CAVY GENETICS

Peter Herman

Caviaria Rusticana

Las Cruces, NM

NOTE: This article was originally prepared for the ACBA guide book in the mid 1980s and revised for the 2013 ACBA Guide Book. It may be saved for personal use but may not be reproduced in any other form or otherwise distributed without the express written consent of the ACBA AND the author! © Peter Herman, 2013

The word genetics causes panic in many cavy breeders. This need not be the case. A few terms and concepts need to be understood first, then all genetics problems become variations or derivatives or the original principles.

The first concept is that every trait is controlled by a pair of factors called genes. One gene comes from the father and the other from the mother. The genes are carried on microscopic structures called chromosomes. There are many genes on a chromosome, and many chromosomes in each cell of an organism. Every cell in a cavy (except sperms and eggs) contains 64 chromosomes, 32 from the mother and 32 from the father. The genes are arranged on the chromosome in a specific order so that every trait has its own particular spot on a chromosome. This spot is called a locus. At each locus there are two or more choices called alleles. For example, at the coat length locus, there are two alleles possible, one for long and one for short. When the two alleles at a given locus are the same, the animal is homozygous. When they are different the animal is heterozygous. In breeders terms, homozygous equals “pure breeding” and heterozygous equals “hybrid” for the trait in question.

As many of you are aware, when a pure Peruvian is crossed to a pure Aby, all the babies will have short coats. This occurs because of dominance. Very frequently, one allele will mask or dominate the expression of another allele at the same locus. The masking allele is called dominant and the masked allele, recessive. Thus, in our example, the babies had a gene for long from the Peruvian parent, and a gene for short from the Abyssinian parent. The gene for short is dominant over the gene for long, making all the babies appear short coated. You can see from this that an animal can look like a purebred and be carrying genes that make it otherwise.

In general, a capital letter is used to represent a dominant trait and a small letter to represent the recessive. In addition, the letter often stands for a word that describes the trait, particularly when it differs from the “normal.” We will use the letter L (for long hair) to represent this locus. L = short, and I = long. If we diagram the cross made in our example, it would look like this:

Peruvian (ll) x Abysslnian (LL)

↓

Abyssinians (Ll)

If we were to take two of the so-called “Abyssinian” babies from this cross and breed them together, we would get both Abyssinians and Peruvians in an approximate ratio of three Abyssinians to one Peruvian.

In genetics, the way an animal looks is called its phenotype. The genetic make-up of an animal is its genotype. The ratio of phenotypes is 3 short:1 long, while the genotypic ratio is 1 LL:2 Ll:1 ll. At this point, let us warn you that we use the term “Peruvian” and “Aby” only loosely in describing the phenotypes of offspring of such a mating. There are many modifying factors other than the gene L which distinguish a good show Aby from a good show Peruvian.

When looking at Peruvians and Abyssinians can see that both breeds have rough coats, whereas Americans and Silkies both have smooth coats. This rough versus smooth character is controlled at the rough locus. The two alleles at the rough locus are the dominant rough (R) and the recessive smooth (r). If we cross a pure breeding American (rr) with a pure breeding Abyssinian (RR) or a pure Silkie (rr) with a pure Peruvian (RR) we will get all rough coated babies. If we then cross these “peruvian” or “Abyssinian” babies to each other, we will have offspring produced in the ratio of three rough to one smooth (three Abyssinians to one American or 3 Peruvians to one Silkie in our examples).

Thus you can see that an animal which shows a dominant trait can either be pure for that trait (homozygous) or carry the recessive as well as the dominant (heterozygous). In order to express the recessive trait, an animal must be homozygous for it. This should help explain why occasionally a breeder will breed two Abyssinians together and come out with an American, or two Peruvians together and come out with a Silkie. In these cases, both the mother and father must carry the smooth gene (r). We diagram these crosses

Finally, after much introduction, we get to the genetic makeup or each of the breeds. As you can see from our examples in the introduction, each breed has its own particular combination of alleles at the rough and long loci. Since some contain dominant characteristics, more than one combination of genes (genotype) can result in the appearance (phenotype) that we associate with each breed.

