollen produced by the male contain the same genetic profile?

...or do all female plants provide the same genetic material?

Are all combinations of the zygote identical...i'm thinking no.

doesn't recombination or mutation effect individuals' downstream?

sorry i'm new to this topic.

So in a few years one could test a given cultivar and know
the lineage?

Breeders be sweating this, good job, we're all counting on you.

I´m not an expert either but I have to agree with Godskronik.

Our genetic make up is a lot more complex than the genetics of plants, we have a lot more traits, we have senses....

The variability in humans is way bigger IMO

Anyway many principles work the same way and in my case helps me to understand better.

trichrider said:

why would you think that?

do all pollen produced by the male contain the same genetic profile?

...or do all female plants provide the same genetic material?

Are all combinations of the zygote identical...i'm thinking no.

doesn't recombination or mutation effect individuals' downstream?

sorry i'm new to this topic.

Click to expand...

As stated above, the number of genes in humans will exceed those in plants. when humans reproduce it is normally 1 offspring at a time. when plants produce it is sometimes in the 1000s of seeds. also the genetic pools which they are drawing from arent as deep as those of humans. I am in no way saying they will all be identical, but if each seed was unique then creating an inbred line of plants would be almost impossible.

I am by no means a genetics expert in plants or in humans. I understand the desire to think of each seed as an individual with unique traits but I just dont think it is the reality.

i'm not understanding that logic.

a cotton plant has more chromosomes than a human, many organisms have orders of magnitude more than us...

human sperm cells are all different, meaning they confer traits others do not. that is why each offspring can be of a different appearance yet quite similar ie: blue eyes blonde hair but still carry traits like left-handedness or buck-teeth...



"For plants, we see a different scenario. Meiosis occurs in flowering plants within the flowers. In future lessons we will look at some of the details in the different groups of plants as to where meiosis occurs. But for now, what we want to note is that when meiosis occurs in plants, such as in the flowers of flowering plants, the immediate meiotic products ARE NOT GAMETES! In plants, the immediate products of meiosis are single, haploid cells called spores. SPORES! IN PLANTS, MEIOSIS PRODUCES SPORES!

Spores develop into plants. Since spores are haploid, the plants that spores form are haploid. The haploid plants will produce the gametes, the egg and sperm. What we have come to in our comparison of sexual reproduction between animals and plants is that plants are more complicated than animals because plants have an additional set of plants, the haploid ones that develop from spores, in between meiosis and the formation of the gametes.

A lot of plant biologists spend their lives studying how different groups of plants form their spores during meiosis, how the spores develop into the haploid plants, and how the haploid plants produce gametes (eggs and sperm) that fuse during fertilization to form the zygote. This is where we started: The zygote is 2n and will develop into a mature, diploid plant.

http://www.ohio.edu/people/braselto/readings/sex_reproduction.html

cannabis probably has fewer chromosomes, but I still believe each plant is unique...as we are also.

i'll need to read some more, but thank you for trying to help me understand this.

bump...

Seed Collection and Plant Genetic Diversity, 1900-1979

by Marci Baranski Keywords: plant genetic resources, plant collection, seed bank, seed collection

Farmers have long relied on genetic diversity to breed new crops, but in the early 1900s scientists began to study the importance of plant genetic diversity for agriculture. Scientists realized that seed crops could be systematically bred with their wild relatives to incorporate specific genetic traits or to produce hybrids for more productive crop yields. The spread of hybrids led to less genetically diversity than normal plant populations, however, and by 1967, plant scientists led an international movement for conservation of plant genetic resources through the United Nations's Food and Agricultural Organization, and later through the Consultative Group for International Agricultural Research, both of which are headquartered in Europe. To conserve plant genetic resources, researchers must collect and store plant germplasm—the genetic material required to propagate a plant—usually in the form of a seed.

In the nineteenth century, farmers, scientists, explorers, botanists, and agriculturalists collected exotic plants and tested the seeds in new environments. Agricultural experimenters and collectors stored germplasm in fields, greenhouses, and botanical gardens. The US government became involved in 1827 when President John Adams instructed the foreign consuls to collect seeds and rare plants and send them to Washington, D.C. Foreign consuls continued to collect seeds through the formation of the US Department of Agriculture (USDA), headquartered in Washington, D.C., in 1862. The USDA distributed foreign seeds to farmers and agricultural experiment stations for testing, and it created the Office of Foreign Seed and Plant Introduction, located in Beltsville, Maryland, in 1898.

