Rat Health Care & Information
Rat genetics is a massive and potentially scary subject. What my article below
will attempt to do is simplify information relating to rat colour genetics and
specific varieties. Most rat colour genetics are simply based on Mendelian
Genetics, which is pretty much the standard genetics that most would learn in
secondary school biology classes and aside from giving a little glossary to
explain some of the key words used in genetics, I am not planning on going into
any depth on the biology of genetics. There are many articles and books that
explain Mendelian Genetics and if you would like further information I can
highly recommend having a look at some of these links: -
Mendelian Genetics links
Useful Genetic and Breeding Definitions
One of the easiest ways to calculate predictions is using punnet squares. You have to remember that each gene pairing is inherited independently of other genes and each baby randomly inherits one gene from each parent.
For a single gene pairing, draw a table with 9 squares, leave the top left corner black and along the top row and down the left column, put in the parents genotype with one gene per space. In the remaining 4 squares, take the genotype from the left column and the genotype from the top row and add them together. This gives the available genotypes of the offspring. From this information, you can calculate the phenotypes. Note that the percentages/ratios listed are theoretical if the offspring followed exact genetic calculations.
I've used the A - agouti locus to demonstrate. All the possibly variations are shown below.
Dominant non-carrier (agouti = A/A) x recessive (black = a/a). All the resultant offspring would be A/a = agouti carrying non-agouti.
Dominant carrier (agouti = A/a) x recessive (black - a/a). 50% of the offspring will be A/a = agouti carrying non-agouti and 50% will be a/a - black.
Recessive (black - a/a) x recessive (black - a/a). All of the resultant offspring will be a/a = black.
Dominant carrier (agouti - A/a) x Dominant carrier (agouti - A/a). Genotype - 25% of the offspring will be dominant non-carrier A/A = agouti, 50% will be dominant carrier A/a = agouti and 25% will be recessive a/a = black. The phenotype would be 3:1 agouti:black as you would not be able to tell visually which agoutis were carriers and which were non-carriers.
Dominant non-carrier (agouti - A/A) x Dominant carrier (agouti - A/a). All the resultant offspring would be agouti phenotype with a genotype of 50% carriers and 50% non carriers.
The above show the simplest form of punnet square for one gene. The below shows a punnet square for 2 genes where both parents are dominant carriers of two genes, the two genes being non-agouti (A/a) and British blue (D/d). You need a 5 x 5 punnet square for this one.
The ratio of phenotypes agouti : black : British blue agouti : British blue is 9:3:3:1 and out of the agoutis and blacks you would not know which are carrying British blue and which are not.
Hopefully the above gives the gist of things. You can do this including as many genes as you like, just add more squares to cover the extra genes.
Coat Colour Genes
Below are a list of the main loci designated in the rat fancy by geneticists. There are many others used by rat breeders that are not officially designated that you may see on websites and in circulation. I will discuss the ones commonly used in the UK later in this article when discussing the varieties. (where /- is used in genetic notation, it doesn't matter whether the gene is in its dominant or recessive state - i.e. A/- can be A/A or A/a and give the same resulting phenotype.)
A - Agouti locus - controls the distribution of yellow pigment through the coat.
A/- = banded hairs (agouti based), a = solid hairs (non-agouti = black).
B - Brown locus - determines whether the eumelanin pigment is black or brown.
B/- = black, b/b = chocolate. It can be combined with agouti to give chocolate agouti A/- b/b.
C - Albino locus - causes the dilution of both yellow and black pigments in the coat. There are 3 known alleles on this locus for rats, but the suspicion is there may be more as yet unconfirmed. ch either combined as chch or chc causes yellow pigment to disappear, and dilutes black pigment to a warm brown or to disappear from most of the body. It also causes the Siamese/Himalayan pattern because the colour of this animal’s fur is determined by the temperature - called acromelanism - the cooler it is, the darker the fur grows; therefore, the extremities (ears, nose, feet, and tail) are dark, and the rest of the body is light.
Certain aspects of the C locus are currently 'work in progress' as it is unclear as to how Burmese and black eyed Siamese/Himalayan/Ivory/Cream/Golden Himalayan fits into the equation. It is suspected that both black eye and Burmese are on a separate locus and behave similarly to the way the pearl locus does to the mink locus.
C/- = full colour, ch/ch = Siamese, ch/c = Himalayan, c = albino (pink eyed white). Combined with agouti only gives a slight difference to extremely dark Siamese on the body in that it will cause a demarcation line down the side. Combining Himalayan/Siamese with any other genes (including agouti) will lighten and change the point colouring and shading on the Siamese.
