My rat litters + hidden gene!

[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.

[sorraia]

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.

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.

[Pythonfriend]

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.

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.

[Mephibosheth1]

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

[sorraia]

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.

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.)

[bunnykit]

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.