Gorignak
member
Farm Facebook page is now up. Stop by and say HI !!
Posts: 569
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Post by Gorignak on Feb 16, 2013 17:27:54 GMT -5
. I don't really have a dog in this fight....yet. But......Aren't most of the described "parents"....Judy's 1300-1400 and the large majority of post 1995-2000 ADCA registered breeding stock the "parents of those new calves". Wouldn't the members with 40 "archaic" tested cows have to re-test with the new protocols. Politically....common ground and common sense usually dictates "grandfathering" and voluntary transitions with rewards prior to fiat and compulsory compliance. DOES THIS MAKE SENSE  ? Re-reading this, I didn't get the sense that folks were calling for the retesting of samples from deceased breeders, or back farther than the current generation. Isn't the problem, the diligent breeders with a couple dozen to 40 -60+ cows who have already tested. Not to mention the "poor folk" who have tested their 3-5-10 cows and bull. I can hear Kirk's arguments echoing from deeper pockets than many might have here. My crazy logger boots cost $450. a pair, and my 21'st century VCR costs $400. While I DO.....ABSOLUTELY...see the value and importance of utilizing any testing tools that would benefit the breed, the argument concerning the loss of animals in the pedigree threads due to inability to shoulder the financial burden has a resonance with me. If testing was implemented before it was VERY affordable, it would support an elitism that may, or may not, be of benefit to the breed. |
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jamshundred
member
Help build the Legacy Dexter Cattle "Forever" Genotype database
Posts: 289 
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Post by jamshundred on Feb 17, 2013 0:27:09 GMT -5
Kirk,
What part of " it isn't needed in this breed" is not getting through?
Microsatellite testing has been fine-tuned and works great in our breed.
We don't need or use the commercial tests that have spurred the SNPS testing in other breeds.
Moving from Blood to the current testing was like going from night to day.
Several steps and expense removed from the testing process not to mention just the cost of packaging and shipping the sample. That is not the case with current tests versus SNPS.
WE do NOT need SNPS and if there is ever a time we do. . . .it is likely science will have found a way to be able to make comparisons between the old and the new.
We have soooooo much to lose and nothing to gain.
Judy
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Post by Cascade Meadows Farm - Kirk on Feb 17, 2013 17:59:27 GMT -5
Kirk, What part of " it isn't needed in this breed" is not getting through? Microsatellite testing has been fine-tuned and works great in our breed. We don't need or use the commercial tests that have spurred the SNPS testing in other breeds. Moving from Blood to the current testing was like going from night to day. Several steps and expense removed from the testing process not to mention just the cost of packaging and shipping the sample. That is not the case with current tests versus SNPS. WE do NOT need SNPS and if there is ever a time we do. . . .it is likely science will have found a way to be able to make comparisons between the old and the new. We have soooooo much to lose and nothing to gain. Judy This isn't about "needs", it's about heading in a smart and logical direction. It's about heading in the SAME direction that everyone else is headed. Most new tests that are coming out are SNP based. For example, I'm pretty certain that the new polled test is SNP based. Older tests are being converted to SNP based testing. The world is moving to SNP for ALL TESTING INCLUDING genotyping and parentage verification. The hereford and angus and simmental and holstein breeds and others have moved to SNP because that's where the world of DNA testing is going. I'll guarantee that down the road we'll be converting to SNP, just like everyone else has been doing. In fact, Dexters are already partially on SNP testing since some of our tests are SNP based. My ONLY point is that it would be a shame (some would call it "stupid") to start testing all females under the old OUTDATED microsatellite method BEFORE we switch to SNP. ALL the other breeds are moving to SNP because that's where the world of DNA testing is going. It's because SNP testing looks at the detail genetic code and is faster and easier and cheaper and more accurate. I don't personally care whether we parentage test or not (I don't feel a need for it).... I'm just saying that if we're going to force everyone to start doing it, then we need to be smart about it and head in the same technological direction as all other breeds. When it comes to technology of any sort, you want to go where the world is going, or you'll get stranded with some outdated or oddball technology. We know the world has been moving to SNP for the past decade. SNP is not "bleeding-edge" technology, it's actually tried-and-true and very well tested for the past 5 years at least. |
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Post by Cascade Meadows Farm - Kirk on Feb 17, 2013 23:44:59 GMT -5
Most DNA labs are using SNP technology in their research because it identifies the detail genetics (where the outdated microsatellite technology fails to do so). The researchers in Germany who recently found the polled gene and developed the test (that UC Davis is using) used modern SNP methods instead of the old clunky expensive and outdated microsatellite methods. www.ncbi.nlm.nih.gov/pmc/articles/PMC3380827/Here's a study explaining that the faster, cheaper, better SNP method HUGELY outperforms the outdated Microsatellite method in parentage verification when identifying animals that are very closely related to each other. Microsatellite genotyping fails to identify one close relative apart from another in highly related herds, where SNP genotyping excels at doing so. www.mendeley.com/research/effectiveness-microsatellite-snp-markers-parentage-identity-analysis-species-low-genetic-diversity-c/PS. On our farm, we don't use any industrial methods at all and could live just fine without any DNA testing at all. We're 100% grass fed, NO GRAIN, 100% pasture raised, no chemicals, no antibiotics, no vaccinations, calves born on pasture with NO assistance 99% of the time. No shots, no vets, EASY TO RAISE. We love our small, and VERY friendly dexter bulls and cows that are raised in a very happy and heritage way. Our 100% grassfed, 100% chemical free dexter beef can't be beat, and our pha-free and chondro-free "shorties" thicken up very fast on grass alone. |
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Post by Olga on Feb 18, 2013 1:09:57 GMT -5
pro·vo·ca·teur noun \prō-ˌvä-kə-ˈtər\Definition: agent provocateur, one who provokes
Example: <a calculating, right-wing provocateur, she has made a career out of controversy for its own sake>
Time and time again I get a feeling that there is an agenda that is being pushed onto the readers of this board. The method of delivery is via a "controversy for its own sake" -- in order to rile up the crowd.
