Double Decker Rabbitry

What does “genotype” mean?

All my bunnies come pedigreed and genotyped.  This means that on their pedigree, for each rabbit, up to 3 generations is genotyped.  A genotype is a series of letters (A,B,C,D, and E that represent color genes), half of which can be determined just by looking at the rabbit (it's Phenotype), the other half can be determined by breeding it, knowing what color it's parents were, and sometimes by other siblings in its litter. Sometimes the genes they carry are unknown, so this is written "-", it can be filled in at any time when more information is available. Genotyping can be useful to purchasers because it allows them to know what their new rabbit carries and might carry so that the purchaser can wisely pick breeding pairs to decrease the probability of unshowable offspring.

Explaining the Letters of Rabbit Genetics.

The letters A, B, C, D, and E each represent different genes coding for color in a rabbit’s genome. It is the combination of these 5 genes that make a rabbit look the way it does.  Each rabbit has some variation on these five letters.  The color of the animal is a result of what variation it has inherited from its parents.  Each rabbit has two copies of each letter- these are called alleles. 

A allele: Determines Pattern of rabbit.
There are only three patterns in rabbits.  (Does not include broken, that is a different allele).  They are Agouti, Tan Pattern and Self.
The alleles (in order of dominance)
A: Agouti. (Ringed Fur) ex.) castor, chin
  Can show up in genotype as AA, Aat, or Aa
at: Tan Pattern ex.) Otter, martin
  Can show up in genotype as atat  or ata
a:  Self Pattern ex.) Black, blue, chocolate, lilac
  Can show up in genotype only as aa

B allele: Determines if the Rabbit is able to produce black color pigment.
There are only two variations that can occur in the rabbit reguarding this allele.  Either it can make Black pigment, or it produces chocolate pigment. 
The alleles (in order of dominance)
B: Can produce Black ex.) castor, chinchilla, black otter, black
  Can show up in genotype as BB or Bb
b: Can produce chocolate only ex.)amber, chocolate chinchilla,chocolate otter, chocolate
  Can show up in genotype as bb only

C allele: Determines color amount that can be produced
This allele determines how much color is on the animal.
The alleles (in order of dominance)
C: Full color ex.) castor, otter, black
  Can show up in genotype as Ccchd, Ccch, Cch, or Cc
cchd: Color, except middle band ex.) chin, silver martin, ermine
Can show up in genotype as cchdcchd, cchdcchl, cchdch, or cchdc
cchl: Shaded color on extremities ex.) Sable Agouti, Sable martin, sable, seal*
  *The C series is codominant, which means that sometimes the “recessives” matter in the phenotype.  This is most apparent in the self sable and seal.  Genetic sables are cchl ch or cchlc.  In order to have a genetic seal, it must be a homozygote: cchl cchl.  But, keep in mind that we show according to PHENOTYPE, not genotype. (Many showable seals are actual dark sables, genetically)

ch:  Californian allele- allows color only where there is a lower body temperature (the extremities)
Can show up in genotype as chch or chc
c: no color, albino ex.) red eyed white
  Can show up in genotype as cc only.  These rabbits HAVE the other gene alleles, you just cant SEE them.  You can figure out what "color" a white rabbit is by testbreeding it.

D allele: Determines if the color can be dilute
This allele determines how the color pigment is distributed in the hair follicle. 
The alleles (in order of dominance)
D: Normal distribution of pigment- black sections are black
ex.) castor, black, black otter
   Can show up in genotype as DD or Dd
d: Diltuion of black pigment- black sections are blue
ex.) opal, blue, blue otter
   Can show up in genotype as dd only

E allele: Determines Extension of middle band color.
The dominant allele allows normal banding of agouti fur and the recessive allele allows only the middle band color to be expressed.
The alleles (in order of dominance)
E: normal extension ex.) castor, black, black otter
  Can show up in genotype as EE, Eej, or Ee
ej: random extension ex) harlequin, magpie, tricolor
  Can show up in genotype as ejej, or eje
e: non-extension ex.) red, tort, fawn, ermine
  Can show up in genotype as ee only

Brokens- The English Spotting Gene

I do not put this allele in my genotype on the pedigree because once you understand the concept of broken genetics it is unnecessary.  There can not be “hidden” recessive genes when dealing with brokens. 
“en en” is the genotype for solid
“En en” is the genotype for broken
“En En” is the genotype for a Charlie marked broken (very little color, usually only a nose spot and ear color, spine markings)

So, solid to solid can only result in SOLIDS.

Broken to Solid will result in about half solid, half broken.

Broken to Broken will result in about half broken, 1/4 SOLID and 1/4 Charlie.

Charlie to Solid will result in 100% BROKEN (this is helpful to anyone breeding tricolors- the solid versions are not showable)

How to Apply this to Breeding?

Now that the color alleles are understood, they can be put together to make colors.  So how does this help on a new rabbit’s pedigree?

Based on what you are after and what you want to avoid in the offspring, you can make informed decisions on what to breed.  Of course, even if the genes are there, it doesn’t mean each parent will contribute the genes you want them to, it is always a probability game.  You find out the most about a rabbits genotype when you breed them and see what colors result.

