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September Skies
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Genetics Explained or: ~ What do those letters mean? ~
Genes are the basic instructions for how everything physical in our body is built. Most people have heard the examples of blue eyes and brown eyes, etc. In dealing with rat genetics of coat colour we are lucky, because it is relatively simple and predictable. In terms of rat psychology or health, understanding the genetics is much more complicated. A copy of all the genes (the DNA) is contained in every single cell in the body. When a male and female mate, their genes (in the gee and sperm) are combined, half from one parent and half from the other. Eggs and sperm are specially designed to carry only half of the genetic information of that individual. So why doesn't a child look exactly like half of one parent and half of the other?. Because it's seriously complicated! Each single gene (and there are millions of them in each strand of DNA) contains information that controls just a tiny piece of the resulting body. For example a gene may control how much red pigment is in the hair, and another may control how much brown pigment, and another may cause dilution of all red and brown pigment to blonde. Many genes counteract and interact with each other. I won't go into that here. As I said, the genes for coat colour in rats are relatively simple, thank goodness! Why do we want to know about coat colour genetics in rats? Because it's interesting, perhaps. But most likely because we want to breed our rats with at least an educated guess as to what colours the resulting rats will be. For example, I wanted to understand coat colour genetics because I was importing only five rats to start a rattery in Tasmania. It would seem logical that if you crossed a mink rat with an argente rat you should get some of each, but as you will see later, the result is likely to be a litter of all agouti babies. I needed to be thoughtful in choosing my rats, so that I could actually breed a range of colours. So, lets go on. In Australia there are ten main coat colours: Agouti, black, mink, cinnamon, argente, beige, silverfawn, champagne, dove and topaz. Overseas they have more possible colours, like blue and coffee. We are slowly finding more colours in Australia, but until the genetics of these colours are understood I will not include them here. With these colours, there are four main genes which control pigments (colours) in the fur. Each of these four genes is designated a letter, namely: A, M, R and P. How can four genes create such a range of colours? We will start There are always two copies of each gene, one from the mother an one from the father. These two copies of the gene can be the same, or different. For each gene there are two possibilities. For example, in the gene "A", the two possibilities are: 1 The hairs have banding (stripes) on them, and 2 the hairs have no banding. If they do, the basic colour is called Agouti (orange and black banding). If there is no banding, the basic colour is black. These two variations of the gene are are either dominant or recessive. What this means is that one gene, the dominant one, can over-ride the other gene (the recessive gene). This means that if the rat has both the dominant gene and the recessive gene in it's DNA, the dominant gene will over-ride the recessive gene, and the rat will display the appearance of the dominant gene. To refer this back to the "A" gene: Because there are two genes always present, we write it as : AA. Now, the dominant version of this genes is written with a capital letter, A, to show that it's bigger and stronger (only joking) than the recessive, which is written with a little letter, a. So, if a rat has two dominant genes, AA, it will show the dominant appearance, in this case Agouti. If it has one dominant and one recessive gene, Aa, it will show the dominant trait, because A is dominant, and over-rides (suppresses) the effect of the recessive gene, a. To show the recessive appearance (black) it must have two recessive genes, aa. For each of the four genes I mentioned earlier, there is a dominant and recessive gene. In the wild, rats are nearly always that brown agouti colour. To be any other colour is likely to attract attention. These different colours have cropped up by genetic mutations, which happen naturally in all living things. These changes in appearance of the coat colour are caused by recessive genes in Australia. What this means is that a rat has to have two recessive copies of a gene before it will show a change in coat colour. The natural colour, Agouti occurs when there is a dominant gene for each of the four colour genes. eg: AA, MM, RR, PP or Aa, Mm, Rr, Pp. As long as there is one dominant for each gene, the colour will be agouti. The recessive genes of these four genes are dilutions of the coat and eye colour. If there are two recessive genes for one letter, eg mm, the rat's coat colour will be diluted (lightened). Now