D - Dilute locus - dilutes the black pigment to a blue/grey colour. This gene has been scientifically notated as British blue, which is also proven as the same gene as American blue, slate blue, powder blue and many other terminologies. No other mutations on this locus are confirmed and the variety of shades of blue are suspected to be down to other modifying or carried genes and selection.
D/- = black, d/d = dilute colour (British blue). It can be combined with agouti to give British blue agouti A/- d/d.
M - mink locus - dilutes to a greyish-brown colour that is distinctively different from chocolate and like the dilute locus can be a variety of shades down to modifying or carried genes and selection. This is another gene with some confusion attached to it as down to imports of USA line 'minks' to the UK, it has been proven that the similar coloured USA mink is not the same gene as the UK mink, although both act in the same way with the pearl gene.
M/- = black, m/m = mink. It can be combined with agouti to give cinnamon A/- m/m
Pe - Pearl locus - this locus only affects mink (and USA mink) rats. It causes each hair to be white with only the tip being coloured. Pearl is semi-dominant in that it is dominant over the mink locus, but in a non-mink rat shows no effect. Homozygous pearl is lethal which means that Pe/Pe kittens will be either reabsorbed in the womb or very occasionally die soon after birth.
M/- Pe/pe or M/- pe/pe = black, m/m Pe/pe = pearl. It can be combined with agouti to give cinnamon pearl A/- m/m Pe/pe. Note that Pe/Pe is lethal in utero so is not viable.
P - pink eye dilute locus - heavily dilutes the black pigment to a very pale creamy colour and also dilutes the eye colour to red. The agouti based version is a pale creamy orange colour.
P/- = black, p/p = champagne (also known as cream in some countries). It can be combined with agouti to give silver fawn A/- p/p (also known as argente, orange or amber in some countries)
R - red eye dilute locus - similar in effect to the p locus, but not quite as intense. It dilutes the eyes to dark ruby (the term red eye dilute is a bit misleading) and dilutes the black pigment to a slightly darker shade than that of the p locus. The agouti based version is a slightly darker version of the p locus version.
R/- = black, although this can seem to be slightly dulled to a dark chocolate, r/r = buff (also known as beige in some countries). It can be combined with agouti to give topaz A/- r/r (also known as fawn in some countries)
Coat Colour Genes Not Scientifically Described
Silvers - There is no separate gene for silvering, but all rats carry an amount of silvering to some degree. Silvers are selectively bred by breeding two rats together which display a larger amount of silvering and repeating the process to achieve a distinctive effect. The colours which display this silvering well are generally Blacks (often known as Silver Greys) and Chocolates.
RB - Russian blue - dilutes black pigment to a metallic heathered blue/grey. The most distinctive trait on all Russian based varieties is the heathering in the coat. Russian blue has not been scientifically described and in some countries it has become fashionable to use the symbol "d" which is scientifically described as the British blue colour so does cause confusion. For ease of understanding Russian blue is commonly referred to as 'rb' in the fancy.
RB/- = black, rb/rb = Russian blue. It can be combined with agouti to give Russian blue agouti A/- rb/rb.
M1 or MO - USA mink - also sometimes referred to as 'mock mink'. This gene seems to act in the same way with the pearl locus as the scientifically described mink gene in the UK, but on test matings with UK minks produced black, proving that these two genes are different. The USA mink tends to be a redder colour than the UK mink and the eye colour is often (but not always) diluted to ruby. Like mink, this gene can be a variety of shades down to modifying or carried genes and selection and also seems to play a part in the genetic makeup of the platinum variety. Combined with UK mink to make a double mink (m/m m1/m1), it gives a greyish colour similar to Russian dove but without the heathering. Further test matings are required to understand this gene fully.
M1/- black, m1/m1 = USA mink. It can be combined with agouti to give cinnamon A/- m1/m1
Be - Black Eyed - still work in progress - see my Black Eyed article for current thoughts.
Bu - Burmese - still work in progress - see my Burmese article for current thoughts.
Cream - still work in progress - see my Black Eyed article for current thoughts.
Golden Himalayan - still work in progress - see my Golden Himalayan article for current thoughts.
Colour Variety Genotypes
Note that carrying genes can change the shade of the variety and is sometimes necessary to 'fit the standard'. A number of these varieties are not UK show varieties and do not have classes at a show. Some are rarely produced because the more recessive the genes it has, the less probability you have of breeding one. Often the variety is not that different from existing varieties, for example a Chocolate Agouti looks very much like a standard Agouti but has a darker top coat and a more muddy appearance.
