Basic genetics explained

[Tom Hill]

I have never heard anything about this,,,,

I think intralocus interaction and degrees of dominance is what's being brought up. Eg red(AA) X white(aa) begets pink(Aa) as apposed to red (Aa).. There are several examples of this even when observing the most basic of traits (eg broad leaf X narrow = intermediate) so really it probably should be covered in even the most basic of text.. -T

 

[Only Ornamental]

I used terms like pheno because most people understand what it means and have seen it used before. I tried to write this so that there wasnt a need to already understand the terms used in genetics. To say my "phrasing is not very sophisticated" is a bit if an unwarranted stab at me. I wasn't trying to write a thesis, just an informal thing on the basics of Mendelian genetics and how some of it could be applied to cannabis.

Again as I wrote in the first post I'm not a big time breeder or geneticist, if the information i gave is wrong you are more than welcome to post your thoughts on it and the correct information. I have not done a mountain of research specific to cannabis genetics and you may have something to add that I am not aware of, like your comment about THC/CBD expression. I have never heard anything about this, so please provide your thoughts on it but let's try to not make our goal to rip apart my post for flaws.

Don't get me wrong, I'm not here to tear your post apart just because I can, although you implemented something like that and I will, if I find enough time, start to correct/complement a bit (which also includes nitpicking, be warned). I'm a bit sarcastic from time to time but never try to offend someone (who doesn't deserve it) even if it may sound like that: so, stay calm!
With my comment about your phrasing I mean the way you describe or rather dramatically simplify things; some stuff you say may not be wrong in the context but is somewhat borderline...

I appreciate your effort although the second part of your post is literally spiked with untruths, half-truths, 'misused' nomenclatures, bad examples and so on and the good things in there get somewhat lost...
We have here quite a few good posts about genetics, breeding (and inbreeding) and I honestly don't know how I feel about going down that rabbit hole again.

To the THC/CBD part: There's an allele for 'THC' and 'CBD' (the B locus): If a plant is heterozygous on that locus (i.e. BT/BD), it will express roughly 50% THC and 50% CBD (or rather the corresponding acids THCA and CBDA).
Use the forum search for a deeper insights, there are tons of infos on that subject!

 

[Only Ornamental]

I still haven't figured out how to poly-cite several paragraphs from one single post, so I'll treat your first post bit by bit.

Now that we have a better understanding of some of the modes of inheritance, and how genes interact with eachother to produce a certain trait, we can now examine the methods that breeders use to produce strains with set, defined, traits, and are true-breeding for those selected traits. There are only a few terms that have been coined by the breeding community to reflect some sructure or template for their breeding. There is simply inbreeding and out-crossing, that's it. You may have heard of backcrossing, line breeding, in line breeding, inbreeding, cubing (a big one used often by cannabis breeders) or any other format on which to structure your breedings. All of the previously listed terms are a way of saying inbreeding, and if its not inbreeding its an outcross, no exceptions. All breeds of dogs and furthermore all "strains", "bloodlines", "sub species", however you would like to refer to them, are inbred and their uniformity and true breeding nature are a direct result of inbreeding.

You didn't mention anything about 'genes interacting with each other'. I suppose you mean one allele dominating over the other... Mentioning that many recessive traits are non-functional mutations and (for reason unknown) most 'wild type' alleles are dominant might have been useful. You write for laymen, right? Maybe you shouldn't use 'nerd' expressions without a definition... like 'true breeding for a certain trait' is the expression used mostly by plant/animal breeders and in case of single gene traits translates as 'homozygous' in genetics.

