IBL vigor

[romanoweed]

hmm, i asume it means, some kind of power needs to go to, or come from Cells, and if one doesent select for This, then this results in Celldeath? ..

Anyway, can someone chemically test if all the mytochondrial thingys are intact? And after every selction i just test it, voila..
Any easy solutions?
This sounds like dacades of work.. man o man

 

[goingrey]

Yeah the science is fascinating but difficult to match to reality. How to identify the non-obviously non-vigorous and cull them...

 

[CannaZen]

Ibl is f1 x f1 progeny parents selectively bred together, depression is like less successive genes locked in. backcrossing to the parent etc may lead towards depression I think in some cases. Thoughts?

 

[djonkoman]

cpDNA is transmitted maternally in most flowering plants, biparentally in a few, and paternally in gymnosperms. cpDNA genes have been shown to transpose to the nucleus and there is good evidence that mtDNA, cpDNA, and nuclear genomes exchange genes. The rate of cpDNA evolution generally appears slow both in terms of primary nucleotide sequence and in terms of gene rearrangement.



I would suggest the same selection tools as mtdna, but also that since it's evolution (alteration) is slow, that it's of far lower concern.

wouldn't the same apply to mitochondrial dna though?

I must admit I've had the same idea about mitochondrial/chloroplast dna possible mattering for vigour, and for that reason I do prefere to use the most vigourous plant as mother in crosses (when I have no other reason to pick one as mother other as father), but I do think actually it's way more likely most available genetic variation that can be used for breeding purposes for vigour is in the genomic dna.

not that there mighrt not be anything usefull to get from mt/cp dna, just that in the grand scheme of things it's a small thing.

 

[GMT]

Hey djonkoman, good to see you, esp in this thread.
I don't think the cpdna is an issue to be honest, at least not something that can be considered as a separate something, to be empirically observed. But mtdna is something that I'm convinced makes a difference, granted in some circumstances more than others. The old question of "Does it matter which is reversed" etc. Seems to have vanished now this is being talked about. I believe it does.
Given poor ATP production leads to reduced cell performance, the theory holds water. And given that this is a variable across populations, it's something that parental choices affect in future populations. Therefore, I believe, an essential, if only small part of the overall program, to consider.

For reference, djonkoman is the guy I message these days, when I get stuck. Props where they're due.

 

[Mudballs2.0]

hmm, i asume it means, some kind of power needs to go to, or come from Cells, and if one doesent select for This, then this results in Celldeath? ..

Anyway, can someone chemically test if all the mytochondrial thingys are intact? And after every selction i just test it, voila..
Any easy solutions?
This sounds like dacades of work.. man o man

Yes but...
a homopolymeric STR pentaplex and a SNP triplex with one chloroplast (Cscp001) marker shared by both methods for quality control. For successful mitochondrial and chloroplast typing, a novel real-time PCR quantitation method was developed and validated to accurately estimate the quantity of the chloroplast DNA (cpDNA), using a synthetic DNA standard
it's not something we can do...or even want to. I like how the actual science is pursued here guys, but i feel like im just setting myself up for more impulsive assaults. Ive witnessed Inbreeding depression once..dealing with it still to this very day actually in one of my lines. Couldn't care less cuz all i gotta do is find the mom i want (f5's) and then cross. Which was always the plan. Meh...these plants lose vigor, yes. Good pollen chuckers can fix it easy peasy.

 

[GMT]

Not by using a female from a depressed line. That's the whole point. Use the male from that line, use a vigorous female to cross to. These aren't meant as assaults, but clarifications.

 

[Mudballs2.0]

Not by using a female from a depressed line. That's the whole point. Use the male from that line, use a vigorous female to cross to. These aren't meant as assaults, but clarifications.

Not by using a fem from a depressed line....hmmmm...

 

[Mudballs2.0]

I dont believe that. Depression comes from something other than strictly mtDNA health..or the cpDNA. Recessive traits (allele sequences) are being passed and replicated, extra and missing chromosome stuff. You can use a depressed line female, sure, cuz at recombination you're at 50% regardless. As a breeder you should have clones of them all and be able to back track bad pairings, but you will have good plants just from the allele frequency ratios...even an f5 x (??)