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Post by Julie on Feb 18, 2013 8:03:05 GMT -5
Kirk - I am (mostly) entertained by you playing devil's advocate, but the first article you referenced doesn't have anything to do with comparing microsatellite to SNP. I read it, and it basically was studying the difference between the Celtic polled gene markers compared to the Holstein-Fresian polled gene markers. The article basically concluded that they could be identified in the breeds they studied, and that a cow could carry genes for C and HF polled. This is interesting, but not related to our discussion! Also, I would question their "science" because they used different tests to compare different SNPs. I couldn't get the second article to open.
I think that what Judy and others keep saying is SO important to remember - Dexters are not involved in any of these large scale studies b/c they are not an "economically viable" breed like Holsteins, Angus, etc. Any time you are evaluating a scientific article, you have to look at who published it, and more importantly, who FUNDED it!
I was just curious, as a newbie to the Dexter breed, what genetic studies specific to Dexters have been done. If we can find some genetic researchers with a specific interest in Dexters, this could be very valuable!
I did a quick search for SNP vs. Microsatellite articles, and didn't find anything good, but I did find this:
A local database was developed that contains over 1.8 million bovine SNP and almost 30,000 genes gathered from the databases at the National Center for Biotechnology Information (http://www.ncbi.nlm.nih.gov.ezproxy.lib.vt.edu:8080/genome/seq/BlastGen/BlastGen). Querying the database provided details on each SNP, including its location and functional class. The SNP that are present in a gene locus can have one of the following National Center for Biotechnology Information-defined functional classes: locus-region, coding, coding-synonymous, coding-nonsynonymous, mRNA-UTR, intron, and splice-site. For SNP not located in a gene, the nearest gene was determined by querying the database for a list of genes on the same chromosome as the SNP, and the gene closest to the location of the SNP was identified.
--From an article titled A Whole-Genome Scan to Map Quantitative Trait Loci for Conformation and Functional Traits in Canadian Holstein Bulls published in the Journal of Dairy Science, July 2008.
Does anyone know if Dexters are included in the NCBI database? I am out of time for this "sidetrack" but it is pretty interesting stuff!
