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aj

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Do Shorthorns have the same markers...…..the same amount of markers that the Angus cattle have? They are the same species. Why won't the Angus 50k test work for Shorthorns? What about the Simi Angus?
 

cbcr

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From our understanding, there are certain alleles that are common among the bos Taurus breeds.  But beyond those common alleles there are differences between the breeds.

So in each trait there is the possibility of having from a few to several alleles.  For example in a single trait there could be say 10 alleles, but within that group the may only be 2 or three of the that are common with other bos Taurus breeds.

This is why companies, such as Neogen/GeneSeek have different tests that are offered.  A basic test looks at those common alleles between the box Taurus breeds.  Then when the higher genomic test are used, they become more breed specific.

Hope that this gives some explanation of the differences.
 

knabe

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The same marker (chapter title) May (will) have different alleles across different populations.

The markers need to be validated in each population

That’s why they don’t work and will sorta never work except on the populations that markers are developed on. They get better and better the more the population is bottlenecked.

I really don’t see much value for them anymore.

The tests need good contemporary groups and there simply isn’t the resources to sample adequately across populations.

Causal genomic features and decorations (methylation) are mot remotely ready for prime time and are mainly a curiosity.

Who in their right mind is going to insure diversity from animals that are otherwise good to find the culprit for no milk or any trait.

It’s simply good enough to try stuff. Most people can’t be bothered with the difference between a terminal bull and a female bull. Much simpler to just buy replacements. For many, it’s just not economically viable to raise replacements.

Etc.
 

knabe

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A few have said there just isn’t that much difference In the breeds with regard to snps.

To me, that is an admission something else is going on that the industry hasn’t been capitalize on commercially.

I don’t see anything on the horizon addressing this.

Vitaferm is doing a methylation Seqg project to see if there is a difference there.

Methylation Seqg is just another strategy to find markers for something.

It may be best used for disease detection and reflex testing (to see if disease still present) and not good for “performance” traits.

Which is why it may help for pregnancy rates if that is associated w something environmental.
 

aj

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Color me as skeptical on the deal. I would think it would take a while before data would even come in. I assume the Angus breed has the numbers to put together a workable program. In the back of my mind...…..I wonder.....does the Shorthorn breed have a "tenderness" gene? If the breed does.....how do you discover it and prove it? Apparently the Red Angus test is slightly different than the Angus test? How much Holstein and Chianina is left in the Angus breed? If Simmental, Shorthorn, Gelbvieh, and Limi's all take the same test's...…..how would this evaluation shake out. If the Shorthorn would have a "tenderness" gene......the breed could rise to next level in the beef industry. Or another breed.....whatever.
 

cbcr

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The GeneSeek Igenity profile was designed and validated for crossbred or straightbred cattle with backgrounds of Angus, Red Angus, Simmental, Hereford, Limousin and Gelbvieh

This test has 16 traits and tenderness is among them.

This test will work for box taurus breeds.  My understanding with talking to them that they have more data on the above 6 breeds, but it can be used for other breeds as well.  Again they are mainly looking at the common alleles that are among the breeds.

To be able to have a test that is more specific for the Shorthorn (or any other breed) a central collection point would need to be done and all of the resulting data collected.  Once there is enough (around 1,000) samples the GeneSeek can be petitioned to evaluate the data.

One thing that we disagree with is that most breed associations want to say that the data belongs to them.  That to us is wrong.  You as the breeder or owner of the animals and you have paid for the testing, etc. are the owners of the data.

If as a group there is interest in a central collection of the data, we would be willing to help breeders in that endeavor.
 

knabe

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Validated with who.

Where is the dada.

Has it been published, peer reviewed and replicated?

Don’t think so.
 

knabe

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The complete lack of ability to produce contemporary groups across even 10% of a breed is impossible.

No one will pay for it.

Cattle are adapted to different regions.

The tests are simply pointless at this point in time.

 

knabe

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What is a test expected to test.

Stayability?

By a bull from a cow that has had 10 calves.

Who can wait for that.

How was she raised?

Etc etc etc.
 

cbcr

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knabe, it seems that you are against genomic testing, that is fine but to each his own.

Genomics are a tool, but I can say that, yes, they are over used and abused.  They are used to market dairy and beef bulls and cows, used in calculating genomic enhanced EPD's and evaluations, etc.

Many breeders and people wonder with the genomics that we have today, how many bulls (and females) that have an impact on breeds would have been overlooked if genomics had been available in their day.  How many animals today that could impact a breed are overlooked because of genomics?

