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Post by Donlin Stud on Dec 21, 2014 23:19:28 GMT
As we move along with our closed herd’s breeding plan, we are noticing the ‘pairing up’ of more numbers against some of the genetic markers.
Which has raised a couple of questions with us given our Dexters have been part of a grade up program:
1. Are the numbers noted in our markers similar to those for ‘traditional-lined’ Dexters?
2. Are we concentrating some of those markers whose numbers would never be found in the traditional-lined Dexter?
It is something we would like to ‘watch’ but have to ask a favour of breeders with traditional lined Dexs if they/you wouldn’t mind sharing with us, solely for personal use only, those numbers?
Don’t want names, age or sex as I am only interested in the numbers found at each marker and how particular numbers relate to numbers of our Dexs.
Happy for a PM or even an email which is available to forum members under my profile if you wouldn’t mind sharing? It certainly can be two-way for those who are interested as we don’t mind at all.
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Post by Donlin Stud on Dec 23, 2014 0:26:32 GMT
Oh am I reading this correctly that there could very well be an identifiable difference between the numbers for those Dexters influenced by an upgrade program and traditional Dexters?
[From Judy's posted article from the Winter Bulletin]:
In the course of this process it was noticed that three alleles (TGLA227/89, ETH10/214 & HEL5/163) out of the 22 loci tested were not present in any pure Dexter sample, either here or in the U.S.A.. It is clear that these must have come from Bullfinch’s sire, Charley Pudding,
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Post by jamshundred on Dec 23, 2014 0:57:54 GMT
Donna,
Oh my goodness! All these interesting conversations starting and I have wrapping! And so much more to get done!
Your question is intriquing. . .and I am not sure if there is an answer.. We have to toss it around a bit. I have wondered if the markers have significance.. and I think they do. .. . . . I think there may be breed specific markers. I know the Angus have markers for their breed. I am working on that now. Because of the Bullfinch issue I have been trying to find a Guernsey herd that does DNA testing to see if there could be markers specific to Guernsey cattle. ( This is absolutely a long shot). They do test for A2 through UCD. . . . and lots of Guernsey's have been tested and this tests does derive some of the same markers as the parentage panel.
I have tested Platinum and he has markers not present in any of the non-Platinum bloodline cows I have tested but he also has markers that are in all of them. I cannot say if there are breed specific markers in Dexters.
As to what they mean. Nothing that I know of yet. . . . . .but as DNA testing progresses me may come to learn they do mean something. For now. . all they mean is that one came from Dad and one from Mom. The current 16 panel are unique markers from the genome that were considered to be the best ones for determining parentage in cattle. All cattle. All cattle breeds. Some of the markers used in the English genotype are not reported in the US and some of the US markers are not reported in the UK markers. . so we primarily only have the ISAG markers to compare.
Lots to think and discuss after the holidays.
Judy
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Post by Donlin Stud on Dec 23, 2014 1:08:52 GMT
Hi Judy - When I emailed you our Dexter herd listing for Legacy, there was a second sheet in the same Excel book listing the reported markers for each Dexter. If (when you have time and get to this after the hols)I would be really interested to know what has popped up in our markers when compared to those of traditional Dexter lines. I am not sure if there is information there which would be useful to us in our quest for a 'real' Dexter or if its just a nice-to-know for possibly sometime down the track but I do want to now know. Im really excited by the possibility  |
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Post by cascade on Dec 23, 2014 2:18:54 GMT
Oh am I reading this correctly that there could very well be an identifiable difference between the numbers for those Dexters influenced by an upgrade program and traditional Dexters? [From Judy's posted article from the Winter Bulletin]: In the course of this process it was noticed that three alleles (TGLA227/89, ETH10/214 & HEL5/163) out of the 22 loci tested were not present in any pure Dexter sample, either here or in the U.S.A.. It is clear that these must have come from Bullfinch’s sire, Charley Pudding,
Be VERY careful not to jump to conclusions when looking at the data. The article in the Winter Bulletin is FULL of unscientific conclusion jumping. If two brown eyed people of English descent have a blue eyed baby, and the mailman has blue eyes, the writer of the article would say "It's clear that there was hanky-panky involving the mailman" But that's NOT clear. Many brown eyed people of English descent carry recessive blue eyed genes. A real scientist would discuss the problems with having too small of samples and would list ALL of the possibilities supported by the data and discuss the probability of each possibility, instead of jumping to a conclusion. |
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Post by Donlin Stud on Dec 23, 2014 2:29:32 GMT
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Post by legendrockranch on Dec 23, 2014 3:44:21 GMT
Oh my, haven't we had enough discussions on what a "real" Dexter is? We have Andrew Sheppys articles with animals that are not "real" Dexters according to some. Dun Dexters aren't real Dexters now? GIVE IT A BREAK. They are all Dexters. Just look at how the breed started. Look at all the time that passed where we had no parentage verification, years and years and years of possible errors. YOUR Dexter is NOT any better/purer than mine and vice versa. Judy you keep talking about the lack of purity with Platinum & Lucifer. I'll keep talking about all the other 100's of other Dexters you are not chasing down and trying to prove purity of lack there of.
