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 AAA genomic enhanced epd's

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PatB



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PostSubject: AAA genomic enhanced epd's   Tue Jan 08, 2013 6:49 am

Take a look at table 1 in the link below.

http://www.angus.org/agi/GenomicUpdateJan2013.pdf

There is another Igenity chip that has not been approved by the AAA as of today that may boost amount of genetic variance account for higher for some traits.

The link to this article is posted for those that might be interested in keeping tabs on genomic developments, Very Happy
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PostSubject: Re: AAA genomic enhanced epd's   Tue Jan 15, 2013 7:29 am



Topigs finds SNPs for litter birth weight, uniformity

Breeding
2480


Topigs has found several SNPs which explain genetic variation in litter birthweight and litter uniformity and can be used to breed sows that farrow large, heavy and uniform litters.


These SNPs have a correlation of almost 0.5 with the animal's true breeding value. This means that almost 50% of the genetic variation for birth weight and uniformity can be explained by these SNPs. The reliability of breeding values of young male selection candidates increases by almost 30% compared to cases where SNP information is not used.

The newly found SNPs speed up genetic progress. The genetic quality of young male selection candidates for litter birth weight and litter uniformity can now be predicted before the end of their performance test. In the past, genetic quality could only be differentiated between full sibs for these traits based on the results of their offspring.

Piglets that start with a high birth weight perform better. High litter birth weights and uniformity in birth weights within litters are therefore highly advantageous for modern pig production systems. Piglets with a higher birth weight are marketed earlier without detrimental effects on carcass quality. Heavy uniform litters make production easier and require less labour. The overall margin is therefore higher for heavy piglets.

With genomic selection technology Topigs is able to speed up the genetic progress for these highly relevant economic traits. Topigs has a unique dataset in which over 500,000 individual birth weights and survival records are collected yearly. Topigs has collected birth weights for several years and now has a database with over 5 million birth weights. Combining this dataset with genomic selection technology offers unique opportunities for creating extra genetic progress.
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PatB



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PostSubject: Re: AAA genomic enhanced epd's   Tue Jan 15, 2013 8:42 am

If the correlation is .5 for a triat then it it explains 25 percent of the variability for that trait.
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LCP



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PostSubject: Re: AAA genomic enhanced epd's   Tue Jan 15, 2013 12:09 pm

MKeeney wrote:


The genetic quality of young male selection candidates for litter birth weight and litter uniformity can now be predicted before the end of their performance test.

Random thoughts, limited by my understanding of genetics and breeding:

I question whether a performance test (I'm thinking of something like Midland) of an individual can ever predict genetic quality of his/her offspring. That would only seem to evaluate the specific combination of genes present in the animal being tested.

I see linebreeding as a genomic test performed over multiple generations.

For someone like myself who has a mixed bag of genetics to being with (commercial or registered alike), it seems like genetic testing for certain traits maybe isn't a terrible thing to do in order to breed like to like. I don't have the advantage of multiple generations of like-to-like breeding, much less close-bred animals. It would seem to me like genomic testing could be used initially to aid in choosing which animals to isolate to begin a line-bred herd. Throw all the stones you want at the tests, they must have at least some merit or else those companies would not be in business, much less be able to charge what they do for the tests.

I'm not saying these tests are the end-all-be-all of genetic selection. But I think today's mainstream thinking of continual outcrossing has made testing more valuable, because there is so much variation to begin with. Anything that can help sort through the mess is going to get some attention.
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PatB



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PostSubject: Re: AAA genomic enhanced epd's   Tue Jan 15, 2013 7:40 pm

I am a frim believer in genetic testing but there are some draw backs to the current tests.

The tests are more accurate for mainstream genetics that went into developing the test. The more ancestors that were tested and the more accurate their epd's the more accurate the test may be and that goes for the number of markers used. The best test only explains little over 50 percent of the variability for some traits and alot less for others. Rumor has it that Igenity has a new test that is 90k and based on alot of work of Iowa state and Dr Taylor, unfortunately the AAA/AGI has not released it yet. If you decide to test at the present time I would suggest testing the herd sires and maybe your cows you would use for linebreeding.
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PostSubject: Re: AAA genomic enhanced epd's   Tue Jan 15, 2013 9:04 pm

PatB wrote:
I am a frim believer in genetic testing but there are some draw backs to the current tests.