For example, if the pedigree says that a broken Castor rabbit has the genotype “AaB_CcD_Ee Enen” you can tell quite a few things by this.  All castors have the genotype “A_B_C_D_E_”, where the lines are unknowns.  From the genotype we know that it carries self (a), albino (c), and nonextension (e).  If you are trying for tricolors and you have only a Harlequin to breed it to (A_B_C_D_ej_enen), will you get tricolors from this breeding?  The answer is, yes, it is possible.  Does it mean that you are guaranteed one in the first breeding? NO- you are still working with probability.  The genes are there to make a tricolor.  For a tricolor (A_B_C_D_ej_Enen) you have the harlequin gene from the harlequin and the broken gene from the broken castor.

Filling in your genotypes once you have bred your stock:

You will find out the most pieces of the genetic puzzle when breeding your pair and observing the colors of the offspring. This is a way for you to "fill in" the unknowns.

An example: 

You buy a castor buck (A_B_C_D_E_) and a black otter doe (at_B_C_D_E_) and breed them.  You get a white baby, a red baby and a blue otter baby.  How did this happen?  What hidden recessives can you fill in for the parents? If there is a white, both parents must carry white (c).  So both parents are Cc.  If there was a red baby, both must carry nonextension (e)- so both are Ee.  The blue otter (genotype at_B_C_ddE_) is more of a puzzle, the “otter” part most likely comes from the black otter doe, but it also could have arisen as a recessive in the castor (we don’t know whats there, so we cant fill in anything).  The blue part must come from both parents carrying blue (d), so their new genotype is Dd.  So from this cross more accurate genotypes were determined.
Castor buck Sire: A_B_CcDdEe
Otter Doe Dam: at_B_CcDdEe
White baby: __ __ cc __ __
Red baby: A_B_C_D_ee
Blue Otter Baby: at_B_C_ddE_

You cannot assume a baby carries any particular allele from the parents.  For example, the red baby may have inherited the unknown recessive of either parent with the dominant A.  There is no way of telling without breeding her to see the outcome. 

Another important genotyping hint- do not assume every rabbit is homozygous for each gene! There are a lot of hidden recessives out there! Ex.) Just because you have an black otter, it doesn’t mean its genotype for pattern is at at.  (It might carry black (a)!)

Genotypes of Recognized Rex Varieties:

Amber  A_bbC_D_E_                                                                                    Black   aaB_C_D_E_
Black Otter  at_B_C_D_E_
Chocolate Otter at_B_C_D_E_                                                                Blue Otter  at_B_C_ddE_                                                                            Lilac Otter  at_bbC_ddE_                                                                       Blue    aaB_C_ddE_
Castor   A_B_C_D_E_
Chinchilla  A_B_cchd_D_E
Californian  A_B_ch_D_E_
Chocolate  aabbC_D_E_
Lilac aabbC_ddE_
Lynx A_bbC_ddE_
Opal   A_B_C_ddE_
Red   A_B_C_D_ee
Sable   aaB_cchl_D_E_
Seal   aaB_cchl cchl D_E_
White   __ __ cc__ __

B/O Tricolor A_B_C_D_ej_


All other Known Genotypes    (recessives only)
Blue Point                          aa cchl_ dd ee
Blue Chinchilla                       cchd_ dd
Chocolate Chin                    bbcchd_
Lilac Chinchilla                   bb cchd_ dd
Chocolate Point/ Cream  aa bb cchl_ ee
Cream Agouti                   dd ee or bb dd ee
Dark Smoke Pearl           aa cchl cchl dd
Ermine- Black                     cchd_ ee
Ermine-Chocolate             bb cchd_ ee
Ermine- Blue                        cchd_ ddee
Frosted Pearl                      aa cchd_ ee
Frosted Pearl- Blue              aa cchd _ddee
Frosted Pearl- Choc.            aa bbcchd _ee
Frosted Pearl- Lilac              aa bb cchd ddee
Gold/Fawn                               bb ee
Californian- Black                 aa ch
Californian-Blue                   aa ch_dd
Californian-Choc.                aabb ch_
Californian- Lilac             aabb ch_dd
Harlequin                                  ej
Harlequin- Blue                       dd ej_
Harlequin- Choc.                     bb ej_
Harlequin- Lilac                       bb dd ej_
Lilac Point (Cream)                  aabbcchl_ddee
Magpie- Black                            cchd_ ej_
Magpie-Blue                             cchd_ dd ej_
Magpie-Choc                           bb cchd_ ej_
Magpie-Lilac                           bb cchd_dd ej_
Otter- Black                                   at
Otter- Blue                                     at dd
Otter- Choc.                                   at bb
Otter- Lilac                                  at bb dd
Red                                                    ee
REW                                                  cc
Sable                                            aa cchl_
Sable Chinchilla                      A_B_cchl_D_E_
Sable Martin                                at_ cchl_
Sable Point                                 aa cchl_ ee
Seal                                          aa cchl cchl
Silver Martin- Black                     at_ cchd_
Silver Martin-Blue                   at_ cchd_dd
Silver Martin-Choc.                     at_bb cchd_
Silver Martin-Lilac                  at_bb cchd_dd
Smoke Pearl/Siamese                 aa cchl_ dd
Smoke