on to what colours come from what genes... Now we've learned that each of the four genes, A, M, R and P, have two variations, a dominant one which causes no change in the coat, and a recessive one which (when there are two) causes dilution of the coat colour. It is the combination of these genes that causes the ten coat colours we have in Australia. I'll explain each gene first (the - next to a dominant gene shows that it doesn't matter what other gene is there, the result is a dominant appearance). A- or aa : The dominant (A) causes banding on the hairs. Two recessive genes (aa) causes no banding on the hairs. M- or mm : The dominant (M) causes no change in the coat. Two recessive genes (mm) causes dilution of the coat. R- or rr : The dominant (R) causes no change in coat colour. Two recessive genes (rr) causes dilution of the coat, and dilution of the eye colour to ruby (very dark red) P- or pp : The dominant (P) causes no change in coat or eye colour. Two Recessive genes (pp) causes dilution of the coat colour, and dilution of the eye colour to pink. Now, the combinations of these genes causes fairly logical results, which I will now explain in terms of coat colours. Agouti : A- M- R- P- : The dominant variations of all the colour genes are present, so the coat is banded in orange and black, and the colour is not diluted. the overall colour is warm brown flecked with black, and with black guard hairs. Black : aa M- R- P- : The only recessive genes present are aa, which means that the banding on the hairs will not show. This is called "solid" colouring, because the individual hairs are all one colour. Because the dominant genes of the dilution genes (M, P, R) are present, the colour is undiluted: black. Other colours are a combination of the mm, rr, and pp dilutions with these first two hair types. If the A agouti gene is present, the dilutions will occur in bands on the hairs, giving a fleckes appearance. If the aa non-agouti genes are present, the dilution will be in the whole hair, un-banded (the hair will be all one colour). This is called "solid" colouring. I will explain the effect of the dilution genes on both of these hair types. --------------------------------------------------------------- Cinnamon : A- mm R- P- : The hair type is agouti (banded), and the dilution genes of mm are present. This dilutes the coat to a warm, flecked, russet brown, with grey at the base of the hair. The coat is evenly ticked with dark brown guard hairs. Eyes are black. Mink : aa mm R- P- : The hair type is non-agouti (solid), and the dilution genes of mm are present. This dilutes the black to "mink", which is a soft, warm grey colour. Eyes are black. -------------------------------------------------------------- Argente : A- M- rr P- : The hair is agouti, and the dilution genes of rr are present. This dilutes the hair to a golden orange flecked with cream, with cream at the base of the hair and silver guard hairs. The eye colour is diluted to ruby (deep red). Beige : aa M- rr P- : The hair is non-agouti (solid), and the dilution genes rr are present. This dilutes the solid coat to beige - a pale, golden fawn. This colour is also called "buff". The eyes are diluted to ruby. --------------------------------------------------------------- Silverfawn : A- M- R- pp : The hair is agouti, and the dilution genes of pp are present. This dilutes the coat to a pale golden fawn, flecked with cream and with silver guard hairs. The eyes are diluted to pink. Champagne : aa M- R- pp : The hair is non-agouti (solid) , and the dilution genes of pp are present. This dilutes the solid coat to a very light creamy-beige colour. The eyes are diluted to pink. --------------------------------------------------------------- Now we get into the slightly more complicated colours, which are created by the combination of agouti/non-agouti with two or more dilution genes. Topaz : A- mm rr P- : The hair is agouti, and the dilution genes of mm and rr are present. This dilutes the agouti coat to a warm golden orange, with ginger guard hairs and a blue-grey undercoat. They eyes are diluted to ruby. Dove : aa mm rr P- : The hair is non-agouti (solid), and the dilution genes of mm and rr are present. This dilutes the solid coat to a pale, warm, dove grey. They eyes are diluted to ruby. --------------------------------------------------------------- I am not certain about what happens when all the diluting genes are present. And I don't know how we get pink eyed whites, sorry! Other colours reported to be found in Australia are cinnamon pearl, and blue, but I will wait for others to work out the genetics of these rats before I publish them here. I thought I'd try to explain the basics of crossing two colours here, but I don't know if it's going to be that basic. I'll try, anyway :) The best way I can find to explain it is by examples. Example one: I want to cross an agouti rat with a black rat. We will ignore the dilution genes for this example, to show the inheritance of just one gene variable, the gene A/a.
