The Agouti Gene

Rabbit coat color is primarily determined by five genes.  Luckily, the denotations for the genes are easy to remember.  They are A, B, C, D, and E.  Thank goodness for small favors.  Unfortunately, it gets a little more complicated from here.  One complication is that there are a few other genes that may change the look of the coat, including the En/en gene discussed on another of my web pages.  Other genes that affect the coat coloring include the blue-eyed white gene and the Dutch marking gene.  But on this page, we will concentrate solely on the "a" gene, which is responsible for a rabbit being agouti, tan/marten/otter, or self. Before going further, let's brush up on our basic high school genetics.  Each parent donates one of a pair of each type of gene to its offspring.  The offspring have two of each gene; one from each parent.  Dominant genes are expressed (you can see the characteristics in the rabbit) and recessive genes are carried to be possibly passed on to offspring.  Each gene, regardless of its dominance or recessive quality, is passed on to roughly half of the offspring. Agouti, Otters/Martens, and Selfs The "a" gene comes in three forms:  "A," which is responsible for agouti rabbits; "at," which is responsible for otters, tans (rare) and martens; and "a," which is responsible for self colored rabbits.  The agouti rabbits include chestnut, opal, chinchilla and ermine, among others.  The "at" gene produces black otters, sable point martens, blue otters, and the like.  The most common four colors of Holland Lops are self colors (produced by the "a" gene).  They are black tortoiseshell (also referred to as "tortoiseshell" or just "tort"), blue tortoiseshell (likewise "blue tort"), black and blue. Varieties of the "A" Gene This gene in its dominant form, denoted as "A," is the agouti gene.  It is dominant to both the "at" and the "a" gene.  The agouti gene, or just "A" gene, is expressed no matter what combination it may be present in.  That is, you will have an agouti rabbit phenotype (phenotype is what you see expressed) whether the rabbit's genotype (genotype is what's genetically going on) is "A-A," "A-at" or "A-a." The second variety is the tan gene, denoted as "at."  The tan gene is responsible for making otters, tans, and martens.  I will use the terms "otter," "tan," and "marten" interchangeably on this page, since they all come from the "at" gene.  In Holland Lops, you see the otters and martens only occasionally since they are not currently showable (black, blue, chocolate and lilac otters are hopefully on their way to being showable).  Personally, I have never seen a tan otter.  Let me know if you have.  (Tans require two recessive wide band genes and an accumulation of rufus modifiers--sounds too complicated to me).  The "at" gene is recessive to the "A" (agouti) gene, but dominant to the "a" gene.  If there is even one "A" gene, you cannot have an otter or marten phenotype.  An otter or marten phenotype is either "at-at" (this can be referred to as a true breeding otter/marten) or "at-a." [By the way, "otters" are full color rabbits (C) with the "at" gene expressed and "martens" are chinchilla (chd), Himalayan (ch) or sable (chl) gene rabbits with the at gene expressed--that's how you will know to say "otter" or "marten" after the color, e.g., black otter or sable point marten.] The "a" form of this gene is recessive to both the "A" gene and the "at" gene.  Only one combination produces the self phenotype:  "a-a."  When you see a self rabbit (for example a black tortoiseshell), you also know the genotype for the "a" gene (a-a).  A self colored rabbit cannot carry an agouti (A) or tan gene (at).  If it did, the agouti or tan gene would express itself and the rabbit would not be a self.   What Happens When You Breed a . . . Now we get to the fun part:  what happens when you breed one rabbit to another.  Knowing what two rabbits' genotypes are (or even just their phenotypes, in some cases) can tell you what the possibilities are for their offspring.  Likewise, looking at offspring (and determining as much of their genotype as possible) can tell you about the unexpressed, or recessive genes, of the parents. Since it does not matter which parent has which set of a genes, there are 21 possible combinations of A/at/a genes in parent rabbits (there are 36 combinations, but 15 of them are duplicates; that is, an "at-a" father to an "a-a" mother has the same outcome as an "a-a"  father to an "at-a" mother).  Fifteen of those combinations involve the agouti gene.  If you have no agouti animals in your barn, your "A/at/a" gene possibilities are much more limited.  Likewise, 14 of the combinations involve the "at" gene.  If you do not have the "at" gene in your barn, you will have fewer possibilities to consider.  If you have only self rabbits, you'll never get anything but self rabbits. Let's just pick one combination as an example to look at so that we can understand the possible outcomes in the offspring.  Suppose you breed an agouti rabbit (let's just say a chestnut) who carries the self gene with an otter who carries the self gene.  The chestnut is "A-a" while the blue otter is "at-a," in this case (other times a chestnut may be "A-A" or "A-at" and the blue otter could have been "at-at").  You can see that, on the average, 50% of the offspring will be agouti rabbits, 25% will be selfs and 25% will be otters or martens (depending on the C gene).

