Genetic Drift?

[englishrick]

fab,,,,but what is the line gravitating to?,,,,

would is the soloution to inbreeding depreshion??,,,,,,,,,,,,[just high Ne numbers?]

 

[englishrick]

sorry i meant::::::what is the soloution to inbreeding depreshion?

thanks dave..

 

[Cuzin_Dave]

Inbreeding depression is the result of the compounding effect of negative recessive alleles as opposed as the mere act of inbreeding a line. A lot of the poly hybrid bunk lines out there today suffer from out crossing depression also known as unstable heterosis. In both of these instances the intermediate phenotype has a low level of relative fitness with the fittest plants being at the extreme ends of the population curve.
A realistic goal might be to have an effective Ne of say between 32 and 64 at F2. Less than perfect indeed, but it will at least afford the opportunity to determine the intermediate phenotype, calculate the dominant and recessive ratios and get some idea if it is worth continuing on with the line.
Most of the genetic drift happened ages ago when the Dutch comercialised the cannabis seed business. None of that can be undone.
What passes for breeding these days is mostly chucking pollen on an unstable poly hybrid Mum clone and sales hype.
It is good to be aware of genetic drift, but there is very little any of us can do about it, save for breeding your own individual lines. Don't expect any international scientific conferences on saving the cannabis gene pool from genetic drift.

 

[DocLeaf]

Bombadil360. Here is my brief explanation of Ne.

Effective breeding population is one of the most basic parameters of population genetics. The idealised Ne is by definition infinitely large and diverse and fully represents all the potential genetic expressions in the population.

The actual calculation is fairly simple arithmetic and goes as follows:
Ne = 4 * (# of Males) * (# of Females) / (# of Males) + (# of Females)

For example a grower selects 1 male and 500 females for breeding. The effective breeding population is; (4) * (1) * (500) / (500+1) = 4. The effective breeding population can never be larger than the number of males selected for breeding. Another example 50 males 10 females Ne becomes 2000/60 or 33.33.

I read the article by DJ Short regarding his breeding of the famous Blueberry wherein he states that he only uses one male for his breeding selections. That might help explain why Blueberry is so resistant to breeding improvement. To quote, "Second, I select only one male from any single breeding project. Again, this simplifies things and avoids mistakes enormously. That male is generally selected at about the third week in the flowering cycle, unless it is a clone from another project".

By and large most cannabis breeders tend to ignore matters like effective breeding population when making their selections for males.

To expand on the basic concept of Ne one must consider how Ne effects the F statistic (Coefficient of Inbreeding).

So let's assume an NE of say 4. The decline in heterozygosity or rate of inbreeding at from the first generation would be: F1 = (1) / (2 * Ne) or 1 / (2 * 4) = .125.

With each subsequent generation the decline in heterozygosity is cumulative. Take generation F6
F6 = 1 - (1 - F1) ^ 6 = 1 - (1 - .125) ^ 6 = .551
By the 6th generation 55% of the genetic diversity will have been lost in the line. By the 12th generation 1 - (.87.5) ^ 12 = 80 % of the genetic diversity will have been eliminated.

The larger the Ne the lower the rate is the actual loss of diversity through inbreeding.

Great post Even I can understand that. Thanks

imo,,,he aquired the intersexed traits because he only used 50 plants a time to select from,,i think he must have picked up some recessive intersexed traits,,dont ya think doc?

Yeah from the Thai sides... although this may or may not have been a recessive trait when selected.

Inbreeding depression is the result of the compounding effect of negative recessive alleles as opposed as the mere act of inbreeding a line. A lot of the poly hybrid bunk lines out there today suffer from out crossing depression also known as unstable heterosis. In both of these instances the intermediate phenotype has a low level of relative fitness with the fittest plants being at the extreme ends of the population curve.

True says.. Cuzin Dave is on fire here

 

[Dalaihempy]

Yeah from the Thai sides... although this may or may not have been a recessive trait when selected.

