Post by genebo on Apr 14, 2015 21:52:36 GMT
I have been voluntarily genotyping and parentage verifying or cattle at Paradise Farm since 2006. I was encouraged to do so by Judy, and have never regretted the decision.
Every once in a while I answer a question about parentage verification in an email. It begins to be repetitive. So I thought it would be good to post one of the old emails on a public forum where anyone who so desires can read it.
This one concerns a bull that was bred here, Armstrong of Paradise. His sire was Brenn of Paradise and his dam was Windridge Bantrybeth. It is dated January 29, 2011.
Ms. Schueler,
A few things about parentage verification, using genotypes:
First, there is an international body that sets standards for parentage verification in cattle. Any lab that complies with the standards they set will produce genotypes that are useful for parentage verification anywhere in the world.
For a long time, they specified 9 markers that must be evaluated on every genotype. Two years ago, they increased the number of required markers to 11. They specify which 11 markers must be used. They offer a list of 20 or 21 markers, and each lab may choose the include any of the additional markers.
UC Davis uses 16 markers while TAM only uses 13 markers, but 11 of the markers are the same. TAM adds 2 optional markers while UC Davis adds 5. Those extra markers may be any from the international list of 20 (9 extra beyond the 11 required) and may not be the same markers. When comparing a UC Davis genotype to a TAM genotype, any that are not the same marker are simply ignored. All the labs belonging to the international association of standards have agreed that 11 markers are enough to establish parentage.
Each marker will have 2 values. Armstrong's genotype starts with marker # BM1818. A single value of 262 is shown. This means that both of his genes at that marker have the value of 262.
Since he inherited the values from his parents, and he gets one value from each parent, then in order to qualify as his parents, they each must have a value of 262 at marker BM1818. They will each have two values at BM1818, but at least one must be 262. It doesn't matter what the other one is.
Look at Armstrong's marker ETH10. His values are 215/217. That means that one of his parents gave him a 215 and the other parent gave him a 217. Brenn's genotype shows ETH10 217/219. Since the only one of Brenn's genes that qualify is the 217, then Beth's ETH10 must contain a 215. It turns out that Beth's ETH10 is 215/217. So they qualify as parents based upon Brenn providing a 217 and Beth providing a 215. Beth also has a 217, but Armstrong got his 217 from Brenn.
Every marker must match in the same way: one of Armstrong's values must be in Brenn's genotype while the other appears in Beth's genotype. Once all of the markers have been compared, and every one of them have a match, then the bull and cow that were submitted for comparison are declared to be qualified to be the parents.
It is remotely possible that another bull or cow might also match. Really closely related animals, heavily linebred, tend to have more and more of their markers match. If you were to line breed long enough, all your animals would have the same markers. Identical twins do have the same markers and parentage verification could not determine which was the true parent. It could only declare both of the twins to be qualified.
This exact same method is used in humans and all other species. Different markers would be chosen for each species, based upon which markers show the most variation among individuals.
There is no database of cattle markers which could be searched to find a parent. All parentage testing on cattle is done by submitting the samples of the suspected parents. I've seen a case where a lady submitted 3 bulls and 1 cow. The lab was able to eliminate 2 bulls and declare the other one to be qualified. The lady was shocked. She was sure it was one of the disqualified bulls that had bred the cow. She was wrong! To give her credit, she did recognize the possibility that it could have been one of the bulls from her other pastures.
I had a situation here where Brenn's younger half-brother had been sold, but the buyer wasn't able to get him on time and he stayed a couple of months after he should have been gone. Meanwhile, a cow had come to visit to be bred. The owner didn't care whether Brenn or his brother did the job, but we had to know. So after the calf was born, I got tail hairs and sent them to be compared against Brenn and his brother. It was Brenn. The calf was then properly registered, with parentage verification.
The results of Armstrong's DNA tests show that:
He is the true offspring of Brenn of Paradise and Windridge Bantrybeth.
He is A2/A2 (it wasn't necessary to test for that, since both of his parents are A2/A2 and he is parentage verified).
He is long legged, chondro free, does not carry the bulldog gene (however you want to state it).
He is black Ed/Ed and does not carry red.
He does carry dun B/b.
I did not have him tested for PHA. Both Brenn and Beth have been tested to be PHA_Free and he is parentage verified, so he could not have inherited the condition. Actually, there was very little reason to test either Brenn or Beth for PHA, since they are not descended from any Dexter that has ever been shown to carry PHA. PHA came to us through a single cow, Woodmagic Wheatear. No Dexter that is not descended from her has ever tested positive for PHA.
You can determine if your Dexters are at risk for carrying PHA by using the ADCA on-line pedigree. Find Woodmagic Wheatear. Bring up her pedigree. On the bottom left is a button labeled "Descendants". Click it and wait for the results. It will take a while. She has a lot of descendants. Once the results are displayed, type Ctrl F (hold the Ctrl key and type F). A search window will open. Enter your Dexter's name in the search field. Each occurrence of your Dexter's name will be highlighted. If your Dexter's name appears on the left side of the page, it is descended from Wheatear and is at risk. It doesn't count if it appears on the right side of the page. That only means that your Dexter once bred a Wheatear descendent. If your Dexter does not appear on the left side of the page, it is not at risk, and you can feel confident that it is not a PHA carrier.
This isn't a perfect method, since an error in listing the correct sire could cause the results to be wrong. However, it is a great tool to use when you're shopping for a Dexter. I use it to discover if a Dexter is at risk. Then I could insist upon a PHA test result before buying, but so far, I've been lucky enough to be able to find Dexters that weren't at risk whenever I shopped for a new one.
Brenn was tested in the first round of tests, before the tests were available to the public, and provided some of the information needed to determine which lines carried PHA. I had Beth tested just so I could answer "Yes" when people asked if she had been tested. I was getting tired of explaining why it wasn't necessary to test her. You're the first one I've told why she didn't need to be tested in a long time. Having her tested saved me a lot of strain on my vocal cords 
Gene Bowen
Paradise Farm
Note that the use of the ADCA "descendants" button has been disabled, so that way of finding the lineage of Dexters is not available to us at present. We should pressure the registrar to re-enable the Descendants button.
