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Post by kansasdexters on Dec 11, 2014 5:50:47 GMT -5
Kirk,
Except that with the chondro gene, since it is partially dominant in the gene pair, it's presence is evident in the phenotype of a chondro-carrier. So, if I had a calf that was an obligate chondro non-carrier by parentage verified pedigree, but that physically appeared to be a chondro-carrier -- then I would test it to confirm whether it was actually a carrier or not. If it was confirmed to be a chondro-carrier, and by pedigree was shown to be from two chondro non-carriers --- then additional testing would be done to identify the proper parents for that calf and the pedigree would be corrected.
Even in two closely related bulls, additional marker panels can be done to identify the correct sire when used in combination with the dam's genotype and compared to the calf's genotype. Other tests such as milk proteins and color genotype, can also be used in addition to the parentage test, to help differentiate between two closely related sires. The presence or absence of the chondro gene serves as a differentiator between the two closely related sires, in the hypothetical example that you proposed. There are also herd records, such as pasture inventories, that help to pinpoint which animals were together (or potentially exposed to each other) during the time frame when the calf was conceived.
Patti
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Post by lakeportfarms on Dec 11, 2014 6:17:26 GMT -5
Who knows, maybe on the non-chondro farm a neighbor's chondro carrier jumped a fence and bred a cow, then jumped back out again. Chondro bulls don't jump...
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Post by RedRidge on Dec 11, 2014 8:00:19 GMT -5
To summarize... if I have a chondro and a non-chondro bull on my farm and I do PV on a calf out of two non-chondro... then the obligate non-chondro status is just as accurate as the PV test. Adding the actual chondro test does not give you more accuracy for the PV. In theory the PV would have determined a non match on the sire if, in fact, the chondro bull was the sire. IOW... We can't make it any more accurate than the human error element. If you have closely related line-bred cattle on your farm and you have a non-chondro bull and his 6 month old chondro son that you assumed was too young to breed, it's possible that this chondro-son has a VERY similar DNA genotype to the non-chondro sire. It's very possible that when you do a parentage verification on your calves, your non-chondro herd-sire bull will verify as the parent even though the chondro son (sneaker bull) is actually the sire of some of the calves. This is NOT human error or computer error. You should get this same result if you redid the parentage verification 100 times. This is due to the way the parentage verification works. If the two bulls aren't related, then the accuracy is pretty good. But if the two bulls are very closely related, then the accuracy falls off a considerable amount. In the case of the sneaker bull, he's often going to be the son of the presumed herd sire, so that alone drops the accuracy of the parentage verification and accuracy drops much further if there is a lot of other interrelatedness. The Chondro test itself is very accurate, but it is prone to a tiny degree of human or computer error. If you got such a human error, and you retested, you would almost certainly get the correct result on the next re-test. The parentage verification test (like the chondro test) is also subject to a small chance of human error BUT it may also only be 90% accurate in the case of very closely related bulls. 90% accuracy may be good-enough for the purpose of pedigrees (the two closely related bulls are very similar in pedigrees anyway), but 90% is probably NOT good enough for the purpose of making certain an animal isn't a carrier of a lethal gene to unknowingly be spread to other herds. This is called "being responsible". ;-) There are a lot of irresponsible people in the world but i am not their conscious or their socialist government.
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zephyrhillsusan
member
Caught Dexteritis in Dec. 2009. Member of this forum since Oct. 2013.
Posts: 1,502
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Post by zephyrhillsusan on Dec 11, 2014 8:55:21 GMT -5
Patti, thank you for bringing this thread back to the original topic--genotypes and parentage verification. I just re-read the four blog posts that I shared in my Original Post, and chondro is not mentioned in a single one of them. So Cascade Meadows Farm - Kirk, if you want to discuss "Chondro non-carrier - Obligate by PV" status, would you please start a separate thread? Parentage verification and the reasons for it are too important a discussion to be turned into a different subject. The beauty of parentage verification is exactly as Patti says, that it is not limited to examining just 13 or 16 markers. VGL has an excellent explanation of what happens when one of two closely related bulls might be the actual sire: Note the part I underlined for emphasis. If a breeder knows they have an intact bull calf of potential breeding age in the pasture, even if they're "sure" it didn't breed anything, all they need to do is submit him along with their herd sire as potential sires. The lab will sort out the real sire. That's the beauty of parentage verification and why it is such an adjunct to responsible breeding.