The last two columns cover any genes that are not scientifically notated.
Agouti group rats (A/-)
I have highlighted the loci which have changed from the Agouti rat.
Non-agouti group rats (aa)
I have highlighted the loci which have changed from the black rat
The albino c locus group rats
Aside from the varieties listed as standards the other genotypes are displayed as ‘any’ because these varieties can contain any of the colours listed above. An Albino rat can be any colour or marking but is displayed as a white animal with pink eyes due to its lack of pigment. This is important to remember when breeding as results can be unexpected and any colour or variety may be produced. The only varieties it cannot carry is Siamese or Himalayan. Both Siamese and Himalayan can be produced in other colours, but because most rat colours are variants of brown it is hard to see the difference. I have included Russian and British blue based Himalayan and Siamese as these do have standards and it shows the specifics of breeding a colour point onto a variety - i.e. if you were trying to breed any other pointed variety you would specify that gene and no others.
The Burmese and Black Eyed Siamese is as yet unproven scientifically so the information below may be subject to change, but it is based on a number of experienced breeders findings to date. (I have not included Golden Himalayan or cream as they are very much work in progress and not enough information available.)
Re - Rex - the rex gene is one of the few dominant genes in rats and causes the effect of a curly coat. The dominance means only one parent needs to be a rex for approximately 50% of the offspring to be rex. The curliness of the coat is mostly by selection, but other coat genes can reduce the rexiness of the coat. Two copies of the rex gene gives 'double rex' which can phenotypically look like anything from rex to hairless.
Re/re = rex, re/re = normal coat, Re/Re = double rex.
Body & Coat Genes Not Scientifically Described
DU - dumbo - this gene has the effect of the ears being lower set on the side of the head rather than on top. No other physical changes are made to the rat and this has been proven by comparing x-rays. It is a straight forward recessive gene so 2 copies are needed to be dumbo.
du/du - dumbo ears, DU/- = normal location of ears on top of the head.
Dwarf - there are several genes described in science that give dwarfing (all of which are recessive) and some of these are associated with health and fertility problems, but several breeders within the fancy have managed to breed them with no problems. The dwarf genes have the effect of the rat being considerably smaller in size, roughly reaching half the size of normal adult rats. (I am not aware of any breeders with dwarf rats in the UK)
Tailless/Manx - tailless does not appear to be a simple recessive, but may be either polygenetic or possibly requiring more than one gene to express. Some lines of tailless rats have had spinal deformities and often the does are infertile or have birthing problems, so in some countries (including the UK) the tailless variety does not have a variety standard and is banned from shows because of health reasons.
Velveteen - this is often given the genetic code of Cu and is a dominant gene, although there has been suggestions that the velveteen rex/wavy coat is just a poor quality badly selected for rex or possibly that Cu is a remutation of the Re rex gene. Velveteen is also known as 'wavy' or 'teddy rex'.
Velvet - the velvet coat is a extremely soft and 'plush' short coat and the inheritance of this coat type of this are unclear. It is probably polygenetic, but to date has most commonly been seen on the Russian blue variety in the UK. The noticeable difference about this coat type is when your stroke the coat against the direction of the coat, it feels extremely soft.
Satin - there seems to be several satinisation genes around that give the coat an intensive sheen. The coat has a real sparkle look on some colour varieties and will intensify many varieties colour as well. It is know there a satin gene that is a dominant and has been found in the UK, but also the 'greasy as kittens' looking satins more commonly seen in the USA are a recessive gene.
Hairless - there are a number of genes that produce visually 'bald' rats, including some 'double rex' as detailed above, but the rest of the 'hairless' genes are recessive. Hairless rats do usually have a thin coat of hair and some have more hair than others (and the more hair, the healthier they seem to be) plus it seems to vary whether they have eyelashes or much in the way of whiskers, but most have extremely tightly curled whiskers. Some hairless genes do have health problems, including 'nude' (Whn) that has no functioning thymus and hence immunodeficiency, 'shorn' (shn) that develop abnormal hearts and kidneys and die prematurely, 'fuzzy' (fz) which suffer kidney nephrosis and die prematurely and 'hairless' (hr) which is believed to be the main gene within the fancy. Some 'fancy' lines of hairless do have lactation problems and many fanciers have general concerns about health and welfare issues with breeding them so in some countries (including the UK) there is no variety standard and hairless rats are banned from shows.
