My rat litters + hidden gene!

I recently got my first rats to keep as feeder breeders. I've had rats as pets before. I feel a bit uncomfortable about buying prekilled because I don't know what they ate, how they lived and how they died, all of which feels very important for me.

I picked the rats up from an animal store, the animals themselves was imported from the neatherlands of all places. It's just that the few big suppliers of rats have had all their contracts here torn because they mass produced and sent out sick animals full of fleas and diseases, and since there are no breeders here they had to import animals from other places. Since I am going to use them as feeder breeders it didn't bother me that much, they were all healthy and nice looking, the males are so nice to handle too, real gentlemen.

I bought two females and two males, all 11ish weeks old from a pet store and brought them home. The lady in the store couldn't guarantee that the rats weren't related, but I figured one mating wouldn't hurt, and decided I'd just get new males for the next generation.

I picked up a black and white hooded male, one really nice agouti male, one mismarked baraback agouti female, and one almost good agouti hooded female.
The black male and the mismarked bareback agouti female mated within days, and I planned on checking if she carried the black gene by doing this cross.

I figured she would have a small litter since she was so young, and only expected agouti hooded het black and possibly black hooded, but they threw a surprise party at me, since this is the 16 babies (!) strong litter:

After 11 hours:

https://fbcdn-sphotos-c-a.akamaihd.n...75355910_n.jpg

After taking this pic, I noticed that a few babies had dark eyes, and a few of them have bright pink eyes. I figured there MIGHT be something going on, OR they may just take a little longer to pigment up.

This is after 48hrs:

https://fbcdn-sphotos-e-a.akamaihd.n...26013545_n.jpg

Still very pink! So I either have albino or pink eye cream body type coloration going on, which is awesome!

This is after 72hrs (3rd day):

http://i42.tinypic.com/14nl24l.jpg

http://i40.tinypic.com/2jchtau.jpg

As you can see I have some hooded babies starting to color up, everyone with dark eyes are currently pigmenting up, but the pink eyes are still bright and shiny! I hope it's cream gene and not albino, because the creme colorations are so pretty O.O

And these babies were born on Friday the 13th! I was so scared something would go wrong, because I always have such bad luck on that day, but instead my young female delivered 16 babies that she is caring for with passion, and also showed me some hidden genes! Now I'm actually glad I mated her to her possible brother, otherwise I would never have known! Getting new males for the females I'm keeping from this mating though, don't want to inbreed them too much.

So far everything is going well, all the babies are plump and fat, and growing like weeds! :D I just wanted to share my first awesome litter of rat pups with you all! I will post more picutres as they put on their fur later, but I think I saw one that's really getting dark fast, the others are more redish-brown dark, so I think the mother is het for black and for albino/creme :D

I'll keep you updated on this litter! I also have three black and white varigated x black hooded (het creme/albino) coming up, and one black hooded (het creme/albino) x roan litter coming up in the next few weeks. Getting all pumped up now! :D

Congratulations! It's always fun seeing recessives come out. :)

Inbreeding isn't too bad in rats, it just depends on what you have. If there are deleterious genes in the animals' bloodline, those may come out with inbreeding. Outcrossing won't make the traits go away, it will just take longer for them to come out, while also risking spreading them throughout the bloodline (so when they do come out, you won't know where to turn and may have to scrap the whole line if its a bad enough trait). With inbreeding you'll find out it's there, and can take appropriate action to breed away from it or get rid of it. Likewise if there are desirable genes (like the recessive coloration you are seeing in this litter), inbreeding can bring those genes out too, and you can select for them. Neither inbreeding, linebreeding, nor outcrossing are bad in and of themselves, they are just tools. What makes them good or bad depends on how you use them. :)

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Originally Posted by sorraia

Congratulations! It's always fun seeing recessives come out. :)

Inbreeding isn't too bad in rats, it just depends on what you have. If there are deleterious genes in the animals' bloodline, those may come out with inbreeding. Outcrossing won't make the traits go away, it will just take longer for them to come out, while also risking spreading them throughout the bloodline (so when they do come out, you won't know where to turn and may have to scrap the whole line if its a bad enough trait). With inbreeding you'll find out it's there, and can take appropriate action to breed away from it or get rid of it. Likewise if there are desirable genes (like the recessive coloration you are seeing in this litter), inbreeding can bring those genes out too, and you can select for them. Neither inbreeding, linebreeding, nor outcrossing are bad in and of themselves, they are just tools. What makes them good or bad depends on how you use them. :)