First, let us consider the American, with its smooth, short coat. As we have seen, smooth is recessive, so all Americans are rr. They can be either Li or LL at the long locus. Thus, a purebred American is rrLL, whereas a Silkie-carrying American is rrLl.

Since the Peruvian has a long coat which is a recessive, all Peruvians are ll. A pure Peruvian is RRIl, while a Silkie-carrying Peruvian is Rrll.

A purebred Abyssinian is RR for rough and LL for short. Other combinations which look like Abyssinians are: RRLI (Peruvian-carrying), RrLL (American-carrying), and RrLl (it is possible to get the four breeds by crossing two of these together). The quality of rosetting in Abys is controlled, in part, by a locus known as rough modifier. This gene, M, suppresses the formation of rosettes. Show Abyssinians are RRmm. RrMM animals can look completely smooth as the result of the rosette suppressing activity of MM, though careful inspection will usually show some hair reversal on the toes.

The thirteen ARBA recognized breeds are all controlled by different combinations of alleles at 6 different loci. In addition to the Rough and Long we have discussed earlier, they are: Star (Dominant) which produces a crest on the forehead, Teddy (recessive) which causes a kinking of the hair shaft and whiskers, Satin (recessive) which makes the hair shaft thinner and translucent in the outer layer giving it sheen, and Rex (recessive) which is very similar to Teddy in its effect on the hair and whickers but which is an independent gene.

LOCUS

BREED	Rough	Long	Star	Teddy	Satin	Rex
Abyssinian	RR	LL	stst	TT	SnSn	RxRx
Abyssinian Satin	RR	LL	stst	TT	snsn	RxRx
American	rr	LL	stst	TT	SnSn	RxRx
American Satin	rr	LL	stst	TT	snsn	RxRx
Coronet	rr	ll	StSt	TT	SnSn	RxRx
Peruvian	RR	ll	stst	TT	SnSn	RxRx
Peruvian Satin	RR	ll	stst	TT	snsn	RxRx
Silkie	rr	ll	stst	TT	SnSn	RxRx
Silkie Satin	rr	ll	stst	TT	snsn	RxRx
Teddy	rr	LL	stst	tt	SnSn	RxRx
Teddy Satin	rr	LL	stst	tt	snsn	RxRx
Texel	rr	ll	stst	TT	SnSn	rxrx
White Crested	rr	LL	StSt	TT	SnSn	RxRx

In addition, there are two rexed breeds recognized in Europe and the UK which sometimes appear in the US that share combinations of these traits

Alpaca	RR	ll	stst	TT	SnSn	rxrx
Merino	rr	ll	StSt	TT	SnSn	rxrx

It should be noted that sometimes crossing breeds can produce unforeseen results because of the way that genes carried by the breeds interact in new combinations. For example, the star gene can interfere with the expression of rough. Though the Rex and Teddy breeds look quite similar, breeding the two together results in normal coated pups.

Variety, or coat color, is controlled by the same sets of genes in all breeds. Remember that the way the animals actually look will not necessarily be the same among breeds, even if they carry the same major genetic information for color. For example, in Americans and other short coated breeds, you are looking primarily at top coat. In Peruvians and other long coated breeds you are looking primarily at under coat. The satin sheen can have a marked effect on the appearance of some colors. Please note that these genotypes only apply to pure breeding animals. As we saw before animals with a breed phenotype are not necessarily pure breeding.

All cavy colors are made from two basic pigments, black and red. The Black series colors are black, chocolate, lilac, beige and slate. The red series colors are red, orange, gold, and cream. All the varieties are comprised of these colors or white, the absence of color. We’ll start by giving a list of the major coat color genes with a brief description of what they do. After that we will go through the varieties and venture a guess as to possible genotypes that yield desirable show phenotypes.

