Cavy Coat Color Genetics
Please excuse our mess while we work on these sections!!!
Okay, for all the non-genetics folk out there, a little terminology 101. Genetics won't be quite as painful once you know some of the jargon. Think of it like starting new in the fancy. I'm fairly sure there were a lot of breed specific and species specific words you had to learn. Genetics is no different. So with that in mind, there are just a few words you need to know the definitions for. Once you've got those, the rest will seem easy. These are going to be my paraphrasing for you for ease of communicating.
Genetics is the study of inheritance. That's about as basic as I can get with that one. Of course there's more to it, but that's generally it (as far as animal breeders are concerned lol).
a Trait is anything we select for based on an animal's appearance. Such as coat length, coat color, eye color, crown, shoulder width, etc.
Phenotype is how an animal looks to us on the outside. We show according to this.
Genotype is the animal's specific lineup of genes on the inside.
a Gene is the mode of inheritance. Merriam-Webster dictionary has this really long definition of a gene, which includes several much longer words that I refuse to utter here. Most of you probaby know what a gene is without having to put it into words. Examples would be coat length, pink-eye color, black coat color. They are quite specific.
In simple inheritance, one gene controls one trait. Most of the things we select for in cavies, are simply inherited.
In complex inheritance, one trait is controlled by many genes. Most of these we are not consciously aware of, as they are difficult to trace. Most of the type traits are complex inherited. Progress is slow as a consequence of the many genes involved.
a Locus is the place where a gene is known (or believed) to exist. (plural is loci)
an Allele is each "type" or alternative form of a gene that can occur at a single locus. So if the gene is the pink-eye gene, there would be 2 alleles, P for non-pink, and p for pink. There are some genes that have more than 2 possible alleles, such as the color locus, where you can have C, full-color; ck, dark dilute; cd, light dilute; cr, ruby-eye dilute; and ca, himalayan. Only 2 alleles can be present at any single locus. So even though there are 5 possible alleles for the color locus, only 2 will be found in any one animal.
Dominant is one allele that asserts it's effects over others. The Black (B) allele is dominant to the brown (b) allele. Agouti (A) is dominant to the solid (Ar) allele, both those are dominant to the tan (at) allele, and all three are dominant to self (a).
Recessive is one or more alleles whose effects may be hidden by other alleles. Pink-eye (p) allele is recessive to the non-pink-eye (P) allele.
(these 2 are actually a little more complex than this, but I'm trying not to confuse)
Homozygous (also homozygosity and homozygote) is where both alleles at a locus are the same. A self is homozygous aa, a Teddy is homozygous wv wv.
Heterozygous (also heterozygosity and heterozygote) is where the two alleles at any given locus are different. A roan is heterozygous Rsrs.
Complete Dominance is where both the homozygous dominant and the heterozygote exhibit the same phenotype. At the agouti locus, AA and Aa will both be agoutis, while only aa will be self. We say that agouti is completely dominant over self.
Incomplete Dominance is where the heterozygote acts as an intermediate between the two homozygotes. At the roan locus, roan is the intermediate between non-roan and lethal. We say then that the roan gene is incompletely dominant.
I think that pretty much covers the basics of the terminology. Next I'm going to mention a few specific genes of interest.
The first locus to look at is the agouti locus. There are 3 possible alleles that can exist here: A is agouti, Ar is solid, and a is self. Since only 2 alleles can co-exist at the locus, you can have AA, AAr, ArAr, Aa, Ara, and aa.
Because agouti is dominant to both solid and self, then AA, AAr, and Aa will all appear as agoutis. We say then that agouti masks the other alleles, they are hidden from out view and could only appear in breeding to a solid or self (or to another agouti that is also masking those alleles)
Solids would appear only as ArAr or Ara. Solids are dominant to self and mask and hide that allele. A solid would only be shown to carry self if either one parent was a known self, or they produce one themselves.
Self is only aa. If you have a self, you know they cannot produce anything but self when bred to other selfs. To produce agouti or solid using a self, you would have to breed to an animal with agouti or solid at that locus.
The next locus to look at is the gene that controls black color. Here the black allele (B) causes normal black pigment, while the recessive brown (b) causes modified black pigment resulting in brown or "chocolate" pigment. (Claus explains though that you need more than this one set of recessives to get good chocolates, that's why I'm using brown and not chocolate!).
So this gene is a simply inherited gene, with only two alleles and is completely dominant in that both BB and Bb will appear black. Only bb will exhibit a brown animal.
