Genetic Sequencing of Cannabis

Breeder's Lab
#1

Nerd alert :smile:

To get an idea of the brave new world plant breeding is likely to be headed now that weed is a mega commercial crop, it’s worth checking out NCBI’s genome sequence data and viewer for cannabis

Basically this process identifies and marks genetic traits on a sequence ‘map’ and allows selection to be done at the level of the individual alleles … and with infinitely more precision than the current methods of ‘that looks pretty good lets suck it and see’. Instead of subjective assessment and observation of the phenotypes, with this approach, specific locations on the plant genome sequence that are responsible for specific traits can be identified, and from these a reference molecular marker map defined. All that the process then involves when a breeder has this information is to test the genome of the plants phenotypes and then use the molecular marker map to identify if the phenotype has the genes in the correct place for the traits you are looking for.

Research paper on the genetic map for Cannabis

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https://genome.cshlp.org/content/29/1/146.full

NCBI’s genome sequence data and viewer for cannabis

https://www.ncbi.nlm.nih.gov/genome?LinkName=nuccore_genome&from_uid=1723451913

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Foundational strains
#2

I haven’t gotten to this level of pollen chucking yet, but I like the sounds of it.

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#3

This is a kit/device that would be incredibly useful for breeding once you have the genetic marker map. And at around $1000 it’s dirt cheap for what it does…

To make use of this a breeder would in theory use the genetic map to identify the markers for specific traits they want to breed into the strain, then it’s a case of growing the offspring out and sequencing out the phenotypes and then comparing them to the marker map, and select the phenotype that is closest for backrossing…

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#4

Wait,

The MinION is commercially available, simply by paying a starter-pack fee of $1,000.

A realtime RNA and DNA sequencer for 1K?!?! That’s within the realm of us plebes. Hmmm, interesting.

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#5

Exactly!
Blew me away especially given the size of the sequences it can deal with… Apparently it had a few accuracy issues early on but it’s now being used in all kinds of situations… like near real time DNA analysis of cancerous tissue that is being cut out during and operation. I figure if the medicos are comfortable enough to use it in anger, then it has to be easily capable of what we could use it for.

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#6

That would be awsome! I have no idea how to use it, or even turn it on, but yea! Lol. If you could pop 100 seeds and test them against what you want within a few days, that would save a ton of time and experimentation. you might even be able to make a map of your perfect strain, then breed for it in a pretty short amount of time.

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#7

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#8

Duuuuuuuuuuuude. That’s sexy af.
@slain Good find

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#9

I’m thinking this needs it’s own topic, @slain

A bit of a potential game changer.

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#10

I’m outta likes for the day but that’s so cool… going to have to wrap my head around understanding a LOT more about genetics I can tell… . Need a genetic engineering for dummies book :stuck_out_tongue_closed_eyes:

If you think there is enough interest in this topic then for sure.

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#11

That company has hundreds of videos on youtube from a couple minutes long up to a couple hours.

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#12

I was asking about this idea a little while back…

How handy would it be to pop seeds strain hunting and run a test on leaf material at 1st/2nd internode ang get an idea if its got the genes you’re chasing.

But the biology is way over my head for now, built some equipment for a dog breeder who screens rescues and their own litters in house for genetic issues.

So tagging along, this new era could be fun

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#13

How many samples can this thing run?

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#14

Minion he linked is 1 at a time.

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#15

Along a similar ‘brave new wold’ vein, CRISPR is the other crazy gene technology worth having a look into. It doesn’t take much understanding about what it is before it’s obvious how this will be used…

https://www.synthego.com/

There is a LOT of information about it on the above website but by way of a simple explanation of the tech as I understand it anyway… .

CRISPR is basically a ‘holy shit’ technology for genome editing to alter DNA sequences and modify gene function. It uses a two step process that performs a double strand break of the DNA at particular loci, and then the next step allows for either knock out of genes from a genome as way to understand the particular function of the targeted gene… i,.e you remove the gene and record how this effects the organism OR it allows you to insert a new sequence at the break point.

It also enables the activation and deactivation of targeted genes as well as allowing the modifying the extent of the activation i.e expression. So in simple terms this means you can remove a gene and see how it effects the plant/animal… because then you know exactly what a specific gene is a specific location does, it also allows you to ‘overdrive’ the signal for activation of a specific gene or genes. i.e. Force a trait to be expressed more that it was before the edit.

It’s all but guaranteed that this tech will be used for breeding/engineering medical 'chemotypes ’ with very predictable ratios and levels of canabadiols for specific medical purposes. Thing is ANYBODY can come up with a gene edit experiment and then get a CRISP ‘kit’ to do what you want. Frankenweed here we come! :grin:

I am pretty sure this is a single sample device, but they do have more industrial sequencers that would surely have to take multiple samples and process them automatically…

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#16

Single sample, as in concurrently? I’m curious how many the unit do before it, or some components in it need to be replaced? Are we talking like 10, or 1000?

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#17

Ahhh okay so yeah that does seem like a slight catch… the device uses consumable ‘flow cells’ with the nanopores for sampling… and they cost $900 a pop…

Taken from their website.

As data is streamed in real-time, a user can choose to stop a run as soon as sufficient data is gathered. A flow cell contains sufficient buffer to run for ~48 hours (under optimal conditions) and a user can choose to run continuously or run, stop, wash, and load a new sample until the buffer and nanopores are exhausted.

I suppose how much use you got per flow cell would have to depend on the complexity of the sample you are trying to analyse? You would really only need to focus on specific sections of the DNA sequence, i.e the parts that you are trying to alter rather than the entire sequence.

Looking at the specs each flow cell has a DNA sequencing yield of between between 15-30GB, to put that in perspective the entire cannabis genome is no bigger than 1333.38 MB according to the genbank genome librrary…

https://www.ncbi.nlm.nih.gov/genome/genomes/11681

Also each of the 10 chromosome fragments is no larger than 120MB, I woudl imagine you would work by targeting specific fragments rather than reading the entire genome.

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#18

I think it was crispr that was build around reusing lab ones, after cleaning obviously.

The manufacturers say don’t do it… Of course but medical/lab grade vs hobbiest…

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#19

Would you happen to have any information regarding how these could be re-used?

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#20
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