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Ah, that actually makes sense :D And I'm glad to see such a big healthy litter, so it doesn't look like they are suffering from it yet like you say. But I sure was surprised, seeing those pink eyes, rofl! I did notice it quick though, I'm happy that I did, or I might have freaked out later, hahaha xD

So, day ten is here now! This picture is taken at 9½ days, and it looks like I've got six colors in total! :D

http://i42.tinypic.com/2qbg3h0.jpg

Rainbow litter, oh yeah! :D Not sure if I've got silverfawn and champange or himalayans and albino, or all of them, rofl. I hope the pale one (got only one) and the orange ones (got two) are silver fawn and champange, because I really want those colors, rofl. They are all female though, so I could mate them back to their father to find out or get more of them.

I meant five colors, rofl! xD

left to right ... looks like

Black, agouti, fawn, not sure, champagne I think, REW aka Red eye white aka albino

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Originally Posted by snakesRkewl

left to right ... looks like

Black, agouti, fawn, not sure, champagne I think, REW aka Red eye white aka albino

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Ahw man, I really hope so! Yeah, there were two blacks and four agouti hooded in the litter, those I'm sure what they are.
I really hope it's fawn/silver fawn though, I LOVE that color. It could still be himalayan or something like that, I think they look creme/brown before they fade out.

Holding my fingers crossed for silver fawn and champange though O.O Have two orange females and that one pale female.

Oh, and they are PEW (pink eye white) if they stay white, since they are pink eye, not red eye :3 and there are two kinds, the albino is a (c) locus mutation, and PEW is a pink eye mutation, not always the same thing genetically but in the end they look the same. For now I just don't know which one I've got.

Gratz, that is a very cool litter.

i completely disagree about inbreeding. i mean, i agree that for one generation its fine. but apart from that, i differ with much of what sorraya says.

these are not BPs but mammals.


for mice or rats with quite a natural gene pool, and maybe some morphs, inbreeding is always bad. it gets worse if it continues. disabilities and deleterious recessive traits will pop up at much higher rates than in ball pythons, or reptiles. ok you did it for one generation, babies look healthy, its fine, dont continue.

then there are the old pure thoroughbred lab mice / lab rat lines. since they are being kept completely seperate from any natural rats/mice, and from other lines, they are basically subspecies. some of these lines are up to 100 years old. their genome is completely different: they are all almost completely genetically identical. a natural mouse is homozygous for some genes and heterozygous for others, and some genes are present only in some individuals. a lab mouse or rat is homozygous for virtually all of the genes present in the genome. here inbreeding does not matter, its meaningless, because differences in the genome between individuals are close to zero and the inbreeding factor / homozygousness is already close to 100%.

lab rats are bred that way to get rid of any randomness, and so that you can just download the full genome online and know that your individual lab rat is a close to perfect copy of the genome you just downloaded.


so you have 2 options: get a pure line of lab rats from a professional lab animal breeder, you should pick a line that is used in so many scientific studies that its all over the scientific literature. keep the line pure, they will all be identical, inbreeding will not matter. absolute purity, but also no morphs, no variation.

or, if you want variety and morphs and stuff, avoid inbreeding, i mean it. they are mammals, and you dont know the genetics but they are obviously diverse, and mammals are very vulnerable to inbreeding.

if you just inbreed a sample of a naturally diverse gene pool, and try to eliminate recessive issues, you are in over your head in a gigantic project that requires dozens of generations, several parralel lines, years of work, and maybe genetic testing. also along the way there will be several setbacks due to serious genetic issues, forcing you to scrap entire lines and to split other lines to replace them. Dont go there. buy a line that some other person purified decades ago and that is proven by full genome sequencing.