So coupling the first locus with this second. Any of the agouti combinations (AA, AAr, Aa) with either BB or Bb will give you the black based agoutis, golden, silver, & lemon. Either of the 2 solid allele combinations (ArAr or Ara) coupled with black (BB or Bb) will give you the black based solids (golden, silver, lemon). And self coupled with the black combinations will give you black. Substitute brown (bb) at the black locus, and you'll get chocolate based agoutis and solids, and chocolate self. This is completely ignoring the pink-eye dilution locus. One step at a time. lol
Black based agoutis:
Chocolate based agoutis:
AA BB
AA bb
AAr BB
AAr bb
Aa BB
Aa bb
AA Bb
AAr Bb
Aa Bb
Black based solids:
Chocolate based solids:
ArAr BB
ArAr bb
ArAr Bb
Ara bb
Ara BB
Ara Bb
Black Self
Chocolate self:
aa BB
aa bb
aa Bb
Bear in mind that you would not
be able to simply look at an animal (with no pedigree or progeny information)
and tell whether it is AA, AAr, Aa or whether it is BB or Bb. So when you
are faced with a black-based agouti animal, you would simply say that it is A-
B- where the dashes account for the fact that it could carry any of the other
recessive or dominant allele(s). The only ones you could be absolutely
certain of just by looking are the homozygous recessives (self and brown).
I was going to skip over the color (C) locus for now, but I think I'll just hit it head on, and anyone with more information than I have can jump in and comment, clarify, or correct.
Okay, so the color locus is one of the most complicated of cavy coat color genes. It's not completely understood how everything works with this one. There are five alleles associated with this locus. The various combinations of the five alleles are what give rise (in large part) to the multitude of varieties (and shades!) we see in domestic cavies. There is no simple dominance associated with the lower alleles, and several of the recessive heterozygote combinations will exhibit the same phenotype. Thus making it that much more difficult to differentiate which of these alleles each individual might carry.
The five alleles are full color (C), dark dilue (ck), light dilute (cd), ruby-eyed dilute (cr), and himalayan (ca). The one dominant allele, full color (C), will mask the four remaining recessive alleles. So in the presence of C, all else is carried. Therefore CC, Cck, Ccd, Ccr, and Cca will all exhibit full color. An example would be red vs orange, the best red will be CC, while a good orange will have some combination of heterozygote recessive alleles.
For the recessives, let's talk about them in reverse order. So ca is himalayan (this is strictly for ease of discussing this particular allele, in reality there is another gene involved in the determination of an animal to be himalayan or white), you could think of this allele as a primary factor of an animal being either himalayan or white. Since cavies have no actual albinism gene, this allele is largely the cause of the lack of body pigmentation in himis and whites. Incidentally, this is also why a himi-smut will result from the crossing of a white to a dark animal. The ca allele also assists in the creation of good creams. Hence the reason many good cream breeders will tell new breeders to cross whites to creams. Okay, so caca will give rise to himalayan and white, and coupled with one of the other recessive color alleles (cd or ck), tends to "lighten" the pigmentation. ca removes all red pigmentation and most of the black. Pink eyes are associated with this allele.
The next recessive color allele to talk about is the ruby-eyed dilute allele (cr). This one seems to have a somewhat similar effect as the ca allele, but rather than removing a large majority of the color, resulting in a "clear" animal, it removes only the red pigmentation (leaving black), resulting in a "silvering" effect. The homozygote of this allele can be found in silvers (agouti and solid), and DEW. A cr allele coupled with a ca allele tends to have similar effects as if you had two ca alleles. Incidentally, ruby cast eyes are associated with this allele. This explains why silvers (not goldens!) should have a ruby cast eye.
The remaining 2 alleles (cd & ck) should be talked about together as they each have very similar effects on the phenoptype of the animal. The difference between the two would be that light dilute (cd) would show about an even amount of red and black pigmentation, while dark dilute (ck) shows just slightly more black than red pigmentation. However, that being said, an ordinary animal breeder would be very unlikely to be able to differentiate these two by merely looking at a cavy's phenotype. The two together and the homoygotes of each (coupled with a few other genes) largely result in buff colored animals (dark cream). These alleles also assist in the production of good chocolates, and good REO's. Matching one of these alleles with a himalayan allele (ca) gives rise to the nicely colored light creams.