At the same time, with genomics being such widely used and touted, if breeds do not utilize them they will be at a disadvantage when it comes to promoting and advancing the general use of the breed.

It seems that today, so many breeders want to breed by numbers.  Gone are the days where the older breeders made breeding decisions with out EPD's or genomics.  Some feel we had better cattle.

Again, while we may like or dislike EPD's and genomics, they are here and will have a continued use now and in the future.

 

knabe

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cbcr said:
knabe, it seems that you are against genomic testing, that is fine but to each his own.


not against it.


there is no validation.


i'm against stuff that doesn't work and is portrayed as such
 

knabe

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cbcr said:
if breeds do not utilize them they will be at a disadvantage when it comes to promoting and advancing the general use of the breed.

It seems that today, so many breeders want to breed by numbers.  Gone are the days where the older breeders made breeding decisions with out EPD's or genomics.  Some feel we had better cattle.

Again, while we may like or dislike EPD's and genomics, they are here and will have a continued use now and in the future.


producers may be required to use only select genomics similar to hogs. genomics won't even be availabe to indifidual producers, because with current implementation, it isn't helpful.


producers have been breeding by numbers for a while without genomics.


epd's and genomics simply don't work for niche breeds (not angus or holstein)
 

doc-sun

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cbcr said:
knabe, it seems that you are against genomic testing, that is fine but to each his own.

Genomics are a tool, but I can say that, yes, they are over used and abused.  They are used to market dairy and beef bulls and cows, used in calculating genomic enhanced EPD's and evaluations, etc.

Many breeders and people wonder with the genomics that we have today, how many bulls (and females) that have an impact on breeds would have been overlooked if genomics had been available in their day.  How many animals today that could impact a breed are overlooked because of genomics?

At the same time, with genomics being such widely used and touted, if breeds do not utilize them they will be at a disadvantage when it comes to promoting and advancing the general use of the breed.

It seems that today, so many breeders want to breed by numbers.  Gone are the days where the older breeders made breeding decisions with out EPD's or genomics.  Some feel we had better cattle.

Again, while we may like or dislike EPD's and genomics, they are here and will have a continued use now and in the future.
I thought he was saying it is hard to rely on testing that has not been published with the methods establishing it disclosed and then validated by an independent source not that testing should never be done. If you use a santa claus test that gives you great results then how can you rely on something that doesn't exist except maybe to make the almighty $.
 

knabe

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with regard to associations adding animals to these tests, i'll use Maine's for an example, the current population has limited milk, more BW, avg or less ww and yw, they don't have the resources or germ plasm access to get a potential cross section that would be representative of reality which would be difficult as well since it's probably not going to include live cover animals in a semi-commercial setting, ie not over fed and given a fair chance to segregate.


really, you need contemporary groups of significant numbers by bulls that represent diversity to fully evaluate animals that are truly significant. additionally, one can think of several useful animals that have negative traits.  most of the niche breeds haven't had time or resources to impose selection like angus has.

At some level, the test is merely a higher resolution parentage verification.

why do maines that used to have milk, growth, etc not have it, but also have a perceived bw issue.  there is sufficient diversity within the breed to address this with current germplasm as well as go back to fullbloods and add other sources including carcass traits that are useful that may be other sources/pathways of marbling/tenderness, cuttability etc.  on the other hand, they could just be the same.


the technology and resources are simply not available to do this now.

Not really sure anymore what the tests offer that selection can’t.

and not that i'm pro or con anything.
 

aj

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I just wonder......if cattle feeders will eventually buy feeder calves by a blood test and pay accordingly for the results. And if the Angus model is the only system that is viable.....that is the system that will be handy to use. That crowds other breeds out. Why mess with another breed except for the heterosis factor? If say Shorthorn cattle are close enough related to Angus maybe the system would reward some Shorthorn cattle. I would wonder that the "British breeds" would be more related to the "exotic" cattle. But I don't know. They may not have a handle on the Shorthorn markers yet anyway to even know. I would like to be a fly on the wall when some of this data is compared.
 

knabe

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cbcr said:
Again, while we may like or dislike EPD's and genomics, they are here and will have a continued use now and in the future.


that is no guarantee. genomics will have to change, just like everything else. the current players have no products that have meaningful impact. the industry will probably consolidate so much it doesn't matter.


maybe Tuli cattle will be a thing.



edsel
pontiac
oldsmobile
buggy whips
compaq
rotary phones
etc etc etc.


genomics needs an upgrade and clear ownership of data now and in the future.
 
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