 

[djonkoman]

Given poor ATP production leads to reduced cell performance, the theory holds water. And given that this is a variable across populations, it's something that parental choices affect in future populations. Therefore, I believe, an essential, if only small part of the overall program, to consider.

true about ATP production, but do you have good reason to think there is (meaningfull) genetic variation among populations there?
my guess would be (but I'll look up if I can find anything more substantial then my instinct) that mitochondrial dna would be pretty conserved.
since ATP production is such a fundamental function, there just isn't a lot to improve/change. a new version would just be a worse version, and get removed by (natural/human) selection. (unless there is a trade-off involved keeping multiple versions around, like one version doing better in cooler temperatures vs. warmer)
I could however see a point in matching compatible mt/cp dna and genomic dna, but I would also think that due to cannabis being a natural outcrosser, that there might not be that many incompatibility problems. because a mt dna that combines well with one specific genomic dna but badly with everything else would be a net negative in evolutionary terms (since in an outcrosser, this good combination gets broken up all the time again), while a jack-of-all-trades mt dna would do better, and become dominant in the population.

which is the mother and which is the father does matter for sure, but there are other mechanisms at play besides the mt/cp dna. so hard to say with certaintity which is the biggest factor.
usually when I'd answer questions on here I will simply say it's just 50/50, since going into the more advanced mechanisms might just end up people focussing on the wrong thing (like in my eyes, I often see people on here exagerate the influence of epigenetics, and neglecting the basics that work in 95% of the cases in favor of it. like it's a thing, it matters, but it's an exception, a smaller factor when practically breeding).
but for example in plants there's also a whole mechanism around fertilisation, when the new embryo has to reset the epigenetic imprint from the parents (think in the way that your skin and liver cells have basically the same dna, but different genes are expressed, so this is not about the sort of epigenetics that inherit). in this process, transposons might activate due to not being silenced anymore, so they need to be re-silenced, and depending on which is the father and which the mother different genes may end up silenced or not in the end of this process.
and there are also lots of cool mechanisms of non-mendellian inheritance that do not involve cp/mt dna.

edit:

Not by using a female from a depressed line. That's the whole point. Use the male from that line, use a vigorous female to cross to. These aren't meant as assaults, but clarifications.

I think in the case of a line that lost vigour in the process of inbreeding (and considering cannabis being naturally an obligate outcrosser, so limited filtering out of recesive delterious genes), it's most likely old muations showing up (recessive deleterious genes), combined with losing the cases of overdominance, instead of new mutations. if it was depressed due to the mt dna being screwed, that would be more likely a new mutation instead.

at least in the case of my s6 line I get vigour back (it's still vigourous enough in it's inbred state, but less vigourous then earlier gens) in f1's while using this line as mother line.


btw, in the vein of mt/cp dna mattering, an interesting detail is also the link between terpene biosynthesis and (chloro)plasts. I still think the genes with usefull genetic variation to breed with probably are in the genomic dna though, but it's an interesting link to ponder about.

edit2:
a quick google search does give some results of plant mt dna being pretty variable (but still slow sequence evolution, low mutation rate), I'll look into it some more, might be the genes left in mt dna (and not migrated over to nuclear dna over time) are mostly highly expressed ones, because highly expressed gemes tend to evolve slowly.

 

[GMT]

I'll take a look for papers. I can't picture there being any DNA that has evolved, without there being variance though just as a first principle. But since it's you, I'll recheck all my assumptions.

On your latter point, this would only affect the non recombining parts of the genome surely, anything else would be distributed among the P stock randomly, making parental selection paramount as opposed to which line took which parental role.

 

[Maple_Flail]

So just had a thought, How much does the Phenotype expression or Set/setting have an effect on vigor? how heavy is it tied to the day to day of the plant, like if its had a good day a step forward in vigor and if its had a bad day step back in vigor.?

 

[GMT]

@djonkoman this is nicely written, and yeah I'll keep looking for plant studies, but it proves the point

 

[bibi40]

Friends ,

smoke a good one please ,
i can' t fix anything about all this learning ,
LOL !

 

[GMT]

@djonkoman
Sorry forgot to share the link

Variation in the link between oxygen consumption and ATP production, and its relevance for animal performance

It is often assumed that an animal's metabolic rate can be estimated through measuring the whole-organism oxygen consumption rate. However, oxygen consumption alone is unlikely to be a sufficient marker of energy metabolism in many situations. This is ...

www.ncbi.nlm.nih.gov

And plants, first is a pdf, second a website, some have preferences.

https://www.google.com/url?sa=t&source=web&rct=j&url=http://www.lifesci.sussex.ac.uk/home/Adam_Eyre-Walker/Website/Publications_files/Piganeau_PO_09.pdf&ved=2ahUKEwio1MzL9-f5AhX7iP0HHVQfCRQ4ChAWegQIBxAB&usg=AOvVaw3XAq-HV0CDpo9POVf2aMaA

Evolving mtDNA populations within cells

Mitochondrial DNA (mtDNA) encodes vital respiratory machinery. Populations of mtDNA molecules exist in most eukaryotic cells, subject to replication, degradation, mutation, and other population processes. These processes affect the genetic makeup of cellular ...

www.ncbi.nlm.nih.gov

 

[romanoweed]

from what i heard, if you Outcross two far related Lines (Afghani x Columbian), you infact get higher Vigor increase than if you cross two Lines that are closer related. (Say a Columbian with another random Columbian Line) .
That was just an anektote i heard. Im not shure, but i once did such close outcrossing and i found it did really only give a visible, but marginal increase. It was still looking a bit ruff and f_ked like Landrace inbreeds/or any IBL can.