Why is it most think by using Thia lines you carry across Hermies if this was the case all haze hybrids and haze like sams would be throwing nannas left and right its not so is it.

I proved more than once a pure Thia will not hermie once its sexed as a female they show up at sexing like a male or female would but not all Thia lines or sativas some don't have them show up in the line at all you will only see a male or female the Thia line i am working with is from 1978 it has males showing up and females and hermies at sexing once the hermies are culled the females and males stay as such i have used it in hybrids and yet to see a single hermie show up at sexing.

After years of growing i am at a belief that in fact the mid to late onset of male flowers showing up in female plants in modern hybrids is the result of indicas not sativas used in these lines.

 

[Sam_Skunkman]

Inbreeding depression is the result of the compounding effect of negative recessive alleles as opposed as the mere act of inbreeding a line. A lot of the poly hybrid bunk lines out there today suffer from out crossing depression also known as unstable heterosis. In both of these instances the intermediate phenotype has a low level of relative fitness with the fittest plants being at the extreme ends of the population curve.
A realistic goal might be to have an effective Ne of say between 32 and 64 at F2. Less than perfect indeed, but it will at least afford the opportunity to determine the intermediate phenotype, calculate the dominant and recessive ratios and get some idea if it is worth continuing on with the line.
Most of the genetic drift happened ages ago when the Dutch comercialised the cannabis seed business. None of that can be undone.

If you use seed varieties developed in the west, this could be true. So start with imported seed from Cannabis areas in the third world.
Clean it up a bit with large populations and then start work.
When I say large populations I mean 2000+ which will keep 99% of the genes intact for dioecious, anemophilous, diploid varieties, 1000 for monoecious.

As for the large numbers required to keep gene loss to a minimum, that is really only important if the varieties are maintained by seed, but most varieties today in the West have been maintained by clones, meaning once the parent clones have been selected no large numbers are required any more for maintenance. Lets hope large population numbers were used for the selection work.
The numbers for Cannabis are set out in the article,

"Crossa, J. et al. 1993. Statistical genetic considerations for maintaining germ plasm collections. Theoretical and Applied Genetics 86: 673-678."

-SamS

 

[Sam_Skunkman]

It is almost impossible to avoid genetic drift unless the Ne or effective breeding population is around 7000 plants. It is a numbers game with respect to preserving alleles in a population and creating a true breeding line. Once a line has been genetically bottlenecked there isn't much one can do to replace the lost diversity.
Pollinating a select clone with a select male plant really doesn't do much to enhance the diversity.
Another term for genetic drift is sampling error and the smaller the effective Ne the higher the probability of that happening, simply as a random event. Its been a long time since I studied quantitative genetics, but the math and probabilities get pretty daunting when the population is very small.

Where did you get the 7000 plant number?
-SamS

 

[englishrick]

sam and dave are cool,,,,,,,

how would one avoid "unstable heterosis",,,,,sam ,dave...???

i feel some old clones like Cheese , Chem D , OG SFV might be worth turning into homozygous lines,,but its a hard job,,,i keep mentioning negative recessive`s but not many people put them high on there priority`s list....

^^how do you feel about working 1 of these clones into a line and upto 0.99???`....an how do you maintain a good healthy line once you hit 0.99??

thanks for your time sam and dave




i agree with you doc,,,,it coulda been a dom intersexed trait from day 1,,,,but i still think his population numbers made him hit a brick wall after a while,,he built-up too mutch bad GuGu "recessive traits",,,,he had the right idea but he tried to make it too simple,,,DJ killed Golioth with a stone ,,that made him king, but his later selection and population numbers changed the empire after a while,,,

 

[englishrick]

i thought Clarke said x2000 was enough to hit good figures,,,

 

[moonunit]

