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Genitics Question

Well if you ask nearly everyone that brings out a black or chocolate they will say.. Its  a naturally occurring variant of the red.... And in some cases this might be true.. In most situations where a Black version (Super dark brown / purple) version os made its a cross with a pimenta De Neyde or similar and they look for the black/purple pheno with the other parents shape and taste etc. 
 
If its a chocolate variety it can be a matter of finding Green versions (rare) and crossing it with a red version and looking for the pheno that holds chlorophyll during ripening giving you brown.. Or once again crossing it to a pepper that holds chlorophyll or going direct to a chocolate secondary parent... It all boils down to applying a colour pheno to the original "strain" you are trying to change the colour of and then looking for the F1+++++ that continues that strain purity with the new colour.
 
I still cant believe how many pepper strains come in the standard three Red Yellow Chocolate varieties and hold very true to the original varieties, that being said though I still believe there are too many so coloured colour variations of varieties that should be classified as a different variety as they vary so much from the original variety.
 
This all being said - If you want to change a colour of a variety its always in your best interest to find a secondary variety that most closely represents the original parent.. Eg. crossing a Bhut with a Naga or Fatalli so pod shape changes are minimized.... Or a Fresno with a serrano etc etc etc.. I guess the most true thing about peppers when it comes down to it is flavour as several varieties can look almost the same but be completely separated by heat and flavour, but at face value its hard to go passed pod shape .
 
A professor friend of mine crossed yellow and red and got brown, which surprised him. He was trying to get orange, lol. I really don't know why that happened. Has anyone tried crossing red and yellow? It would be easiest to cross a brown pepper though. Brown seems to be a deep red.
 
Question phrased in such a way that I am not sure what you want to do.

Create a New Pepper - Easy, start with black / brown varieties, cross away, see what you get, and then years of selective seed saving and you might have a stable new pepper.  CPI has a fantastic guide to crossing chili peppers. 

Change Color of Existing / Established Pepper - My opinion is can't be done because I feel that once you cross two peppers, the offspring are no longer the original pepper.

Let Nature Take its Course - What Kraken said about natural varients I believe very much.  I have chocolate reaper growing.  First year had a single plant, saved seeds, horrible germination rate.  Next year, grew true to mama plant.  Saved seeds. Kind of thinking the germination rate improves with time due to auto culling. 

Long story - Birds do not fully digest pepper seeds.  Bright colors attract birds.  So chances are natural selection would cause brightly colored peppers to expand their domain much more than chocolate / black peppers.  Thing is, mother nature doesn't tend to throw away dna.  Instead, the genes that failed wind up in the mix somewhere but recessive.

Now this is real sixth grade earth science, fruit fly, eye color stuff.  It is much, much, much more complicated.  But this is the basics of what I think is going on.  I -think- the darker colors are recessive but generally in there.  When two peppers of the same variety cross pollinate, if both have the recessive gene for brown then some of their offspring will have only that recessive gene for color. 

BR = Brown Gene (recessive)
RD = Red Gene (dominant)

Parent A is Red but has both genes - BR n RD
Parent B is Red but has both genes - BR n RD

Offspring Could be:

BR n RD - Will be Red cause is dominant.
RD n RD - Will be Red cause that is all that is in there.
BR n BR - Will be brown because that is all that is in there.

Where a monkey wrench is thrown into my thinking is that peppers tend to self pollinate.  That being the case, I would imagine lots of folk should have noticed chocolate reapers.  I have only red about three people thus far.  Two in the US and on one in the UK.  The one in the US sold his seed stock right off the bat, so I imagine we will hear more about it soon.  Then again, there was the horrible germination rate that I observed, so maybe not till it is grown out a bit.

In closing, take note of the whole thing on how this comes from sixth grade earth science.  I am no expert and constantly humbled by mother nature's roulette wheel. Got two health, bright, intelligent kids.  No clue how that happened.
 
You can never be assured of what colour things will turn out .. Unless.. You know that the peppers you are using a Homozygous .. eg. you have a red pepper and a red pepper... that have no recessives.. eg. a yellow.. The result will be red .
 
If oyu mix a yellow and a red to try and get orange.. Unless you know what you have 100% results will always vary.  One of your mates peppers most likely had a chlorophyll retaining gene.. and as red is dominant as is the Cl gene they have both come forward and created brown ..  
 
If he was harvest those brown pods for seeds and grow them out.. his chances of getting an orange may be closer to 1/8 or 1/16 or similar.. depending on what genes are present.  The F2 stage or second generation of a cross is were all the magic happens.
 
Brown is completely different than red. You have red or yellow, red dominate, yellow recessive. For your oranges and whites, there are two parts responsible for the intensity of the red/yellow. Those two missing, you get your light oranges and whites. Browns are the result of not losing the green as the pods ripen. Get a red with no green loss, you get brown. Get a white with no green loss, you just get green. Your shades of brown come from the original shade of green unripe and the shade of red or yellow.
 
rhm3769, good information.  Learned about the chlorophyl dying off while trying to figure out what makes a purple bell pepper.  Was trying to figure out why the purples and other colors took so much longer to ripen / take on their color.  From what I read, it is usually due to cooler temperatures.

How things evolved, natural selection, the reason some attributes are wide spread and some are rare is absolutely amazing.
 
Did a bit of color research a few years ago for my cross breeding interest. Purple is a completely different process from the other color aspects, but similar to the retention/loss of chlorophyll....

Red is dominate over yellow, the higher amounts of red/yellow is dominate over less amounts, and losing chlorophyll is dominate over retaining it.

Treating it as a simple process like the classic bio/gene/color of peas/flowers problem, because of dominance, the majority of pods are red.
I'd have to find my notes again to double check the rates....
 
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