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Originally Posted by Pythonfriend

i completely disagree about inbreeding. i mean, i agree that for one generation its fine. but apart from that, i differ with much of what sorraya says.

these are not BPs but mammals.


for mice or rats with quite a natural gene pool, and maybe some morphs, inbreeding is always bad. it gets worse if it continues. disabilities and deleterious recessive traits will pop up at much higher rates than in ball pythons, or reptiles. ok you did it for one generation, babies look healthy, its fine, dont continue.

then there are the old pure thoroughbred lab mice / lab rat lines. since they are being kept completely seperate from any natural rats/mice, and from other lines, they are basically subspecies. some of these lines are up to 100 years old. their genome is completely different: they are all almost completely genetically identical. a natural mouse is homozygous for some genes and heterozygous for others, and some genes are present only in some individuals. a lab mouse or rat is homozygous for virtually all of the genes present in the genome. here inbreeding does not matter, its meaningless, because differences in the genome between individuals are close to zero and the inbreeding factor / homozygousness is already close to 100%.

lab rats are bred that way to get rid of any randomness, and so that you can just download the full genome online and know that your individual lab rat is a close to perfect copy of the genome you just downloaded.


so you have 2 options: get a pure line of lab rats from a professional lab animal breeder, you should pick a line that is used in so many scientific studies that its all over the scientific literature. keep the line pure, they will all be identical, inbreeding will not matter. absolute purity, but also no morphs, no variation.

or, if you want variety and morphs and stuff, avoid inbreeding, i mean it. they are mammals, and you dont know the genetics but they are obviously diverse, and mammals are very vulnerable to inbreeding.

if you just inbreed a sample of a naturally diverse gene pool, and try to eliminate recessive issues, you are in over your head in a gigantic project that requires dozens of generations, several parralel lines, years of work, and maybe genetic testing. also along the way there will be several setbacks due to serious genetic issues, forcing you to scrap entire lines and to split other lines to replace them. Dont go there. buy a line that some other person purified decades ago and that is proven by full genome sequencing.

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I have to disagree with you, pretty much completely.

Lab rats and mice are not a subspecies, they are the same species as pet/feeder rats and mice. They are no different morphologically, their chromosomes are the same, and the only differences in genetics is what genes and alleles were selected for or against in the lab rats and mice. Lab rats and mice were inbred for many generations, and during that time different lines and strains were developed for different purposes. Some were developed for control purposes, some selected for cancers, some for diabetes, some for obesity, etc. This was all achieved through carefully recorded, well monitored, and highly selective inbreeding. Through inbreeding those genes coding for that desired trait were selected for, while those genes coding for undesired traits were selected against.

The same thing can be and is achieved in pet/feeder rats and mice. The keys again are records, monitoring, and selection. It does not take hundreds of years either. It doesn't have to take many generations, it depends on what you are starting with, how often you breed, how good your records are, and how careful your selections. Is inbreeding going to bring out deleterious traits? Sure is, but not because it is causing those traits, it's because those traits are already there. BECAUSE of inbreeding you KNOW those traits are there and can select against them. If you don't inbreed, the trait is still going to be there, but you don't know it. You keep breeding the rats and potentially spread that trait throughout your entire colony (can't call it a bloodline if you aren't linebreeding or inbreeding). When it does pop up, you don't know where it came from or how to get rid of it, and you WILL have to scrap ALL your rats. Will you have to scrap some lines while inbreeding or linebreeding? Sure will, that's part of breeding. Nothing is ever assured, and nothing is ever perfect. That's why you have to have goals and you have to select for those traits you desire.

Just speaking from my personal experience, I bred pet show rats for 10 years (and now with my feeder colony my experience breeding rats is greater than 10 years). During that time I practiced careful, well monitored and recorded, and selective linebreeding and inbreeding. I worked with a number of different lines, some of which were unknowns, some of which were partially unknown, some of which weren't the greatest and some of which had good records for many generations. I saw the MOST and QUICKEST improvements in my rats, in health, temperament, and confirmation, when I did inbreed and linebreed. The slowest and most inconsistent improvements, if there were any at all, occurred in outcrossing. In my personal experience of breeding rats for more than 10 years, real improvements only occurred with inbreeding and linebreeding, while outcrossing really served no purpose except to produce more rats. During the last 3 or 4 years I was breeding pet show rats, I was doing some very heavy inbreeding and linebreeding. By this I mean father to daughter, full siblings, grandoffspring to grandparents, etc. I was NOT breeding many litters either, only 2-6 litters PER YEAR (that's an average of 1 litter every 2 to 6 months, not litters every week as most feeder operations have). During that time, with that number of litters, I saw a decrease in ALL health problems. Hind-end degeneration decreased to almost 0%, congestive heart failure was eliminated, respiratory disease decreased from nearly 25% to less than 10%, tumors decreased from 30-40% by 2 years of age to less than 18%, and life expectancy increased from an average of 20 month to over 24 months. If inbreeding was so awful, I would not have seen those kinds of results, and in 10 years of breeding, even with the low number of litters I had each years (especially the last few years), that is not a matter of luck either. Like I said before, the key is careful selection, record keeping, and monitoring.