A-a x at-a		Blue Otter
		at Gene	a Gene
Chestnut	A Gene	A-at Agouti carrying otter/marten	A-a Agouti carrying self
	a Gene	at-a Otter/Marten carrying self	a-a Self

Since otters are hopefully on their way to being showable, let's now look at what happens when you breed an otter that carries the self gene with another otter that carries the self gene.  On the average, out of every four babies, you could expect three to be otters and one to be a self.  Two of those otters would carry the self gene while one of them would be a true-breeding otter.

at-a x at-a		Black Otter
		at Gene	a Gene
Black Otter	at Gene	at-at True Breeding Otter	at-a Otter/Marten Carrying Self
	a Gene	at-a Otter/Marten Carrying Self	a-a Self

Please note that the self rabbits produced from two such otter parents do not carry the "at" gene.  Self colored rabbits (black tortoiseshell, blue tortoiseshell, black, blue, chocolate, lilac, etc.) cannot carry either the otter gene or the agouti gene.  If a rabbit has the agouti gene, it will be expressed.  If a rabbit carries the otter gene, the self gene will be hidden under it (not vice versa).  Thus, a black rabbit cannot "carry" the otter gene. Since there are so many combinations of "A/at/a" genes when breeding rabbits, I won't attempt to make a complete table for each one.  But below you will see the possible combinations and the expected outcomes for each.  (Remember, these are averages--your exact results will vary, except when the percentage is 100., of course.)

Parent 1 4 Parent 2 6	A-A	A-at	A-a	at-at	at-a	a-a
A-A	100 % A-A					Key
A-at	50% A-A 50% A-at	25% A-A 50% A-at 25% at-at				Agouti A-A, A-at, A-a Otter/Marten at-at, at-a Self a-a
A-a	50% A-A 50% A-a	25% A-A 25% A-at 25% A-a 25% at-a	25% A-A 50% A-a 25% a-a
at-at	100% A-at	50% A-at 50% at-at	50% A-at 50% at-a	100% at-at
at-a	50% A-at 50 % A-a	25% A-at 25% A-a 25% at-at 25% at-a	25% A-at 25% A-a 25% at-a 25% a-a	50% at-at 50% at-a	25% at-at 50% at-a 25% a-a
a-a	100% A-a	50% A-a 50% at-a	50% A-a 50% a-a	100% at-a	50% at-a 50% a-a	100% a-a
Parent 2 5 Parent 1 4	A-A	A-at	A-a	at-at	at-a	a-a

