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Invisibletruskool
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Domestication
    #11187565 - 10/05/09 05:01 PM (8 years, 1 month ago)

So I am receiving a cube print from a place where there is no stantard cube from.  This was collected wild and an isolate from a clone was made this isolate was grown out to print several times.  The largest fruit was picked and the process was done again.  I am told that the ms innoculations grow very different.  I take it cause this is unstable.  How would I go about domesticating the cube.  Would I isolate and go thru several generations?  How many if this is the process.  Or am I completely off base and something totally different has to be done and if so what?


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OfflineWorkmanV
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Re: Domestication [Re: truskool]
    #11188193 - 10/05/09 06:37 PM (8 years, 1 month ago)

7 times is the magic number :wink:

Check my post here.

http://www.shroomery.org/forums/showflat.php/Number/10242476#10242476


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Re: Domestication [Re: Workman]
    #11188283 - 10/05/09 06:50 PM (8 years, 1 month ago)

7 only! Fuck I was well out with a guess on a previous thread of 20 plus.

Good info^^^

Maybe i will try to cross two cubes.


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Re: Domestication [Re: badman]
    #11189809 - 10/05/09 10:19 PM (8 years, 1 month ago)

Workman if you haven't already you should write a "How to breed mushrooms for dumbies". I read your post and it makes PERFECT sense. Now I'm just curious what kind of DNA/genetics mushrooms have. I wanna play, I wanna play.


Edited by smaerd (10/06/09 01:18 AM)


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Invisible13shroomsM
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Re: Domestication [Re: smaerd]
    #11190972 - 10/06/09 01:05 AM (8 years, 1 month ago)

the man beat me to it, I thought I could shed some light on this thread but I see the light is already here.:sun:
I'll put the info up anyway.:shrug:
the more its posted the easier it is to find in the search engine.:stoned:

Quote:

Ah, thats pretty simple actually.  You need to do around 6 sequential generations from multispore selecting for the best specimen at each generation.  By the 6th generation, almost all of the heterozygosity will be lost and the strain stable.  The early generations are the most important for selection.  Heterozygosity is reduced by 50% for each generation by multispore, so you can mathematically see how this works.

Generation zero - wild specimen heterozygosity 100%
F1 multispore of wild specimen 50%
F2 multispore of F1 specimen 25%
F3 ....12.5%
F4 ....6.25%
F5 ....3.12%
F6 ....1.56%

and so on.

After the F6 generation there is so little heterozygosity (variability) left that all the mushrooms generated by multispore are virtually identical and the strain is considered stable.  It almost acts like a single clone since all the multispore strains are so similar and do not antagonize each other within a multispore tray.

I hope this makes sense.




Leave it to the pros to make it sound so simple :super:

13:mushroom2:


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Invisibletruskool
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Re: Domestication [Re: 13shrooms]
    #11191023 - 10/06/09 01:15 AM (8 years, 1 month ago)

:lmafo:
Thank you tho 13shrooms


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OfflineWorkmanV
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Re: Domestication [Re: truskool]
    #11192541 - 10/06/09 11:40 AM (8 years, 1 month ago)

I should point out that common sense dictates that inbreeding is bad since it can expose recessive genetic defects or undesirable traits.  Ideally you want high heterozygosity to give a particular mushroom strain a wide range of available genes, which in turn makes it better adapted to unpredictable environmental conditions.  This could be achieved by cloning a wild vigorous specimen or by crossing two very different strains.  In my experience, the mushrooms resulting from such a cross are very vigorous and productive (hybrid vigor).

The problem is that to keep this strain going you have to keep the mycelium going.  This isn't a problem with edible cultures but we need stable spores.  The spores from a high heterozygosity strain will be genetically recombined and won't produce the original strain  (although with aggressive isolation you could get something close).  Multispore grows will be terrible, not because the newly generated strains are bad, but because they are so genetically different from each other.  These different strains don't get along nicely in the same tray which reduces productivity.  If we can reduce the differences between the strains generated by multispore to some minimal level, they tend to cooperate better with each other and act more like a single strain.

The point is that we are dealing with spores not clones.  Many (most) Psilocybe growers use syringes to generate multispore grows with no isolation. In this context, stabilized strains are desirable.  If everyone could trade/sell mycelium this wouldn't be an issue.


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Invisiblefastfred
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Re: Domestication [Re: 13shrooms]
    #11199902 - 10/07/09 01:17 PM (8 years, 1 month ago)

Quote:

I should point out that common sense dictates that inbreeding is bad since it can expose recessive genetic defects or undesirable traits




This isn't really true.  Our cultural norms have led us to anthropomorphizing this to other species. 