Agouti: AA Black: aa (We will assume for this example that the agouti parent carries AA, though there is always a possibility that an agouti rat is Aa. The black parent must always be aa, because otherwise the agouti A gene would dominate) So, here is a diagram, and the text below explains it:
It shows that the agouti parent is AA, and the black parent is aa. Each parent only gives one gene from its pair to the pup, because otherwise the pup would end up with four copies of the genes. When each parent gives one gene, it is always a fifty-fifty chance which gene it gives. In this case it doesn't matter, because each parent has two identical copies of the gene, so it only has one kind of gene to offer. One gene from each parent's pair is passed down to the pup, so that the pup end up with two genes. Because one parent can only give A, and the other only a, the pup must have the genotype (genetic make-up): Aa. You can hopefully see this in the picture. The outward appearance (phenotype) of this rat pup will be agouti, because A is dominant over a. But, this pup carries the recessive a gene, and so there is a possibility of it having black pups of its own. We'll see this in the next example. Example two: We want to cross two agouti pups from the above litter. Their genotypes are both Aa (of course, this is inbreeding, but for example's sake :) Each parent gives one gene from it's pair to the pup, and
its 50:50 which gene it gives (that is, there is an equal chance of it giving
either A or a). Another picture: Now, because each parent has two different copies of the gene, there are four different possible results when you cross these. The difficult way to work out the results is with arrows: (don't do it!)
The easiest way to calculate what you will end up with is to do what's called a "punnet square". I can really only show you how. Draw up a table (1):
Write in the two genes from the mum at the top (2), and then the two genes from the dad along the left (3). Then you work down and across each row and column, filling in the blank squares with the genes from the corresponding row and column. For example, in the first row the gene is A. And in the first column the gene is A, so the two genes in the top left blank square = AA. Here is this punnet square worked through, so you can see what I mean:
So, this punnet square shows us the four expected genotypes (genetic make-ups) of the offspring (babies) of this cross. These are: AA, Aa, aA, and aa. In fact, there are only three types here, because Aa and aA are exactly the same, just backwards. So, one quarter of the offspring will be AA, half of the offspring will be Aa, and one quarter will be aa. In terms of appearance (phenotype), these rat pups will be three quarters agouti (Aa and AA), and one quarter will be black (aa).
Aa Aa Aa aa -------------------------------------------------------------------------- Congratulations, you made it this far! It's really not as bad as it looks. I'm very interested to hear what you have to say about this example, I'd love to test it out on someone and see if they actually understood, but here I am at my end of the computer, and there you are at yours.... Maybe you could tell me how terrible ; ) it is through my comments page? I'd appreciate it :) -------------------------------------------------------------------------- Okay, so now lets carry these ideas over to a more complicated example. What happens when all the genes are involved? Example 3: We want to cross a cinnamon rat with a mink rat. I will assume that the genotypes are: mum: cinnamon - Aa mm RR PP dad: mink - aa mm RR PP Now, the only thing that is different between these rats is the
presence of the A agouti gene in the cinnamon rat. They both have double
recessive (mm) genes for the mink dilution. So, we know that all either of them can give
to their babies is little So it's the same as before. We draw up our punnet square, and
put the A/a genes from mum (Aa) along the top, and dad (aa) down the sides (1)
and fill in the blank squares with the corresponding two letters (2)
From this filled in punnet square, we can see the genotypes will be: Aa, Aa, aa, aa. ie: half will be Aa and half aa. The phenotypes (appearance) of these pups will be: 50% cinnamon, Aa mm RR PP 50% mink, aa mm RR PP Well done! -------------------------------------------------------------------------- Example 4: Alright, lets get a bit more complicated.... What about a mink mum with an argent dad? Lets say their genotypes are:
Mink: aa mm RR PP Argente: AA MM rr PP The only thing these two rats have that's the same is PP, so we'll ignore that, knowing that their children must all be PP. But we'll have to draw up punnet squares for three genes: A, M and R. Starting with the agouti genes A/a: Draw your punnet square and fill, in the parents details, one along the top and one down the left side (1). Then fill in the blank squares with the corresponding letters from each row and column (2).
