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I have wanted there to be a thread like this for years, and there are frequent enough genetics questions scattered about in random threads that I feel like enough people are interested. However I am not the type of sperg to make an initial effortpost like some of our other spergs. But I'd like this thread to be a general discussion/question thread about animal genetics and genomics. I know a lot of you are involved in science in various capacities so I think a lot of people could contribute good knowledge! So whether it's talking about your experiments with making your food rabbits look pretty before you off them, or questions about the inheritance of eye diseases in cats, or more general discussions about inbreeding/line breeding or ~hybrid vigor~ and doodleshits - let's do it! All levels of questions/discussions welcome here, from how 2 punnett square to debate about determining relative significance of multiple QTLs. Hope this takes off. 
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| # ? Jan 28, 2013 22:10 |
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| # ? May 22, 2013 00:00 |
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 What's the difference between leucistic and albino? What goes into breeding these five-digit snakes?
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| # ? Jan 28, 2013 22:52 |
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A good part of my bread and butter is breeding danios in an academic setting- making transgenic fish, mapping mutants and the like. A lot of the high-throughput sequencing techniques are getting to the point where covering an entire genome or entire transcriptome would be achievable for a small business or even something like a group of hobbyists pitching in together to get it done. Most of the academic work on the molecular underpinnings of traits that hobbyists are interested in (pigmentation genetics, disease, etc) are studied intensively in a handful of species (D. rerio, medaka, goldfish, etc) and less so in others. It struck me recently that there might be some interest in the hobbyist community to try to make detailed genetic data available for particularly widely-bred species that have not yet piqued the interest of the academic community, but I don't know if there's any demand for it. If anyone has thoughts on that I'd be interested in hearing them.
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| # ? Jan 28, 2013 23:21 |
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This is sort of a question and discussion but I hope that's ok. One of the breeds of sheep I have, the Jacobs, is used as a model for Taye-Sachs disease in humans after some lambs with a nervous system issue popped up in a flock in Texas. They shipped the affected sheep to Auburn University where some vets identified the source of the issue as a mutation called the G444R mutation. The original flock bred some more affected lambs and they are used for gene therapy trials now. You can read more about it here and here. The disease usually ends up with lambs dying by 4-6 months old which probably resulted in the culling of any ewes producing lambs with the disease even before people knew what it was. This means that even though it the gene is present in the population no one is particularly worried about it. This all happened in 2009-2010 before I got in to sheep and now the free testing researchers were offering has been canceled due to lack of interest. Breeders have identified the original carrier of the mutation as a ram called Turner 183K who is in the background of every major flock in the US so there's really no getting away from it unless you are able to trace your flock all the way back to when they were imported to the US without running in to him. Not easy to do when there is an open studbook and two different registries to dig through. I've been trying to ask around to see if any breeder still get their flocks tested and haven't gotten any clear answers. It seems most people who wanted to test their flocks did so when it was free and simply culled out any carriers then. Do any vet/vet students know if any of the vet schools are still doing testing for the mutation? I'm planning on testing most of my flock for scrapie susceptibility at least on codon 171 but I would love to test some of them for the G444R mutation as well if someone is still doing it.
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| # ? Jan 28, 2013 23:24 |
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Instant Jellyfish posted:Do any vet/vet students know if any of the vet schools are still doing testing for the mutation? I'm planning on testing most of my flock for scrapie susceptibility at least on codon 171 but I would love to test some of them for the G444R mutation as well if someone is still doing it. How many animals do you want tested? The cost of getting sequencing to identify carriers of a particular SNP isn't particularly high to begin with (I pay $10/reaction plus whatever it costs me to extract the DNA and my primer costs, which might add a buck or two), it could be even cheaper if you did it in high enough volume or the SNP produces a restriction site polymorphism or something like that where you can just run samples out on a gel.
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| # ? Jan 28, 2013 23:30 |
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I only have about 20 Jacob sheep and probably wouldn't test them all. Scrapie testing is about $10 plus the cost of either blood cards or vaccutainers but it's common for sheep registries to require testing for that and/or spider lamb syndrome in order to register your lambs so there are a lot of commercial labs that can run that test and they keep their prices competitive. Shepherds are cheap bastards.
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| # ? Jan 28, 2013 23:38 |
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Hooray, I've been waiting for this thread.  I'm not in any sort of science field, I'm just interested to learn a bit about genetics, which is something I'm less than knowledgeable about.