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Post by Deleted on Dec 23, 2014 14:58:59 GMT
donlindexters, maybe interesting to know but keep in mind you are looking at 16 markers out of 3 billion. You could breed for those 16 markers and if the other 3 billion were way off you would have something that did not even resemble a dexter. Now if you only new the other 3 billion you would be all set |
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Post by genebo on Dec 23, 2014 15:57:24 GMT
ISAG is the organization that selects which markers shall be used for parentage verification. They specify 20 markers that have been used by various member labs. A core of 13 of these markers are the most commonly used. Genotypes suitable for international acceptance must include these 13 markers. It is optional for the testing lab to use more than 13 markers. Each lab is free to select which additional markers they use, selecting from the 20.
A disclaimer says that these 20 markers are chosen by the individual labs based upon the amount of variance noticed in them in all breeds' genotypes. This seems to make sense to me, since there would be no purpose in testing for a marker that was the same in all cattle. The disclaimer states that none of the markers used in parentage verification have been shown to be in control of the traits of the cattle. That means that none of them can tell you what color the animal is, or whether it is male or female, or any other traits. The information that controls the animal's traits is buried in other locations.
Based upon that, it would be a big assumption to think that any of those markers could be useful in determining breed. Mr. Sheppy tried to deduce any such association with an animal's breed in the Carlisle report, and could not. The only difference in then and now is that he now has a genotype that was developed in England that disagrees with a genotype for the same animal that was developed at UC Davis.
When this was pointed out to him, Mr. Sheppy said that it was too late to change his paper. It had already been prepared for publication
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Post by legendrockranch on Dec 23, 2014 16:32:27 GMT
I have still not received an answer as to if SNP's we used in this new testing as opposed to microsatellite markers. Mr. Sheppys first article mentioned SNP's however in my mind it is still inconclusive as to what was used. |
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Post by jamshundred on Dec 23, 2014 18:02:23 GMT
Barb,
The Cardiff project was done with microsatellite markers. I am guessing that is what was used in any analysis. I don't think all the samples were re-done using snips. I do not think this is any new project. I think it was merely a different view of existing data. I don't know for sure. . . and note I am stating that I am speculating. . . but I think Sponenberg is the basis of this new article. I believe he visited England and did some "consulting" ( may be a loose description maybe "discussion" would be better ) with folks over there. I know he was working on color research because Dr. Lawson referred me to him regarding research on the Colorado herd. I never followed through because he was busy with some other things at the time. It would seem Dr. Sponenberg's theory of determining introgression is strongly connected to this recent article.
Kirk is right. This is an article heavy in observation and opinion. . . . not science. But it freshens and old discussion.
My own curiosity is wondering what the "new" science referred to in the article with reference to Agriculture is about!
Judy
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Post by jamshundred on Dec 23, 2014 18:12:28 GMT
Donna,
I did not look at the markers! I just needed the case numbers. . . . . . and I do NOT use markers on which I have not paid for the testing unless I specifically have permission from an owner and they are fully informed as to any reason I would want them. If you want me to I will do that after the holidays. There is little to learn from the markers currently because we don't have other breeds available for comparison. My curiosity has been jiggled and I am going to try and see if there are breeds who now have established breed markers other than Angus. Or maybe someone else with boundless curiosity and time for research would find that an interesting project to take on?