Your statement 'There is simply inbreeding and out-crossing, that's it' comes from botany and refers to plant species which self-pollinate (notably each flower pollinates itself) and species which depend on other specimens/flowers as pollen donors: Only in case of 'inbreeders' does the species really inbreed, 'outbreeders' may also inbreed . Plus, you don't give any definition of inbreeding like '5 generational connections'. Check out THAT thread wherein I give some.
Then again, there are several fields like thoroughbred breeding, agricultural breeding, pedigree breeding, 'scientific' breeding and so on and everyone has their own definitions and uses for terms like 'line breeding'. In science, it is impossible to line breed for two different ancestors whereas pedigree breeding has no problem with that.
Another example: Cubing, if done with non-stable parents, is virtually neither nor and should (in principle, although most breeders aren't aware of that) result in something new although similar to the first cross due to A) maintaining heterozygosity and B) multiple crossing overs and other 'gene-mixing' mechanisms.

In cannabis breeding it's not principally about inbreeding but about selective breeding, wherein some steps are often inbreeding to speed up things. Another effect used is hybrid vigour where you obtain an F1 (outcrossing): Is an F1 out-bred to the male or female line or to both? A stupid question because the breeders seldom uses an F1 to go further on so there ain't no line (that is a bit exaggerated and not 100% correct, I admit).

The statement 'All breeds of dogs and furthermore all "strains", "bloodlines", "sub species", however you would like to refer to them, are inbred and their uniformity and true breeding nature are a direct result of inbreeding.' is simply and completely wrong.
Dog breeds suffered tremendous inbreeding in the last century but the original breeds are not truly inbred and are a result of a very long (nature and human driven) selection process (inbreeding is only a by-product).
A 'strain' is a term used nearly exclusively in microbiology and in vitro breeding and one of the biggest 'abuses' in cannabis culture whereas a subspecies is a naturally occurring 'species' and subject of taxonomic caprices; there's no direct link to inbreeding or outcrossing or whatever subject we're discussing here.
A 'bloodline' is rather obsolete unless used in pedigree/thoroughbred breeding. A stud may be of two different unrelated bloodlines and hence be the product of outcrossing ; notably, this is rubbish from a scientific point of view.

Only a strain (a real one, not a cannabis 'strain') is true breeding, all others are true breeding for one or the other trait but the whole population could show mutations on every allele. What you define as inbreeding was involved in the whole evolution... but in breeding we don't use inbreeding in that sense but a more strict one and that likely contributed to the extinction of more species than to the development of new ones.
Also, uniformity may come from inbreeding or rather very loose inbreeding aka line breeding involving thousands or millions of individuals (and that's usually not called inbreeding anymore) or it can result from selection or absence of mutations. The closer the inbreeding, the faster the homogeneity obtained; but you can also get something homogeneous with selection and nearly no inbreeding (at least one step in common breeding is usually necessary unless you happen to come across two different varieties with the same allele)... I would simply not put it the way you do. It's to generalised and focussed on the same time involving different fields/nomenclatures and that doesn't work out very well.

 

[Only Ornamental]

One thing to always remember is that inbreeding neither adds nor subtracts from the line. It simply doubles up on what is genetically there, creating new possibilities.

If you double say the 'male allele', you loose the female part .
Sure, you can not obtain a new allele (using only Mendels rules) and the new possibility is just heterozygosity or rather hybrid vigour.

Inbreeding is not bad, nature is imperfect!

Who said inbreeding is bad? And why do you think nature is imperfect? Most things in nature have their use which may or may not correlate with human desire...

Inbreeding does not create problems, deformities, or disease, but it does rapidly bring masked recessive traits to the surface where they can be selected for or against, recessive doesn't always mean bad, it means its recessive.

What else would you call it when a strategy results in disaster other than it creates problems? It does not create mutations but only (eventually) reveals them, if this is what you mean...

