Genome Has Been Sequenced

[VerdantGreen]

not totally on topic but i thought this was an interesting side-issue

Heather Miller Coyle, an associate professor in the Henry C. Lee College of Criminal Justice and Forensic Sciences is setting up a national databank that will allow law enforcement to track marijuana DNA.

http://www.msnbc.msn.com/id/44644719/ns/technology_and_science-science/#.Tn3J6XPN5l0

 

[GreenintheThumb]

Apparently they don't understand that cuttings get passed around.

 

[VerdantGreen]

imagine them trying to get a database of all the multi hybrids in circulation!

 

[OLDproLg]

Hahahaha!

POWER IN NUMBERS................
Millions of chem combos to be had,it cant be done.

 

[GreenintheThumb]

Another technology that would probably be useful as far as tracking allows someone to discern what reservoir the plants were watered with. Don't think it's ever really been used and RO water would prevent that from working but it's interesting...

 

[Highlight]

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[Phaeton]

The police in my town use water analysis to differentiate local grown weed from imported. Why? I do not know.

The DNA program is much more useful, it tells us what is out there and popular.

 

[HempHut]

http://www.cbc.ca/news/canada/saskatchewan/story/2011/10/19/sk-marijuana-genetics-111019.html

Marijuana genetics revealed

The genetic make-up of marijuana has been mapped out by a group of researchers who hope the information can help both the hemp industry and those who are developing medicines from marijuana.

Different types of the plant species known as Cannabis sativa can produce strong fibres or the key ingredient in marijuana that produces a high.

The scientists, at the University of Saskatchewan and the University of Toronto, are set to publish the genome of the plant.

"We hope to be able to use that genome sequence to shed light on ... questions about how did hemp arise and how did marijuana arise," Jon Page, a plant biochemist at the University of Saskatchewan, said.

Page, who co-led the research project to decode the genetic underpinnings of the cannabis species, said the plant likely originated in Asia, around modern-day Afghanistan and surrounding area.

Archeological evidence shows hemp textiles were used in China at least 6,000 years ago and shamanistic material from a Chinese tomb dated about 2,700 years ago was likely from the marijuana-type plant, he said Wednesday from Saskatoon.

Page said people likely recognized the plant had several uses: it was the source of fibres to make rope and cloth, as well as seeds that produce oil and contain protein.

"But they also realized that the flowers of ... the female plant were full of a chemical that could relieve pain and cause a sort of pleasant intoxication," he said. "So maybe what happened over time was those two uses — the medical and psychoactive — started to be separated from the rope and food use, and different types of strains were being grown for those uses."

That suggests that early farmers may have been engaging in selective breeding even thousands of years ago.

Co-investigator Tim Hughes, a molecular biologist at the University of Toronto, sequenced the genomes of both Purple Kush, a marijuana strain widely used for medicinal purposes, and the Finola variety of hemp.


Hemp differs from marijuana

He then looked for differences to explain why marijuana produces THCA, or tetrahydrocannabinolic acid, the precursor of the active ingredient in marijuana, while hemp strains contain a non-psychoactive component.

Page said analysis showed that the THCA synthase gene, an essential enzyme in THCA production, "is turned on in marijuana, but switched off in hemp."

The researchers, whose report will be published Thursday in the journal Genome Biology, are making the cannabis genome publicly available for researchers worldwide.

Page said the data could help scientists better understand the plant's properties and lead to expanded uses.

For instance, because Cannabis sativa "puts on a huge amount of biomass each season ... there's the idea that it could be used for producing biofuels in an efficient way."


Better painkillers

On the medical side, knowing the genetic makeup of cannabis could aid the development of drugs to treat pain, without the side-effects of straight marijuana, added Hughes.

"People want a painkiller, but they don't necessarily want to be mentally incapacitated," he said. "So if you could make variations in the molecule, that would increase the painkiller effect but decrease the effect on your mental capacity. For most people using it, that would probably be a step in the right direction.

"Although for others," he said, laughing, "it might not matter."

Page said there is also a potential forensic use for the genetic data, with law enforcement interested in tracking illicit marijuana.

For instance, he said one police force wondered if stalks left in a harvested field suspected to have been a marijuana crop could be DNA-fingerprinted and the results used as evidence in court.

