How many phenotypes are there in an s2 generation?

[ICGA]

If an s1 generation has 4 phenotypes how many phenotypes are in an s2 generation?

Also for example would this be different for an s1 of a polyhybred or supperpolyhybred VS. an s1 of an F1 line etc.

Also does anyone know if all 4 phenotypes from the s1 generation are identical genotypes; what I mean is if you take 100 s1 seeds and separate them into the 4 groups of the 4 phenotypes, will all the seedlings in each group be genetically identical, or just generally phenotypically identical?

Really what I want to know is this; during mitosis when the chromosomes split up does the deck shuffle on an epigenetic level because of "helixing" or does half of "chromosome a" from parent A always unzip and match with the half of "chromisome a" from parents B; Obviously this is the case to some extent as the sequences for a particular trait are supposed to line up some being dominant, recessive etc. But what about the so called "junk DNA" containing epigenetic information and latent genetic contingency. Or genetic contingency that is still forming out of the superstructure of "junk DNA" ?

Another even further out question is this; how does recent data suggesting nonrandom mutations are emerging based on the specific kind of adversity in the environment inform us about genetic drift? Does this actually mean genetic drift can be directed by creating a specific kind of environmental adversity, which would trigger the plant to "have to" mutate a specific way in order to adapt to the intentionally created adversity?

 

[goingrey]

If an s1 generation has 4 phenotypes how many phenotypes are in an s2 generation?

Also for example would this be different for an s1 of a polyhybred or supperpolyhybred VS. an s1 of an F1 line etc.

Also does anyone know if all 4 phenotypes from the s1 generation are identical genotypes; what I mean is if you take 100 s1 seeds and separate them into the 4 groups of the 4 phenotypes, will all the seedlings in each group be genetically identical, or just generally phenotypically identical?

Really what I want to know is this; during mitosis when the chromosomes split up does the deck shuffle on an epigenetic level because of "helixing" or does half of "chromosome a" from parent A always unzip and match with the half of "chromisome a" from parents B; Obviously this is the case to some extent as the sequences for a particular trait are supposed to line up some being dominant, recessive etc. But what about the so called "junk DNA" containing epigenetic information and latent genetic contingency. Or genetic contingency that is still forming out of the superstructure of "junk DNA" ?

Another even further out question is this; how does recent data suggesting nonrandom mutations are emerging based on the specific kind of adversity in the environment inform us about genetic drift? Does this actually mean genetic drift can be directed by creating a specific kind of environmental adversity, which would trigger the plant to "have to" mutate a specific way in order to adapt to the intentionally created adversity?

It's an interesting question how quickly a phenotype can be stabilized via selfing.

The genome size for female cannabis plants is about 1636 millions of base pairs:

Cannabis Genetics: A Genetic Approach to the Cannabis Plant | Good Cannabis Guide

Cannabis is an annual plant genus belonging to the Cannabaceae family. Cannabis, whose fibers in its stems are used in yarn, weaving, and fabric production,…

goodcannabisguide.com

I suppose some of that is what you call junk DNA. But even so a lot isn't. How many of the genes are responsible for a certain phenotype I suppose is the key question here.

It is my understanding that the pairs are not a "zipper" but rather can be shuffled as visualized by Punnett squares, and S2 generation plants that exhibit four phenotypes have way more than four genotypes with recessive alleles and unobvious genes hidden from the naked eye.

 

[goingrey]

And regarding your question about using intentionally created adversity... seems like yes actually.

...rice plants that were exposed to drought-simulation treatments displayed increased tolerance to drought after 11 generations of exposure

Transgenerational epigenetic inheritance - Wikipedia

en.wikipedia.org

2017 study so not super recent, if someone has newer info please share.

 

[zif]

If you mean phenotype as in the observed form of a specific trait, then it's a straightforward question.
How many genes are involved in the trait?
How do the different pairs of alleles in the population combine to determine which phenotype is expressed?
What alleles are present in the S1?
If you can't answer these questions, then you make crosses that allow you to answer them. Once you know, you'll have a good idea of how many phenotypes any generation will express.

If you mean phenotype as in the totality of observable traits of a plant, then only in very rare cases will it seem like every plant in a population is identical (give or take, environmental variability always plays a role). In other words, almost every plant in almost every seed population is going to be noticeably different, or, that is, have a different phenotype. You'll see N phenotypes if you grow N seeds to maturity, in every generation.