It's our numbers, and diversity, and cultural aversion to inbreeding that have generated such a large number of detrimental recessive genes in our population.  Non-human animals don't really know their lineage to any extent, so they inbreed all the time naturally.  This works to remove detrimental recessive genes from the gene pool, making inbreeding not a problem.

There's still the diversity issue.  It's good to have diversity in nature, but generally you don't want it in your cultivated genetics.

Quote:

13shrooms said:
the man beat me to it, I thought I could shed some light on this thread but I see the light is already here.:sun:
I'll put the info up anyway.:shrug:
the more its posted the easier it is to find in the search engine.:stoned:

Quote:

Ah, thats pretty simple actually.  You need to do around 6 sequential generations from multispore selecting for the best specimen at each generation.  By the 6th generation, almost all of the heterozygosity will be lost and the strain stable.  The early generations are the most important for selection.  Heterozygosity is reduced by 50% for each generation by multispore, so you can mathematically see how this works.

Generation zero - wild specimen heterozygosity 100%
F1 multispore of wild specimen 50%
F2 multispore of F1 specimen 25%
F3 ....12.5%
F4 ....6.25%
F5 ....3.12%
F6 ....1.56%

and so on.

After the F6 generation there is so little heterozygosity (variability) left that all the mushrooms generated by multispore are virtually identical and the strain is considered stable.  It almost acts like a single clone since all the multispore strains are so similar and do not antagonize each other within a multispore tray.

I hope this makes sense.







DOH!  That's completely wrong for our situation!

The Hardy–Weinberg rule states that both allele and genotype frequencies in a population remain constant unless specific disturbing influences are introduced.

The specific disturbing influence you're describing is non-random mating via inbreeding.  So this is described by the inbreeding coefficient.  The inbreeding coefficient is unstable as the expected value approaches zero, and thus not useful for rare and very common alleles.

While it's hard to see how that applies to us, here's the explanation.  We would expect a very high inbreeding coefficient, but that's not the case.  This is because for all alleles for which there is only one in the population you must discount from the equation.  Since the population is already highly inbred and homozygous across the entire species you end up with a relatively small proportion of genes with multiple alleles.  So when you factor this in you actually end up with a small inbreeding coefficient, making the calculations inaccurate.

To simplify, an already inbred population's allelic frequency is much less affected by inbreeding.


-FF


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Re: Domestication [Re: fastfred]
    #11200095 - 10/07/09 01:52 PM (8 years, 1 month ago)

^I kind of understand some of that, but your on a whole different level with science then I am:confused:. Is there anyways you can bring it into more common language for me(and probably some other people:smirk:). I was thinking about experimenting with gene's and stuff but I don't want to spend a bunch of time doing it wrong :laugh:.

Thanks for your time.:peace:


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Invisiblebadman
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Re: Domestication [Re: smaerd]
    #11200674 - 10/07/09 03:25 PM (8 years, 1 month ago)

>Since the population is already highly inbred and homozygous across the entire species you end up with a relatively small proportion of genes with multiple alleles.

Is this an assumption?


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Invisiblefastfred
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Re: Domestication [Re: smaerd]
    #11200677 - 10/07/09 03:26 PM (8 years, 1 month ago)

If you have specific questions I'd be happy to answer them.

In respect to what 13shrooms posted... Those numbers only work out with a normal population as a comparison to your inbred line vs the rest of the population.  It won't work with inbred populations like mushrooms.  The normal sexual cycle for mushrooms is mating between siblings.  They're already very inbred.  There's also no real comparison since your population is going to be only one line.

Smared, I suggest you check out some breeding texts.  There's a lot of information out there.  Genetics works the same way in any species.  You just have to understand the differences in sexual cycle.


-FF


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Re: Domestication [Re: smaerd]
    #11200682 - 10/07/09 03:28 PM (8 years, 1 month ago)

double post


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Invisibletruskool
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Re: Domestication [Re: badman]
    #11200758 - 10/07/09 03:42 PM (8 years, 1 month ago)

So lets see if i have any idea wat is going on.  FF you are saying that mushrooms are so inbreed all ready that what workman posted isn't true because the genes of said mushroom is already close enuff?  Am I even in the right ballpark.  And if this is true it wouldnt take that long to domesticate a wild cube?


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Invisiblefastfred
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Re: Domestication [Re: badman]
    #11200791 - 10/07/09 03:47 PM (8 years, 1 month ago)

Quote:

>Since the population is already highly inbred and homozygous across the entire species you end up with a relatively small proportion of genes with multiple alleles.

Is this an assumption?




No, it's just a basic feature of their sexual cycle.  The vast majority of spore matings is the equivalent of a full brother and sister mating (or closer depending on how you figure it).  It can't get any more inbred than that.