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| # ? Jan 28, 2013 23:38 |
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Thumbs up good thread
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| # ? Jan 29, 2013 00:03 |
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Instant Jellyfish posted:I only have about 20 Jacob sheep and probably wouldn't test them all. Scrapie testing is about $10 plus the cost of either blood cards or vaccutainers but it's common for sheep registries to require testing for that and/or spider lamb syndrome in order to register your lambs so there are a lot of commercial labs that can run that test and they keep their prices competitive. Shepherds are cheap bastards. Looks like the G444R test can be done by REN digest. If you can't find anyone to do that work for you, PM me. I have the reagents needed to perform that assay.
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| # ? Jan 29, 2013 00:04 |
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Paper Mac posted:Looks like the G444R test can be done by REN digest. If you can't find anyone to do that work for you, PM me. I have the reagents needed to perform that assay. Can you link to your source for determining that you can do this genetic test?
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| # ? Jan 29, 2013 00:34 |
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Instant Jellyfish posted:I only have about 20 Jacob sheep and probably wouldn't test them all. Scrapie testing is about $10 plus the cost of either blood cards or vaccutainers but it's common for sheep registries to require testing for that and/or spider lamb syndrome in order to register your lambs so there are a lot of commercial labs that can run that test and they keep their prices competitive. Shepherds are cheap bastards. Yeah, unfortunately I don't think the gangliosidosis genetic test for use in Jacob sheep is commercially available at this time, because it would likely not be profitable enough for any place to run it in high volume. Topoisomerase fucked around with this message at Jan 29, 2013 around 00:44 |
| # ? Jan 29, 2013 00:38 |
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redmercer posted:
In albinios, there is a lack of melanin production (melanin is a dark, brown pigment, and is the pigment responsible for different shades of brown skin. So an albino person (or other mammal) will have very fair skin and hair. Reptiles, on the other hand, have other pigments besides melanin, including different yellows and reds. So, an albino reptile will often have yellow and/or red coloration, but no darker melanin. An albino red-eared slider turtle, for example, is pale yellow with orange-red "ears." A leucistic animal, on the other hand, has a reduction in all pigments, and in the case of reptiles this is how you get a really white snake. A leucistic animal will also have normal colored eyes, compared to the red eyes of an albino, because the pigment in the iris originates from different cells than the rest of the pigmented cells and is not affected by leucism. It is generally affected by albinism, so the lack of pigment makes the eyes appear red (from blood vessels being visible). I believe leucistic animals are more difficult to breed than albinos because more genes tend to be involved. There can be one gene for albinism (lack of melanin) but for a leucistic snake you might need the gene for no melanin, a gene for no red, and a gene for no yellow. If they only had one of these mutations, they would be amelanistic/albino (no melanin), axanthic (no yellow), or anerythristic (no red). Snake-breeding people, did I get all of that right? I tend to just trust owners when they tell me their snake is a particular color morph or pattern because there are too many to keep straight.
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| # ? Jan 29, 2013 00:51 |
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Topoisomerase posted:Can you link to your source for determining that you can do this genetic test? Its been a while since I've done any molecular biology, but if all he's doing is using restriction endonucleases and then running gels and poo poo, that doesn't seem too incredibly strange or off the wall to me. Here's a paper explaining some of the ways in which the mutation was identified and can/ could be tested for. http://www.sciencedirect.com/scienc...096719210003021
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| # ? Jan 29, 2013 01:09 |
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Topoisomerase posted:Can you link to your source for determining that you can do this genetic test? Are you asking me for the paper I was looking at regarding the G444R mutation, or asking me how I determined I'm able to do it? If it's the latter, I've been doing benchwork for a decade, and have extensive experience with genotyping in a variety of species- that kind of thing is bog-standard stuff for me.