So a summary of the color
gene:
CC found in good reds & blacks
Cck, Ccd, Ccr found in good
chocolates
cdcd, ckck, & cdck result
in buffs (does not act alone, requires another gene)
cdca & ckca result in good creams
caca results in himalayans and whites
crcr results in DEW or silvers
Other unknown modifiers may be involved with these, but that's about as basic as I can get with the color locus and still be understood (and understand myself)
Genetics doesn't have to be complicated. I'm trying to make it as simple as I can and still make it understandable. If I don't quite manage it, question! lol I question everything, and believe me, some of this stuff is stumping me. lol I'm going to be referring to other papers and another group to try and get some answers. I find that Harry Claus is causing more holes than filling them with his book. lol (I expected that though)
...one other thing, don't get too caught up with all this stuff I'm writing down. I'm trying to break it down first so can understand what each gene does individually. But remember, there is no such thing as a cavy with only one or two of these genes, so most of these interact to give us the various colors. So first I'm breaking it down, then I will put it together (might make more sense then), and then I'll go through some examples.
btw, I'm probably a day late on
asking this....but if anyone would prefer I not continue this thread, I will
stop. I know some people probably would just prefer to skip all this
stuff. Just say so, if you aren't comfortable saying so in the thread,
send me a pm.
Reply to : Falls-Acre
Please continue! It is really helping me understand cavy genetics more. Keep it coming!
I am sure you have these links, but if not, here are a few places on the internet to find more papers written on cavy genetics.
Cavy Genetics by Peter and Cell Herman (this is also found in the Claus book)
Basic Color Genetics by Pip Squeak Caviary
Sigi's Sauhaufen Cavy Genetics
Cavy Genetics: An Exploration by Nick Warren
Colour Genetics of the Cavy by Catherine Whiteway (can also be found in the "file" section of the Cavy Colors group)
Some great links Leslie, thanks.
Alright, moving on, the next gene to consider would be the Pink-Eye (P) dilution gene. This one is another simply inherited gene, completely dominant. So both PP and Pp would have dark (non-pink eyes). This gene affects the eye color of the animal separate from the effects of the color locus (so you can have a white or albino that is PP or Pp at this locus, and they would still have pink eyes! This is partly why it Is possible to produce dark eyed animals from whites and himis)
The allele P causes normal coat color pigmentation to be produced, it completely masks the effects of the recessive allele, so an animal carrying one pink-eye allele will still have dark eyes and normal coat pigmentation.
The presence of the homozygous recessive at that gene causes a large reduction in the amount of black pigment that is made, with no effect on red pigment. So black gets diluted to lilac and chocolate gets diluted to beige. Red becomes REO, and DE cream becomes RE cream, but because there is no effect on the red pigmentation of the animal, the coat color of these two varieties would remain virtually unchanged. This is why it is possible to have a REO with a coat as dark as a red, and a RE cream, with a coat as pale as butter. The only change caused by the P gene in those animals is to change the eye color.
So now, putting the the agouti, black, and pink-eye genes together, we can have:
black based agouti = A- B- P-
black based solid = Ar- B- P-
black self = aa B- P-
chocolate based agouti = A- bb P-
chocolate based solid = Ar- bb P-
brown self = aa bb P-
lilac based agouti = A- B- pp
lilac based solid = Ar- B- pp
lilac self = aa B- pp
beige based agouti = A- bb pp
beige based solid = Ar- bb pp
beige self = aa bb pp
For right now I'm going to be skipping both the extension locus and the white spotting locus and will come back to those a little later. You'll see why when I do get to them. lol
For now, I want to discuss the two genes that are responsible for roaning. Yes I said two, because there are two genes that are accepted as being able to cause white and color intermixing. However, in heterozygote form only the actual roan spotting (Rs) gene will give showable roans. The other gene is the silvering gene (showable roans with this one are homozygous recessive). In this post I'll go in depth with the roan spotting gene, and cover silvering in the next post.
Most breeders that have ever owned roans for show and breeding know the basics of the roan spotting gene. But there's more to this one than meets the eye. The roan spotting gene is incompletely dominant, meaning that there are three phenotypes associated with the various allele combinations. The heterozygote is intermediate between the two homozygotes. There are only two alleles, the non-roan allele (rs) and the roan allele (Rs), which means that rsrs will be our ordinary non-roaned pigs, Rsrs will be roans, and RsRs will be the lethal micropthalmics. (I know, old hat to many of us)
This gene will have the same effect on all colored pigs, regardless of what is found at the other loci. So we can have agouti roans (little or hard to see roaning on the belly due to the belly band), solid roans, and self roans. Even whites can be "roaned" but we cannot see it becuase white intermixed with white will still be white.
So what's so different and interesting about this gene? Well, it is unclear which modifiers cause the differences between roans and dalmatians. It has been shown that the same gene (Rs) causes both, but the modifiers which result in spots rather than intermixed hairs have not been identified.