I have always been an advocate for more diversity within lines, and not selecting males unless A: You can progeny test the male
and B: You have a clear goal for the line and create it for the end flower grower,
otherwise use all the males and only select on the fem side.
I think heavy inbreeding has its place, as a way to use ones breeding lines ( maintained with as much diversity as possible) to produce a product for the flower grower with a very narrow hybrid range or ne, but all to many are using these inbred geneticaly narrow lines as their breeding lines and thats the prob imho.
much respect
moonunit

 

[englishrick]

being able to take a line from Heterozygous to Homozygous is a skill a real breeder needs!,,,,,making things heterozygous is as easy as making a true F1

 

[kopite]

i thought Clarke said x2000 was enough to hit good figures,,,

Clarke got the info from the doc SamS has cited . I remember in the big thread that got butchered by the gestapo and erased Hyb in caused some panic.

http://www.internationalhempassociation.org/jiha/iha02106.html
http://www.springerlink.com/content/56034178641n0363/
http://hempworld.com/hemp-cyberfarm_com/htms/research_orgzs/iha/ihagenetic.html
http://ddr.nal.usda.gov/bitstream/10113/14626/1/IND20368598.pdf
http://crop.scijournals.org/cgi/reprint/44/6/2246

Kopite

 

[englishrick]

hay Kopite..

how do you feel about taking a supirior genotype like the Cheese clone and makin it hit 0.99 in a skunk line??..

how would one maintain the germplasm and observed taraits [without keeping clones] once the line hits 0.99??,,,,

 

[Jones]

.

 

[kopite]

How did you get the 2000 plants number?

According to the article you refer to the number of plants needed to preserve '99%' of genetic diversity is directly dependend on the number of alleles and locii. What are these numbers for cannabis? Crossa talks about maize...

How do you exercise gamete control (which is one premise of Crossa's work) in a population of 2000+?

There's is ircc a revised version of Crossa's work (from 1998?) which addresses some shortcomings of the 1993 article.

Edit: Attached Crossa 1993

table 3 is only time you see 2000? I don't know if they used the GRsim that wang developed?

and Rick what makes the "cheese" superior? I think a backcrossing program is best suited to it, but I'd just spread the clone myself.

Kopite

 

[englishrick]

yeh,,,i also think a BackCrossing program is best for the cheese too...

i wish i could put some cheese in freezer,,,,i cant have a propper holliday because my mothers demand so so mutch attention and i fear losing my PROPPER weed

the cheese is supirior to me, because everytime i see a skunk it looks waterd down compard to cheese,,,,,nothing is as strong in smell,,,,its agressive,,,,it shouts IM HERE!!! IM HERE!!,,,,its usaly 1 of the first jar to get smoked!

 

[DocLeaf]

Numbers are objective! The major difference between sowing a 10 pack and 1000 pack is space. That's all ,, so dont be blagged by hype!

In numbers then uniformity and rogue elements can be observed a whole lot easier,, but otherwise, as already stressed in this thread the number involved are ultimately related to the number of parent, and grandparent, and great-grandparent plants involved.

When crossing onto clones,, only the male selection is really involved,, (on it now with Rainbow Kush) which is totally different to actual "breeding" i.e. selecting traits from male and female parent stock in the expectation of continuing traits,, or even making a "winning" line from it. That's a different ball park,, Sam and Shantibaba already won that one.

We see it like dogs (or anything that breaths),,, only the most mindful breeders hold the most mindful, healthy, and non-temperamental stock,, otherwise you end up with crazy temperamental hybrids (BS),, that will take extra work hours,, both in line,, and out of it... we guess this is where the "drift" in lineage is involved, when breeding.

Otherwise anyone that doesn't breed plants on a annual basis ,, is chatting out their ass,, get back to the books kids ! (no disrespect to anyone) Otherwise these 'clone-onlys' are short lived in the grand scale of things and grow weaker with age,, face it up!