Inbreeding depression is a term used when inbreeding is abused and a general lack of vigor, fecundity, and health is lost throug h successive generations. When this occurs breeders usually look for an outcross to bring the inbreeding coefficient down and promote vigor and fertility. Inbreeding depression can happen to any organism but inbreeding is not to blame. Again nature is imperfect, you doubled up on a piece of genetic information already in your line, and now you have a problem, inbreeding didn't cause the problem, it just made it visible. Now that a negative trait has been expressed, its not necessarily time to find an outcross, just select against that trait for future breedings. There are strains of lab mice that are a result of 100s of generations of brother - sister breedings to keep the line uniform and genetically, nearly identical for testing purposes of pharmaceuticals. These lab bloodlines have exhibited no apparent loss of health, vigor, or fertility, with an inbreeding coefficient (a measure of to what extent a specimen is inbreed written in percent) of 95% and in some cases higher. How is this? The original breeding stock was of superior quality, and the breeders culling process was thorough and rigorous, only selecting the best specimens for future breedings.

Inbreeding depression is not necessarily linked to abuse and strictly speaking starts in case of cannabis already in the F2 (although you won't notice it at that point ).
Don't forget to explain what the inbreeding coefficient is (not for me, I do know).
Why do you think inbreeding depression can happen to every species if there are inbreeding ones like tomatoes?
If you find a damaging recessive mutation in your breeding program, you won't use the individual who expressed it because it's homozygous and you can't remove it but you will use a heterozygous parent or sibling for the 'removal process'.

Pleas get your knowledge on lab animals, or rather true inbred lines, updated. The poor suckers suffer tremendous inbreeding depression and no IBL of higher animals has not several severe problems with vigour, fertility, litter size, health, lifespan and so on.
The inbreeding coefficient is usually above 99.9% and not just 95%.
And there was not much of a selection involved (eventually only in the first few generations if a certain trait was desired), then the breeders simply had to take what survived... and usually only survives in a more or less sterile/clean lab environment. Again, the original stock was just some healthy animals (like wild mice allegedly found in the sewers), no extraordinary whatsoever. Besides, it is impossible to know in advance what will survive a complete inbreeding program and what not. And the only animal being culled where mercy killings. That way one avoids that selecting for heterozygous animals (the usually more vigorous ones in the litter). That means, the successive sibling crosses have to be random to remain close to the mathematical probabilities and far away from biased crosses. Well, nowadays one also uses gene tests (e.g. PCR, ELISA) to enhance the inbreeding process of transgenic animals. In plant breeding one has the possibility to get it done in one go by producing 'doubled haploids'... again, there's no true selection involved; the few survivors simply have to prove themselves in subsequent F1 crosses.

 

[Only Ornamental]

And what has the part with the allosome linked traits to do with cannabis breeding?
The publication cited by Sam has a minor flaw insofar as it states in the abstract the X being the biggest one but the rest of the article says it's the Y... Anyway, it doesn't matter.
What does is that we don't know if cannabis is evolutionarily somewhere between bisexual becoming dioecious or whether it once was purely dioecious and returned partially towards monoecious or whatever... everything is possible and has for example been shown in reptiles where we have a lot more species and genetic data to compare with. That said, we will likely never know why cannabis is subdioecious, although the version of (deliberate?) incomplete evolution is regarded as most likely.
I don't get at what you're aiming with second last paragraph, the one about 'hermies' and breeding. Furthermore, it is purely speculative because (see above phrases). Selective cannabis breeding has not much to do with what's natural but with what humans want and desire.

cannabis does not grow so we can get high

Maybe it does (or does grow so we can get high, sated and dressed etc.)? There are several crops only existing in cultivated form with no wild relatives (one example is ginger); who knows for sure if that's the case or not for cannabis?
And yes, 'herms' are the end of the world, at least for a sinsemilla grower .

I think, now I have said everything 'important'...

 

[mofeta]

I haven't read the OP or most of the comments in this thread, but Only Ornamental brings up something that has been bugging me:

The publication cited by Sam has a minor flaw insofar as it states in the abstract the X being the biggest one but the rest of the article says it's the Y... Anyway, it doesn't matter.

Here are some quotes from the paper:

The Y chromosome is larger than the autosomes, and carries a fully heterochromatic DAPI positive arm and CS-1 repeats only on the less intensely DAPI-stained, euchromatic arm. The X is the largest chromosome of all,...