Judy
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Post by Donlin Stud on Dec 23, 2014 20:53:03 GMT
Donna, I did not look at the markers! I just needed the case numbers. . . . . . and I do NOT use markers on which I have not paid for the testing unless I specifically have permission from an owner and they are fully informed as to any reason I would want them. If you want me to I will do that after the holidays. There is little to learn from the markers currently because we don't have other breeds available for comparison. My curiosity has been jiggled and I am going to try and see if there are breeds who now have established breed markers other than Angus. Or maybe someone else with boundless curiosity and time for research would find that an interesting project to take on? Judy Hi Judy Absolutely understand why you wouldnt have looked at the markers in my spreadsheet but I intentionally sent them If I didnt want you to have our stud's genotypes then I would have removed that sheet before sending it to you But in future I will put such into writing for you as I do completely understand where you are coming from I cant and dont see what the deal is [sharing genotypes] and maybe that is because we (Aussies) have a grade up program with a well-established genotyping and PV requirement. Information is gold ! Your experience and knowledge is something I only dream about having, so I am more than happy to share any information that can/may be of assistance. Maybe because we do have the grade up program and we do genotype, this sort of information can be used as a comparison/controller in endeavours similar to the articles posted on this forum? Our stud wants the same [traditional] but we are starting way behind the 8 ball but that doesn’t mean we throw our hands up in the air and say its too hard because its not. |
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Post by Donlin Stud on Dec 23, 2014 21:13:34 GMT
The only difference in then and now is that he now has a genotype that was developed in England that disagrees with a genotype for the same animal that was developed at UC Davis. When this was pointed out to him, Mr. Sheppy said that it was too late to change his paper. It had already been prepared for publication Hi Genebo My thought from reading this info went straight to: When did the UK begin their grade up program? And the UK only requires PV of bulls for registration. Could this have had any influence on the differences with UCD I wonder? Its all very interesting........ |
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Post by jamshundred on Dec 24, 2014 14:50:38 GMT
Donna,
No. I think the issue with the differences in the genotype of Pardon Bullfinch in the Cardiff research and that of UCD is a matter of the scientist reading the test results. Rounding off usually means a number is one or two digits different. The Bullfinch number is off 6 digits on one and 8 digits on the other. That is a major difference that can only be attributed to error. . . . and the error HAS to be in the UK genotype. Bullfinch has offspring that have confirmed with the UCD genotype. . and . . . . most important. . . . UCD reports to the ISAG standard which is a standardized method of reading and reporting the markers. You have seen the example that Gene gave on the rounded numbers from the Texas lab. . . . . well, there is another lab that does DNA in the Dexter breed here in the US and they round as well, and sometimes as much as three digits. . . and some of the tests from that lab were transferred to UCD and then offspring parentage compared. Talk about a nightmare! The animals all had to be redone. The testing lab refused to redo the tests and report to the standard.
Apparently there are a couple ( sometimes three) of locus in the ISAG panel which are more difficult to read and report. These are the locus that labs tend to "round-off" to the nearest number. ( I do not consider "nearest number" to be three digits off).
The most often found is the BRR that Gene discussed and TGLA126. These two are usually where the reading differences between labs are found that cause parentage non-confirmed.
All the markers in the Bullfinch ISAG panel were off by at least one digit with the exception of SPS115 which matched, TGLA126 was off 3 digits in each marker type, ETH225 being 3 digits on both marker types, but then in TGLA 227 the UK markers were 89/99 while the UCD markers are 81/93. That is too many digits. There IS a problem. Since that IS the marker that was specifically used as comparison in the article. . . the analysis is faulty.
Also, for the sake of comparison, in this locus (TGLA227) the 81 can be found in Legacy animals from the Piehota herd, ( no Bullfinch)and in one Legacy animal from the Martz herd. The 93 marker is found in the US herd in animals that did not have Bullfinch in the pedigree and is often found in animals in my herd or that I have tested. It is in all the Colorado animals for instance. That does NOT mean that all the Bullfinch markers are found in the Legacy and traditional cattle that do not descend from him There are a couple markers that I do not have in any of my animals. So there is nothing that proves the status of his lineage either way. Yet.
Judy
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