Now if I saw those kinds of results with 2-6 litters a year in just a couple years, imagine what kind of results I would see if I bred my feeder rats like that. The improvements would happen in a much shorter span of time, and I'd have a much greater gene pool to work with, since I would be producing much higher numbers.

The major problem with outcrossing is you simply do NOT know what you are working with. Inbreeding brings it all out, outcrossing does not. Outcrossing gives you multiple "hidden genes", some good, some very bad. Eventually those hidden genes are going to come out, but you don't know when, or in what way, or how many animals will be or are affected. Inbreeding is like opening the closet door and letting those skeletons out. You inbreeding, and it brings them out, now you can see them, now you know what you have, now you know where it came from, and you can take some action to eliminate it. Is it easy? Not always. Does it have to be hard? Well I guess that depends on what you consider "hard".

Think about it biologically too. I've seen it said multiples times on this forum that ball pythons are very tolerant of inbreeding. Why? Because in the wild they aren't holding large territories and moving around a lot, they have to breed with what they've got, whether or not that animal is their mother, father, brother or sister. So how does that differ from mammals? Depends on the mammals. Genetically meiosis and mitosis work the same way. When mammals breed, the offspring get half their genes from one parent, and half from the other parent, same way it happens in snakes. Inbreeding doesn't make the genes mutate, same as snakes. The difference between mammals and snakes is what genes do and don't occur, and perhaps the rate of natural mutation (which is variable, and may be due to encoding errors or due to environmental factors such as radiation or goodness knows what else). But look at the biology of rats... they are a small mammal, food to many other animals, live in colonies, don't hold large territories, and don't exactly travel over large distances. Those last two traits are two of the very reasons given for why it's ok to inbreed ball pythons, hmmm..... If an animal is living in a colony, the only thing that's going to prevent inbreeding in the wild is natural dispersion. Some species do disperse, others don't. Rats generally don't. When wild rats are weaned and leave their nest, they don't suddenly decide to run off for miles and miles to make sure they don't breed with their father or mother, they stay pretty close. Moving away from the colony is a death sentence, because the rats don't know where food resources are, where shelter is, and emigration increases their chances of encountering a predator. Staying close to home means inbreeding IS going to occur naturally. Thus, rats (and mice) are actually very tolerant of inbreeding. That's why the laboratories can get away with inbreeding for so many generations. If the animals were not biologically tolerant of it to start with, the labs can't change that (these animals aren't computers). This DOES differ from other species, such as many big cats, where offspring are forced to disperse away from their natal territory. Pack animals, such as canines or many species of livestock, may have some inbreeding or linebreeding occurring naturally, but because they are so much more mobile, and hold so much larger territories, the rate is much smaller than in relatively immobile animals such as rats. Migrating animals are especially less likely to inbreed naturally because they are moving around and thus encountering other groups who are bringing in other genes. This is why inbreeding is less tolerated by species such as horses, dogs, and cats.

Ignoring the giant walls of texts arguing inbreeding...
What is the hidden gene? Rats from breeders and petstores can carry a variety of markings,colors and coat types that won't show up unless bred to other rats with those specific genes. I've bred rats for a while and have talked to many long time breeders. Unless you have one color and repeatedly inbreed over generations to breed out anything else they could be carrying, most rat litters are pretty unpredictable with the exception of dominant colors (or sometimes color points). I just bred a Russian Blue variegated and a Blue Beige who came from seperate breeders. The Blue beige carries hairless, but the breeder of the Russian blue (to my knowledge) has no hairless rats in their collection(currently), yet about a quarter of her litter had hairless babies in it. Honestly, thats part of the fun about breeding them. With bps, there are only a couple of morphs possible, and you usually know exactly what the possibilities are. Whereas, you can spend years reading about recessive colors and marking combinations but still be unprepared when your litter colors up.