LOCUS	Gene (allele) Name	Symbol	Function
AGOUTI	Agouti	A	A causes ticked hairs to be produced in the presence of black pigment. Each hair has a base derived from the black series of colors and a tip derived from the red series. The belly color is the same as the tip color, appearing untipped.
	Ticked Belly Agouti	A^r	A^r produces the solid agouties. They have ticked hairs all over so that the belly color and back color are the same. Ar is recessive to A
	Tani	a^t	A^t produces the Tan Pattern (belly, eye circles, nostrils, pea spots and brindled sides) in the Tan and Marten Varieties. a^t is recessive to A.
	Non-agouti	a	Animals with black series pigment that are non-agouti are aa. You cannot tell if a red is aa, Aa or AA because black pigment must be present to express the agouti trait.

EXTENSION	Extension	E	Allows The production of black pigment to extend throughout the coat, producing self animals of black series colors or agoutis.
	Partial Extension	e^p	Allows black pigment to extend partially through the coat, leaving patches of black series and red series pigments
	Non-Extension	e	Restricts black pigment to the eye, leaving a red series colored coat. Recessive to E and e^p .
BLACK	Black	B	Causes normal black pigment granules resulting in black color
	Chocolate	b	Modified black pigment granules are produced by bb animals, converting black to chocolate. Gives eye a ruby cast.
PINK-EYE	Non-Pink-Eye	P	Normal pigment is produced.
	Pink-Eyed Dilute	p	The presence of pp causes an 80% reduction in the amount of black pigment produced, with little effect on red. The reduction of black pigment dilutes blacks to lilacs, and chocolates to beiges. The eye color is pink because the diminished black pigment allows the blood in the eye to show through. Reds and creams carrying pp are REQ and RE Creams respectively.
	Grey Pink-Eyed Dilute	p^g	The presence of p^gp^g causes an ~50% reduction in the amount of black pigment produced, with little effect on red. This allele is responsible the slate color in the Blue Tan variety
ROAN	Roan	Rn	Show Roans are Rnrn. Homozygous RnRn animals are all white, ruby blue eyes, and frequently deformities. This gene is responsible for both the Roan and Dalmatian varieties depending on which pattern modifying genes are present
	Non-Roan	rn	Non-roaned animals are rnrn
WHITE SPOTTING	White Spotting	s	Animals with ss usually have over 50% white. Animals with Ss are usually less than 50% white
	Non Spotted	S	Animals that are SS are not usually spotted. On occasion, they will have white toes or a white blaze.
DILUTE	Full Color	D	Normal Pigment produced
	Dilute	d	Pigment diluted. This gene has been recently been discovered/rediscovered in Denmark and is being worked with extensively in Scandinavia and the UK. Even more recently the gene has been imported into the US. It is analogous to D in rabbits and produces a color similar to the blue in Dutch rabbits. While there are skeptics that the locus exists, the preponderance of data gathered thus far supports its existence

These genes, and those of another locus, the C locus, interact as the major factors that produce the color varieties that are in the show standard. We should emphasize that there are many unknown, or uninvestigated modifiers which can cause an animal to be close to the show standard while another animal of the same basic genotype without the modifiers might be pet stock.

The C locus is quite complex because there are five possible alleles. To make matters worse, there is no simple dominance. There are a number of different heterozygotes of lower C alleles that have the same phenotype. Below is a table that shows basically what effect the different C alleles have on black and red pigment production.

Allele	Symbol	Red	Black	Eye color
Full Color	C	++++	+++++	Dark
Dark Dilute	c^k	++	++++	Dark
Light Dilute	c^d	+++	+++	Dark
Ruby—Eyed Dilute	c^r	-		Dark with ruby cast
Albino/Himalayan	c^a (also commonly called c^h)	-	++ (on points only, in presence of E or e^P^)	Pink

The alleles of the C series interact in sometimes strange ways. Below is a table of the relative amount of red and black pigment (percent relative to full color) produced by the various combinations of C alleles in the absence of other modifiers. (extracted from Searle, 1964)

