Landrace Seed Collection: Destinations???

[darwinsbulldog]

EDIT: some of the below is incorrect, i clarify in the next comment. i'll fix this up later.

you'd have to use the primers they've already found. those primers will show up in australian cannabis (we don't have landraces but we've got very old lines), they show up in all cannabis, but in different combinations, i think it's sort of like if you have markers 1-15, some a landrace from africa may have 1,3,7,9 whereas one from aus may have 1,4,5,11,15. so you'd compare the combination to see what those "unknown" old seeds match closest to. if they're 1,4,5,11,13 you may see that they're closely related so it's probably been outcrossed with another strain that had the 13. i'm still yet to learn the specifics of this stuff but that's the impression i have so far. and yeah as far as i know the older we go back the more common landraces were, reduced level of inbreeding/outbreeding like today, but that said a lot landraces themselves are actually strains that have been bred up by native people from original wild cannabis so it'd be interesting to test wild populations as well as landrace ones still being used by native peoples to see what has or hasn't changed and where they got their strains from originally. like the african ones, i don't think cannabis originated there, it would've been transported there so those landraces will have origins in asia somewhere, who knows how pure they are, that's what you'd want to find out. it'd be interesting though if you worked out that the african stock wasn't from the closest parts with natural cannabis like the middle east, but if instead it'd been transported from china or somewhere else much further away. hope that helps, lol it's got me thinking much more about it all too so thanks

 

[darwinsbulldog]

sorry i confused myself a little, the primers aren't what you're looking at specifically.

ok so when you use microsatellites in examining the dna of whatever it is you're looking at, effectively what you're doing is looking for tiny mutations/changes in the dna (microsatellites are nucleotide base pair repeats, so AAAAAA in the length of one side of the dna for example the other side would be TTTTTT i just can't put them beside each other in here. they can also be repeats like GATGATGATGAT etc.

here's an example

so one cannabis plant would have had a mutation causing a microsatellite to appear in a specific part of its DNA, this will be passed onto all its progeny and say it was very successful and eventually was a common ancestor of all the cannabis plants in a population, so all the plants had the AAAAAA/TTTTTT microsatellite at the same place. now there would be more than one that will have built up in a population. then this original cannabis population will have split due to maybe a river being created, too big for pollen to traverse, so there was no interbreeding between the newly formed 2 separate populations. over time both would accrue different microsatellite mutations from members of each population, because they're not interbreeding they can't share these microsatellites in their DNA with each other so they are unique to each population.

someone will take both these populations' DNA and run it against one another to see where the microsatellites are, and to see where they differ. the primers are just locations on the DNA stands either side of these microsatellites that enable the researcher to CUT these microsatellites out for isolation/analysis so they don't have to compare the entire DNA strand, instead they just compare the parts of the DNA that have the microsatellites, some may be the same, but some will be different and as these populations would have spread spatially over time and become separated into many 10s or 100s of populations that aren't interbreeding, they can determine how closely related each population is and where the genes have flowed, but comparing how many microsatellites they have in common. if we know of 50 microsatellites over all the populations and 2 populations share 49 of them, we know that these two populations probably live very close to one another and were split very recently, if they share only 1 our of 50, we know they must have split a VERY long time ago. etc etc. by adding up the amount of differences between all the populations, you can then make a phylogenetic tree which has the populations ordered by how related they are (how many microsatellites they have in common). however, if you have taken all these (we'll say landraces) landraces and crossed them together repeatedly, outbreed, inbreed, selfed, etc then that is going to have mixed up all of the microsatellites that once made them distinct. now the strain will have a whole jumble from everywhere. but this is good in a way because you'll be able to distinguish it from the landraces easily enough. and you'll be able to compare it to them to see which one's it's related to. anyway hope that clarifies it a bit. i'll go search for some pictures and try and add them in

here's a phylogenetic tree of races and how they are linked (how they evolved effectively).

the letters A-E in the above tree are what are called "clades" or groups. for cannabis you would have an african clade, an east asia clade, a middle eastern clade i'm guessing (you'd have to examine this stuff to know for sure). you never know what surprises might pop up where the african stuff may be more closely related to stuff on the other side of asia than to the middle east because they will have be transported there by humans many 1000s of years ago.

you can have these at any level of taxonomy. so you can have it between kindoms, families, genuses, species, populations, even individuals (ie. your family tree!)