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| # ? Jan 29, 2013 01:19 |
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redmercer posted:
So reptiles express color totally differently from mammals. Almost all color in mammals and birds expressed during development can be traced back to the pigment melanin, produced by melanocytes, which is a sort of brown/black type pigment (simplistically). "Albino" simply means that melanin production is absent or markedly reduced to the point of being essentially nondetectable, though the melanocytes are present. So an albinic mouse, for instance, pretty much lacks expression of the only type of pigmentation it has, which is why it appears white with pink eyes. On the other hand, an 'albinic' snake (I'll use corn snakes since that's the only type I have real experience with) lacks black/brown pigment but still has the ability to express the yellow and red pigments, resulting in the red/pink eyes and lack of black. They call those amelanistic but that is what an albino is as well. A leucistic animal has a defect in distribution of an early precursor cell to ALL pigment-producing cells derived in early development from the cell population that would later spread the pigment-producing cells over the skin/feathers/scales/etc. So the leucistic animal lacks all pigments in areas affected by this defect in distribution/migration. Consequently, the cells aren't actually present in the skin/hair/scales/feathers of this animal to produce the pigments, but if they were present, they could produce them just fine. Since the precursor cells that form the eye are not derived from the same population as the affected cells, they are still capable of expressing melanin, so the eyes are generally normal colored, as would be any other areas not derived from the damaged cell population. I hope I explained that okay. Both are recessive traits, but the 'rarity' would depend on the frequency of the gene in a population. A recessive trait is not necessarily a rare trait, to put it another way. So if the leucistic gene were rare in the population, when a leucistic animal is bred I guess it'd be worth more money. Dr. Chaco posted:In albinios, there is a lack of melanin production (melanin is a dark, brown pigment, and is the pigment responsible for different shades of brown skin. So an albino person (or other mammal) will have very fair skin and hair. Reptiles, on the other hand, have other pigments besides melanin, including different yellows and reds. So, an albino reptile will often have yellow and/or red coloration, but no darker melanin. An albino red-eared slider turtle, for example, is pale yellow with orange-red "ears." Not quite on the leucistic mechanism. See above. Topoisomerase fucked around with this message at Jan 29, 2013 around 01:25 |
| # ? Jan 29, 2013 01:21 |
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Topoisomerase posted:
Got it. So would a snake with the amelanistic, anerythristic, and axanthic mutations look like an albino mammal then, all white with red eyes?
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| # ? Jan 29, 2013 01:32 |
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Paper Mac posted:Are you asking me for the paper I was looking at regarding the G444R mutation, or asking me how I determined I'm able to do it? If it's the latter, I've been doing benchwork for a decade, and have extensive experience with genotyping in a variety of species- that kind of thing is bog-standard stuff for me. Yes that's what I wanted, the paper. It's more well written than what I'm used to in veterinary genetics literature, and clearly repeatable which is refreshing. A lot of the labs in the business of developing genetic tests for animals are also interested in patenting those tests. I assume that since this is primarily a human lab interested in using the sheep strictly for a model they don't care so much. edit: because the primer sequences are there and everything. Topoisomerase fucked around with this message at Jan 29, 2013 around 01:42 |
| # ? Jan 29, 2013 01:33 |
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Topoisomerase posted:Yes that's what I wanted, the paper. It's more well written than what I'm used to in veterinary genetics literature, and clearly repeatable which is refreshing. Sure thing, I just glanced at the first one I saw that did some screening: http://www.sciencedirect.com/scienc...096719210003021 In Fig.5 a TaiI/MaeII digest is shown. Basically just need a little bit of tissue to extract from, PCR, digest, run the gel and bob's your uncle.
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| # ? Jan 29, 2013 01:44 |
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I've found this Dog Coat Color Genetics website to be pretty excellent. It's illustrated and very well written. Does anyone have any similar resources for rat coloring/marking genetics?
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| # ? Jan 29, 2013 02:17 |
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Invalid Octopus posted:I've found this Dog Coat Color Genetics website to be pretty excellent. It's illustrated and very well written. Does anyone have any similar resources for rat coloring/marking genetics? I found a bunch of newish papers on rat coat colour genetics. I don't know for sure, but since work is still ongoing, you might not find as comprehensive a single resource for rats as that site on dogs. Here are some of the papers: http://www.ncbi.nlm.nih.gov/pubmed/22531792 http://www.ncbi.nlm.nih.gov/pubmed/21800996 http://www.ncbi.nlm.nih.gov/pubmed/21224527 Looks like a group at Hokkaido University interested in those sorts of things. If you're interested in those findings but don't have journal access or whatever I can try and answer specific questions from the paper or post figures etc. Paper Mac fucked around with this message at Jan 29, 2013 around 02:34 |
| # ? Jan 29, 2013 02:31 |
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Work is still very much ongoing in the dog too. And that site is awesome!!