"So DNA is a useful way of finding out the identity of a sample. People are identified by their DNA samples; plants can be as well."

Page said Cannabis sativa is the first medicinal plant to have its genome sequenced, following the decoding of non-medicinal plants like rice and corn.

Surprisingly, the genome for the opium poppy has not yet been sequenced, perhaps in part because it is estimated to be three to four times larger than that of Cannabis sativa.

"But the way things are going," said Page of the speed at which sequencing can now be accomplished, "I would fathom it's right around the corner."

 

[highonmt]

McKernan has assured himself a place in scientific history that is for sure. In the process he has made geeky taxonomists everywhere even more sweaty and nervous. The very murky definitions of all linnean nomenclature so long and hard fought over by dorky zoologists and botanists, mycologists, etc are now laid open to the unblinking eye of systematic genomics.Assignments will be made based on genetic variation under the purview of mere computer jockeys. You can almost see tear drops falling on a neatly folded plaid sweater vest cant ya...

Me, I can hardly wait till I can sprout 500 seeds and save the ten best based on chemotype and phenotype, all while they are only 2 inches tall...Makes basement breeding of uber cannabis a reality. Of course it will be 20 years or more before prices are realistic for carrying out said basement dream.
HM

 

[filtr0w]

chemovars

chemovars

did you by chance give them any of you cannabinoid specific chemovars? Seems like a no brainer.

hello there

any chance anyoen can point me to any topic about the chemovars developed by SamS?

thanks!

 

[filtr0w]

found something

https://www.icmag.com/ic/showthread.php?t=73239&highlight=chemovars&page=4

 

[Oregonism]

Insanely fascinating topic, my question is from this statement, "The production of cannabinoids and their associated terpenes in Cannabis is subject to environmental influences as well as hereditary determinants".
-Pate, D.W., 1994. Chemical ecology of Cannabis. Journal of the International Hemp Association 2: 29, 32-37.

Can a phenotype determine a genotype? it has been some time since I broached biology, but can RNA transcription occur during an environmentally influencing event(s)? In essence taking a phenotype's characteristics from environmental influence and creating a seperate genotype.
This is where I as a botanist would argue that we aren't all useless, lol. But I would agree that identifying genotypes SEEMS to be more accurate than outward phenotype identification. I would also think though that there are several unanswered questions about day to day plant evolution and the ability to transcribe new code on the fly, that will again delineate from "concrete genotypes." Hope that makes sense, even though my RNA theory needs some brushing up I will admit.

So in essence, just because a genotype or chemotype has been identified, doesn't mean it can't or won't change, needing more sequencing? Or is it that if DNA is identified as changed within a genotype, that only, THAT block needs to be sequenced and not the whole overall?

 

[GreenintheThumb]

Genotypes are not determined by phenotype. Sometimes an environmental affect can be inherited for a few generations and this field of study is called Epigenetics. It doesn't actually change the genotype or dna, it's a change in gene expression; not a change in the genes themselves. These affects 'wash out' after a few generations.

 

[mofeta]

"The production of cannabinoids and their associated terpenes in Cannabis is subject to environmental influences as well as hereditary determinants".

Can a phenotype determine a genotype? it has been some time since I broached biology, but can RNA transcription occur during an environmentally influencing event(s)? In essence taking a phenotype's characteristics from environmental influence and creating a seperate genotype. ....

.....So in essence, just because a genotype or chemotype has been identified, doesn't mean it can't or won't change, needing more sequencing? Or is it that if DNA is identified as changed within a genotype, that only, THAT block needs to be sequenced and not the whole overall?

If I understand your question correctly, GreenintheThumb's answer, in the context of plant breeding, is a good a good statement of the conventional wisdom on acquired traits. If you are interested in this topic, Google "Lamarckism".


The genomes talked about in this thread are for individual plants. For all practical purposes, the genome of an individual organism does not change over its lifetime.

 

[Oregonism]

Thank you for the answers and ideas! Of course Lamarck, that is so Bio 101, lol, should have remembered. I guess what is most important is that it is the opposite of natural selection to a point. But, my above post was convoluted and for that I apologize, but excellent answers. I have been reading furiously for a few hours, so thank you for the motivation.

Another question, define: mutation?


