Going F2 and higher

[BobChronic6505]

Ok so I'm not really sure how to title this post but I have a few general questions about breeding that I hope the pros here can help with.

So if i understand correctly, F2 generation follows mendels law of separation, where all the recessive traits show themselves....so are these recessive traits now considered dominate? If so, is it only for the F2 generation?
I made some F2s and now I'm sprouting them....I want to find a male and breed it back to one of the same F1s. Would this be considered an IBL or just a regular backcross? Also, let's say I do the F2 into F1. Are those dominate traits, that may only show during the F2, are they now going to be dominate traits in the resulting seeds? Are those seeds considered F3? Or is F3 only for putting the F2 to F2?

Also has anyone here bred some landrance shit into a fairly indica dom? Realistically, are those seeds going to be any good? Or are they going to be mutants? I know people do this all the time but I've always been skeptical about buying those kinds of seeds.

Thanks in advance

 

[Nannymouse]

Well, first of all, we have to determine if our language is with the standard horticulture or if it is with the old stoner language. Then, there are widespread stoner interpretations.

recessive traits will show in f2 (stoner f2 terms).

Dominant. Hmmm. A recessive gene doesn't ever become a dominant gene (as far as i know). You probably are talking about...does that recessive trait then show itself all the time, if that particular recessive trait is mated with a plant that has the same recessive trait. Yes, if it is a simple recessive trait. (not all traits are simply 'dominant or recessive', sometimes a trait shows itself only when a certain number or combination of genes is present) That is one on one breeding.

In a group/field breeding, if all the males show your trait and the females do not, it varies. If the females are sisters of the males and they don't show the recessive trait, it is probable that some females do carry the recessive trait. How many? Depends. If half the girls carry the recessive trait, those that do should average out to having half their seed show that recessive trait and the other half of the seeds will not show, but will carry the gene. Even the seed from the females that do not carry the gene, will carry one gene from the fathers that had two of the genes.

We have to be careful how we use the words 'dominate' and 'dominant'.

Also, a trait can be caused by different genes. For instance, the white color in cats can be caused by five different genes. A pure white cat could have gotten it's color from a dominant white gene, or a recessive white gene. Then there are the 'spotting' genes. AND, to make it more confusing, the cat could have any combination of those, sometimes only passing to it's progeny, just some or all.

As far was to what is considered an IBL, there may be a real definition in horticulture. In stoner world, it seems there are many opinions.

In the critter world, some of the breeds view the F1 and F2, etc. differently from stoner world. In stoner world, the f2 (etc) is brother to sister, with pedigrees always being 50/50. In other fields, say, a herd of cattle or goats, an f5 would only show one 'non-purebred', six generations back. BIG difference in terms.

Well, if that is confusing, i say yes. In simple terms, just keep breeding for the traits that you want. How long does it take to get an inbred line? Sort of depends on if you are just looking at a pedigree or if you are talking about getting a seedline that produces consistently, what you are looking for.

Crossing 'landrace' into existing lines...this is how many 'strains' have come about. Probably comes down to selection, sometimes over time. 'Good' depends on personal judgement. If you want "indica dom", then don't cross to non "indica dom". There are 'Indica' landraces.

 

[troutman]

It's segregation and not separation. What you plan on doing
is a backcross if you cross an F2 with an F1. It helps to grow
as many F2's as possible. Because the more traits you're after
the more plants you will need to find that special plant.

I'm actually testing an Afghani Landrace crossed with an old Indica.

They're not mutants.

 

[BobChronic6505]

@Nannymouse thanks man and I apologize about the wording, alot of this is new to me. Ok so recessive traits can dominate, but not be dominant? I think that is what you were saying and maybe what I'm trying to say. So what happens when we breed with those? Do those recessive traits dominate? Or will it be a crap shoot all of the traits? I hope this makes sense man

 

[BobChronic6505]

@troutman thanks man

 

[Nannymouse]

If you keep breeding for the traits that you desire, you will likely make a larger percentage of those traits in each future generation of mating...as long as you do not outcross to something that doesn't show those traits. That goes for either dominant or recessive traits.

You don't need to apologize.

I was taught about punnet (sp?) squares, back in high school(they're probably teaching it grade school, nowadays, ha)...doesn't hurt to refresh yourself, especially the more advanced squares showing the percentages when breeding for two or more traits at the same time.

There was also some sort of chart that listed traits of cannabis, showing which traits were recessive and which were dominant, and i should have bookmarked it, or something, cuz i have no idea which site it was posted.

Good luck. I also look forward to answers to your questions about what an IBL is.

 

[goingrey]

@Nannymouse Not sure what the "critter world" is' but the "stoner" definition of filial generations is the same as what is generally accepted by the scientific community and even Merriam Webster and other dictionaries.

Filial generation
Offspring generation. F1 is the first offspring or filial generation; F2 is the second; and so on. Successive generations of progeny in a controlled series of crosses, starting with two specific parents (the P generation) and selfing or intercrossing the progeny of each new (F1; F2; . . . ) generation.