The rise of genetic theories and the professionalization of plant breeding in the early twentieth century contributed to early theories of plant genetic diversity. Scientists in Europe such as Rowland Harry Biffen, Hugo de Vries, and William Bateson along with Liberty Hyde Bailey in the US popularized Charles Darwin's concept of natural selection and Gregor Mendel's genetic laws and their application to plant breeding. Based on de Vries's mutation theory, which indicated to scientists that they might be able to create new species from old ones if they learned how to mutate them, scientists recognized an importance for genetic variation to plant breeding.

Governments in the US, Europe, the Soviet Union, Australia, and New Zealand supported early efforts at plant germplasm collection. In the early 1900s the US commissioned Frank Nicholas Meyer, who trained under Hugo de Vries and for whom the Meyer lemon, Citrus meyeri, is named, to collect plant germplasm from locations in Asia, Russia, and Europe. In his travels, he met Nikolai Ivanovich Vavilov, who worked in Russia during the first half of the twentieth century and helped found theories of plant diversity, origin, and evolution. Vavilov studied plant genetics in England with Rowland Biffen and William Bateson at the University of Cambridge between 1913 and 1914. In the 1920s and 1930s, Vavilov publicized the loss of plant genetic diversity due to the dominance of a small number of genetically similar crops, a fact that help ground a movement for the conservation of plant genetic resources.

In the 1920s Vavilov proposed the theory of Centres of Origin of Cultivated Plants, which were eight areas of the world classified as the origins of food crops. These areas were thought to contain the most diverse wild relatives of the crops due to evolution and genetic variation. Despite repression of Vavilov's theories by Trofim Lysenko and Joseph Stalin in the Soviet Union, scientists worldwide embraced his theories. Vavilov's work inspired botanists, plant breeders, and explorers in the second half of the twentieth century to lead the movement for conservation of plant genetic resources, including Jack Rodney Harlan, Erna Bennett, John Gregory Hawkes, and Otto Herzberg Frankel. The theory of Centers of Origin increased the importance of crop wild relatives for plant germplasm collection and plant breeding. Many scientists later viewed Vavilov's Centers of Origin theory as a theory about the centers of diversity, because there is not always a clear genetic origin of plant varieties.

In 1943 the Rockefeller Foundation, headquartered in New York, New York, funded the Mexican Agricultural Project (MAP), to improve basic crops through the collection of plant germplasm in Mexico. The MAP began an era of systematic collection, evaluation, and storage of plant germplasm, in this case, maize, wheat, and potato germplasm. The MAP preceded the formation of the first long-term seed storage facility, the US National Seed Storage Laboratory in Fort Collins, Colorado in 1958. Prior to the National Seed Storage Laboratory, most germplasm collection facilities only provided short-term storage. After World War II, many countries, including India, Brazil, and Japan had established seed banks for long-term storage of plant germplasm.

The Food and Agricultural Organization (FAO), an international organization headquartered in Rome, Italy, became concerned about the loss of plant genetic diversity in wild as well as in domesticated relatives of food crops in the 1960s. The FAO had stored information about plant exploration since 1948 by cataloging plant varieties, and it had mediated between participating countries. The FAO also oversaw plant germplasm collections in countries around the world. In 1967 the FAO created a department of Crop Ecology and Genetic Resources, led by Erna Bennett and R. J. Pichel.

In 1967 the FAO and the International Biological Programme in England, organized the 1967 Technical Conference on the Exploration, Utilization and Conservation of Plant Genetic Resources in Rome, Italy. The conference popularized the term genetic resources and established a set of standards and plans for storage of plant genetic material outside of natural habitats and in seed banks. Two scientists involved in the conference, Bennett and Otto H. Frankel, argued about this strategy. Bennett advocated for conservation in the field through farmers' participation, while Frankel advocated the seed banking approach. Like the FAO, Frankel favored the seed banking approach to conservation because it allowed plant breeders to selectively draw from stored collections of plant genetic material.

Participants at the 1967 FAO conference also coined the term genetic erosion to describe the loss of plant genetic diversity due to agricultural expansion. Genetic erosion became a pressing international concern after a 1970 outbreak of corn blight in the US and the spread of coffee rust in Brazil. Echoing Vavilov, scientists highlighted the drawbacks of genetically homogenous crop populations. In 1972 the US National Research Council in Washington, D.C. authored the report, Genetic Vulnerability of Major Crops, stating a similar argument.

The FAO advocated long-term germplasm conservation as a solution to genetic erosion. Yet the FAO was not a research organization, and it lacked the funding and the ability to enact conservation methods. The FAO could not oversee the rise of international agricultural research centers in the 1960s, such as the International Rice Research Institute in Los Baños, the Philippines. In 1971 eighteen international agricultural research centers, organizations, and countries formally joined together and became the Consultative Group for International Agricultural Research (CGIAR), directed by the World Bank, headquartered in Washington D.C. The CGIAR helped FAO reach its goal of long-term germplasm conservation.