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Post by rezzfullacres on Feb 18, 2013 8:23:46 GMT -5
Does anybody remember Super 8 movie film? If you do, that is a good comparison for what is going on with DNA testing. DNA testing is moving ahead in leaps and bounds. Super 8 film did everything that the home movie maker wanted and did it well, we still have some old reels laying around that we can still watch. Now we went from there to VHS/Beta now to DVD and with each generation the quality got better. But as these new technologies came out the same refrain was heard, it won't be around long, it'll never work, nothing can replace the Super 8, BUT they did........Now to my point........The current DNA testing that is being utilized by most Dexter breeders is very good, but it is becoming outdated. Does that mean we should switch, no BUT it does mean we should be having this conversation.....As more and more commercial labs switch to SNP based testing outside lab options for Dexter owners will be restricted, is that a good thing, I don't think so. There are some labs that are trying to convert older results into SNP they are not there yet but they are working on it. If we stay with the current testing, which is good testing, we will at some point in the future be very restricted in the labs we will be able to utilize. My opinion is this, SLOW DOWN.......Do a little more research and speak to some qualified, unbiased scientists and get some outside opinions. Go to VA Tech for an opinion go to Kansas State, Utah State etc etc....All of these schools have Animal Science programs dealing with genetics and they do not have a dog in this fight...Get opinions from these people or other qualified people and than make a decision. I am concerned that if we stick with the testing we are now using we will, in 20 years be looking for a Super 8 film to DVD format converter for DNA, I may be wrong BUT I would like to hear that from someone qualified to answer the question, is that too much to ask? ?? I want to make an informed decision based on science not based on "what we are doing is working great so why change"................. ask Kodak how that worked for them.... Just my opinion... |
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Post by kansasdexters on Feb 18, 2013 8:31:03 GMT -5
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Post by Cascade Meadows Farm - Kirk on Feb 18, 2013 11:28:10 GMT -5
Kirk - I am (mostly) entertained by you playing devil's advocate, but the first article you referenced doesn't have anything to do with comparing microsatellite to SNP. I read it, and it basically was studying the difference between the Celtic polled gene markers compared to the Holstein-Fresian polled gene markers. The article basically concluded that they could be identified in the breeds they studied, and that a cow could carry genes for C and HF polled. This is interesting, but not related to our discussion! I am NOT playing "devils advocate". I am presenting factual DNA science that is 100% related to this discussion. The article that discusses using SNP methodology in finding the polled gene is completely relevant because it shows that DNA researchers have moved to SNP in their research because it is so very effective. SNP is more powerful and more accurate and can be 100% automated (unlike the old outdated semi-manual and error-prone microsatellite technology). SNP-based tests can be bundled together and run in a single automated pass. Here's the text of the second article that explains the FAILURE of microsatellite technology to distinguish between closely related animals (in genotyping), where SNP technology easily does so.
"The European bison (Bison bonasus) has recovered successfully after a severe bottleneck about 90 years ago but has been left with low genetic variability that may substantially hinder parentage and identity analysis. According to pedigree analysis, over 80% of the genes in the contemporary population descend from just two founder animals and inbreeding coefficients averaged almost 0.5, whereas microsatellite heterozygosity does not exceed 0.3.
We present a comparison of the effectiveness of 17 microsatellite and 960 single nucleotide polymorphism (SNP) markers for paternity and identity analysis in the European bison.
Microsatellite-based paternity and identity analysis was unsuccessful because of low marker heterozygosity and is not a practical approach in this species. Simulations using SNP markers suggest that 80-90 randomly selected loci, or just 50-60 of the most heterozygous loci, would be sufficient to ensure successful paternity and identity analysis in this species. For the purpose of standardizing future analysis, a panel of 50-60 bovine SNPs characterized by high heterozygosity and an even distribution in the genome could be selected. This panel of markers could be typed using VeraCode (Illumina) or similar SNP genotyping systems.
The low cost of these SNP genotyping methods compared with a 16 locus microsatellite survey means that off-the-shelf SNP genotyping systems developed for domestic species represent powerful tools for genetic analysis in related species, and can be effective even in bottlenecked species in which heterozygosity of other markers such as microsatellites may be very low." This is article is basically saying the Microsatellite technology is UNABLE to distinguish one close relative from another close relative and is one of the MANY reasons that outdated Microsatellite technology is being abandoned by many labs. www.nature.com/hdy/journal/v103/n4/full/hdy200973a.htmlBy the way, in dexters there is at least one known case where the microsatellite parentage test was WRONG because it confused a young bull with the young bull's sire. |
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Post by Cascade Meadows Farm - Kirk on Feb 18, 2013 12:19:15 GMT -5
Does anybody remember Super 8 movie film? If you do, that is a good comparison for what is going on with DNA testing. DNA testing is moving ahead in leaps and bounds. Super 8 film did everything that the home movie maker wanted and did it well, we still have some old reels laying around that we can still watch. Now we went from there to VHS/Beta now to DVD and with each generation the quality got better. But as these new technologies came out the same refrain was heard, it won't be around long, it'll never work, nothing can replace the Super 8, BUT they did........Now to my point........The current DNA testing that is being utilized by most Dexter breeders is very good, but it is becoming outdated. Does that mean we should switch, no BUT it does mean we should be having this conversation.....As more and more commercial labs switch to SNP based testing outside lab options for Dexter owners will be restricted, is that a good thing, I don't think so. There are some labs that are trying to convert older results into SNP they are not there yet but they are working on it. If we stay with the current testing, which is good testing, we will at some point in the future be very restricted in the labs we will be able to utilize. My opinion is this, SLOW DOWN.......Do a little more research and speak to some qualified, unbiased scientists and get some outside opinions. Go to VA Tech for an opinion go to Kansas State, Utah State etc etc....All of these schools have Animal Science programs dealing with genetics and they do not have a dog in this fight...Get opinions from these people or other qualified people and than make a decision. I am concerned that if we stick with the testing we are now using we will, in 20 years be looking for a Super 8 film to DVD format converter for DNA, I may be wrong BUT I would like to hear that from someone qualified to answer the question, is that too much to ask? ?? I want to make an informed decision based on science not based on "what we are doing is working great so why change"................. ask Kodak how that worked for them.... Just my opinion... Well said and I agree. I'm NOT suggesting that we quickly move to SNP, I'm just suggesting that we SLOW DOWN on genotyping females until a fully informed decision is made on moving to SNP. The Angus folks and Hereford folks and Simmental folks and Holstein folks and others struggled with this too. They did the research and the answer was clearly SNP (even though the decision caused a lot of grief for folks with large herds already tested under the old microsatellite approach). |
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Post by rhonda on Feb 18, 2013 15:40:21 GMT -5
Sounds to me that we as members need to make sure the genotyping of cows and heifers be put on hold till this is sorted out.