The tests are more accurate for mainstream genetics that went into developing the test. The more ancestors that were tested and the more accurate their epd's the more accurate the test may be and that goes for the number of markers used. The best test only explains little over 50 percent of the variability for some traits and alot less for others. Rumor has it that Igenity has a new test that is 90k and based on alot of work of Iowa state and Dr Taylor, unfortunately the AAA/AGI has not released it yet. If you decide to test at the present time I would suggest testing the herd sires and maybe your cows you would use for linebreeding.

Curiosity finally got the best of me- and I submitted the home raised Juanada Rito bull yesterday....Just curious to see if what they say matches to what I see... I will also probably test the Bannon 2 BY bull I also plan to use this spring....
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outsidethebox



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PostSubject: Re: AAA genomic enhanced epd's   Wed Jan 16, 2013 6:35 am

It is my belief that these genetic tests are both worthless and useless...in other words-a scam. Their popularity can be attributed to "There is a fool born every minute". Their contributions to either quality or quantity are nonexistent. The human's ability to rationalize remains our most remarkable feature and here is "exhibit A" . This reminds me of religion-man defining a God we know nothing about yet claiming to be fully knowledgeable. We would be light years ahead of our current position if we only decided to pay attention to the "simple" empirical evidence that smacks us in the face every day.
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PatB



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PostSubject: Re: AAA genomic enhanced epd's   Wed Jan 16, 2013 7:09 am

Oldtimer wrote:
PatB wrote:
I am a frim believer in genetic testing but there are some draw backs to the current tests.

The tests are more accurate for mainstream genetics that went into developing the test. The more ancestors that were tested and the more accurate their epd's the more accurate the test may be and that goes for the number of markers used. The best test only explains little over 50 percent of the variability for some traits and alot less for others. Rumor has it that Igenity has a new test that is 90k and based on alot of work of Iowa state and Dr Taylor, unfortunately the AAA/AGI has not released it yet. If you decide to test at the present time I would suggest testing the herd sires and maybe your cows you would use for linebreeding.

Curiosity finally got the best of me- and I submitted the home raised Juanada Rito bull yesterday....Just curious to see if what they say matches to what I see... I will also probably test the Bannon 2 BY bull I also plan to use this spring....

I hope you used phizer for the test.
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MKeeney
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PostSubject: Re: AAA genomic enhanced epd's   Wed Jan 16, 2013 7:26 am

outsidethebox wrote:
It is my belief that these genetic tests are both worthless and useless...in other words-a scam. Their popularity can be attributed to "There is a fool born every minute". Their contributions to either quality or quantity are nonexistent. The human's ability to rationalize remains our most remarkable feature and here is "exhibit A" . This reminds me of religion-man defining a God we know nothing about yet claiming to be fully knowledgeable. We would be light years ahead of our current position if we only decided to pay attention to the "simple" empirical evidence that smacks us in the face every day.
would it be sacreligious for me to say...Amen cheers Smile
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larkota



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PostSubject: Re: AAA genomic enhanced epd's   Wed Jan 16, 2013 8:53 am

outsidethebox wrote:
It is my belief that these genetic tests are both worthless and useless...in other words-a scam. Their popularity can be attributed to "There is a fool born every minute". Their contributions to either quality or quantity are nonexistent. The human's ability to rationalize remains our most remarkable feature and here is "exhibit A" . This reminds me of religion-man defining a God we know nothing about yet claiming to be fully knowledgeable. We would be light years ahead of our current position if we only decided to pay attention to the "simple" empirical evidence that smacks us in the face every day.

little late but better then never, happy birthday.
my present to you.


We shall not grow wiser before we learn that much that we have done was very foolish.
Friedrich August von Hayek


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PostSubject: Re: AAA genomic enhanced epd's   Wed Jan 16, 2013 10:25 am

outsidethebox wrote:
It is my belief that these genetic tests are both worthless and useless...in other words-a scam. Their popularity can be attributed to "There is a fool born every minute". Their contributions to either quality or quantity are nonexistent. The human's ability to rationalize remains our most remarkable feature and here is "exhibit A" . This reminds me of religion-man defining a God we know nothing about yet claiming to be fully knowledgeable. We would be light years ahead of our current position if we only decided to pay attention to the "simple" empirical evidence that smacks us in the face every day.

Sure wish good sense like this would spread as fast as BS.
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LCP



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PostSubject: Re: AAA genomic enhanced epd's   Wed Jan 16, 2013 2:04 pm

outsidethebox wrote:
It is my belief that these genetic tests are both worthless and useless...in other words-a scam. Their popularity can be attributed to "There is a fool born every minute". Their contributions to either quality or quantity are nonexistent. The human's ability to rationalize remains our most remarkable feature and here is "exhibit A" . This reminds me of religion-man defining a God we know nothing about yet claiming to be fully knowledgeable. We would be light years ahead of our current position if we only decided to pay attention to the "simple" empirical evidence that smacks us in the face every day.