However clones do NOT tend to drift anyway from anyone,, unless they put em on a boat and sail em overseas! hehe

Hope this helps in the scale of this relative

we're do'in it! http://www.youtube.com/watch?v=Za9x3VRmLB4

 

[Cuzin_Dave]

Sam, I should have metioned that my argument was based on my recollections of constructing those statistical tableaus with Ne on the left hand side and very small numbers on the top of the matix.So your argument about Ne at 2000 would be correct insofar as preserving almost all of the alleles. Anyways doing too much math makes my head hurt. The little ^ symbols I used are exponentials.
There are methods for estimating the probability of genetic drift and underscoring its devastating impact on unsystematic shifts in allele frequencies where Ne is small.
The formula is: Prob. = (1 - frequency) ^ 2 ^ Ne
For example, lets say there is a less common allele (w) in a white widow clone that occurs say 5% of the time (.05) and further for arguments sake Ne = 2.
So. (1.- .05) = .95
(.95) ^ (2)(2) = 81.4% probability of elimination
Make Ne = 50
(.95) ^ (2)(50) = .00592 probability of elimination.
As is the case with any algorithm, the answers will change depending upon what numbers one intends to plug into the formula.
The higher the frequency of an allele in a given population the greater its likelihood of surviving a genetic bottleneck with the opposite being true of lower frequency alleles surviving when Ne is very small.
To expand on the basic concept of Ne one must consider how Ne effects the F statistic (Coefficient of Inbreeding).
So let's assume an NE of say 4. The decline in heterozygosity or rate of inbreeding at from the first generation would be: F1 = (1) / (2 * Ne) or 1 / (2 * 4) = .125.
With each subsequent generation the decline in heterozygosity is cumulative. Take generation F6
F6 = 1 - (1 - F1) ^ 6 = 1 - (1 - .125) ^ 6 = .551
By the 6th generation 55% of the genetic diversity will have been lost in the line. By the 12th generation 1 - (.87.5) ^ 12 = 80 % of the genetic diversity will have been eliminated.
The larger the Ne the lower the rate is the actual loss of diversity through inbreeding.
Let's take a hypothetical example:
Breeder X grows out 20 plants and gets 6 males and 14 females.
Effective breeding population will be:
(4)*(6)M*(14)F / 20 Plants Total =16.8

Change in inbreeding per generation:
1 / (2)*(16.8)= 2.9%

The "best" effective size calculation in this example:
16.8/20 = 84%

Fun with numbers for sure. I posted these examplea to underscore that genetic drift is quantitatively measurable.

 

[englishrick]

Dave...

when you say:::::::"the decline in heterozygosity is cumulative",,,

am i right to asume that things are being put in homozygote positions?

So let's assume an NE of say 4. The decline in heterozygosity or rate of inbreeding at from the first generation would be: F1 = (1) / (2 * Ne) or 1 / (2 * 4) = .125.
With each subsequent generation the decline in heterozygosity is cumulative. Take generation F6
F6 = 1 - (1 - F1) ^ 6 = 1 - (1 - .125) ^ 6 = .551
By the 6th generation 55% of the genetic diversity will have been lost in the line. By the 12th generation 1 - (.87.5) ^ 12 = 80 % of the genetic diversity will have been eliminated.

 

[Sam_Skunkman]

How did you get the 2000 plants number?

According to the article you refer to the number of plants needed to preserve '99%' of genetic diversity is directly dependend on the number of alleles and locii. What are these numbers for cannabis? Crossa talks about maize...

How do you exercise gamete control (which is one premise of Crossa's work) in a population of 2000+?

There's is ircc a revised version of Crossa's work (from 1998?) which addresses some shortcomings of the 1993 article.

Edit: Attached Crossa 1993, Wang et al. 2004 (Statistical Genetics and Simulation Models in Genetic Resource Conservation and Regeneration)

Math is not so easy for me but I will reread the article and get back to you, originally Robert Clarke did the numbers after consulting the Crossa paper and talking with gene bank folks. As far as I know there is no count of the number of alleles and locii found in Cannabis. I can ask Rob when I see him next week.
Do you have a copy of the revised (1998?) Crossa paper?
My only copy of the original Crossa paper was on paper, so thanks...
-SamS