beef and sheep business

A forum for discussion of these genetic measurement tools.

Re: beef and sheep business

Postby Joe Emenheiser » Wed Jul 11, 2012 3:17 pm

Ebenezer wrote:So, the question comes down to the EBVs in sheep and EPDs in Angus cattle. .....How is the easiest way to increase them? Either outcross lines or use the growthest parents or both.


EPDs are adjusted for known inbreeding. Linecrossing is detected, even within breeds.
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Re: beef and sheep business

Postby Judy Lewman » Wed Jul 11, 2012 10:20 pm

Warren, the additional info much appreciated. And I should clarify my earlier post. I'm new to NSIP and still learning how to best utilize it for our small flock. But we've had sheep for more than 40 years and, due to a number of unexpected circumstances, have been "distilling" (thanks for that term) our current breed for more than 20. So far, so good but I'm always on the lookout for trouble.

Joe, your April 2011 post on Coefficient of Inbreeding was extremely helpful . . . the best I've ever read on the subject. I believe that someone mentioned earlier that LambPlan calculates COI back 4 generations. Is that your understanding, or can it go back further if the pedigree info is available? Or is 4 generations considered adequate for BLUP?

Brian, do you recall offhand John's rule-of-thumb for linebreeding? It was in an article he wrote for The Shepherd Magazine years ago (10?) but I haven't been able to dig it up. I've been working with my own shorthand version but remember his as more concise and I'd like to review it.

Again, thanks to all who take the time to share your knowledge, and to Bill for this Forum . . . an incredible resource.
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Re: beef and sheep business

Postby Joe Emenheiser » Wed Jul 11, 2012 11:06 pm

outsidethebox wrote:The registered Angus business has turned into a number chasing game...chasing maximum performance. The problem with this is that, while it is well documented that fertility is the most important economic trait, our natural predisposition to worship that phenomenal individual wins out over our better judgment. So, several things happen: 1) The critical functional traits are compromised. 2) The phenoms cannot reproduce themselves. And 3) There is tremendous variability in the offspring.


Outsidethebox:

You raise several interesting and valid points; however, your point about variability above is either underdeveloped, contradictory to your stronger point about linebreeding, and/or flat wrong.

One of the greatest potential risks of BLUP selection is the LOSS of genetic variation in the offspring, which stems from only breeding from the top percentile (e.g. Holsteins). You are not alone among breeders of closed, linebred strains who argue against EBV selection. I will offer my opinion that the main reason you feel there is less variability in the offspring of your herd/flock is that you have not collected the data to demonstrate otherwise.
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Re: beef and sheep business

Postby Joe Emenheiser » Wed Jul 11, 2012 11:15 pm

Judy Lewman wrote:Joe, your April 2011 post on Coefficient of Inbreeding was extremely helpful . . . the best I've ever read on the subject. I believe that someone mentioned earlier that LambPlan calculates COI back 4 generations. Is that your understanding, or can it go back further if the pedigree info is available? Or is 4 generations considered adequate for BLUP?


I cannot speak specifically for LAMBPLAN, but I would be very surprised if the relationship matrix only uses 4 generations. With a simple 3-column pedigree file with individual, sire, and dam, it is quite simple to calculate inbreeding using the entire known pedigree.
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Re: beef and sheep business

Postby DonDrewry » Wed Jul 11, 2012 11:28 pm

Joe Emenheiser wrote:
Ebenezer wrote:

EPDs are adjusted for known inbreeding. Linecrossing is detected, even within breeds.


Joe, it's been some years since I used NSIP and even longer when Dave Notter told me I would screw up my data if I was inbreeding. At that time we weren't getting the results I had hoped for so it wasn't a problem to stop doing it but it looks like several advancements have been made in the last several years.
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Re: beef and sheep business

Postby Joe Emenheiser » Wed Jul 11, 2012 11:39 pm

DonDrewry wrote:Joe, it's been some years since I used NSIP and even longer when Dave Notter told me I would screw up my data if I was inbreeding.


Hmmm.....I'm certainly no Dave Notter, I will have to pick his brain about this!
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Re: beef and sheep business

Postby outsidethebox » Wed Jul 18, 2012 6:38 am

Joe Emenheiser wrote:
outsidethebox wrote:The registered Angus business has turned into a number chasing game...chasing maximum performance. The problem with this is that, while it is well documented that fertility is the most important economic trait, our natural predisposition to worship that phenomenal individual wins out over our better judgment. So, several things happen: 1) The critical functional traits are compromised. 2) The phenoms cannot reproduce themselves. And 3) There is tremendous variability in the offspring.