The FAO approached the CGIAR in 1971 with the idea of integrating conservation of plant genetic resources into their existing agenda of international agricultural research. The CGIAR and FAO met in 1972 in Beltsville, Maryland, and discussed a global system for plant genetic conservation. The CGIAR relied on plant genetic resources for plant breeding, and it already had some collections of germplasm. In 1974 the CGIAR and FAO formed the International Board for Plant Genetic Resources (IBPGR), which currently operates as Bioversity International.

Under the direction of the FAO's Pichel, the IBPGR, later based outside of Rome, Italy, coordinated the collection, experimentation, and information dissemination of plant genetic conservation projects around the world. The IBPGR partnered with the CGIAR's other international centers and national agricultural research centers to fund and create seed banks. These seed banks had multiple goals: long-term conservation, medium-term experimentation and propagation of germplasm for agricultural research, and short-term field experiments leading to new crop varieties.

In 1975, fewer than ten seed banks existed in the world. This number increased under direction of the CGIAR and FAO, but not without controversy, both within and outside of the IBPGR, about to whom the genetic resources belonged, and about whose responsibility it was to guarantee the security of their storage. The IBPRG changed leadership in 1979, when Trevor Williams replaced R. J. Pichel as executive secretary of the IBPGR. Publication of Pat Roy Mooney's Seeds of the Earth: Private or Public Resource? sparked public controversy over access to seed banks.

- See more at: http://embryo.asu.edu/pages/seed-co...etic-diversity-1900-1979#sthash.Ag03snoa.dpuf

Trich is right.........A lot of species have a lot more chromosomes than we do....Plants and animals.

Danny

Interesting project I think I heard about this on the Adam Dunn Show

Check out this fern: http://en.wikipedia.org/wiki/Ophioglossum
1260 chromosomes


And this ant with only 2 chromosomes in females and 1 in males: http://en.wikipedia.org/wiki/Jack_jumper_ant

i'd like Sams take on the question of individual/unique genetics since he's involved with some genealogical investigation of hemp.
actually would like anyone with his level of expertise to consider the question:

is each plant a unique individual?

or, in other words, does each seed carry unique coding?

awesome ..I can wait to hear the data..

trichrider said:

is each plant a unique individual?

or, in other words, does each seed carry unique coding?

Click to expand...

I'll take a shot at this one...
Like most things in this life, the truest answer is "It depends."

If the two parents of the seeds are completely homozygous across their genomes, then: No, each seed will technically be an individual, but will definitely not be unique since they will all have the same genotype (coding), not taking into account a tiny bit of variation due to mutation which is overwhelmingly either unseen or fatal.

Likewise, clones are individuals but are not unique again since they share the same genotype as their source plant, ignoring again somatic variation or mutation as being statistically rare, unexpressed, or minor.

If the two parents of the seeds have any segregation (heterozygosity), then the seeds will each be an individual, and will be unique to a degree proportional to the amount of heterozygosity present in the parents. Cannabis seeds in general seem to be released with this being a safe assumption to some extent.

In most cases the answer is that yes, Cannabis seeds each can be thought of as a unique individual. The amount of expressed genetic variation present can be visualized by noting the amount and magnitude of segregating expressed traits in the progeny.

Sam,
Will you want IBL's of specific strains, such as DJ Short Blueberry? How about fems? Thanks. -granger

IntelliGeneS said:

I'll take a shot at this one...
Like most things in this life, the truest answer is "It depends."

If the two parents of the seeds are completely homozygous across their genomes, then: No, each seed will technically be an individual, but will definitely not be unique since they will all have the same genotype (coding), not taking into account a tiny bit of variation due to mutation which is overwhelmingly either unseen or fatal.

Likewise, clones are individuals but are not unique again since they share the same genotype as their source plant, ignoring again somatic variation or mutation as being statistically rare, unexpressed, or minor.

If the two parents of the seeds have any segregation (heterozygosity), then the seeds will each be an individual, and will be unique to a degree proportional to the amount of heterozygosity present in the parents. Cannabis seeds in general seem to be released with this being a safe assumption to some extent.

In most cases the answer is that yes, Cannabis seeds each can be thought of as a unique individual. The amount of expressed genetic variation present can be visualized by noting the amount and magnitude of segregating expressed traits in the progeny.

Click to expand...

thank you so much.
that squares with my perception and is completely adequate an explanation.

wont amount to a hill of beans, pun intended.

wouldn't it be possoble to trace lineage the way we can in humans...certain genes are passed only from your mother..perhaps there is a gene in plants that is easy to trace regardless of how the genes combine...my 2

I wonder how much that info is going to be worth to big pharma after its completed?

Certainly alot?