-FF


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Re: Domestication [Re: fastfred]
    #11200951 - 10/07/09 04:18 PM (8 years, 1 month ago)

Seen seen. thanks for the clarification.


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Re: Domestication [Re: truskool]
    #11201038 - 10/07/09 04:33 PM (8 years, 1 month ago)

This is all pretty damn confusing, but really interesting and useful information.

So in response to fastfred, if mushrooms are an inbred organism, and that is how they reproduce, how to do they create variations in nature?  Isn't it necessary for the livelihood of an organism to produce random genetic mutations somehow, so that if variables in the environment occur, there is a chance that the organism will continue to survive by creating an offspring that is suited to these conditions by chance?

Also, you say that mushrooms are extremely inbred, and thus are by nature homozygous, but still there is a great deal of variation between different races.  What causes these variations?  And if the method that workman and 13shrooms posted is not effective, what is the proper method of domesticating/stabilizing a strain/race?


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Re: Domestication [Re: libertaire]
    #11201138 - 10/07/09 04:50 PM (8 years, 1 month ago)

I don't agree that mushrooms are naturally inbred since they do reproduce sexually.  There has to be a benefit to mushrooms to take the extra effort for sexual reproduction.  There are even mating-type factors to discourage inbreeding.  Granted, 100% heterozygosity is unlikely but I used this theoretical number as a "worst" case scenario.  The sequential multispore grows to reduce heterozygosity is still valid and 6 or 7 generations should more than do the trick.


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Re: Domestication [Re: badman]
    #11201209 - 10/07/09 05:01 PM (8 years, 1 month ago)

Quote:

So lets see if i have any idea wat is going on.  FF you are saying that mushrooms are so inbreed all ready that what workman posted isn't true because the genes of said mushroom is already close enuff?  Am I even in the right ballpark.




Yes.  The idea of inbreeding as different from normal mating is mostly a human idea.  Most animals and organisms have no idea who they're related to.  They naturally inbreed all the time.

If you take dogs for example, pretty much all pure bred dogs were created through extensive inbreeding.  A few breeds have problems because of this, but the majority of breeds do just fine.  The ones with problems are the result of poor breeding, not any inherent problem with inbreeding it's self.  The breeders should have been more careful to weed out those recessive genes which end up cropping up frequently in small gene pools.

And in fact inbreeding is a great way to weed out detrimental genes from the population.  There are even some human cultures which practice inbreeding.  Hindus and Muslims of India and Africa practice inbreeding for cultural and religious reasons, Amish, Mennomites and Hutterites practiced it because they were isolated.  Even Western societies practiced it before the 19th century.  Egyptian commoners also frequently practiced full brother-sister marriage.

Some have even claimed that inbreeding is the human norm and it's only recently that cultural taboos have reduced it's incidence.

But back to the point... The main argument against inbreeding is that it can expose recessive genes which otherwise would have a very low probability of coming together.  This doesn't matter with an already inbred population.  Especially if you consider inter strain mating.  While they have differing genetics they're both highly inbred sub-populations and after crossing them you shouldn't have any problems inbreeding them.

The other main issue is limiting the gene pool.  Desirable traits can be lost this way and once they're gone it's hard to recover them without starting from scratch again.

> And if this is true it wouldnt take that long to domesticate a wild cube?

Even wild cubes are pretty inbred.  But in any case, with random mating (spores will mate randomly  amongst compatible mating types under normal conditions) the frequency of any given allele will remain constant.  That's a more important point than the inbreeding coefficient, and one that I forgot to mention earlier.

Domesticating wild cubes isn't hard.  All you really have to do is keep growing them.  The selective pressure of whatever conditions you put them under will end up giving you what you want.


-FF


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Re: Domestication [Re: fastfred]
    #11201800 - 10/07/09 06:45 PM (8 years, 1 month ago)

What you are saying makes no sense.  What you are saying is that developing traits in mushrooms is impossible, because the frequency of traits is always averaged out after multispore, which it clearly is not, based on many people's experience.

How would the frequency of an allele remain constant if you select only specimens that do not express that attribute?  Eventually, you would get to a point where the allele is completely bred out of the genes after so many generations.  Or I guess in this case, it would become accustomed to the indoor conditions eventually because any detrimental genes would not represent themselves in those conditions. 

Am I mistaken?  I really know nothing about genetics, so I'm only basing this on logical analysis of the information I've been given.


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Re: Domestication [Re: libertaire]
    #11201889 - 10/07/09 06:56 PM (8 years, 1 month ago)

Quote:

Or I guess in this case, it would become accustomed to the indoor conditions eventually because any detrimental genes would not represent themselves in those conditions.




that is exactly what Im trying to accomplish here with Libs.:stoned:


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