 

[gronko]

Scarily enuff that actually makes perfect sense. However would that mean someone would have go through all the clades one by one and document each unique signature for each plant type. (Assuming it hasn't been done before - which is where you step in )

It would be good if there was an online resource like wikipedia where ppl from different parts of the world could submit a lab report of what the signature might be like. Then it could be even verified by other independent labs. Hell it could even speed things up a notch in the grand scheme of things.

sorry i confused myself a little, the primers aren't what you're looking at specifically.

ok so when you use microsatellites in examining the dna of whatever it is you're looking at, effectively what you're doing is looking for tiny mutations/changes in the dna (microsatellites are nucleotide base pair repeats, so AAAAAA in the length of one side of the dna for example the other side would be TTTTTT i just can't put them beside each other in here. they can also be repeats like GATGATGATGAT etc.

here's an example

so one cannabis plant would have had a mutation causing a microsatellite to appear in a specific part of its DNA, this will be passed onto all its progeny and say it was very successful and eventually was a common ancestor of all the cannabis plants in a population, so all the plants had the AAAAAA/TTTTTT microsatellite at the same place. now there would be more than one that will have built up in a population. then this original cannabis population will have split due to maybe a river being created, too big for pollen to traverse, so there was no interbreeding between the newly formed 2 separate populations. over time both would accrue different microsatellite mutations from members of each population, because they're not interbreeding they can't share these microsatellites in their DNA with each other so they are unique to each population.

someone will take both these populations' DNA and run it against one another to see where the microsatellites are, and to see where they differ. the primers are just locations on the DNA stands either side of these microsatellites that enable the researcher to CUT these microsatellites out for isolation/analysis so they don't have to compare the entire DNA strand, instead they just compare the parts of the DNA that have the microsatellites, some may be the same, but some will be different and as these populations would have spread spatially over time and become separated into many 10s or 100s of populations that aren't interbreeding, they can determine how closely related each population is and where the genes have flowed, but comparing how many microsatellites they have in common. if we know of 50 microsatellites over all the populations and 2 populations share 49 of them, we know that these two populations probably live very close to one another and were split very recently, if they share only 1 our of 50, we know they must have split a VERY long time ago. etc etc. by adding up the amount of differences between all the populations, you can then make a phylogenetic tree which has the populations ordered by how related they are (how many microsatellites they have in common). however, if you have taken all these (we'll say landraces) landraces and crossed them together repeatedly, outbreed, inbreed, selfed, etc then that is going to have mixed up all of the microsatellites that once made them distinct. now the strain will have a whole jumble from everywhere. but this is good in a way because you'll be able to distinguish it from the landraces easily enough. and you'll be able to compare it to them to see which one's it's related to. anyway hope that clarifies it a bit. i'll go search for some pictures and try and add them in

here's a phylogenetic tree of races and how they are linked (how they evolved effectively).

the letters A-E in the above tree are what are called "clades" or groups. for cannabis you would have an african clade, an east asia clade, a middle eastern clade i'm guessing (you'd have to examine this stuff to know for sure). you never know what surprises might pop up where the african stuff may be more closely related to stuff on the other side of asia than to the middle east because they will have be transported there by humans many 1000s of years ago.

you can have these at any level of taxonomy. so you can have it between kindoms, families, genuses, species, populations, even individuals (ie. your family tree!)

 

[darwinsbulldog]

Scarily enuff that actually makes perfect sense. However would that mean someone would have go through all the clades one by one and document each unique signature for each plant type. (Assuming it hasn't been done before - which is where you step in )

It would be good if there was an online resource like wikipedia where ppl from different parts of the world could submit a lab report of what the signature might be like. Then it could be even verified by other independent labs. Hell it could even speed things up a notch in the grand scheme of things.

yeah definitely would be nice if they could just do it, but the primers are normally in the form of a liquid you order and mix with dna and using lab techniques it separates all the microsatellites, complex stuff needing decent equipment. and it costs 1000s to find the primers so people probably don't often want to give it away to just anyone for free, normally they'll share them between universities etc. but yeah i'd say if it hasn't been done someone would have to do it yes. i probably couldn't do it personally as i'm not a pure geneticist that knows the ins and outs of processing that stuff in a lab, but you'd be able to pay a uni team or company to get primers for whatever samples you had. as stated above though it's often 1000s of bucks. doable though. the main thing to start with though would be to hypothesize what the clades are (what you think they are anyway) and try and sample each one. you can analyse that and then get much more specific (more sampling around each clade's area). just all depends on time and money and accessibility of some of these strains. unfortunately it seems cannabis landraces come from many dangerous countries in africa, asia and the middle east, i don't know if i'd have the balls to personally go to some of these countries lol but who knows what may happen. just have to communicate with people who have samples etc as well.