The species’ estimated haploid genome sizes are 818 Mb for female plants and 843 Mb for males, indicating that the Y chromosome is larger than the X...


In male plants, one of the largest chromosomes showed brighter DAPI staining on one heterochromatic arm relative to the other euchromatic arm of the chromosome (Fig. 1a, b). This chromosome was likely the Y chromosome. The second largest chromosome without homologous DAPI positive bands on both subtelomeres was probably the X chromosome. A pair of these chromosomes was detected in female plants.

The Y chromosome can be distinguished from all the autosomes by its larger size,

The largest chromosome was assumed to be the X chromosome, and carries CS-1 subtelomeric repeats on both arms. No morphological or significant size differences were detected between the X chromosome and the autosomes

The X chromosome was not clearly differentiated from the autosomes because they have a similar size

Our results show that the Y is larger than the autosomes and the X chromosome in C. sativa.

I haven't had the time to really scrutinize the paper properly yet. Usually when I read a technical article in a peer-reviewed journal, I assume what seem to be errors are really a lack of understanding on my part- scientists are generally very careful, and the peer review process is supposed to catch anything the authors miss.

So, I thought maybe they were talking about two different types of size- actual physical length vs. information (bp) size. But no, the X is both longer, and by virtue of it's heterochromatic (dense) arm, more bp.

I am really having a difficult time reconciling the incongruity of the statements from the paper that I quoted above. I will give the paper proper reading when I can, but that might be a while. Maybe someone who actually knows about this stuff can save me the time. *cough cough Chimera cough cough*

It is not impossible that these are actually the glaring errors they seem to be on the face of it, (language barrier maybe, but peer review should have caught that, even in a cursory skimming this just pops right out) but I find that unlikely. If I can't get a satisfactory explanation after further study and input from you guys I will email the authors and ask them.

 

[Tom Hill]

If a 4 year old walked into the room and he somehow digested the topic,, he would ask us all why we are talking about corn,, instead of strawberries,, since medicinal cannabis (not to be confused with fiber or seed hemp) more closely follows the breeding of strawberries..

We would tell him well son cannabis is a diploid etc,, and he would quickly retort yes but you have been propagating it asexually/clonally for decades, why?!! and then we can all sit here with a stupid look on our face because that 4 year old is absolutely correct.

Cannabis -medicinal cannabis anyway- is too complicated of an organism to be treated in the same way as hemp or other much less complicated organisms. And that elephant has been in the room so to speak ever since the very first elite clone rooted.

 

[dannykarey]

Hey Tom, good to see ya posting again man.

Danny

 

[Tom Hill]

thanks danny, its been a minute, just getting warmed up.

 

[dannykarey]

Really great to hear buddy.......we missed you for sure.

Danny

 

[Raco]

Hey Tom, good to see ya posting again man.

+1


Eg red(AA) X white(aa) begets pink(Aa) as apposed to red (Aa).. There are several examples of this even when observing the most basic of traits (eg broad leaf X narrow = intermediate) so really it probably should be covered in even the most basic of text.. -T

PCK P1 x Uzbek male P2 ...ejemplo tio?

 

[Tom Hill]

hermano familla jefe si claro. See what happens if we fail to cover all of the scenarios (especially the most prominently experienced ones) is the neophyte quickly observes something different his first time out and then our simple previous explanation gets used for kindling at the next barbeque, jejeje,, biglove bro.

 

[Tom Hill]

Only Ornamental nailed it properly,, but only the upper echelon knew what he was talking about.. I knew i could speak the jive of us commoners better than that.. ..and that is what i have to say to the OP.. if we lose the upper echelon,, we have nothing,, we need to keep them,, show them something, bring to them new realizations, as well as at the same time not be a huge downer for the neophyte.. It's easier said than done believe you me

 

[mofeta]

If a 4 year old walked into the room and he somehow digested the topic,, he would ask us all why we are talking about corn,, instead of strawberries,, since medicinal cannabis (not to be confused with fiber or seed hemp) more closely follows the breeding of strawberries..