GENOTYPES
PIGMENT	c^ac^a	c^rc^a	c^rc^r	c^dc^a	c^dc^r	c^dc^d	c^kc^a	c^kc^r	c^kc^d	c^kc^k	C_
Red	0	0	0	30	30	40	30	30	40	35	100
Black	20	40	80	35	70	60	80	90	90	95	100

The genotypes we have listed are our best guess of the desired show genotypes based on extensive reading, 40+ years of breeding experience, and lengthy conversations with other knowledgeable breeders. They are by no means the only possible genotypes to achieve the desired show phenotypes. As we have said before, unknown or unstudied modifiers can have tremendous influence on an animal’s appearance.

For convenience we have grouped the varieties genetically rather than by the Standard of Perfection (SOP). The Solid varieties of the SOP have been moved to Agouti or marked, depending on their genetic affinities.

SELF COLORS

The Standard lists nine self colors. All the other varieties are made up of some combination of these. In the chart below we have listed only the important loci for each variety. The notation c^x indicates an unspecified lower C allele.

Variety	Genotype	Comments
Black	aa EE BB SS CC PP	C produces the darkest color, unknown modifiers strengthen the under color
Chocolate	aa EE bb SS CC PP	bb converts black to chocolate
Lilac	aa EE BB SS c^xc^x pp	pp dilutes black in eye and coat
Beige	aa EE bb SS c^xc^x pp	pp dilutes chocolate in eye and coat
Red	ee bb SS CC PP	bb tends to produce proper ear and foot pad color, C produces most intense top color, unknown modifiers influence undercolor
Red-Eyed Orange	ee bb SS c^xc^x pp	lower C allele desirable for orange color
Cream (Dark-eyed) Cream (Pink-eyed)	ee bb SS c^xcx PP ee bb SS c^xc^x pp	The presence of pp converts Dark-eyed to Pink-eyed Cream. The best color is produced by one of these genotypes c^dc^a, c^kc^a. c^dc^r. Creams with the genotype c^kc^k & c^dc^k are usually dark or “hot creams”.
Gold (Dark-eyed) Gold (Pink-eyed)	ee bb SS c^dc^d PP ee bb SS c^dc^d pp	c^dc^d produces the correct gold shading. In Europe, DE Golds are called Buff and PE Golds are called Saffrons
White	ee c^a c^a	ee produces clear points
Danish Blue (unrecognized color under development)	aa EE BB SS CC PP dd	dd converts Black to Danish Blue, a color simolar to blue in rabbits.

AGOUTI VARIETIES

All agouti varieties must carry E to express the tipped agouti hairs throughout the coat. Animals with the genotype e^pe^p or e^pe will have spots of agouti color. There are two basic agouti colors, Golden and Silver. There are Solid Goldens and Solid Silvers as well. Below are the genotypes

Variety	Genotype	Comments
Golden Agouti	AA EE BB SS CC	the basic agouti color and the genotype of wild cavies
Silver Agouti	AA EE BB SS c^rc^r	c^r eliminates the red color leaving a white tip. It also dilutes the black base color to silver
Solid Golden	A^rA^r EE BB SS CC	A^r causes the narrow tipped belly hair
Solid Silver	A^rA^r EE BB SS c^rc^r	c^r eliminates the red color leaving a white tip. It also dilutes the black base color to silver. . A^r causes the narrow tipped belly hair.
Dilute Agouti		These animals have any of the diluting factors (pp,c^x,bb) which act on black or red pigment. Note: the combination of tip and base color must appear in the SOP to be showable

MARKED VARIETIES

There are several genetically related sets of varieties in this group. An Examination of the chart below will point them out.

