At least for the Sour D project, the primary question is which cuts are really Sour D and which are something else but named Sour D. Then, maybe the second question would be which Sour D cuts have the greatest genetic relation to the Chem 91 and each other.
As far as I know, the AJ Sour D is the original, even though it may suffer from clonal decay and seem unlike like the original. I hope to get the Sour D cut Bro spoke about last year, which should be the same as AJ’s, but maybe it has fewer somatic mutations.
In terms of traits, using genomic testing to identify specific traits seems like the best route (especially for breeding projects). But more traditional measurement and analytical tests may suffice when choosing the ‘best’ Sour D cut to grow. I agree human bias is a significant concern. I forget the specific term, but it’s akin to visual bias, like, ‘oh, this plant grows faster’ or is ‘healthier.’ That’s why I harp on measurement, not opinion - using data-driven decision-making as much as possible.
the 91 from fcg was confirmed fake by someone on the forum he sent it to get genetic tested it was the Chem D. It is ultimately from Phinest where they were selling it as 91 TC
When i was growing sour d out here there was only 1, the chem lines where still being guarded heavily. The chem d made its rounds and there was 1 og for about 2-3 yrs before sfv started showing up. That and the sour were the bread and butter for yrs. Never ran the head band when it came out around the sfv time. Just my experience from here 12-15 yrs ago. My SD was supposed to be AJ’s cut, i have handed it out on here and they can chime in and give there two cents. Never ran any other of the sour cuts ( that i know of) but man before gavitas even existed we were getting those numbers in soil with the sour cut. Then came the blue dream……
To take the Sour D project one step further, I have this project flow in mind:
Identification of the ‘real’ Sour D cuts using whole genome sequencing based on comparison to Chemdog 91, AJ’s Sour D, and agreed upon Sour D trait identification @silverstudent suggested
Detection of DNA methylation through tissue culture of the selected Sour D cuts and the Chemdawg 91 cut. (This step may be unnecessary because it’s probably safe to assume the ~27-30-year-old genetic age of the cuts has introduced significant senescence-driven DNA methylation.)
Restore clonal fidelity of the selected Sour D cuts and Chemdog 91 with genome-wide epigenetic reprogramming through passive or active DNA demethylation during tissue culture regeneration. And at the same time, eliminate any diseases affecting clone health and phenotype expression (fungi, bacteria, viruses, and viroids). So they grow, smell, taste, and produce cannabinoids like (or close to) the first Sour D and Chemdog 91 moms of the early '90s. (Assuming somatic mutations aren’t causing clonal decay and fidelity loss, a.k.a. in bro science as “genetic drift.”)
@silverstudent@cyclopath, are somatic mutations a concern regarding whole genome sequencing when identifying the ‘real’ Sour D cuts? In other words, could they skew results making identification more difficult?
I don’t personally, i never noticed it when i kept my mom for yrs. I then got it back from someone i had given it too and never mom’d it out or really ran it like before so I couldn’t say now. Over the yrs of running it i never saw any difference in it.
It would be great to compare its whole genome sequence against a clone only Chemdog 91. And DNA demethylation is a natural process during sexual reproduction. So, a selfed Chemdog 91 would show less DNA methylation (e.g., senescence-driven) loss of fidelity/vigor/secondary metabolite biosynthesis, etc., compared to clone-only Chemdog 91.
With enough depth of coverage you could probably work out how many individual mutations you were looking at. When I was last worried about somoclonal variation (I’m of the camp that doesn’t draw a line between tissue culture induced vs “natural” genomic/phenotypic changes) we didn’t have access to massive sequencing…so I have to admit I haven’t seen data on exactly the kinds/scope/range of mutations or their frequency. I could make the same guesses I would have 20 years ago, re: deletions and expansions at repeats (be they trinucleotide or transposon associated), but I imagine there is actual hard data at this point.
As it turns out you and I (and all the boys and girls) are mosaics, so yeah, when you clone you can go off phene, and the smaller (fewer cells) that clone is, the greater the probability that your clone won’t look like Mom… just because the length of the genome is so long, every copy is different (every copy contains approx one error by by the last estimates I saw).
the bigger issue might be epigenetic changes…either direct DNA modification, or presence/absence/modification of histones…what I often refer to collectively as “decorations” when discussing with non-molecular biologists. turns out we change the decorations as we age… and “redecorating” is associated with reinvigoration when looking at tissue culture based methods.
Thanks for the info! This is a topic where I know what I don’t know is vastly greater than what I do know. So, I love that you’re on this site and willing to share your expertise I have to stop by and buy you a beer or twenty the next time I’m on the west coast .
Is it your opinion that somaclonal variations and somatic mutations are the same (or have the same result) but are from different causes? With the former mainly caused by newly induced mutations from some TC processes, and the latter caused by unnaturally extended plant age through vegetative cloning?