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Originally Posted by SarWildDog

Ignoring the giant walls of texts arguing inbreeding...
What is the hidden gene? Rats from breeders and petstores can carry a variety of markings,colors and coat types that won't show up unless bred to other rats with those specific genes. I've bred rats for a while and have talked to many long time breeders. Unless you have one color and repeatedly inbreed over generations to breed out anything else they could be carrying, most rat litters are pretty unpredictable with the exception of dominant colors (or sometimes color points). I just bred a Russian Blue variegated and a Blue Beige who came from seperate breeders. The Blue beige carries hairless, but the breeder of the Russian blue (to my knowledge) has no hairless rats in their collection(currently), yet about a quarter of her litter had hairless babies in it. Honestly, thats part of the fun about breeding them. With bps, there are only a couple of morphs possible, and you usually know exactly what the possibilities are. Whereas, you can spend years reading about recessive colors and marking combinations but still be unprepared when your litter colors up.

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I think the OP's "hidden gene"(s) is either red-eyed dilute or pink-eyed dilute, and possible a c-locus recessive (either albino and/or the himalayan gene). From what I can see on my screen, it looks like there's fawn and beige in the litter (red-eyed dilute), and either albino or himalayan (c-locus recessives).

It's funny to see how long certain genes can be carried. I once had a litter of rats which included a couple of beige babies. When I went back through the pedigree, there was NO beige in the direct line for at least 6 or 7 generations. So that gene had to be carried, unexpressed, for at least that long. Considering the generation time for a rat, that would have been at least a couple years timespan. With my current colony I'm trying to tease out all the recessive color genes I can. So far all I'm seeing is red-eyed dilute, and a few c-locus recessives (so far either poor quality Siamese or Himalayan, no albino yet). I have a mink female, and I'm hoping I can pull out more mink from some future litters.

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Originally Posted by sorraia

I have to disagree with you, pretty much completely.

Lab rats and mice are not a subspecies, they are the same species as pet/feeder rats and mice. They are no different morphologically, their chromosomes are the same, and the only differences in genetics is what genes and alleles were selected for or against in the lab rats and mice. Lab rats and mice were inbred for many generations, and during that time different lines and strains were developed for different purposes. Some were developed for control purposes, some selected for cancers, some for diabetes, some for obesity, etc. This was all achieved through carefully recorded, well monitored, and highly selective inbreeding. Through inbreeding those genes coding for that desired trait were selected for, while those genes coding for undesired traits were selected against.

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umm, no. time for some sources.

http://en.wikipedia.org/wiki/Knockout_mouse

"A knockout mouse is a genetically engineered mouse in which researchers have inactivated, or "knocked out," an existing gene by replacing it or disrupting it with an artificial piece of DNA. The loss of gene activity often causes changes in a mouse's phenotype, which includes appearance, behavior and other observable physical and biochemical characteristics.
Knockout mice are important animal models for studying the role of genes which have been sequenced but whose functions have not been determined. By causing a specific gene to be inactive in the mouse, and observing any differences from normal behaviour or physiology, researchers can infer its probable function."

so no, the varieties of lab rats / mice you mention are not line-bred. they are genetically engineered by selectively destroying one of their genes. no carefully selected inbreeding. you take the digital mouse genome, scan for the gene, synthesize a new strand of DNA that contains a destroyed version of the gene, splice that into stem cells of the mouse, put these into a zygote, fertilize it and implant into a female mouse, and you get a "het for knockout" baby. breed back to get homozygous knockout mouse.


check out this one:
http://en.wikipedia.org/wiki/BALB/c

it went through 26 generations of sibling to sibling inbreeding from 1920 to 1935. one substrain reached its 235th generation of inbreeding in 2005. inbred lab mouse strains are typically inbred for over 100 generations.

there is only one trait that would require the insane amount of 100+ consecutive generations of sibling to sibling inbreeding, and that trait is a simplified genome from which randomness and heterozygousness are almost totally eliminated.