[Thanks guys, hope I am not segueing out of the subject. I just have some unanswered questions. ]

 

[mofeta]

allele = the various forms of a gene at a given spot on the chromosome

wild type allele = the allele that appears with the greatest frequency in a population

mutant allele = any allele other than the wild type

The popular use of the word mutant, to describe an individual with some deformity or unusual trait is incorrect.

 

[Mycel]

Just read the plants sequenced were

Sativa - CHemdog ! Hah , local strain with a lot of mystique , is what the company's founder said

Indica- La Confidential - Guys from DNA recommended it , for it being bx'd 3x + and close to landrace or some bs

 

[Nunsacred]

Massive outpouring of jargon, what can ya do?

Massive outpouring of jargon, what can ya do?

Cannabis genome sequence releases are quite exciting but
don't believe the hype!
Genomic sequencing is no different to any other industry...simplistic half truths are announced to keep shareholders happy, and most scientists have dismal imagination/foresight.

I used to work in genomic sequencing and I know first hand how difficult it is to resolve the repetitive parts of the sequence. I also know that these parts tend to contain important control areas, where divergence is occurring between subspecies. So the value of draft releases is severely limited because they lack much of the critical info.

Ok, let's pretend we do actually have pristine nuclear genome sequence for say 20 strains. We do some comparative studies and we identify a load of useful stuff from the conserved regions. Cool, this exciting and should come in our lifetimes.
But the differences we're really interested in are swamped by complexity. We can't detect most associations using GWAS. Marker maps get better but still the real situation is obscured.

I believe the problem here is that the nuclear genome sequence is only a fraction of the important info. There are other chromosomes in a cell separate to the nuclear ones, and anyway, selection occurs at the level of the individual organism, not the chromosome. Someone dismissed epigenetics as 'washing out in a few generations' but I don't think that's true. Scoff at Lamarckism all you like, but if you're wrong, you're going to really kick yourself in hindsight.
There are pools of RNA handed down the maternal egg cell line in eukaryotes which persist for many generations.
Reference : worms-can-pass-a-trait-down-for-100-generations-without-using-dna
This provides a possible mechanism for Lamarckian inheritance of traits, and was only discovered recently. Remember we're talking about control of genes, not genes themselves, so it wouldn't need to be large unique amounts of RNA sequence.

Finally I want to mention polyploidy. Again someone dismissed this as though it doesn't matter about extra copies of DNA.
But the inconvenient truth is that it's a key divergence mechanism and the switch to activate one copy instead of another is probably the most important aspect of plant genetics.
Someone might dismiss this, saying that most cannabis (if not all) is diploid, and that we know epigenetics well enough to say that its the maternal-derived chromosomes which have the patterning inherited and it's well-understood. I say it's not well-understood and it isn't simple. All higher plants are amphidiploid, meaning that what looks like a simple haploid complement is actually multi-copy, in fact it looks like there were 2 or 3 ancient duplications in plant ancestors and therefore we have a damn good explanation of why plant chromosomes are so packed with repetitive blocks much larger than viral elements etc.
If you don't believe me, google paleo-polyploidy.

In other words, almost no genes in cannabis are single copy and therefore the genome sequence tells us very little. The real information is in expression studies, and for those to work properly we need non-invasive transcriptomics. What this means is that traditional breeding still rocks, and technology has a long way to go before we can identify proper informative genetic marker sets to really replace phenotype selection.

Sorry if I seem negative I'm just trying to sum up my frustrations with the field after working in it for a while.
Genetics is exciting and holds a lot of promise but don't believe the hype in the press releases....

 

[mofeta]

Wow, great comment. You are thinking along the same lines I have been.

I believe the problem here is that the nuclear genome sequence is only a fraction of the important info. There are other chromosomes in a cell separate to the nuclear ones,...

This is so true. The success of the Mendelian paradigm, and its emphasis on the gene, has caused people to ignore the cytological inheritance that is so important.