Assuming plants are pathogen-free, it sounds like you think epigenetic changes through histone modification (H3K9 methylation) and DNA methylation may be the primary causes of clonal decay (affecting genetic fidelity, which negatively affects vigor and secondary metabolite biosynthesis) - so-called ‘genetic drift.’ And in contrast, somaclonal variations and somatic mutations are less likely to be the cause. If so, that’s also what John Brunstein (Ph.D. in biochemistry) believes and what other molecular biologists and geneticists I have listened to think. But other researchers have recently found measurable clonal decay caused by somatic mutation-induced genetic mosaicism from vegetative cloning, albeit with significant caveats:
Assuming clonal decay of old clone-only strains that growers report is primarily caused by epigenetic changes, what is your opinion of active and passive DNA demethylation and histone demethylation, and the implication of their cross-talk, through TC regeneration as a whole-genome ‘reset’ to revert the unwanted epigenetic changes? I’m currently looking for TC labs that can do demethylation. Also, from the limited papers I have (thus far) read on the subject, it seems like advances in tissue culture understanding and processes avoid inducing somaclonal variation; is that correct?
Interesting. Top cut clones could have more mutations from the og DNA due to epigenetics and cutting from the bottom of mother’s could help prevent that… So, there is nothing better than some F1 from tissue culture.
I would say they are both from the same underlying mechanisms. mistakes are made. one cell becomes a clone of cells. either a sector in a plant, or on a petri dish. yeah, you probably get MORE mistakes during tissue culture, but only because you’re replicating faster or more times. not because there is anything intrinsically mutagenic about the process.
if there was a SINGLE DNA strand that was copied repeatedly (same master for each copy) the problem would be different. but we get copies, of copies of copies of copies…so we get errors, and they are compounded.
as for “unnaturally extending the plant’s life”, yeah, that really is the primary issue (with cannabis). the assumption would be that it has evolved a genetic fidelity that works with its life cycle. mistakes are problematic, but fidelity is expensive. happy balance is where mistakes don’t (usually) affect reproductive fitness.
no. I think that epigenetic changes are currently too hard to measure on the scale we would need to measure them, to have any clue. ie when I say
I mean we can now perform whole genome sequencing with relative ease, so we can SEE the mutation derived changes. we can’t yet measure the “epi-mutations” that might be responsible for some of the changes cheaply/easily enough to actually investigate thoroughly.
if I were to propose a mechanism for accelerated DNA mutations in TC vs normal plant growth, I would certainly wave my hands in the direction of “DNA decorations”…along the lines of “…dude, no time for decorations, we need another copy of the whole genome, NOW!!”, where methylation (and other mods) just couldn’t keep up with the rapid cell cycle.
CpG methylation is actually part of the error correction process.
“hey, these two don’t match! which strand is methylated? That’s the old one. match that.”
…so if you get behind on the decorations you can start making more mistakes (or be less able to fix those errors correctly).
methylation also keeps transposons quiescent. I haven’t seen anyone actively playing with them in cannabis, but they’re there and could certainly be rattled back into activity with a little effort (ionizing radiation/breaking chromosomes works great)
the one I worked on in maize may have been awoken on bikini atoll. deliberately.
the first one I stumbled over (as an undergrad), we woke with a Cobalt 60 source.
successful tissue culture does need to minimize/mitigate. so yeah, solving would count as an “advance”. pretty sure we are still just “aware of and monitoring” rather than “have solved this”, on that front.
…but it’s been a long while since this was my primary focus
Stochastic changes in allele frequency NOT due to selection.
except in cannabis…where apparently folks apply that to what I would call “Clonal Fading”.
As Dr Brunstein states, genetic drift is NOT the correct term.
What is Genetic Drift?
Now we’re ready to define what genetic drift actually means. It is a change in the allele frequencies at a locus in a population. If you have a single plant – or even if you have a group of genetically clonal plants such as from cuttings – that’s not a population in the genetic sense of the word, there’s only (at most) two alleles for each locus, and there’s no change over time in the relative frequency of each allele – it’s either 100 percent or 50 percent.
The words “genetic drift” can only be applied to heterogenous populations of a species over normal reproductive cycles – for any of you looking for more reading, it also only occurs when said population is not in Hardy-Weinberg equilibrium, which is a fancy way of saying some form of non-random mating or selective pressure is occurring to alter allelic frequencies over reproductive generations. If all of that lost you, the bottom line is genetic drift, by definition, doesn’t occur in a single individual organism.
As far as his exploration/explanation; sounds great, needs data.
The Canadian data does lend support to the gradual accumulation of somatic mutations (base pair changes)…and given the lack of selection for cannabinoid or terpene production during vegetative growth, the concept that changes in or near those genes accumulate at a greater frequency is not unreasonable.
I have to stop by and buy you a beer or twenty the next time I’m on the west coast 
.