"worthless and useless" to whom? I would agree with you, if everyone was using cattle that breed true. There would be no need to test, because the "ancestral pen of cattle" that contributed to the individual is known. I have a cow that is 10 years old. She's a good cow, good enough anyhow, and if I were to start my own line, I'd pick her to be the foundation. I don't know her dam or sire. No idea what is in her pedigree, other than its black. What can I tell about her genotype by just looking at her? This is where I believe these tests might have a place. Again, if you have consistency in a pedigree, I would say that it eliminates the need for much testing of any sort, genetic or otherwise.

Do I understand you correctly that you think the numbers from the tests have no correlation to what is actually found in the animal's genetic makeup? What do you base your opinion on? I can respect your opinion if you substantiate it with facts.

Let's say for the sake of argument that there is a genetic test someday that does correlate to reality. What percent correlation would it take to make the test worthwhile? How much would it be worth to have that information for relevant traits? What if they identified markers for libido, or udder quality, or mothering ability? Maybe this question is better asked of LL - What would it have been worth to have a tool that helped identify the carriers of unwanted (or desired) genetic material, rather than having to wait on their offspring to reveal it?

My opinion might not be popular here. However, I find it puzzling that amongst people who are so interested in genetics, there is so little interest in viewing and selecting them other than through the phenotype said genetics produce. I know the phenotype is what we are after. If it is possible to get a thumbnail sketch of what that phenotype potentially could be by looking at genetic markers, then I'm interested at the right price.

My analogy is like this - I want to build a house. I might not be good at reading blueprints, but if I could get blueprints that show even 30% of what the house will be like, that's better than just taking the carpenter's word for it and waiting until its done to figure out if its what i want. Maybe if I had more confidence in the carpenter my thinking would be different.
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outsidethebox



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PostSubject: Re: AAA genomic enhanced epd's   Wed Jan 16, 2013 10:40 pm

Simply put, the genome is far too complicated for these tests to be meaningful. And I do not see such a course ever being pragmatically useful...there are simply too many variables. Close breeding, line breeding and like-to-like breeding offer much better options for building an optimal genome than a narrow test.
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PostSubject: Re: AAA genomic enhanced epd's   Wed Jan 16, 2013 11:06 pm

outsidethebox wrote:
Simply put, the genome is far too complicated for these tests to be meaningful. And I do not see such a course ever being pragmatically useful...there are simply too many variables. Close breeding, line breeding and like-to-like breeding offer much better options for building an optimal genome than a narrow test.

The line One herd has been selected for one trait for 84 yrs and they have identified the snp for yr wt and can predict that trait with 7% more acc than a random calf from a sale barn. IMO that is a remarkable start to Gene testing. But for that acc, to earn my dollars that % needs to be way higher than 60% and they have a long way to go at this time. Ten twenty years from now they may be where they need to be but today the 50k chip is nothing more than advertising, to increase the sale Avg. By us using that as a tool today is merely funding the laboratory.
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PatB



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PostSubject: Re: AAA genomic enhanced epd's   Thu Jan 17, 2013 5:50 am

W.T wrote:
outsidethebox wrote:
Simply put, the genome is far too complicated for these tests to be meaningful. And I do not see such a course ever being pragmatically useful...there are simply too many variables. Close breeding, line breeding and like-to-like breeding offer much better options for building an optimal genome than a narrow test.

The line One herd has been selected for one trait for 84 yrs and they have identified the snp for yr wt and can predict that trait with 7% more acc than a random calf from a sale barn. IMO that is a remarkable start to Gene testing. But for that acc, to earn my dollars that % needs to be way higher than 60% and they have a long way to go at this time. Ten twenty years from now they may be where they need to be but today the 50k chip is nothing more than advertising, to increase the sale Avg. By us using that as a tool today is merely funding the laboratory.

The research community is moving to the 770k chip and higher. There has been work done in sequencing the whole genome of select bulls and more will come as the price continues to fall on this procedure. The genome test of today is like the personal computer of early 90's not that poweful but useful. In 10 years we should have a far greater understanding of genetics and actual inheritance of genetic material.
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larkota



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PostSubject: Re: AAA genomic enhanced epd's   Thu Jan 17, 2013 8:25 am

PatB wrote:
W.T wrote:
outsidethebox wrote:
Simply put, the genome is far too complicated for these tests to be meaningful. And I do not see such a course ever being pragmatically useful...there are simply too many variables. Close breeding, line breeding and like-to-like breeding offer much better options for building an optimal genome than a narrow test.