So What Does This All Mean to My Breeding Program? Many phenotypes are easy to detect just by looking at the rabbit.  Some are a bit more tricky.  Knowing what the choices are from the parents' phenotypes (or better yet, genotypes, if you know them), can help you figure out what color an animal actually is.  It can be difficult to tell the difference, for example, between a broken orange (which is an agouti color), a broken orange otter (sometimes referred to as a tort otter) and a broken black tortoiseshell (tort, a self color) that has brighter fur.  Broken Orange, an agouti color. Picture Courtesy of Mary Justice. Broken Orange (or Tort) Otter.  Picture Courtesy of Mary Justice. Broken black tortoiseshell.   If you determine that both parents are self colors, then you know that the rabbit is a broken black tortoiseshell who just happens to have a brighter color of fur.  If the parents are agouti or otter, you must consider the other options.  To determine the true color, in this case, test-breed the questionable colored rabbit to a black rabbit (the best choice is a true breeding black, who is aa BB CC DD EE).  If the rabbit produces chestnut babies, it is an orange (the"A" is needed to make chestnut).  If it produces a black otter, it is an orange otter and if neither is produced (with a sufficient number of offspring to account for chance), then the rabbit is a broken black tortoiseshell (tort).  There's no way to confuse a chestnut with a black or black otter.  Photo courtesy of Mary Justice. The black otter is distinctive from the black and chestnut.  If a black otter is born of the test-breeding, the "at" gene is present. A resulting black isn't proof conclusive, but repeated litters with only selfs is a convincing argument that the test-bred rabbit is a self. Other colors are difficult to determine as well, such as the difference between a sable point and a sable point marten (the rabbit on the left is a sable point marten, the rabbit on the right is a sable point).  Again, if both parents were self, the rabbit would be sable point.  If either parent was agouti or otter, then the rabbit could be a marten.  A test breeding could help you make a determination in this case as well. Another great use for understanding the a gene is in the development of otters.  I am particularly fond of black otters and hope to devote some space to their development in the not-too-distant future.  Because otters are rarer in Holland Lops (they were culled out as non-showable for years--now we want them back!), your first otter may very well be an otter carrying self ("A-a").  Your first goal would be to produce true breeding otters, that is, otters that have two at genes (at-at) and the correct pairs of the other color genes for the color you are attempting, of course.  You can tell from the chart a few paragraphs above that you cannot produce a true-breeding otter from an otter and a self.  You can get some true-breeding otters, though, from breeding two self-carrying otters (at-a).  But, only 25% of your offspring from two self-carrying otters will be true-breeding otters.  Twenty-five percent won't be otters at all, and that's easy to determine.  But of the otters, you will not be able to tell by looking at them which are the true breeding otters.  By watching their offspring, however, you will be able to tell whether they are true-breeding or not.  If an otter ever produces even one self baby, it is not true breeding.  (You can go to the chart and follow the "at-at" line across or the column down and you will not find one single "a-a" offspring.) In case it is not apparent, let me specifically state that the advantage to having true breeding otters when you are developing an otter line is that you will more reliably produce otters.  You will need the greater numbers of otters to work with in improving their conformity to the standards.  Usually this improvement is done by breeding true-to-type black tortoiseshell back into your otter line (which are a-a, of course).  If you try to work with self-carrying otters, only half of your resulting offspring would be otter (on the average).  I recently had a litter like that with five kits and got no otters at all--how frustrating!  Had I a true-breeding otter, all of the kits would have been otters (100% at-a). Let me know other ways that using your knowledge of the agouti gene is useful in your breeding program.  I love to share useful information with others . Color Families Rabbit colors can be grouped many ways.  Although "color families" is not an official term that I know of, on this page I'd like to use it to group together rabbit colors that vary only in the A/at/a gene.  By way of example, let's look at the most prevalent Holland Lop color, the black tortoiseshell.  It's genotype (with ? for unknown genes) is aa B? C? D? ee.  If we change only the a gene to "A," we get A? B? C? D? ee which is an orange rabbit.  If we change the gene again, this time to "at," we get at B? C? D? ee, which is an orange otter (sometimes called tort otter--and now you see why).  So let's put black tortoiseshell, orange and orange otter together in a family.  The table below lists some other useful color families for the Holland Lop.

Agouti

Tan/Otter/ Marten

Self

Orange	Orange Otter	Black Tortoiseshell
Fawn	Fawn Otter	Blue Tortoiseshell
Chestnut Agouti	Black Otter	Black
Opal	Blue Otter	Blue
Chinchilla	Black Silver Marten	Sable (self chin)
Lynx	Lilac Otter	Lilac

The goal for understanding any of the color genes is the same:  to know what you've got and be able to produce the colors you want.  Although there are no points for color in the Holland Lop standard, the rabbit must be a showable color.  But aside from that, color is just plain fun.  I hope that this information on the agouti gene has been helpful.  As always, if you have a question about the agouti gene, please do not hesitate to contact me.  I'd love to answer your question or research the answer and learn along with you.