Filial generation definition

Same for inbred lines (also called inbred strains). A line that is uniform (homozygous) as a result of inbreeding.

Inbred lines (aka inbred strains)
Inbred strains are defined as the product of 20 consecutive generations of brother–sister matings. Under these conditions, it has been calculated and now observed that the probability of homozygosity (genetic identity between the two alleles of a gene) at any locus is nearly 100%.

https://www.sciencedirect.com/science/article/pii/B9780123749840009815

 

[Nannymouse]

@goingrey , thanks for that. I was going by what some of the cattle and goat registries have done in the past, in order to achieve 'purebred' status. Depending on the registry, they wouldn't call it purebred until the generation was up into the 90+percent to the 'pure blooded'. They did use the 'F' terms as i described.

Wow, Mice =20 generations...i would have guessed fewer generations than that. If the scientific definition is that the homozygosity at any locus is near 100%, then i would think that the number of chromosomes that a specie has, would then determine how many generations. I did read that one page that you referenced, and it was just getting interesting, at the end of the page...but that was all that was available to read. They started getting into backcrossing to parents.

As far as inbred lines, i would think that most of your animal breeders would, in a practical way, say that a line would be considered 'inbred' long before 20 generations of brothers x sisters.

 

[goingrey]

The "BX" lines are called Inbred Backcross Lines in scientific literature.

This article (blog post) suggests a minimum of 8 generations to stabilize them:

Inbred Backcross (IBC) Lines and Populations – Plant Breeding and Genomics

Significantly less than the 20 for mice IBL... but there's no reference to any type of genome.

Mice genome is 20 pairs, cannabis 10. Would a cannabis strain be an IBL after 10 generations? Maybe? The important part is if it breeds true.

 

[djonkoman]

chromosome pairs number doesn't lead to faster/slower reaching homozygosity. but what does matter is if selfing is possible, which in animals usually isn't the case.

in case of selfing, the math is pretty easy. you take the classic punnet square for a single gene, and you extrapolate that to all genes.
i.e., for a single gene, the offspring in the next generation will be 25% AA, 50% Aa amd 25% aa.

now, take a single individual from this next generation. this single individual has 25% chance of having AA, 50% chance Aa, 25% chance aa. both AA and aa are homozygous, so for 1 random gene that was heterozygous in the f1, there is a 50% chance this gene is homozygous in a random f2/s1 individual.

this aplies to all genes.

so let's say we have an f1 with 100 genes being heterozygous. we take 1 plant and self it.
now statistically ~50 of those 100 genes will be homozygous in any plant of this s1 generation.
we again take 1 random plant from this generation. now these 50 genes that have already turned homozygous will not segregate anymore, so we are left with 50 heterozygous genes which will still segregate in the next generation.
same 50% chance, so now in the s2 we will be left with only 25 heterozygous genes.

so, after 6 generations of selfing, we are left with only 1,5625% of the genes that were heterozygous in the f1 still being heterozygous. the other 98.4375 % have turned homozygous.

the exact cut-off generation for speaking about a homozygous line is a bit arbitrary. the first generations give the biggest steps, going from 6th generation selfing to 8th generation selfing takes you only from 98.4375 % to 99.609375 % homozygosity.

(the same math can be aplied to backcrosses)

now, if you can not do selfing, this progress will be slower. because while any random plant from the f1 will have 50/100 genes turned homozygous, those will not be the same 50 genes in different individuals. so if you self, these 50 are locked in for the next generation. but if you're using brother/sister crossings, some of these 50 will turn back to heterozygous since the 2 parents are different for those genes.

and besides whether you self or do fillial crosses, another consideration for the cut-off generation to speak of an inbred line would be what you're going to use the line for. in a lot of cases for breeding purposes 6th generation is probably plenty homozygous, and any extra generations also means more work, more time, more investment.
I've also seen a youtube video from some american company talking about making cannabis f1 hybrids (I think it was oregon cbd?) where they only took the parent lines to the 4th generation of selfing and considered it finished already at that point.

 

[goingrey]

chromosome pairs number doesn't lead to faster/slower reaching homozygosity. but what does matter is if selfing is possible, which in animals usually isn't the case.

in case of selfing, the math is pretty easy. you take the classic punnet square for a single gene, and you extrapolate that to all genes.
i.e., for a single gene, the offspring in the next generation will be 25% AA, 50% Aa amd 25% aa.

now, take a single individual from this next generation. this single individual has 25% chance of having AA, 50% chance Aa, 25% chance aa. both AA and aa are homozygous, so for 1 random gene that was heterozygous in the f1, there is a 50% chance this gene is homozygous in a random f2/s1 individual.

this aplies to all genes.

so let's say we have an f1 with 100 genes being heterozygous. we take 1 plant and self it.
now statistically ~50 of those 100 genes will be homozygous in any plant of this s1 generation.
we again take 1 random plant from this generation. now these 50 genes that have already turned homozygous will not segregate anymore, so we are left with 50 heterozygous genes which will still segregate in the next generation.
same 50% chance, so now in the s2 we will be left with only 25 heterozygous genes.

so, after 6 generations of selfing, we are left with only 1,5625% of the genes that were heterozygous in the f1 still being heterozygous. the other 98.4375 % have turned homozygous.

the exact cut-off generation for speaking about a homozygous line is a bit arbitrary. the first generations give the biggest steps, going from 6th generation selfing to 8th generation selfing takes you only from 98.4375 % to 99.609375 % homozygosity.