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| # ? Jan 29, 2013 02:48 |
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Invalid Octopus posted:I've found this Dog Coat Color Genetics website to be pretty excellent. It's illustrated and very well written. Does anyone have any similar resources for rat coloring/marking genetics? AFRMA seems to have a fairly extensive list of color/marking genetics. This one has pictures though. Both are layman friendly. Also I think this big list of genetics calculators has rats somewhere. I waste so much time with those things. Paper Mac posted:Sure thing, I just glanced at the first one I saw that did some screening: What kind of tissue sample would you need? A blood card, whole blood, skin tissue, cheek cells? It's been forever since I've done a PCR. I did as little molecular bio as I could get away with in college. Field work 4 life. I may just PM you about doing it though, thanks for the offer. I found another shepherd with supposedly current testing done so I'm going to ask where she had it done first. I figured no one was doing it commercially. Curse you rare, heritage breed sheep  vvv Grad students need to make money somehow vvv Instant Jellyfish fucked around with this message at Jan 29, 2013 around 03:03 |
| # ? Jan 29, 2013 02:55 |
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lol my grad adviser always told me that people would offer to run genetic tests in their garages and poo poo but I thought she was just being a paranoid loon.
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| # ? Jan 29, 2013 03:01 |
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Instant Jellyfish posted:AFRMA seems to have a fairly extensive list of color/marking genetics. This one has pictures though. Both are layman friendly. Also I think this big list of genetics calculators has rats somewhere. I waste so much time with those things. One could do cheek as long as the person collecting the sample knows what they're doing and gets a good scraping. Myself, I wouldn't go for blood, ideally you'd get an ear punch when you had the animal ear tagged (assuming they are) and drop that in extraction buffer or just freeze and send. If there are people doing it commercially they're probably doing it to GLP standards so if you need the assay done for some kind of regulatory thing rather than interest, you probably want to go that route. quote:lol my grad adviser always told me that people would offer to run genetic tests in their garages and poo poo but I thought she was just being a paranoid loon. I could also do it in a GLP-certified custom assay CRO, but it would be MUCH more expensive and if you don't actually need that level of rigour, there's no point in paying for it. Paper Mac fucked around with this message at Jan 29, 2013 around 03:33 |
| # ? Jan 29, 2013 03:30 |
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This is my only little contribution. I always thought it was neat, it's a giant Punnett square of coat colors in GSDs. http://www.ehretgsd.com/genetics.htm Edit: Oh yeah!!! This page also has a really neat lecture (under that first segment of text) that shows examples of some really neat breeding experiments in dogs to see how traits are passed. Go watch it!! WolfensteinBag fucked around with this message at Jan 29, 2013 around 04:33 |
| # ? Jan 29, 2013 04:28 |
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It's interesting that the GSD page considers a dog to be "extensively linebred" when the inbreeding occurs in 9 or more generations. My big ASI handbook has a list of the effects of each 1% increase in COI on performance traits which includes a -0.244 lb change in lamb weaning weight, -2.78 lambs weaned per 100 lambs born, and -1.4 ewes lambing per 100 bred (from "Effects of Inbreeding in Sheep" by Lamberson and Thomas in 1984). Has anyone done similar studies on inbreeding in dogs? I can't imagine the level of inbreeding in the average purebred dog is doing anything good for them.
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| # ? Jan 29, 2013 04:56 |
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Funny you should ask that...for a long time it was kind of one of my little future 'pet projects' to do exactly those sorts of studies, on inbreeding in dogs and how it affects various parameters, and also to look at IBD as estimated by various pedigrees and compare it to estimates derived from real genomic data. I think there are some smaller studies out there, but not NEARLY what's been done in production species on that sort of topic. But sadly I've kind of gone away from the population genetics world and become interested in a more specific subset of inherited disorders that fit my discovered clinical interests better.
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| # ? Jan 29, 2013 05:09 |
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This thread is neat. My degree programme involves several units on population genetics, evaluating genetic health, proper breeding etc. but not for a few years yet. The Dog Coat Colour Genetics website is wonderful to read. We have a Labrador with somatic mutation at the daycare where I work. She is mostly yellow but has a black patch on the back of her neck.
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| # ? Jan 29, 2013 07:25 |
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Topoisomerase posted:lol my grad adviser always told me that people would offer to run genetic tests in their garages and poo poo but I thought she was just being a paranoid loon.
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| # ? Jan 29, 2013 08:51 |
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Rixatrix posted:If I had a garage I'd just grab some old equipment off of people moving their lab or something and do all kinds of stuff on my dogs DNA. I probably wouldn't sell it as a service though. A good chunk of the CROs I'm familiar with started out as graduate students doing things after-hours (with, of course, the PI's blessing), or in a spare room/garage. People might sneer at that, but I used to get requisitions for patient genetic testing for a heriditary osteodystrophy from confused doctors all the time when I worked in a lab that did some basic bone research. It was easier to just do the work and send them an invoice than to return the cultured blood samples and the req forms. Weird side-contracts are how specialist assays that are unprofitable on a commercial scale get done. A lot of this stuff isn't anywhere near as expensive or time consuming as it once was, so I think there's probably room for hobbyist breeders or just pet owners to move past off-the-shelf commercial assays in cases where it's necessary or desirable to do so.