 

[GMT]

Couple of notes

It's not always the recessive genes that you want rid of, they can be what you want to keep. Dominance isn't always good.

I'm not saying that the only possibility of a depressed line is the mitochondria. I'm saying in a breeding program, they should be considered, and that knowledge used.

 

[Mudballs2.0]

Ibl is f1 x f1 progeny parents selectively bred together, depression is like less successive genes locked in. backcrossing to the parent etc may lead towards depression I think in some cases. Thoughts?

i always start a new line with a backcross...once i find the mom i like i dig through f1's from that mom and find something to backcross to her and then i start normal breeding methodologies. I wouldn't say backcrossing 'leads' towards inbreeding depression, that first cross is a pretty safe move, genetic recombination and whatnot...after that a breeder should be more aware of his/her plants and genes being thrown around.

 

[djonkoman]

from what i heard, if you Outcross two far related Lines (Afghani x Columbian), you infact get higher Vigor increase than if you cross two Lines that are closer related. (Say a Columbian with another random Columbian Line) .
That was just an anektote i heard. Im not shure, but i once did such close outcrossing and i found it did really only give a visible, but marginal increase. It was still looking a bit ruff and f_ked like Landrace inbreeds/or any IBL can.

yes, basically, although if you go a bit deeper, it isn't necessarily always that the furthest related ones give the best result. but it's a good simplification.
this phenomenon that an f1 between 2 far related lines gives increased performance is called hybrid vigour or heterosis.

there are multiple explanations as to why it occurs, one is indeed recessive genes that get canceled out. there is also overdominance, where for a particular gene an individual that is heterozygous (Aa) outperforms both homozygotes (AA and aa). and there might be epistatic interactions between specific genes that play a role.
not a single answer can solve hybrid vigour, it's a combination of all these mechanisms.

I also once saw/heard some research about finding which particular chromosome or parts of chromosomes had the best contribution to hybrid vigour in a specific cross (like you might see that a cross between line A and B performs 50% than expected without hybrid vigour, but you might then find that for example 30% of that higher performance can be explained by only the combination of chromosome 2 of A with B, and you might even find that for some chromosomes the hybrid combination has a - on performance, eventhough the average combination performance is still positive).

but anyway the point is some specific lines/populations might just combine very well.
for example, with maize people found that combining american dent maize with european flint maize gave very good hybrid vigour.

however, the opposite can happen as well, that a hybrid between 2 populations performs worse than expected from just the average of the 2.

@djonkoman
Sorry forgot to share the link

Variation in the link between oxygen consumption and ATP production, and its relevance for animal performance​

It is often assumed that an animal's metabolic rate can be estimated through measuring the whole-organism oxygen consumption rate. However, oxygen consumption alone is unlikely to be a sufficient marker of energy metabolism in many situations. This is ...

www.ncbi.nlm.nih.gov

And plants, first is a pdf, second a website, some have preferences.
https://www.google.com/url?sa=t&sou...ChAWegQIBxAB&usg=AOvVaw3XAq-HV0CDpo9POVf2aMaA

Evolving mtDNA populations within cells​

Mitochondrial DNA (mtDNA) encodes vital respiratory machinery. Populations of mtDNA molecules exist in most eukaryotic cells, subject to replication, degradation, mutation, and other population processes. These processes affect the genetic makeup of cellular ...

www.ncbi.nlm.nih.gov

I'll have a look into it and get back to this later.
at least 1 quick thing I already see in the abstracts:
the first paper talks about there being a trade-off, apparently more efficient ATP production isn't always the best, but depends on circumstances. so this could then indeed be a driver to keep variation around, since there isn't a single best version for all situations. (next question though, is this variation actually in genes that are on the mtdna? because there are also genes in the nuclear dna where the product is targeted to the mitochondria, so even if the final function/work is done within the mitochondria, the gene behind it doesn't have to be on the mt dna).

the 2nd paper seems, very quickly looking over it, about dynamics of the pool of all mitochondria within a single cell, since they're all seperate mitochondria they could have some variation in dna between them.

 

[GMT]

Can levels of glucose become toxic? Sounds ridiculous I know, but it would explain led shock mechanism, or sun shock.
Given that more chloroplasts are produced in low lighting, and less in higher lighting, as we switch suddenly from one to the other, are we creating a demand on the mitochondria that they can't keep up with?

Just idle musings