(the same math can be aplied to backcrosses)

now, if you can not do selfing, this progress will be slower. because while any random plant from the f1 will have 50/100 genes turned homozygous, those will not be the same 50 genes in different individuals. so if you self, these 50 are locked in for the next generation. but if you're using brother/sister crossings, some of these 50 will turn back to heterozygous since the 2 parents are different for those genes.

and besides whether you self or do fillial crosses, another consideration for the cut-off generation to speak of an inbred line would be what you're going to use the line for. in a lot of cases for breeding purposes 6th generation is probably plenty homozygous, and any extra generations also means more work, more time, more investment.
I've also seen a youtube video from some american company talking about making cannabis f1 hybrids (I think it was oregon cbd?) where they only took the parent lines to the 4th generation of selfing and considered it finished already at that point.

That's great info but because of some stubbornness within me I can't understand how the amount of chromosome pairs would not affect the number of generations needed to reach homozygosity with sibling crossings. Would be interesting to see the mathematical model they used to determine the 20 generations for mice, though it's probably quite advanced math and difficult to validate one way or another.

And sure, it is just theoretical. In practice breeders may well call their line IBL if it breeds true for the traits they feel are important. Sometimes their customers may not agree at that point yet though. I can think of a couple of famous examples from the canna world where inbreeding so-called IBL's has resulted in disappointments.

 

[djonkoman]

I think the maths for sibling crosses is relatively simple too, I do remember seeing a graphic illustration of it in some paper about cannabis breeding a while ago, let's see if I can find that image again, then I'll edit it in here.

chromosome number really doesn't mean much in this case.

-chromosome number doesn'rt say anything about the number of heterozygoyus genes in the f1: you could have a cross where most genes are the same between both parents
-it's about percentages. with the maths example I gave I took 100 genes as an example, fill in 1000 there and the math works out the same.

edit: here's the graph, look at panel D (ignore the rest, there are a few details which look like errors, like the sts is pointed to the wrong row in panel E):

from this paper:

Frontiers | Potentials and Challenges of Genomics for Breeding Cannabis Cultivars

Cannabis (Cannabis sativa L.) is an influential yet controversial agricultural plant with a very long and prominent history of recreational, medicinal, and i...

www.frontiersin.org

edit:
also found this snippet relating to the 20 generations for mice, but can't open the referenced source, so don't know the exact formula.
but guessing it could be reasoned through calculating how big the chance is of a random individual having the same allele, as also explained on the same page:

Mouse Genetics by Lee M. Silver, chapter 3

Figure 3.2 shows the level of homozygosity reached by individual mice at each generation of inbreeding along with the percentage of the genome that is fixed identically in both animals chosen to produce the next filial generation according to the formulas given by Green (1981). After 20 generations of inbreeding, 98.7% of the loci in the genome of each animal should be homozygous (Green, 1981). This is the operational definition of inbred. At each subsequent generation, the level of heterozygosity will fall off by 19.1%, so that at 30 generations, 99.8% of the genome will be homozygous and at 40 generations, 99.98% will be homozygous.

 

[goingrey]

I think the maths for sibling crosses is relatively simple too, I do remember seeing a graphic illustration of it in some paper about cannabis breeding a while ago, let's see if I can find that image again, then I'll edit it in here.

chromosome number really doesn't mean much in this case.

-chromosome number doesn'rt say anything about the number of heterozygoyus genes in the f1: you could have a cross where most genes are the same between both parents
-it's about percentages. with the maths example I gave I took 100 genes as an example, fill in 1000 there and the math works out the same.

edit: here's the graph, look at panel D (ignore the rest, there are a few details which look like errors, like the sts is pointed to the wrong row in panel E):

from this paper:

Frontiers | Potentials and Challenges of Genomics for Breeding Cannabis Cultivars

Cannabis (Cannabis sativa L.) is an influential yet controversial agricultural plant with a very long and prominent history of recreational, medicinal, and i...

www.frontiersin.org

edit:
also found this snippet relating to the 20 generations for mice, but can't open the referenced source, so don't know the exact formula.
but guessing it could be reasoned through calculating how big the chance is of a random individual having the same allele, as also explained on the same page:

Mouse Genetics by Lee M. Silver, chapter 3

Incredible papers, thanks for looking them up!

From the mice paper:

In mathematical terms, the fraction of loci that are still heterozygous at the Nth generation can be calculated as [(1/2)N-1], with the remaining fraction [1 - (1/2)N-1] homozygous for the inbred strain allele.

So the math is indeed simple. The amount of heterozygous loci is cut in half every generation.

My interpretation is though that the chromosome count does matter. And If you are starting with half (mice 20 vs cannabis 10) then homozygosity will be achieved one generation earlier.