Most people don't realize that although we inherit nuclear DNA from both our parents, we inherit the cytology of our bodies from our mothers. The various organelles and the expressive machinery are handed down in a much different way than the nuclear DNA, it is direct and unshuffled in the way the nuclear components of inheritance are. We are all the result of a single cell from our mothers. Here is a great quote from Richard Lewontin on this subject:

DNA is a dead molecule, among the most nonreactive, chemically inert molecules in the world....[It] has no power to reproduce itself. Rather it is produced out of elementary materials by a complex cellular machinery of proteins. While it is often said that DNA produces proteins, in fact proteins (enzymes) produce DNA. The newly manufactured DNA is certainly a copy of the old, ...but we do not describe the Eastman Kodak factory as a place of self-reproduction [of photographs].....Not only is DNA incapable of making copies of itself, ...but it is incapable of "making" anything else. The linear sequence of nucleotides in DNA is used by the machinery of the cell to determine what sequence of amino acids is to be built into a protein, and to determine when and where the protein is to be made. But the proteins of the cell are made
by other proteins, and without that protein-forming machinery nothing can be made. There is an appearance here of infinite regress..., but this appearance is an artifact of another error of vulgar biology, that it is only genes that are passed from parent to offspring. In fact, an egg, before fertilization, contains a complete apparatus of production deposited there in the course of its cellular
development. We inherit not only genes made of DNA but an intricate structure of cellular machinery made up of proteins.

This becomes clear in the study of human disease. Some diseases are thought to be defects in organelle dysfunction (like mitochondria), that have little to no relation to genetic inheritance. This, and other epigenetic forces help explain the reason the Human Genome Project have not been the silver bullet that it was hyped as.

...and anyway, selection occurs at the level of the individual organism, not the chromosome.

Boy, this is an interesting concept to discuss! I too am not a "gene centered", Dawkinsian. I believe that it is the phenotype, not the gene that is visible to natural selection. In various evolutionary contexts, even units higher up the chain (like species) can be considered the unit of selection.

Someone dismissed epigenetics as 'washing out in a few generations' but I don't think that's true. Scoff at Lamarckism all you like, but if you're wrong, you're going to really kick yourself in hindsight.
There are pools of RNA handed down the maternal egg cell line in eukaryotes which persist for many generations. Reference coming here when I get to my work PC. This was found recently and provides a neat mechanism for Lamarckian inheritance of traits.

This too is extremely interesting. There is that woman working with Arabidopsis that postulated a "RNA template" scheme a while back. She was roundly criticized, and her results were refuted by a number of people. She is still working on it though, and I am real interested in her research.

There is also that guy working with soybeans, who has noticed something similar in his work. His results are more robust. He has taken an interest in the woman's work I mentioned above, I think they may be collaborating now?

When I have more time, I will provide the names and citations for this stuff.

Finally I want to mention polyploidy. Again someone dismissed this as though it doesn't matter about extra copies of DNA.

I think that may have been me. I think in the context of this thread, induced polyploidy doesn't have much utility in determining the genome of a certain individual.

But the inconvenient truth is that it's a key divergence mechanism and the switch to activate one copy instead of another is probably the most important aspect of plant genetics.

In a evolutionary context, I would agree with you there.

Someone might dismiss this, saying that most cannabis (if not all) is diploid, and that we know epigenetics well enough to say that its the maternal-derived chromosomes which have the patterning inherited and it's well-understood. I say it's not well-understood and it isn't simple.

Again, I agree.

All higher plants are amphidiploid, meaning that what looks like a simple haploid complement is actually multi-copy, in fact it looks like there were 2 or 3 ancient duplications in plant ancestors and therefore we have a damn good explanation of why plant chromosomes are so packed with repetitive blocks much larger than viral elements etc.
If you don't believe me, google paleo-polyploidy.

Once again, this is very interesting.

Although I do think that you are correct, I tend to feel that the duplication in Cannabis is very archaic, and has been smoothed out, diplodized, pretty thoroughly, as opposed to something like broccoli.

The real information is in expression studies, and for those to work properly we need non-invasive transcriptomics. What this means is that traditional breeding still rocks, and technology has a long way to go before we can identify proper informative genetic marker sets to really replace phenotype selection.

I agree, but I still think that being able to inexpensively, quickly, accuratelly genotype individual plants will have a profound effect when it comes to breeding plants. Not replacing traditional breeding, but allowing for breeding that is not solely based on observable phenotype. I think that is a big deal.

Sorry if I seem negative I'm just trying to sum up my frustrations with the field after working in it for a while.

I don't think you are being negative at all. Your post maybe the best one in this thread.

