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Selecting Parents
There are many things to consider when choosing two rats to breed. It is important to keep in mind that the next generation must be better than the one before, or there is no point breeding. Things to take into account are health, temperament, type and colour, generally in that order.
Selecting for health:
Rats, sadly, are prone to so many hereditary illness and conditions, not to mention problems due to their delicate chests. As breeders, it is our responsibility to produce animals that are strong and healthy, with minimal risk of early mycoplasma, tumours etc. This is done by breeding rats of known background that have been monitored for generations and by removing rats from the gene pool that are sickly or prone to illness. The first couple of generations of a new line are risky - you are having to breed more rats before the first have reached old age, so to start with it is difficult to judge what is a healthy line, which is why it is best for new breeders to work with an excellent, established line to start with. Breeding from an unknown rat is very risky - while that particular animal may be very healthy and friendly, that does not mean that it's family are and the rat itself might be hiding genetic faults - for example, a buck from a line of does that are prone to mammary tumours may not get tumours himself, but he'll pass the weakness on to his daughters, or a doe might carry a genetic tendancy from her male ancestor's testorone fuelled agression. You may breed a doe at 6 months old, to find that she develops mycoplasma at 1 year old and is dead by 18 months old. Your foundation animals should come from a line where records are kept of all breeding and homed rats, their dates and causes of death and general lifelong health. Breeders should be willing to share this information with you, and if not don't take the risk.
Selecting for temperament:
Temperament is equal to health in my opinion - there is just no point breeding agressive miserable rats. Breeding rats should come from a line of happy, contented pets who love to be with other rats and their humans. Breeding rats for temperament is more ambiguous than breeding for health - rat owners are agreed about what makes a healthy rats, but temperament is entirely dependant on your opinion of what makes a good pet. I prefer my rats to be quite calm and laidback, so this is what I breed towards, but others prefer very in-your-face attention-seeking troublemakers. On top of this criteria I breed only rats that are happy to accept other rats, which has resulted in a line of rats that are easy to introduce to one another at any age. Your breeding animals should be a joy to be with, whether to you that means snuggling up on your shoulder or entertaining you with their amusing antics. They should show no aggression or bullying to their cagemates and should be happy to meet strangers.
Selecting for type:
Breeding animals with good conformation is important - rats are meant to be rat-shaped. Type is partly dependant on genetics and partly on diet. A scrawny, narrow-headed buck will not breed typey offspring, but poorly fed kittens from a typey buck will not not reach size/shape potential. Type is very dependant on line - my silver fawn marked line produced bucks with quite poor and effeminate type, but the does were such stunning, pretty girls.
Your stud bucks should be large, chunky but not fat, with a large, broad head. Does are to be racy and fairly slender with finer heads. From there it really is down to personal preference. Larger eyes and ears are generally more preferred, and a good thick, round tails.
Selecting for colour:
This can be difficult, particularly as health, temperament and type should take priority, you don't always get a nice choice. Do you keep the weedy nicely marked variegated in a litter or the strong-looking mis-marked berkshire? Health, temperament and type must always come first - markings can be improved but a line is easily ruined by selecting nicely coloured poor quality rats.
Assuming the rats in question already have good health, temperament and type, then selective breeding must occur to improve the varieties and outcrosses must be carefully thought out, as they can improve or ruin the colour you're aiming for. For example, a black rat used to outcross a chocolate line would darken the chocolate, a blue outcross would dull the chocolate, and a buff outcross would lighten it. Therefore, if you had a line that is too dark you would use a buff outcross and so on. Animals with rusting (a fault common in darker self varieties that makes the fur colour turn a patchy orange) will breed rusty offspring, therefore rusty individuals should not be bred.
Selective breeding is made easier by only breeding one colour - if you have a litter of 12 Russian blues, with two runty ones and 10 big, strong, healthy ones, you have 10 kittens to choose the best colour from. If you have a litter of 12 with 3 Russian blues, 4 blacks, 2 russian doves, and 3 minks, you only have 3 Russian blues to choose from. If two of those are weedy or not the gender you need, you are left with one Russian blue and the need to keep some typey ones of the wrong colour. The same occurs with markings. Markings like variegated and berkshire are heterozygous, which means statistically only half of a litter will be variegated/berkshire, which only gives you 6 to choose from in a litter of 12.
Your breeding rats should have all the qualities previously discussed as well as a good, even colour as much to show standard as possible, with minimal rusting and without a kaleidoscope of different colours in the line.
Examples:
Below I have examples of rats I own and a critique of their strengths and faults as a visual guide.

Hamlet is a good solid typey lad, weighing around 800grams. He has one of the nicest heads I've ever seen - it's very broad and quite blunt. His colour is poor though, it's much too pale and orange for an agouti - but he has bred lovely coloured chocolates.

Faelen has a very typey, muscular build and a very handsome, broad head with nice sized eyes and ears. In his prime he weighed about 700 grams, but he's lost a bit of weight recently. All through his life he's had a very even, deep, rich chocolate colour.

Unfortunately Caolan's picture does him no justice at all and it was taken during a moult, but he has a lovely solid type and broad head. Sadly his eyes and ears are on the small side. This was corrected in his offspring by breeding him to a doe with large ears and nice ears - in this case I felt that Caolan had enough good points with his general conformation and colour to warrant trying to correct the fault with his eyes.

Another terrible picture as Enya is a very active doe, but you can see that type-wise she is a very small and dainty doe, and looks quite fragile. She does have the prettiest face though, with large intelligent looking eyes and nicely positioned alert-looking ears.

Tishalulle has the worst type for a doe that I've ever seen - she's quite small and a bit blocky and stumpy looking, with a large head and small eyes. Her colour is beautiful and even and she has a lovely triangle, which unfortunately bleeds down her belly in a thin line, but despite these she wouldn't be bred because I feel her type would be detrimental to the line.

Shannon is a very racy and fit doe, with a slim but quite toned body. She is quite large for a doe, whilst still keeping her essential feminine features. She has a pretty face with nice shaped eyes and ears. She had a very rich chocolate colour in her youth, but it has faded now she's getting on.

Aislinn is one of the most attractive does here - she's racy and fit, with the pretty, intelligent looking head that Concord's offspring seem to have in common. Her colour is quite a bright, dairy milk shade, probably due to her being a berkshire.
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