We would tell him well son cannabis is a diploid etc,, and he would quickly retort yes but you have been propagating it asexually/clonally for decades, why?!! and then we can all sit here with a stupid look on our face because that 4 year old is absolutely correct.

Cannabis -medicinal cannabis anyway- is too complicated of an organism to be treated in the same way as hemp or other much less complicated organisms. And that elephant has been in the room so to speak ever since the very first elite clone rooted.

Hi Tom

It is good to see you back. I hope things are good in your part of the universe.

Like usual I am in complete agreement with your position on this. The massively multifactorial traits that separate fire from hay yeild only to large numbers. Polygenic quantitative qualities=needle in haystack.

I've stated on here in the past that I thought there was one big stumbling block in this kind of breeding. Most people usually boggle at the growing of such large numbers of plants. This aspect is actually trivial though, as shown by a number of the members of this very site.

The actual problem is evaluating the individuals. What good is growing a million plants if you can't check every one of them? Even if you had the massive budget to hire and expertly train the equivalent of sommeliers for weed, the individual differences in neurochemistry would make standardized results impossible.

The only answer to this one non-trivial problem is the sharpening of our analytical tools. There is a LOT of work to be done to realize the goal of accurate machine testing so necessary to find the truly transgressive individuals that will parent the next generation of weed.

It really is good to see you back! You seem bright-eyed and bushy-tailed too.

 

[mofeta]

For those who don't get where Tom is coming from, and would like to start to understand, here is the "Word Of The Day To Look Up:

EPISTASIS

 

[Raco]

eg broad leaf X narrow = intermediate)

DC x Hz -F2...

 

[Tom Hill]

I almost went there mofeta re if not for things falling outside of the OP's scenario more often then not,, hybrid vigor would not exist

And thank you brother Mofeta for the previous, i been saying closer to strawberries than corn for a decade around here but i never still have found quite the correct language to get it out enmass.. We are talking about nothing less than reclassifying medicinal cannabis as Allard speaks of plants according to the way they are bred. In this case, flip to the back of the book and read about plants that are propagated asexually. Indeed, when we reshuffle 100 some odd entourage inputs, it may as well be a friggin octoploid - we are not breeding hemp. In the case of drug type cannabis, this is not up for discussion,, it has been in fact for a very long time propagated asexually and for very good reason. Even a 4 year old could see it. -T

 

[Tom Hill]

if we solved this actual problem sir,, i believe we will only be confronted with another. namely,, the horrendous maths involved in the recombination of 200+ inputs that actually matter.

I dig that you used that word transgressive,, i love even more that i know what u mean..

but until technologies eg reverse breeding are borne out,, i think we'll be propagating and capturing said transgression asexually.

Hi Tom

It is good to see you back. I hope things are good in your part of the universe.

Like usual I am in complete agreement with your position on this. The massively multifactorial traits that separate fire from hay yeild only to large numbers. Polygenic quantitative qualities=needle in haystack.

I've stated on here in the past that I thought there was one big stumbling block in this kind of breeding. Most people usually boggle at the growing of such large numbers of plants. This aspect is actually trivial though, as shown by a number of the members of this very site.

The actual problem is evaluating the individuals. What good is growing a million plants if you can't check every one of them? Even if you had the massive budget to hire and expertly train the equivalent of sommeliers for weed, the individual differences in neurochemistry would make standardized results impossible.

The only answer to this one non-trivial problem is the sharpening of our analytical tools. There is a LOT of work to be done to realize the goal of accurate machine testing so necessary to find the truly transgressive individuals that will parent the next generation of weed.

It really is good to see you back! You seem bright-eyed and bushy-tailed too.

 

[Tom Hill]

You see Padre CH? You need to brain fuck them all, get them high on acid and inform them that they've been studying the wrong fucking plant. That gets their attention.

 

[Tonygreen]

Basic genetics? I'm wondering if we had a plant with GFP reporter gene if it would encourage itself to show intersex characteristics.