The line One herd has been selected for one trait for 84 yrs and they have identified the snp for yr wt and can predict that trait with 7% more acc than a random calf from a sale barn. IMO that is a remarkable start to Gene testing. But for that acc, to earn my dollars that % needs to be way higher than 60% and they have a long way to go at this time. Ten twenty years from now they may be where they need to be but today the 50k chip is nothing more than advertising, to increase the sale Avg. By us using that as a tool today is merely funding the laboratory.

The research community is moving to the 770k chip and higher. There has been work done in sequencing the whole genome of select bulls and more will come as the price continues to fall on this procedure. The genome test of today is like the personal computer of early 90's not that poweful but useful. In 10 years we should have a far greater understanding of genetics and actual inheritance of genetic material.

why select bulls and not random. seems like they need the answer before the why.
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PostSubject: Re: AAA genomic enhanced epd's   Thu Jan 17, 2013 11:16 am

Quote :
In 10 years we should have a far greater understanding of genetics and actual inheritance of genetic material.

Should I freeze dry the cows and wait until 2023 to get myself on the right track? At least by then I should be old enough to know better. What happens in 2023 when you find out that all of your cattle are junk? This 10 year stuff seems rough when the cows eat every day and I have to ponder if they are worth the feed. Decisions, decisions. Good thing I have linebred sheep to fall back as I wait to get my decade away cattle gene report.
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PostSubject: Re: AAA genomic enhanced epd's   Thu Jan 17, 2013 11:57 am

Larkota

I have no idea own the selection criteria that was used for selecting which bulls would be sequenced. I know EXt and 036 were whole genome sequenced. I do not know who and how many total have been done or planning to be done.
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PostSubject: Re: AAA genomic enhanced epd's   Thu Jan 17, 2013 12:08 pm

EddieM wrote:
Quote :
In 10 years we should have a far greater understanding of genetics and actual inheritance of genetic material.

Should I freeze dry the cows and wait until 2023 to get myself on the right track? At least by then I should be old enough to know better. What happens in 2023 when you find out that all of your cattle are junk? This 10 year stuff seems rough when the cows eat every day and I have to ponder if they are worth the feed. Decisions, decisions. Good thing I have linebred sheep to fall back as I wait to get my decade away cattle gene report.

You are free to use what ever tools you like in your breeding program. I started using computers in the early eighties and compared to todays computers they were limited. Even the early PC was more capable then the electric typewriter which was better than the manual typewriter which was a improvement over hand written letters. If you choose not to take advantage of the current technology that is your choice but why ridicle the process for those that do.

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PostSubject: Re: AAA genomic enhanced epd's   Thu Jan 17, 2013 2:10 pm

PatB wrote:
EddieM wrote:
Quote :
In 10 years we should have a far greater understanding of genetics and actual inheritance of genetic material.

Should I freeze dry the cows and wait until 2023 to get myself on the right track? At least by then I should be old enough to know better. What happens in 2023 when you find out that all of your cattle are junk? This 10 year stuff seems rough when the cows eat every day and I have to ponder if they are worth the feed. Decisions, decisions. Good thing I have linebred sheep to fall back as I wait to get my decade away cattle gene report.

You are free to use what ever tools you like in your breeding program. I started using computers in the early eighties and compared to todays computers they were limited. Even the early PC was more capable then the electric typewriter which was better than the manual typewriter which was a improvement over hand written letters. If you choose not to take advantage of the current technology that is your choice but why ridicle the process for those that do.

What are doing now with this "beyond the typewriter" info? Am I ridiculing the process or wondering why you are excited over something that you and others are guessing might, could, should, would happen (but will not in the form that you are guessing) in about in ten years? With all of the modern stuff you cite, do you not think that the current gene technology will be old news and out of date in 10 years? We'll send our robot out in the pasture or we'll be aiming a ray gun or our cell phone "i pencil" at a cow and it will tell us everything we want to know or we'll look on Google Maps and zoom in to a cow in the pasture and read her DNA. What about making a GM cow that poops and pees herbicides so we no longer have to spray weeds? Dream BIG!