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Post by kansasdexters on Feb 18, 2013 17:21:27 GMT -5
This is not something that can be "put on hold". The ADCA currently assigns obligate status for PHA non-carriers and Chondrodysplasia non-carriers, if the sire and dam are shown in the registry as being non-carriers. This designation is given without any parentage verification. It shows up on the pedigree certificates of the newly registered animals and that's what the new owner receives. This "automatic obligate status" is just not acceptable. No animal should receive a designation as a non-carrier unless it has either been tested or has been parentage verified to non-carrier sire and dam.
The first bull that we purchased when we started our herd, we had carefully selected from an experienced breeder. We paid to have this yearling bull examined by a veterinarian for breeding soundness. We drove all the way to Cincinnati, Ohio (from Overbrook, KS) to pick up this bull. We used this bull for 4 years, and he was a wonderful Dexter bull. Then, the requirement for genotyping of herd sires came about. We genotyped him and found out that his sire of record was not his sire. After additional genotype testing (which we paid for) we were able to determine the correct sire. We did further testing on our bull, and found out that he was a PHA-carrier. We then had to test every offspring that he had sired to determine their PHA-status. If our first bull had been sire and dam qualified before he was registered, none of this would have been necessary.
Requiring the genotype and parentage verification of every registered heifer and bull, prior to designating obligate status for PHA or Chondrodysplasia is just common sense. This is something that cannot be put on the back burner for years and years. Every single year that passes results in more and more animals that have errors in their pedigrees. Some of these errors will be very costly to whomever gets stuck with the case(s) of mistaken identity.
Just ask anyone that's had to go through this process of correcting a dam or sire of record. It usually isn't the breeder that gets stuck with this, it ends up being the owner that wants to have a properly registered herd with valid pedigree certificates. It is irresponsible and a detriment to our breed to put off a requirement for parentage verification any longer. We have the technology available, it is affordable ($25 per test), and it should be done by anyone that is offering their registered breeding stock for sale to others. It should also be demanded by any buyer of registered breeding stock.
Patti
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Post by rezzfullacres on Feb 18, 2013 17:58:30 GMT -5
This is something that cannot be put on the back burner for years and years. Every single year that passes results in more and more animals that have errors in their pedigrees. Some of these errors will be very costly to whomever gets stuck with the case(s) of mistaken identity. Patti I agree with you on this point. I just want to make sure we are making the RIGHT choice. There are also several other concerns...... What would be the procedure when a mistake is found, you know there will be some found.. For example......A 15 year old registered cow, Sire still alive and genotyped, has had 13 calves, 8 heifers, 5 bulls....All of the heifers have had at least 2 calves some have 8 calves...3 bulls were steered 2 were used as herd sires and had multiple calves registered both heifers and bulls.....Now we DNA verify and find out the sire is incorrect and there is no matching DNA on file, what is the ADCA procedure for this? If this question can not be answered, we as an association are not ready..... Just asking |
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Post by rhonda on Feb 18, 2013 18:20:42 GMT -5
I'm not saying put testing on hold for years and years..I'm saying settle on a lab first! I personally can't afford to do testing and then do it AGAIN if we switch labs or procedures in the next year or month or whenever. If we start the testing with the understanding that ADCA pays for the switch if it happens--that's another story!
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Post by rezzfullacres on Feb 18, 2013 18:48:02 GMT -5
Rhonda;
I agree with you but will take it 1 step further..... My opinion of what needs to happen is this:
1) Experts need to be consulted as to which scientific tests will best suit the dexter breed now and going forward.
2) Decide which lab offers the ADCA the best deal for all required testing...
3) Implement the plan
We are not talking about years and years we are talking months to make sure that this gets done right, not halfway and than the association ends up spending more time and effort to fix a poorly thought out and implemented plan...
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? Re-reading this, I didn't get the sense that folks were calling for the retesting of samples from deceased breeders, or back farther than the current generation. Isn't the problem, the diligent breeders with a couple dozen to 40 -60+ cows who have already tested. Not to mention the "poor folk" who have tested their 3-5-10 cows and bull. 
