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breeding Discussion: Breeding Program Best Practices

Edaxflamma

Edaxflamma

This may only apply to a handful of growers but I am interested in discussing best practices for long term pepper breeding in the hobbyist setting.
 
Whether it someone is trying to stabilize a new phenotype, or someone actively crossing two varieties, what are some of the best ways to go about it?
 
For example:
Let's say you have Plant A and Plant B; you cross them and grow out two really interesting but really different F1 phenotypes, Plant C and Plant D.
 
I would guess that most people would begin isolations of Plant C and Plant D to try and make them breed true and that would be the end of it. 
 
For most people, the size of their operation will dictate what resources they can devote to their breeding program. But if someone really wanted to chase specific traits, in a perfect world what would they do?
 
Would they overwinter / take cuttings and repeat the original cross with the original parent material?
Repeat the original cross with independently isolated seed from the original two parents?
If yes to either, how many times?
Given the interesting phenotypes of Plant C and Plant D, how many times would they review the cross?
What are some personal metrics for evaluating crosses?
How many seeds of each generation would need to be evaluated before making your next cross or isolation?
How many generations down the road before your variety is "pure"? (Conventional wisdom is 8+ correct?)
 
I know this is a fairly open ended question but I would really like to see what comes of the discussion. Everyone has their own ideas and constraints but I'm sure there are some ways we all could improve. I'm sure there are a few more people here with industry experience that have some metrics, rules of thumb, or tricks of the trade that could be useful for anyone willing to implement them.
 
Another way of phrasing it:
 
What would be the ideal set of best practices for a breeding program?
Which of those would be most important for the hobbyist grower?
Which of those would realistically be able to be implemented for the hobbyist grower?
 
As hobbyists, most of us don't have the resources to think in terms of "Best Practices".  I tend to think in terms of "Perfect is the Enemy of Good Enough".  As a hobbyist I'm not sure my practices even live up to that standard.
 
But I can clear up one major misconception you're holding.
 
It's counter-intuitive because we're all so used to seeing the results of humans or other animals breeding.  But stabilized pepper varieties are different.  In the animal kingdom, what we do with peppers would be considered wildly inbred.  But peppers are different.
 
If you cross two well-stabilized pepper varieties, the F1 generation is very consistent.  This is because a stabilized variety doesn't have many recessive traits hiding behind dominant genes.  If they did, the subsequent generations would express these recessive genes, and everyone would know that pepper isn't really stabilized.
 
The F2 generation is where you start to see a wider variety of peppers.
 
There's no point of repeating the original cross unless the parents aren't as stable as you thought they were, or if the seeds you saved from your F1 peppers go bad.
 
 
 
If you cross two well-stabilized pepper varieties, the F1 generation is very consistent.  This is because a stabilized variety doesn't have many recessive traits hiding behind dominant genes.  If they did, the subsequent generations would express these recessive genes, and everyone would know that pepper isn't really stabilized.
Click to expand...
 
This was something I hadn't really stopped to think about. I guess I keep going back to the old Pink Tiger cross how the original phenotype that everyone loved hasn't really been repeatable all that much. Or the White Hot Lime as another example where the strong lime flavor didn't really persist as much as it once had. 
 
Have we unintentionally overlooked some traits with mixed or shared dominance in our strains by the nature of how our stabilization process works?
 
But that having been said, in a hobby where all the plants have a tendency to cross pollinate and stability isn't always guaranteed, is there extra anything we could be doing to ensure success (within reason)?
 
Edaxflamma said:
 
This was something I hadn't really stopped to think about. I guess I keep going back to the old Pink Tiger cross how the original phenotype that everyone loved hasn't really been repeatable all that much. Or the White Hot Lime as another example where the strong lime flavor didn't really persist as much as it once had. 
 
Have we unintentionally overlooked some traits with mixed or shared dominance in our strains by the nature of how our stabilization process works?
 
Click to expand...
 
Some traits are a complex expression of several genetic traits.  The coloration of the Pink Tiger and the unique flavor of the White Hot Lime are probably good examples of traits that may require several genetic rolls of the dice to hit them exactly (as well as the growing conditions that year).  There's always several other traits you're also trying to retain.  After the F1 generation, it can be really difficult to get all the traits you want in a single pepper plant.  The F2 generation has a lot of variability.  The only way I know to compensate for this is to grow a lot of examples of the F2 generation.  It might take 40 or 50 plants, or even more if you have a number of traits you're trying to retain.
 
Most people who grow as hobbyists can't manage that many examples of a single variety, so they just have to make do with what they can handle.
 
Edaxflamma said:
 
But that having been said, in a hobby where all the plants have a tendency to cross pollinate and stability isn't always guaranteed, is there extra anything we could be doing to ensure success (within reason)?
Click to expand...
 
Absolutely!  There's a variety of methods to isolate peppers to prevent cross pollination.  If the goal is to develop a stabilized variety, then some method isolation is usually employed.  But not always.  The extent to which peppers will cross pollinate on their own varies widely.  Some growers find that their varieties are "stable enough" without any special isolation.  The opinions on this vary widely and are hotly debated.
 