 

[moonunit]

Darwin is onto something extremely important here, that i would be willing to help fund under the right circumstances. The genetic database of and the phylogeography of Cannabis sativa L. would both be better off with said research taking place. It would also make the life of real breeders much easier and allow for much more productive work to be achieved within the scene and science. Microsat took over where early rapd left off, as we build the data base , things get easier and better.
Kudos m8, most of the academia types here just circle jerk and partake in peeing comps about their own knowledge but contribute very little practically, this could potentialy contribute in a big way and needs to be done.
much respect
moonunit
much respect

 

[darwinsbulldog]

thanks for the kind words moonunit means a lot! i really do hope to get this up and running one day, i'm wondering if there are any well known companies or universities that anyone knows of out there that would be interested in this sort of work? i'll have to have a good look in the next year or two, i'm guessing there'd be nothing here in aus with any interest at all but i've high hopes that somewhere in europe there'd be interest and funding for it. i definitely think you're right that this sort of research would strengthen 10 fold the cannabis community's breeding work and hopefully make the lives of a lot of people much easier.

i'm going to start traveling in a few years with a couple of cannabis loving mates once we move to europe and will start collecting samples. if anyone in the mean time is interested in helping this sort of project along, please feel free to collect any form of landrace sample - need to be 100% certain of it's exact origin, if it hasn't been picked by you personally and stored in a plastic tube or the like in a freezer. might be a big ask, maybe not. but it will one day definitely come in handy

 

[englishrick]

i read that paper ages ago, but i didnt understand it,,,,i know il be coming back to this

darwin,,,if i can help you in any way, just ask,

i can tell your gona be something special when you become an old man.....i very mutch value you as a person,,,,,you have all the right ideas,,,,your a star bro

il come back to this,,,,

 

[Feb2006er]

cheers mate, yeah phylogenetic tree i'll probably have to aim for a select few sites from the main areas Cannabis occurs naturally. i'd have to take maybe 5+ samples per site, then you'd run microsatellite dna analysis on it (i'd have to look into the specifics of doing it in botany, in zoology you also use mitachrondrial dna, plants don't have this though, but i believe the chloroplast dna acts much the same way). then you'd run the dna against one another to and use computer programs to work out which populations of Cannabis are the closest related all the way to most distant and the computer will form the most likely phylogenetic tree. it'd be nice to see which country has the most ancient population of Cannabis, as well as the most genetically diverse populations. and i'd also be able to see where the genes have flowed through space and time, and be able to examine natural barriers (these are barriers that would separate populations = no gene flow) so there may be populations out there within 10s of kms that are less related than other populations 100s of kms away because of a mountain range, or big river etc. it's really interesting stuff just have to find a university or organisation that'd take me on and fund the project etc. few years away yet though



thanks mate!

I would reccomend New Guinea, Uzbekistan, Colombia, Congo, and NW India for the starting 5. All of those places still have landraces, and a great distance between them, so the genetic variation should be the greatest.

 

[Feb2006er]

You can start a dna lab in you house no problem. Once you have started collecting data you can use computer software to do all of the analysis for you. No reason to get a university or organization to help. ICmag has unfathomable resources for helping to further this project- there have been landraces picked up by members from all over the world. Once you have done the research you can then publish your work and get an honorary doctorate and then some university or organization will sponsor more post-doctoral research. Make magazine had a great article about doing home dna research for cheap a while back. I'll see if I can find that article for you

 

[TeaHateSea]

Always inspiring Darwin.
Best of luck and let me know if you need a cheap pack mule.

 

[darwinsbulldog]

You can start a dna lab in you house no problem. Once you have started collecting data you can use computer software to do all of the analysis for you. No reason to get a university or organization to help. ICmag has unfathomable resources for helping to further this project- there have been landraces picked up by members from all over the world. Once you have done the research you can then publish your work and get an honorary doctorate and then some university or organization will sponsor more post-doctoral research. Make magazine had a great article about doing home dna research for cheap a while back. I'll see if I can find that article for you

i don't think it'd be that easy to get a dna lab in your own house going, i mean sure you could start saving and storing the samples but the equipment used to analyse the dna you'd never find in anyone's home. that's what you need before you can analyse it using computer software, you have to have chopped up all the dna, run PCRs etc and have it read into the computer first. but yeah once it gets up and going it'll be interesting to see how it goes, by the looks of things there'd be many people/organisations out there interested in supported the project which gives me hope

Always inspiring Darwin.
Best of luck and let me know if you need a cheap pack mule.

thanks teahatesea, no doubt it will require more than just me to do it, but it's a few years off yet, though i'll keep you all updated on here with how things go

 

[TeaHateSea]

*updates expected*

Adventure travel based resume with border running expertise referenced and documented is in the works.