From this worked punnet square, we can see that the genotypes for all four outcomes are the same, Aa. Now, we write this down and put it aside for a moment, while we work out the other genes. For M/m: Write up your punnet square (1) and fill in the blanks (2).
Again, the results are four of the same thing: Mm. And for the last gene, R/r. Write up the square (1) and fill it in (2).
And, no surprise, the results are four of the same, Rr. Do you understand why this is happening? When both parents have the opposite pairs of genes, (eg one has AA and the other aa) then then the only possible result is one of each gene for the babies (Aa). The resulting genotype of this is: Aa Mm Rr PP and the resulting phenotype is Agouti, because there are no pairs of recessive genes present, so all the dominant genes over-ride the recessive genes, and you get agouti colouring.
Agouti: Aa Mm Rr PP...... -------------------------------------------------------------------------- Lets work out one where we have a chance of some interesting colours! Example 5: A dove rat crossed with one of the agouti babies from above.
Dove: aa mm rr PP Agouti: Aa Mm Rr PP The pink eyed genes are all the same, so we'll leave these out of our calculations. The other genes however, are all different, so lets do it: A/a: draw up your punnet square, with mum along the top and dad down the left (1) (it makes no difference which goes where) . Fill in the blank squares with the corresponding row and column letters (2).
You can see there are two different results here: Aa and aa. Let's keep this aside and do the next one, M/m. Draw up the square (1) and fill it in(2).
Again, there are two different results from this square, Mm and mm. Now, let's do the last one, then we can put our results together. R/r: draw your punnet square (1) and fill in the blanks (2).
And again, there are two different results: Rr and rr. Now, how do we put this together? The results written out again are: Aa or aa, Mm or mm, Rr or rr. You have to manually write out all the possibilities here. It's easiest to do it methodically, changing one at a time, beginning with the agouti type (Aa) colours: Aa Mm Rr Aa Mm rr Aa mm Rr Aa mm rr then the non agouti type (aa) colours: aa Mm Rr aa Mm rr aa mm Rr aa mm rr As you can see, just to make it interesting I've picked one of the most complicated crosses to work out, because I have faith in your new-found genetics-calculation abilities! So what do all these genotypes mean, in terms of the appearance of the baby rats? I'll write them out again, and put the pictures in this time: Aa Mm Rr Agouti
Aa Mm rr Argente
Aa mm Rr Cinnamon
Aa mm rr Topaz
then the non agouti (aa) colours: aa Mm Rr Black
aa Mm rr beige
aa mm Rr mink
aa mm rr dove
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Now, let's continue, (thanks for your inspiration Trisha!) How do I work out my rat's genetics? Now we need to work out what our own rats are, from what their parents are, so we can work out what babies our rats might have if we cross them. I'll start with an example from my own boys. Working out your rat's genetics can be difficult, because of the way that dominant genes mask the second gene, so we can't always be sure what is hidden there. In some cases, we know for certain, and in other cases we know there's a possibility it's there, and we find out for certain when the babies come out! When you work out the genetics of your own rats, you need to look at the other babies the parents have had, and what colours the grandparents were, and then you can get a pretty good idea. Example 1 My spotty black boy, Jesse His mum was dove: aa mm rr P* (the star means we don't know what gene was hidden there). His dad was black: aa M* R* P* Now, this mating only produced black babies, no other colours, so we can learn a bit about the parents' genetics from this. Because the mum was dove, she passed down only recessive genes for non agouti, mink and ruby eyes. So, if the dad was carrying any of these recessive genes, hidden by the dominant genes, we could expect them to show up in the litter. For example, if he was aa Mm RR PP, the punnet square would go like this:
Which means we would have a 50% chance of getting mm and a 50% chance of Mm for that gene. This would most likely have showed up as some of the babies being mink, aa mm R* P*. In fact, in the real world, there is a small chance that all the babies would randomly turnout to be Mm, anyway. But with 8 brothers and sisters, the chances of this happening are slim. So, we can see from the offspring that the dad's genetics was most likely to be aa MM RR P* (we still don't know about that P gene, it could be hiding there somewhere!). Learning this doesn't actually help us in this situation, because the baby's genes are easy to learn about by combining what we know about the parent's colours, and what we know about his colour. That is, we know that the mum was dove, aa mm rr, and we know our boy is black, which means he must have a dominant gene for all but the agouti genes, aa M* R* P*, and because his mum was dove, she could only give him the recessive genes, a, m and r, so because he's black, his genotype has to be aa Mm Rr P*. But it's important to look into the parents other offspring because it's not always this straight-forward to work out the genes. ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Example 2 An argente doe out of an argente mum and a mink dad. We start with what we know about our doe. If she's argente, she must have genetics like this: A* M* rr P*, so we need to learn what's hiding behind the dominant genes. The mum is argente, therefore A* M* rr P* The dad is mink, so his genes have to be: aa mm R* P*. We know that because your baby is argente, the dad must also have given her an r, so his genes are actually: aa mm Rr P* What can we find out from this? The dad has to have given your girl an a and a m, so we add this to what we know, and your girl's genes look like: Aa Mm rr P*. Now, how do we find out about that P gene? Well, we can look at both the siblings from this litter, and also the history of the parent rats. The siblings are: 7 argente and 6 agouti. This doesn't tell us about the pink eye gene, but it tells us a little bit more about the parents. Because all the babies were agouti type, and none were cinnamon or mink, I'd expect that the mum's genes are AA MM rr P*, in other words, she's not carrying the m or a genes. We still don't know about the P genes, so we look back further. The father of the mink dad (your baby's grandfather) was champagne. That means he was aa M* R* pp. So, your baby's dad must have inherited the pink eye gene. There is no silverfawn in the history of the argente mum's family, and no pink eyed babies turned up in their litter, so it's safe to assume that the mum carries no pink eye genes. Therefore, the parents genes look like this: Mum: AA MM rr PP Dad: aa mm Rr Pp So, let's do our punnet square for the pink eyed genes, and see what we get.
So, we have a 50 % chance that our baby is PP and 50% chance that it's Pp. We won't ever know, until we breed her, and even then we'd need to breed her to a boy who is carrying or displaying the pink eyed gene for it to show up. Hidden genes like this one can be carried down the generations, and surprise you! Example 3 Neena, who came from a pet shop... Now, this is tricky, because I know nothing about her parents! All I know about her is that she's black, so her genetics must be : aa M* R* P*. However, when I bought her from a pet shop, most of her brothers and sisters were still there, so I know what colours they were. There were black, champagne and mink babies in that litter, so that tells me quite a bit about her parents. For a start, we have no agouti based colours, so I expect her parents were both non-agouti. Because she had champagne (pink eye dilute) siblings, I know that both her parents must have carried a little p. Because there were mink babies in the litter, I know that both the parents must have carried a little m as well. So, that means her parents were probably something like this: aa Mm RR Pp, perhaps. We'll never really know, unless we find her breeder :-) However, because her parents were each carrying at least one p and one m, we know that for each gene there is a fifty percent chance that Neena carries the recessive hidden behind her dominant. The probability is that she has two copies (homozygous) of the dominant R gene, because she had no siblings displaying that gene, and I know there aren't many ruby eyed rats in Tasmania ;-) So, her genotype could be one of four possibilities, which one we won't know unless we breed her to the right male :-) The possibilities are: aa Mm RR Pp, or aa MM RR Pp, or aa Mm RR PP, or lastly, aa MM RR PP. If we knew her mum was pink eyed and her dad a mink, we'd know for certain that she carries the pink eye and mink genes (aa Mm RR Pp) The Genetics of Markings Ok, the next step is to look at how markings are defined by genetics. It's not as "black and white" as the genetics of coat colour, but still as predictable. I will work here with the three basic markings: hooded, Berkshire and self. I plan to begin to explain the DownUnder markings afterwards. * The variants of bareback, Irish, and even blazed are, I think, just extreme versions of these three marking types, and so cannot really be predicted. It's just like a colour, say, silverfawn. Now, we know the genetics which cause the colour dilution to silverfawn, but there is still a large range of variation within that colour. Some silverfawn rats are really orangey ginger, and some are a washed out yellowish cream. We can't predict exactly what shade of silverfawn our rats will be, just as we can't predict the unusual markings our rats may be born with, but we can increase the chances of getting what we want by breeding selectively - choosing two parents who have the attributes we are looking for. * So, on with the show! First, a description of what each marking is: Hooded: This is the "typical" appearance of pet rats the many people recognise. The rat has a coloured head, the colour reaching down the chest to between the front paws, and also a tripe of colour running from the "hood" down the back, to the tail. For show standards, the stripe should be even, one inch wide, and the colour should extend down about 2/3 of the tail. the paws should be white, and the demarcation between white and coloured fur is to be straight and well defined. The colour of the hood can be any recognisable colour variation, and should conform to the standards for that colour. In reality, a hooded rat can be anything from the bareback marking (no stripe) to a blotchy, half-spotted stripe, to a 3 inch wide stripe. Berkshire: A Berkshire rat has colour all over it's body, except a well-defined white area on the belly, which covers the whole belly area, and extends down the inside legs, giving the rats white "socks". It's a very pretty marking. In real life, the white marking can range from a triangle between the front legs (Irish) to a white squiggle down the tummy, to a paint-splash, but generally they have white feet, or at least white toes. The main colour can be any recognised colour. Self: I have never seen a self in person, but it sounds quite beautiful. The rat's body is completely all the same colour, with no white markings at all. The natural patterning of colour on a rat usually makes the belly a lighter colour than the rest of the rat's body, especially in agouti-based rats. Selfs can come in any colour, from champagne to black and everything in between. Now, what are the genes which control these markings? Well, it's all controlled by one gene, the "H/h" gene. How this happens is by a process call incomplete dominance. I think I'll show you, then explain it, ok? :-) Hooded: hh Berkshire: Hh Self: HH The HH and hh (homozygous) genotypes create the two extremes of marking, one with most of the body white, and one with no white. The combination of the two variations, Hh shows how the big H is not completely dominant. It does not mask the presence of the little h, it just tempers the effects of it, so you end up with a marking which is half-way between the two: Berkshire. So, how do we calculate what markings we might get from a cross? It's just the same as colour genetics, so draw up those wonderful punnet squares! If you cross a hooded with a hooded, the only possible outcome is 100% hooded babies. The same if you cross two selfs together. The fun part happens when you cross two berkshires, or two different markings. Example One: Berkshire x Berkshire Each parent is Hh, so put them into your punnet square.
So, what do we have? 25% of the offspring are HH (self) 50% are Hh (Berkshire) and 25% are hh (hooded). The only difference between these results and those of the coat colour genetics is that there can be three different results fromt he one cross. I hope this explains the basics of coat markings! It's really fairly straightforward :-) I'll write a bit more about DownUnder markings sometime! Ta Dah! How was that? Want more?! Well, you'll have to request it! :-) If you email me with anything you'd like to know, I'll write about it both here and in an email back to you :-) You can email me at jessica_b@iprimus.com.au <:B )~~~
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Created on the 13th Feb 2004. Last updated 10/4/05. |
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(agouti
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