MARKED VARITIES

Variety	Genotyp~	Comments
Himalayan	c^ac^a EE BB PP EE.	EE and SS are required to insure a complete set of points. BB and PP improve point intensity. e^p_, Ss or ss will often result in missing points.
Tortoise/Brindle	e^p_ BB PP SS	Unknown modifiers determine the distribution of patches. Animals that are e^pe have more red on the average than e^pe^p animals.
Tortoise Shell and White	e^p_ BB PP ss or Ss	The presence of s increases the clarity of patching. Animals with ss usually have more white than Ss animals.
Broken Color (with White)	Any color and sS or ss	Animals with ss usually have more white than Ss animals.
Dutch	Any Color with Ss	Dutch pattern is not fixed by a known locus. There are unknown modifiers that increase the tendency toward getting the patches in the right place
Broken Color (2 colors no White, or 3 Colors)	e^p with A_ or bb,or pp, (s)	These are basically modified Tortoise Shells that carry genes that modify the black or red. White is added by s
Roan	Rnrn with any color	Amount of roaning and pattern controlled by modifiers. Heads are usually not roaned
Dalmation	Rnrn with any self color	Amount and clarity of spotting controlled by modifiers.
Tan - Black Tan - Blue Tan Chocolate Tan - Lilac Tan - Beige	a^ta^t EE BB SS CC PP a^ta^t EE BB SS c^xc^x p^gp^g a^ta^t EE bb SS CC PP a^ta^t EE BB SS c^xc^x pp a^ta^t EE bb SS c^xc^x pp	a^ta^tconverts the corresponding self variety to tan.
Marten - Black Marten - Blue Marten Chocolate Marten - Lilac Marten - Beige	a^ta^t EE BB SS c^rc^r PP a^ta^t EE BB SS c^rc^r p^gp^g a^ta^t EE bb SS c^rc^r PP a^ta^t EE BB SS c^rc^r pp a^ta^t EE bb SS c^rc^r pp	a^ta^tand c^rc^r converts the corresponding self variety to Marten. If the aninal is c^rc^h instead ofc^rc^r the anmals will have the silver markings of a Marten but the body color will be shaded rather than the called for even color.
Otter - Black Otter - Blue Otter Chocolate Otter - Lilac Otter - Beige (group under development)	a^ta^t EE BB SS c^rc^r PP a^ta^t EE BB SS c^rc^r p^gp^g a^ta^t EE bb SS c^rc^r PP a^ta^t EE BB SS c^rc^r pp a^ta^t EE bb SS c^rc^r pp	a^ta^tand c^dc^x(where c^x is c^h or c^r ) converts the corresponding self variety to Otter. If c^xis not c^h or c^r , the cream color of the Otter markings will not be correct
California (variety under development)	Kk with any color	The incompletely dominant gene K produces dark coloration on the nose, ears and feet against any color background. KK animals are much more heavily marked tha Kk animals and tend to have body smut. The current development standard calls markings produced by Kk

Sometimes you can produce a show phenotype with totally different genetics from the ones listed above, however, you can usually tell by analyzing the pedigrees or their offspring what is going on. An example from personal experience is a black and white broken color which had no white spotting gene in its genetic make up. This particular animal was c^rc^ae^pe. The c^rc^a converted the red pigment in a tortoise shell to white giving the appearance of a Black and White. I have seen some “pseudo roans” of the same genotype where the red brindling was converted to white. The moral of this story is that there is ALWAYS a reasonable genetic explanation to what you get. In addition, that explanation is almost never that a new mutation has occurred in your herd. While mutations do happen, they are so extremely rare that a better explanation can almost always be found in looking at new combinations of existing genes. Remember that recessive genes can lurk in the background for many generations and pop up only when you make the “right” mating. We had a case where we had to go back over a dozen generations in our pedigrees to locate the source of a recessive allele which suddenly popped out.

My goal has been to introduce you to the basics of cavy genetics. It is far from a complete treatment of the topic. I hope I have given you some basic tools and have whetted your appetite for more information. With the advent of the internet, it is becoming easier and easier to find many of the primary sources. Look especially for work by Sewell Wright who is the father of cavy genetics. With a working knowledge of genetics, good pedigrees and careful records of the pups your matings produce, you can figure out a great deal about the genetic make-up of your herd and be in a far better position to make the correct matings for the varieties you want to produce.