BTW, when we cross in a broken to a roan, we cause spotting in the roans, essentially a broken roan, but I'll get more into that a bit later.
Hey, you guys are going to love this! There are three, not 2 different ways for a cavy to be roan in color. I was going to talk about silvering here, and I will, but first I want to talk about the other way a cavy can be roan, although this one would be a "false" roan, since the only way to perpetuate it would be to breed two "roans" together! See, genetics can be fun! lol
The "false" roan could also be called a silver brindle (per Catherine Whiteway). If you look back to the post on the color locus, one of the alleles (cr) removes all red pigmentation, leaving nearly all black pigmentation, giving the animal a "silvered" appearance. This is seen in silvers, where it removes the red tips of the golden and makes them white. A brindle is red and black intermixed. So if a brindle has crcr at the color locus, it would remove all red pigmentation, leaving a black animal with white intermixing hairs. I love genetics! lol (incidentally, a brindle pig with crcr and white patching are our magpies)
BTW, this will only work with red/black brindles and the derivatives (chocolate/red, lilac/reo, & beige/reo) If you had a cream/black, well remember that cream is a lower c heterozygote, that would be replaced by crcr and you'd still have a false black roan (silver brindle). Chocolate/red would yield a false chocolate roan, lilac/reo would be a false lilac roan, and beige/reo would be a false beige roan. You would know that strawberry roan, reo roan, and cream roan could NOT be crcr (remember that the effects of cr is to remove all red pigmentation!). In those cases, you'd have whites.
Okay, now for the silvering gene (Si). This one is incompletely dominant (just like Rs), where the heterozygote will yield some intermediate between the two homozygotes, but rather than the intermediate giving the best roaning, the homozygote silvered (sisi) pig usually has the best roaning. Once upon a time, it would seem that most roan cavies were silvered, roan spotting was apparently a mutation that grew in popularity (first reported by Catherine Whiteway in 1973). Si is the normal, non-silvered allele of this gene, the si allele causes a dark face, and white hairs intermixed over the body. It's important to note that silvering cannot yield a dalmatian. Only the roan spotting gene can cause spots (and dapples). So if you've got a roan on your hands that is spotty, it's probably a good bet that it's Rsrs, while a complete lack of spots may (but is not guaranteed) be sisi. Of course, the two may be present together as well, and we would not know what these were by phenotype alone.
We already know that RsRs produces micropthalmics. sisi all by itself will not produce lethals. However, sisi coupled with another gene called Diminished (Dm) can result in sickly whites that die young. Dm is the normal form of the gene, dm in homozygous form and coupled with sisi is what yields the sickly whites. If you are fortunate to have a line of perfect roan cavies, that happen to be sisi DmDm, breed them together and you'll never get a lethal! (yeah right, like there are really any of these left out there! lol)
In other words, when dealing with the roan spotting gene, it's best to cross roan to non-roan. When dealing with the silvering gene, it's best to cross roan to roan (to maintain homozygosity of the recessive and maintain the best roans), however, crossing these without knowing what they carry at the dimished locus may also yield sickly whites. lol Aren't roans a blast?! I never even realized how much fun they could be until I started looking into this stuff. lol
There are two other genes that give the "appearance" of being roans, but aren't. They are the grizzling gene (gr) whose homozygous recessive can cause white hairs to begin to appear on cavies after about 4 months of age (not born with it). And also the whitish gene (w), which causes white hairs to appear in black and brown cavies, but which may come and go with hair growth. I think what we all know as "grizzling" of chocolates is actually the result of this whitish locus, since it usually appears around weaning and is gone by senior age (generally).
Now for genetics terminology 102. :)
Wild Type is the (believed) original genetic code, no mutations. It generally consists of all dominant alleles. In cavies, the believed Wild Type is the golden agouti. So the dominant allele may also be referred to as the Wild Type or WT.
Pleiotropy is the
Epistasis is the
Inbreeding is the act of breeding two related individuals, regardless of what that relation might be. Mother x son, father x daughter, aunt x nephew, full-sibs, half-sibs, cousins, etc.
Linebreeding is generally believed to be the act of breeding within a family line. Father x daughter and mother x son. Also grand-mother x grandson and grand-father x grand-daughter.
Crossbreeding is the act of breeding two different breeds. Such as Peruvian to Silkie, American to Teddy, or (according to ARBA) Satin Abyssinian to Abyssinian.
Outcrossing is the act of crossing two genetic lines within the same breed. Lines are created through linebreeding (inbreeding), and outcrossing is when you introduce non-related individuals into the line.