From personal experience with lab mouse strains, it's true they aren't subspecies, but the inbreeding is not what made the genetic change. The genetic change was made, and the resultant mutated mice were bred together for 25+ generations to allow for the mutation to be passed down. The resulting mice (B6J, BALB/c, etc) are now inbred AND knockout

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Originally Posted by Pythonfriend

umm, no. time for some sources.

http://en.wikipedia.org/wiki/Knockout_mouse

"A knockout mouse is a genetically engineered mouse in which researchers have inactivated, or "knocked out," an existing gene by replacing it or disrupting it with an artificial piece of DNA. The loss of gene activity often causes changes in a mouse's phenotype, which includes appearance, behavior and other observable physical and biochemical characteristics.
Knockout mice are important animal models for studying the role of genes which have been sequenced but whose functions have not been determined. By causing a specific gene to be inactive in the mouse, and observing any differences from normal behaviour or physiology, researchers can infer its probable function."

so no, the varieties of lab rats / mice you mention are not line-bred. they are genetically engineered by selectively destroying one of their genes. no carefully selected inbreeding. you take the digital mouse genome, scan for the gene, synthesize a new strand of DNA that contains a destroyed version of the gene, splice that into stem cells of the mouse, put these into a zygote, fertilize it and implant into a female mouse, and you get a "het for knockout" baby. breed back to get homozygous knockout mouse.


check out this one:
http://en.wikipedia.org/wiki/BALB/c

it went through 26 generations of sibling to sibling inbreeding from 1920 to 1935. one substrain reached its 235th generation of inbreeding in 2005. inbred lab mouse strains are typically inbred for over 100 generations.

there is only one trait that would require the insane amount of 100+ consecutive generations of sibling to sibling inbreeding, and that trait is a simplified genome from which randomness and heterozygousness are almost totally eliminated.

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Not quite. You are talking about two very different things. What you are quoting here is about genetically engineered animals. Genetic engineering is an entirely different model and method from ordinary selective breeding, regardless whether or not inbreeding, linebreeding, and outcrossing are used in those selections. Genetic engineering is not even comparable to what we as breeders are doing. It's an entirely different process to create and force genetic mutations in the lab, than it is to selectively breed for natural-occurring (and thus unpredictable and random) mutations.

Also these "knockout mice" you are quoting are a specific strain of lab animal, they are NOT the only strain of lab animal in existence, nor the only strain in use, nor are they the first strain created. Not all lab animal strains were produced through genetically engineering, many of those in existence and used today were created through ordinary selective breeding (including intense inbreeding generation after generation). This far down the inbreeding line, these animals are pretty much genetically identical to others in their strain, but it is NOT because of genetic engineering. You are also wrong in claiming the strains I mentioned were created through genetic engineering. They were not. Some of these strains were started and produced before genetic engineering was even possible. Try looking up the individual lab strains and you will see many were in fact created through traditional breeding methods, including inbreeding.

And I hate doing this, but as a scientist I have to... Wikipedia really should not be used as a research source. It can contain some good information, but it can also contain a lot of inaccuracies. Your best bet is to go to scientific journals, or straight to the source and talk to professionals in the field. The big problem with Wikipedia is that it is created and edited by anyone, including you and me. Some people do their research and include citations (your links have a few citations), others don't. Even those who include citations should be considered with a grain of salt, because unless you go back to those sources cited, you are only reading someone else's paraphrasing. If you want to do full research, make sure you use good references. Also when researching a subject, you don't stop on the first article you find, you need to look up multiple other sites. By stopping with that one article about a specific strain of lab mouse, you concluded that all lab strains that were created for a specific purpose were genetically engineered, which is simply not true.

Here are a few sources to help you out:
http://www.labome.com/method/Laborat...-and-Rats.html
http://www.informatics.jax.org/mgiho.../strains.shtml
http://www.informatics.jax.org/exter...earch_form.cgi
http://www.harlan.com/products_and_s...esearch_models
http://www.janvier-labs.com/rodent-r...bred-rats.html
http://www.nature.com/ng/journal/v9/.../ng0195-63.pdf
http://link.springer.com/article/10....0285115#page-1
http://www.karger.com/Article/Abstract/131333
http://link.springer.com/article/10....9900031#page-1
http://ilarjournal.oxfordjournals.or.../38/3/104.full


(By the way... besides working as a biologist now, I used to work in a DNA lab as an undergraduate, which included replicating and isolating DNA. I also had a special interest in genetics, part of which involved long involved discussions with my professors after class. So I know a little bit about how these topics.)