But, are you and "they" (whoever they are) exhausting every possible tool that is available to mankind today to find out the value of individual cattle or is this just a far-off brass ring that is something to keep us wanting and waiting? What are you doing TODAY to make your cattle better? That's the point. And what difference has gene technology made so far for you? Are Angus better? Are you making more money? Are your cows more fertile and have extra longevity? Are your bulls more fertile? Are your steers more tender? Have you been able to delete out all of the non- Angus genes? What do you want and why can you not improve it now? It reminds me of busy work.
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LCP



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PostSubject: Re: AAA genomic enhanced epd's   Thu Jan 17, 2013 6:54 pm

outsidethebox wrote:
Simply put, the genome is far too complicated for these tests to be meaningful. And I do not see such a course ever being pragmatically useful...there are simply too many variables. Close breeding, line breeding and like-to-like breeding offer much better options for building an optimal genome than a narrow test.

I agree that strategic breeding is a more reliable option for building the desired genotype, at this point anyhow. The disadvantage of relying solely on breeding is time. Perhaps I'm too optimistic, but I think DNA tests will get reliable enough to be used in helping make breeding decisions.

EddieM wrote:
Dream BIG!

Would have you believed they could make rootworm-resistant corn 20 years ago? People thought the world was flat too. Technology is exploding. Never say never.

I also agree that there are many who will not use the proven "technology" of breeding systems. That doesn't seem like a good enough reason to throw cold water on the possibilities of new technology. In the meantime, I'm going to use the Tru-Line approach but keep my ear to the ground on what could be.
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outsidethebox



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PostSubject: Re: AAA genomic enhanced epd's   Thu Jan 17, 2013 9:34 pm

"I agree that strategic breeding is a more reliable option for building the desired genotype, at this point anyhow. The disadvantage of relying solely on breeding is time. Perhaps I'm too optimistic, but I think DNA tests will get reliable enough to be used in helping make breeding decisions."

LCP, we simply have very different perspectives on this matter. I do not believe you could be more wrong than you are here but that is your prerogative...and mine too. As I see it, there is no reliability within the current data base and, in this regard, I do not believe there will ever be sufficient information to produce optimally functioning cattle. I agree with Eddie. Quit looking for a flash in the pan and get on with the business of breeding the best propotent cattle you can to suit your purposes. EBVs and this genetic profiling may have some value if you know how to capture it. However, if your breeding system is not holistic in its approach it is an utter waste of time and effort-you will absolutely not save any time...you will always be chasing your tail and opening another can of worms.
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PostSubject: Re: AAA genomic enhanced epd's   Thu Jan 17, 2013 9:50 pm

outsidethebox wrote:
"I agree that strategic breeding is a more reliable option for building the desired genotype, at this point anyhow. The disadvantage of relying solely on breeding is time. Perhaps I'm too optimistic, but I think DNA tests will get reliable enough to be used in helping make breeding decisions."

LCP, we simply have very different perspectives on this matter. I do not believe you could be more wrong than you are here but that is your prerogative...and mine too. As I see it, there is no reliability within the current data base and, in this regard, I do not believe there will ever be sufficient information to produce optimally functioning cattle. I agree with Eddie. Quit looking for a flash in the pan and get on with the business of breeding the best propotent cattle you can to suit your purposes. EBVs and this genetic profiling may have some value if you know how to capture it. However, if your breeding system is not holistic in its approach it is an utter waste of time and effort-you will absolutely not save any time...you will always be chasing your tail and opening another can of worms.

The new test's will not stop for a long time when they do they may have some crediblity untill then we are freeze drying cows. Iain tell me how to thaw them out .....
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PostSubject: Re: AAA genomic enhanced epd's   Thu Jan 17, 2013 9:55 pm

I would love to "look inside" and find true inbreeding levels; and that can be done right now; just costs too much...about all this amounts to at the moment is the registered breeder financing the genetic companies test development...nice of the breeders to do this; in return, they can promote they have, and the commercial buyer pays for...isn`t that the way it always works?? the commercial producer payyyyyyyysssssssss...does he get return?
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PostSubject: Re: AAA genomic enhanced epd's   Thu Jan 17, 2013 10:06 pm

MKeeney wrote:
I would love to "look inside" and find true inbreeding levels; and that can be done right now; just costs too much...about all this amounts to at the moment is the registered breeder financing the genetic companies test development...nice of the breeders to do this; in return, they can promote they have, and the commercial buyer pays for...isn`t that the way it always works?? the commercial producer payyyyyyyysssssssss...does he get return?

Mike the commerical man gets the sastifaction of saying B.O.H.I.C.A. Bend over here it comes again. And the sad part is dosent even get any pleasure out of getting screwed.
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