Fuzz - aside from the knowledge that this is a recessive gene, little is known about the 'peach fuzz' rats and they appear to have disappeared within the UK. The coat of the fuzz is very short all over, a bit like having been shaved with a 'no 1' cut all over.
Harley - the harley rat appears to be a longhaired rat. Aside from proving that at least one of the gene(s) required to reproduce the variety is recessive, little seems to be known still about this variety. There is speculation that it may be a combination of the recessive satin gene and possibly either the dominant rex or velveteen gene. At the time of writing, harley is still relatively new and only available in a few countries and no doubt test matings will confirm in time whether this is a combination of known genes or something new.
Recessive rex - this is possibly the recessive wv (wavy) gene and can be visually hard to distinguish from the dominant rex gene. The wv gene was first reported in 1981 and studied by both Robinson and Greaves. It is not allelic to the dominant rex gene and according to their studies when the Re and wv genes are combined it produces rats with extremely sparse and downy coats. Recessive rex recently re-emerged in the UK, but unfortunately test matings were not completed to confirm the above.
Any breeding program requires a bit of knowledge of at least basic inheritance of genes, but working with marked genes requires a greater understanding and knowledge of genetics and also lineage. Marking genes are so heavily influenced by polygenes, incomplete dominance and outside factors such as even crossing different marked lines makes accurate predictions almost impossible and one genotype can look almost identical to another with a completely different genetic make up.
There is also the issue with the use of 'mismarked' in marked rats - for example a Berkshire can have a varying amount of white marking on the belly to fit the standards and the term 'mismarked Berkshire' is used for pretty much anything between a too wide hooded and a too big irish marking, but a hooded breeder would probably see an overwide stripe as a 'mismarked hooded' while an irish breeder, would see a too big irish marking as a 'mismarked irish'. In some countries, their fancy has tried to come up with names for all these mismarks and inbetween markings, but the genotypes are often very different and you need to know the lineage to describe them accurately.
With marked breeding, one of the considerations is the close relation of the pigment genes to the genes that control the central nervous system. During embryonic development the cells that produce skin pigment are in close proximity to the ones that form the central nervous system. A mutation that prevents pigment attachment (which is how white markings are formed) sometimes also causes changes in the nervous system. This is what causes megacolon/megacecum in rats and also deafness in some lines of white rats and the mutations are usually related to the facial markings. It also needs to be made clear that pigment does not always cause problems in the nervous system, and white face markings aren't always linked to megacolon/deafness and even with those affected varieties, good breeders have successfully bred white spotted lines without health issues.
H - Hooded locus - in rats, most markings are created by mutations on the h locus. Marking genes are more complicated and do not follow the simple recessive and dominant rules, instead following incomplete dominance where the effects are almost 'blended'. They interact to produce different effects and some when homozygous can be lethal or when mixed with other white spotting genes causing problems like Megacolon. There are many opinions on what alleles actually exist on the h locus, but there does seem to be a few that are agreed on and pretty much proven: -
As you can see from below, each marking has several proven genotypes and can mock other varieties.
Downunder is relatively new to the fancy, but tests to date point to it to looking to be a heterozygous lethal and the gene has tentative been given hdu as its notation. It can be combined with H or h or other combinations of marked genes to give a variety of new patterns. The downunder marking leaves the main marking as is but adds a stripe (or a line of spots) across the belly. H/hdu gives a berkshire downunder and h/hdu gives a hooded downunder.
Roan/striped roan is not on the H locus, but the markings can be affected by H locus varieties. The gene causes fading to the colour which can in some paler colour varieties turn the rat completely white as it matures. It is thought to mostly be a simple recessive although it shows incomplete dominance in its heterozygous state. Striped roan appears to be roan with additional extra modifiers rather than a separate gene. What needs to be made clear is there is some confusion where the term husky/banded husky is used for these rats - the UK roan/striped roan is the same as what is often termed European husky/European banded husky, BUT is not the same as similar fading gene in the USA also referred to as husky (or sometimes roan). The USA husky/roan is often associated with megacolon, where the UK roan is not, although care needs to be taken when mixing with some of the extreme marked genes or chinchilla.
There are no official symbols applied to the roan gene, but many breeders are using ro. An Ro/Ro is the wild type and shows no change. Ro/ro gives small amounts of markings on the belly - often termed 'belly irish'. ro/ro gives roan and ro/ro + modifiers gives striped roan.
Chinchilla - ?
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Last modified: February 08, 2017