 

[An Old Friend]

i'd have to take maybe 5+ samples per site,

Transkei - South Africa

Swazi
Transkei
RooiBaart
Durban Poison
Leshoto Highlands
Pondo

Across the way is mauritius, Mozambique and close by is the Angolan area and their strains

Pure Sativa's but some SA sativa's, Durban Poison, may be a little muddied with indica genetics coming from India and the surrounding areas.

Best of luck and if in SA, please feel free to give me ashout for any advise.
Kind Regards,

 

[darwinsbulldog]

saw a documentary on cannabis today, called cannabis : The evil weed? on bbc knowledge, foxtel. it stated that cannabis evolved in the last 50 million years in Kazakhstan and was then distributed to other places in asia and africa like china, india, etc so it'd be really interesting to test the genetics of wild (non landrace - unchanged by human agriculture) to those landraces in surrounding and distant countries. i wonder how much has changed in the last 3000 yrs or so since humans started using and cultivating it.

also it'd be interesting to look at populations that now grow wild in countries where it didn't originate where it was introduced and escaped from farmers into the wild. what would the ecology of the plant be like with the surrounding environment? i know that the dingo here in australia was introduced about 5000 yrs ago from asia and is now relatively balanced in the ecosystem of australia compared with more recently introduced species like the cane toad, rabbit, fox, etc. would there be different levels of this adaptation to environments cannabis now grows wild in? and you wonder what sort of adaptations the plant has had to gain in places much different from the environment of kazakhstan like the dry deserts of Afghanistan compared with the wet forests of india and africa.

i think cannabis is going to be an amazing plant to study this in because it is still relatively primitive with respect to agriculture by humans, compared to vegetables and fruits and grains etc that are now grown on industrial scales, genetically modified etc, cannabis is still grown in these landrace countries the same way it was 1000s of years ago... i think this would be unlike most other plants so it will have an interesting story to tell! and may open our eyes and expand our understanding of how we treated our more ancestral crops and now incredibly domesticated foods and animals. it'll be a nice step back into the past i think!

 

[nlvigour]

I applaud your work

I applaud your work

I suspect that you've read some of Michael Pollan's work. It may be wise to take cues from his exceptional work. I've attached but a single link... but with a bit of hunting and gathering you'll be able to draw upon his narratives to bring about a well articulated and informed thesis.

http://michaelpollan.com/?s=cannabis

In addition, I'd be honoured to assist your efforts. Whether it be gas-chromotagraphy, chemical or geographical distributions of this plant over time and geography.

As previously mentioned, you have you have a solid foundation to probe your thesis and illucidate your findings to a wide audiance.

Bravo.......

 

[darwinsbulldog]

hey nlvigour, sorry only just saw your post, thanks heaps mate, i'll suss it out tomorrow (2am here and i'm gonna hit the hay) and i'll get back to you. i'll keep everyone posted with how it all goes though it'll be a work in progress for a fair few years i'm sure. cheers for the interest and support

darwin

 

[Masterlow]

holy crap this is some interesting stuff.. pulled up a chair, and will def check this out again in the morning when i'm sober (dam quarts) Thanks for the oodles of info guys.

Oh and Darwin, an old friend is right!! Pull through South Africa on your global round trip, get some pure genetics, get blazed and fly on.. sounds good no?

ML

 

[burningfire]

what about la reunion? there's lots of zamal ( cannabis ) growing there.. and I think it,s probably safer than most southern locations

 

[darwinsbulldog]

hey ML and burningfire cheers guys, hehe yeah la reunion would be a nice place to see, i could work on my french too while there hehe

 

[ksmokey]

hey darwin! awesome thread and best of luck in your work with landraces

i'm waiting on MOZAMBIQUEN POISON, malawi gold, and mulanje gold from mulberry seeds.

the breeders info on the mulanje gold said it was a strain of malawi gold but i'm not sure if mozambiquen poison is related to durban poison. guess that'd be where you come in haha


btw have you come across http://en.**********.eu/ the site has a cool feature that lets you see strain genetics mapped out if you press the mapthisshit button.