[SIZE=10.5pt]Following up on good information from DP, for someone who [/SIZE]truly[SIZE=10.5pt] wants to get a reasonable handle on the basics of breeding peppers, I suggest approaching it this way:[/SIZE]
 
1.  Understand very basic genetics, especially monohybrids, dihybrids and trihybrids and the associated punnett square distributions.
2.  Understand the allele combinations that generate the main color variations in mature pods and which are dominant over others, i.e., "y," "c1," and "c2." 
3. Understand the SW allele series for chlorophyll-based immature pod color variations and the effect they have on the primary mature pod colors.
4.  Understand the basics of the cl, A, MoA, and anthocyanin-retainer alleles and how they interplay with mature and immature colors.
5.  Start with mother and father plants that are homozygotic as to the genetic loci you intend to select for.
6.  Understand that the F1 generation of homozygotic parents will result in what are essentially genetically identical heterozygotic plants.  They are not the starting point for selection, their F2 progeny are.  All you should really need is one F1 seed if you do things right (a simplification, but most of the time it should work)
7.  Assess whether you're selecting for monohybrid, dihybrid, or trihybrid expressions and plant a number of F2 seeds that should statistically 
generate your desired phenotype based on the relative punnett square distributions. Full recessive combinations are 1:4, 1:16, and 1:64, respectively.
8.  Bear in mind that the immature pod color can be relevant to stabilization. 
9.  You can never be certain that your new cross is stable, ever.  Statistically, around F8 the odds are pretty strongly in your favor if you haven't been seeing much variation among the recent generations of plants or if you're dealing with simple recessive pairings.
10.  Understand that unless you're growing a minimum of 50 to 100 plants each season that continue to your next generation, your new variety simply won't have the genetic diversity to flourish outside controlled conditions, so it should not be expected to be commercially viable, but only a hobby pepper.
 
The following basic articles are a great place to start and cover a wealth of information succinctly.  Beyond these basics, learning more about specific pepper genetics requires reading research papers.
 
http://kdcomm.net/~tomato/gene/genes.html
 
http://kdcomm.net/~tomato/gene/genes2.html
 
https://the-biologist-is-in.blogspot.com/2015/05/the-color-of-peppers.html
 
https://the-biologist-is-in.blogspot.com/2015/11/the-color-of-peppers-2.html
 
http://sites.science.oregonstate.edu/genbio/otherresources/punnett%20squares.htm
 
CaneDog said:
[SIZE=10.5pt]Following up on good information from DP, for someone who [/SIZE]truly[SIZE=10.5pt] wants to get a reasonable handle on the basics of breeding peppers, I suggest approaching it this way:[/SIZE]
 
1.  Understand very basic genetics, especially monohybrids, dihybrids and trihybrids and the associated punnett square distributions.
2.  Understand the allele combinations that generate the main color variations in mature pods and which are dominant over others, i.e., "y," "c1," and "c2." 
3. Understand the SW allele series for chlorophyll-based immature pod color variations and the effect they have on the primary mature pod colors.
4.  Understand the basics of the cl, A, MoA, and anthocyanin-retainer alleles and how they interplay with mature and immature colors.
5.  Start with mother and father plants that are homozygotic as to the genetic loci you intend to select for.
6.  Understand that the F1 generation of homozygotic parents will result in what are essentially genetically identical heterozygotic plants.  They are not the starting point for selection, their F2 progeny are.  All you should really need is one F1 seed if you do things right (a simplification, but most of the time it should work)
7.  Assess whether you're selecting for monohybrid, dihybrid, or trihybrid expressions and plant a number of F2 seeds that should statistically 
generate your desired phenotype based on the relative punnett square distributions. Full recessive combinations are 1:4, 1:16, and 1:64, respectively.
8.  Bear in mind that the immature pod color can be relevant to stabilization. 
9.  You can never be certain that your new cross is stable, ever.  Statistically, around F8 the odds are pretty strongly in your favor if you haven't been seeing much variation among the recent generations of plants or if you're dealing with simple recessive pairings.
10.  Understand that unless you're growing a minimum of 50 to 100 plants each season that continue to your next generation, your new variety simply won't have the genetic diversity to flourish outside controlled conditions, so it should not be expected to be commercially viable, but only a hobby pepper.
 
The following basic articles are a great place to start and cover a wealth of information succinctly.  Beyond these basics, learning more about specific pepper genetics requires reading research papers.
 
http://kdcomm.net/~tomato/gene/genes.html
 
http://kdcomm.net/~tomato/gene/genes2.html
 
https://the-biologist-is-in.blogspot.com/2015/05/the-color-of-peppers.html
 
https://the-biologist-is-in.blogspot.com/2015/11/the-color-of-peppers-2.html
 
http://sites.science.oregonstate.edu/genbio/otherresources/punnett%20squares.htm
Click to expand...
 
I found these articles really awesome since I plan to dip my toes in crossing peppers.
 
After going through them, I found this one: http://kdcomm.net/~tomato/Tomato/mutant.html. A similar one for peppers would be amazing since it will cut down a lot of the guesswork (e.g. what is the % chance of getting the traits I'm looking for?). Some of the links suggest that such a document exists, but they seem to be out of date (broken). Does anybody have something like this?
 
Thanks!
 
HeatMiser said:
 
I found these articles really awesome since I plan to dip my toes in crossing peppers.
 
After going through them, I found this one: http://kdcomm.net/~tomato/Tomato/mutant.html. A similar one for peppers would be amazing since it will cut down a lot of the guesswork (e.g. what is the % chance of getting the traits I'm looking for?). Some of the links suggest that such a document exists, but they seem to be out of date (broken). Does anybody have something like this?
 
Thanks!
Click to expand...
 
https://pdfs.semanticscholar.org/02cb/c24c92eb348b05319ed811ecbd68decc7fa3.pdf
 
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