I too see the hype, I participate in it! I also participated in the hype surrounding the Human Genome Project, and witnessed the deflation in peoples perceptions as it failed to deliver as promised. It's just that these projects, although not the end all that they are hyped as, are absolutely necessary to advance to higher understanding. The quicker we do these things, the quicker problems arise that lead to paradigm shifts and better understanding. Maybe a little (or a lot) of hyping helps speed the process?

Genetics is exciting and holds a lot of promise but don't believe the hype in the press releases....

Yeah, I think it's in the same book I mention above where Lewontin mentions how all the prominent genome-hypers, and in fact most famous molecular geneticists all have vested interests, or even own outright the companies doing this work, and manufacture the apparatus to do the work. I say more power to them. Cut through the quagmire of publicly funded, government research and get the work done. The profit motive has always been, and will continue to be the main driver in human innovation.

 

[Nunsacred]

Wow, great comment. You are thinking along the same lines I have been.

Thanks, I'm really grateful you understand.
---- been insulted & mocked by a subgroup of scientists/colleagues before for these kind of rants, as you can imagine.

I've put the reference in my post above. ^^

In various evolutionary contexts, even units higher up the chain (like species) can be considered the unit of selection.

Yes agreed.
Overall I tend to think selection is about population bottlenecks..... until mankind came along and started really accelerating diversion and local environmental change.
It's interesting because people talk about wheat being our oldest farmed crop with the most stratified global population as a result but I wonder if cannabis beats it, actually.
Again this confounds Genome Wide Assoc Studies.

There is also that guy working with soybeans, who has noticed something similar in his work. His results are more robust. He has taken an interest in the woman's work I mentioned above, I think they may be collaborating now?

When I have more time, I will provide the names and citations for this stuff.

Yes please, I don't have access to journals anymore and I've never really been a good student when I did.

I think that may have been me. I think in the context of this thread, induced polyploidy doesn't have much utility in determining the genome of a certain individual.

Yep agreed. Sorry to drag it out of context and maul it. I promise that wasn't intentional.

In a evolutionary context, I would agree with you there.

Although I do think that you are correct, I tend to feel that the duplication in Cannabis is very archaic, and has been smoothed out, diplodized, pretty thoroughly, as opposed to something like broccoli.

Yeh I guess you're right....conserved variants, then, would be a clue to the importance of duplicates.
Particularly conserved non-coding sequences which don't match their homologues.

I agree, but I still think that being able to inexpensively, quickly, accuratelly genotype individual plants will have a profound effect when it comes to breeding plants. Not replacing traditional breeding, but allowing for breeding that is not solely based on observable phenotype. I think that is a big deal.

Yeh I agree with that. We will be able to spot combinations of markers which occur rarely and enrich them to finally understand the major confounding factors ....
and it'll really speed things up for breeders.
I suppose I need to clarify why I'm so doubtful about it being as good as promised.

I don't think you are being negative at all.

Cool.

I too see the hype, I participate in it! I also participated in the hype surrounding the Human Genome Project, and witnessed the deflation in peoples perceptions as it failed to deliver as promised. It's just that these projects, although not the end all that they are hyped as, are absolutely necessary to advance to higher understanding. The quicker we do these things, the quicker problems arise that lead to paradigm shifts and better understanding. Maybe a little (or a lot) of hyping helps speed the process?...
..... Cut through the quagmire of publicly funded, government research and get the work done. The profit motive has always been, and will continue to be the main driver in human innovation.

Yeh I absolutely agree.
I'm going to come right out and say that J.C.Venter is a hero of mine even though I worked in the public-funded 'opposition' quagmire.
He's no saint but that's life.
The public effort here ceased investment as soon as the race was 'drawn'.
Which I thought was worse than Venter's wrongs, in all honesty, the biggest single resource in that field, just left to rot?

Anyway politics never was a strong point of mine.

Most of my concerns are about loss of diversity through commercialism.
I think we'll get some marker sets, and then a load of improved strains. And some old heirloom strains will get replaced in people's collections because the progress will be so great with the small amount of new stock.

And then, maybe 10 years later, someone will have a MUCH improved marker set, capable of 'efficiently rescuing' superb subtle traits from heirlooms, and we'll wish we'd kept viable seed stock of that old Thai chemovar which took 17 weeks and was susceptible to mites.....but was heaven's own high....