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Post by Cascade Meadows Farm - Kirk on Dec 11, 2014 11:45:06 GMT -5
Patti, thank you for bringing this thread back to the original topic--genotypes and parentage verification. I just re-read the four blog posts that I shared in my Original Post, and chondro is not mentioned in a single one of them. So Cascade Meadows Farm - Kirk, if you want to discuss "Chondro non-carrier - Obligate by PV" status, would you please start a separate thread? Parentage verification and the reasons for it are too important a discussion to be turned into a different subject. Zephyhillsusan, YOU introduced the tightly related subject of parentage verification and lethal gene testing in your second post above as you can see right here: I hope that once people realize the benefit to them in not having to test every calf for PHA and chondro, it will be done more frequently. My scientific point is that if you have cleansed your herd from lethal genes and do a good job of keeping lethal genes OUT, then yes, simple parentage verification/obligate status can help assure others that your calves are free from lethal genes.... But if you continue to host lethal genes on your farm, then a simple straight-forward parentage verification alone may not be sufficient in many cases, and may require the extra effort that Patti detailed. I'd trust an expert like Patti, to be able to do that extra effort, but not everyone has that expertise.
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Post by RedRidge on Dec 11, 2014 13:45:16 GMT -5
My scientific point is that if you have cleansed your herd from lethal genes and do a good job of keeping lethal genes OUT, then yes, simple parentage verification/obligate status can help assure others that your calves are free from lethal genes.... But if you continue to host lethal genes on your farm, then a simple straight-forward parentage verification alone may not be sufficient in many cases, and may require the extra effort that Patti detailed. I'd trust an expert like Patti, to be able to do that extra effort, but not everyone has that expertise. "Cleansing my herd of lethal genes" Reminds me of eliminating Jews or a socialist government thinking taking away guns is a good idea. None of those ever proved to be anything but a nightmare btw. ;-) I'm guessing my neighbors would tell you that my teenager behind the wheel, or my Italian Maremma guarding the livestock, or the 9mm I carry, are all potentially more lethal than any dexter I own. ROFL
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Post by RedRidge on Dec 11, 2014 14:21:29 GMT -5
Sorry Susan, I tend to read threads from the bottom up when on my phone. Chondro topic moved. Apologize for that...
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Post by lonecowhand on Dec 11, 2014 14:29:21 GMT -5
C'mon Kirk, can't you think of something else to harp on? Lethal genes, lethal genes, lethal genes...blah, blah blah.
You don't have any, what do you care?
Kind of the "Boy who cried Wolf" after a while.
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Post by kansasdexters on Dec 11, 2014 15:11:50 GMT -5
lonecowhand,
Here's the irony in all this conversation: "No one can presume that their cattle are completely free of lethal genes".
Once you test a Dexter for the Chondrodysplasia mutation and the PHA mutation, and the tests come back as "non-carrier", then you only know that the animal is free from those two specific genetic mutations.
What you don't know is anything about the other lethal genes that are commonly found in cattle, or those that can also occur as the result of a new mutation. If the frequency of occurrance of any lethal gene, in any particular breed, is very low, then the chances of a calf inheriting a lethal gene from both parents is very low. Lethal genes that are "carried" in viable animals are recessive genes, when they occur in a gene pair (one normal allele/one mutated allele) the normal gene is dominant and codes for the necessary processes that allow the animal to grow, mature, and reproduce. Recessive genes can go unnoticed for many generations, until the number of animals that carry them become significant enough that the Carrier X Carrier matings start to occur at a high enough frequency for Severely Affected (homozygous for the mutated allele) calves to be produced. At that point, if enough people are willing to pay for it, researchers are then financially motivated to develop a genetic test, and breeders begin testing their stock to positively identify the carriers of that mutation.
Since cattle have never been "Homozygous Perfect", it's only reasonable to test for the mutations that can result in significant negative consequences for any particular cattle breed.
Patti
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Post by lonecowhand on Dec 11, 2014 16:24:20 GMT -5
Thanks, Patti. I agree that all breeders should test, and manage conditions if applicable. If they don't want to test, they should eat them, not breed them. IMO My point was, folks come here for information, not to see how many times one can use "lethal gene" in a sentence.
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Post by rawlingsdexter on Dec 12, 2014 5:59:10 GMT -5
Hi all, I have found this thread very interesting, but just want to point out that genetic mutations do occur. We had one cow who produced two calves with genetic mutations on the same marker in two separate calves. The PV for those calves came back as not from the nominated dam. I knew that they were definitely the nominated cows calves as she would not suckle any other calf.
When questioned the DNA profile was retested to include a larger panel of markers, which was then concluded that the calf was in fact from the nominated dam.
DNA testing is not without it challenges, but it does give more assurances that calves are actually the progeny of the nominated parents, and it them goes to prove invaluable in identifying potential carriers in the case of PHA with more accuracy.
Well done to everyone who is adopting this quality assurance in breeding their Dexters, it makes the integrity of Dexters way above those of other breeds of cattle.
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