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| # ? Jan 29, 2013 17:23 |
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This isn't about genes so much as combating the really dangerous stuff, but what do you guys think it would take to finally get the AKC on board with required screenings for breeding stock? In 1996, the American Quarter Horse Association determined that HYPP was enough of a threat to the future of the Quarter Horse that now every QH foal born in 1998 or after is required to be tested for HYPP, and if they are homozygous for it, they are not able to be registered with the AQHA. Naturally, this has caused some changes in halter showing, since Impressive (the stallion to whom the disorder was first linked) was a very prolific and popular sire for halter-bred Quarter Horses, but the AQHA still made the determination to require screening and bar registry if necessary. Will the AKC ever take these steps, or are we just going to leave it up to the individual breed clubs and pray that someday dog owners will get educated enough to actually go through those clubs to find a breeder?
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| # ? Jan 29, 2013 18:25 |
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Paper Mac posted:A lot of this stuff isn't anywhere near as expensive or time consuming as it once was, so I think there's probably room for hobbyist breeders or just pet owners to move past off-the-shelf commercial assays in cases where it's necessary or desirable to do so.
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| # ? Jan 29, 2013 19:48 |
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I have an orange tabby with Dichroic Ojos Azule eyes. They are a beautiful cornflower blue with small slices of brown at the top of each. Apparently it's a pretty rare mutation and she was a stray in Houston that a friend found. Cat Eye Color and Coat chart: http://culex.us/ig/catstut6.jpeg Ojos Azules: http://en.wikipedia.org/wiki/Ojos_azules
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| # ? Jan 29, 2013 21:40 |
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D-Pad posted:I have an orange tabby with Dichroic Ojos Azule eyes. They are a beautiful cornflower blue with small slices of brown at the top of each. Oh my god, I'd love to see photos of this if you have any!
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| # ? Jan 29, 2013 22:03 |
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ButWhatIf posted:Oh my god, I'd love to see photos of this if you have any! I really wish I did. I've never been able to properly capture it in a photo. Even in a bright light situation her pupils are always so big it looks like her eyes are black when she is inside. If she is in direct sunlight however her pupils become small and you can really see how beautiful her eyes are. I'll try to get her outside and see if I can get a proper photo tomorrow, but she doesn't cooperate very well.
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| # ? Jan 29, 2013 22:47 |
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The mention of New Mexico interests me (I grew up there) as for a long time it was one of the most isolated areas of the New World Spanish empire, a fertile ground for all sorts of interesting genetic poo poo to crop up. We have three-horned goats, too, but I can't find anything on the Internet about them.
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| # ? Jan 29, 2013 22:50 |
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Like, the two normal ones, and then one in the middle like a unicorn? I want a unigoat so bad now. edit: Also, I can scrape together an effortpost for you later, once I have my drat brain back. Remind me if I forget.
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| # ? Jan 29, 2013 23:19 |
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This might be a simple (stupid) question, but perhaps I'll get a cool answer. My two cats are from the same litter. One is a brown tabby with "sleek" fur, while the other is black with "plush" fur. Is this due to a possibility of different fathers, or is this just how the genetic lottery doled out their fur colors?
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| # ? Jan 30, 2013 00:03 |
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Pile of Kittens posted:Like, the two normal ones, and then one in the middle like a unicorn? I want a unigoat so bad now.
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| # ? Jan 30, 2013 01:22 |
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| # ? May 22, 2013 00:00 |
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four lean hounds posted:This might be a simple (stupid) question, but perhaps I'll get a cool answer. My two cats are from the same litter. One is a brown tabby with "sleek" fur, while the other is black with "plush" fur. Is this due to a possibility of different fathers, or is this just how the genetic lottery doled out their fur colors? They could definitely have come from the same father. Both are technically black cats genetically (if by 'brown tabby' you mean it has black stripes). The tabby markings are a pattern, rather than a coat color. They differ at the locus that determines whether they express the tabby pattern or not. Tabby is dominant to self (solid) coloring, so even if both parents were tabbies, they could produce a black kitten if they were both heterozygous for the tabby markings.
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| # ? Jan 30, 2013 01:35 |
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