I can honestly say I missed this thread getting so many responses O.O It was interesting to read though!

As for the one question asked in my direction the answer is that the hidden gene(s) that popped up in the first litter of brother x sister rat was pink eye dilute and albino (not the same gene for both things).
Meaning that the parents are PePe and Cc het animals. I also got a champagne female (black with PePe) and a few black hooded babies, so mom who is agouti is also het for black. Dad for this litter was black hooded. Mom was agouti hooded.

They have a brother and sister who is both agouti hooded (brown/white x brown/white), and in their first litter I got champagne, silver fawn, roan, champagne roan, agouti, and something that I think is siamese or something similar. They have color, but the head is washed out with no clear hood, and I recognize it as different from the champagnes and silver fawns.

The black hooded male, dad to the first litter, was mated to an adult roan female, but produced no roans in 16 babies, meaning he is most likely not het roan like his agouti hooded brother. It did however produce some albinos, so there is the c mutation sneaking around in the roan.

So as for now the genes I know about, after one generation, are as such;

Female 1; Aa-Cc-HOHO-PePe
Female 2; Aa-Cc(sia)-HOHO-PePe-RoRo
Male 1; Aa-Cc(sia)-HOHO-PePe-RoRo
Male 2; aa-Cc-HOHO-PePe
Roan female 1; Aa-Cc-RORO

Then I have one black variegated female, one black berkshire, and their first litters were just like I thought they would be, mated to my black male they produced all black and white babies, no recessives that collided there, so no albino or pew that I can see from the first litters.

This is what I know from what I can see after one generation. I have many generations to go before I have the results I desire and know how many recessive traits and colors that my rats carry, but I will get there eventually.

And after looking around, reading about it, thinking about it, and talking to breeders my opinion is that inbreeding and line-breeding is a sword that will do what you make it do. If you aren't careful and don't pay attention, or on purpose breed on bad mutations or traits, it's a bad tool that will harm your breeding. If you select healthy animals and select mates that compensates each others ups and downs you will eventually get animals that carries both the desired traits, and thus the tool can be good. It will only be good though if you pay attention and are SELECTIVE, not random, and pay attention to the animals, not 'just' their color. Temperament, health, growth speed, litter size, body type, outgoing or reserved, energy level, etc, there is many things you might need to select from and prioritize from depending on what you're breeding for. As these are feeders I will prioritize;

1. Litter size
2. Growth speed
3. Health
4. Temperament
5. Coloration

I do wish to make PRETTY animals that you can handle and who have nice personalities, but I need them to produce too and be healthy. I have realized what people say is true, out crossing to often will probably bring more harm then good. In dogs it's not recommended to cross them with different breeds or crossbreed for too many generations, since this tends to give them more of a 'messy' mental composition and bring them closer to a wild dog behavior. This is a natural thing to happen and I can see it happen with rats and other animals too.

Many people don't select when they breed. They produce.
And in that they don't get improvement in their stock/line because they didn't make such improvement happen, instead they blame the tool they used. It's like saying that fire can burn your house down, thus it's bad, but if you use it right it will probably keep you and your house warm without burning the building to the ground.

So will this work for me? I honestly don't know, but I'd be darned if I were to be an lazy ass about it now that I've gotten started. I've decided to start with the few sibling pairs of females I've got ( 2 variegated females, 2 roan females, 2 hooded females) and the two males, and then take the half siblings and cousins from their crossings and start out there. Lot's of work, but it's a fun challenge.

The first generation is already 5 weeks old, and I've decided on which ones to keep. Out of the 16 pups there is only 4 left, one absolute keeper, the rest depends on the coloration of the next few litters. Nice temperament in all of them though, but one of them (the champagne hooded) is slightly better than the rest on all aspects, from coloration, temperament and contact seeking. Litter size and such is impossible to know since she is so small, of course.