Outsidethebox:

You raise several interesting and valid points; however, your point about variability above is either underdeveloped, contradictory to your stronger point about linebreeding, and/or flat wrong.

One of the greatest potential risks of BLUP selection is the LOSS of genetic variation in the offspring, which stems from only breeding from the top percentile (e.g. Holsteins). You are not alone among breeders of closed, linebred strains who argue against EBV selection. I will offer my opinion that the main reason you feel there is less variability in the offspring of your herd/flock is that you have not collected the data to demonstrate otherwise.


Joe, I think we are talking about different things. I know I do not know what you are talking about...BLUP????

I am referring to the building/maintaining of brood stock lines that indeed are more narrow in their genetic makeup. If one selects from the more average/center of the herd/flock the variability will be reduced significantly...and I am talking about culling the outliers from both ends of the bell-curve. There will certainly be loss of performance within these lines due to loss of hybrid vigor. However, when crossed with a terminal male there will be more consistency and more growth performance will be captured.

EBVs and EPDs simply informs one of the expected average. They do not inform one of anything about variability...please explain this otherwise. And it is a total genetic crap-shoot to explain the differences experienced here.
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Re: beef and sheep business

Postby DonDrewry » Wed Jul 18, 2012 7:53 am

outsidethebox,

Joe's term BLUP is just the name behind the math that calculates EPD or EBVs.

best linear unbiased prediction (BLUP)
acronym for a statistical method of predicting the breeding values of animals. Fixed effects of environment and genetics on observed phenotypic values are estimated simultaneously and, therefore, genetic differences between herds are accounted for. BLUP animal models are now used in many countries for a number of species, including dairy and beef cattle, swine, sheep and fish.
Saunders Comprehensive Veterinary Dictionary, 3 ed. © 2007 Elsevier, Inc. All rights reserved

The is a tendency when EPDs are used for diversity to shrink pretty much for what I think is one of your points. Everyone wants to use the genetics from the extremely EPDs. Combine the power of AI with BLUP to identify the high outliers pretty soon a few studs are in the pedigree of most of the breed.
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Re: beef and sheep business

Postby Janet McNally » Wed Jul 18, 2012 9:34 am

While I am a total fan for balanced trait selection, I disagree that we should be selecting only from the middle, or should be striving to limit variability by line breeding. Variability is the essence of genetic improvement. Eliminating variability through inbreeding and culling both the top and bottom end serves only to stifle genetic improvement. This is fine if you love your breed just the way it is, but if you would like all of your animals to perform like your top end, and would like to have a steady sure way to get there, then you need to make use of genetic variability and objective performance measurement (EBVs).

EBVs are nothing more than a way to reflect genetic performance with a higher degree of accuracy. Selection indexes* using these EBVs combined with old fashioned note taking and visual appraisal help select for balanced animals. Improvement in any one trait will be slow, but steady. *(even indexes require an eyeball of the data to weed out some extreme individuals, in my own flock, extremely lean animals can be the issue).

While I agree that inbreeding can be used to develop consistency, one can also do this using EBVs with unrelated animals without suffering the consequences of inbreeding (lowered performance through inbreeding depression, narrowing of the gene pool).

My rule on inbreeding is to use it only when that related individual is the best option available, or to test the genetic integrity of the line. But never do it just for the sake of inbreeding. Over the course of a breeding program a certain amount of line breeding will occur without having to seek it for its own end.

As to the comment that EBVs can also lead to narrowing of the gene pool, this is true. One needs to set up sire lines and make sure that one line does not dominate the entire breeding program. What has happened in the past, such as in the Holstein, is one sire has dominated the breed at the expense of the rest. When it turns out that one sire has a serious genetic recessive flaw, it can be disastrous. This has happened with and without EBVs, I believe there is also an example in the horse, and dog world, where EBVs are not involved.

I realize crossing unrelated line bred lines helps add to the 'pop' of hybrid vigor, but as noted above, some line breeding is bound to happen in any program that is reaching maturity.

Janet
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Re: beef and sheep business

Postby outsidethebox » Wed Jul 18, 2012 12:13 pm

Janet, you clearly do not understand what I have presented. The expectations, belief and confidence in EBVs is seriously flawed. When I have time I will consider how I might restate the value of close breeding.
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Re: beef and sheep business

Postby Joe Emenheiser » Wed Jul 18, 2012 12:47 pm

outsidethebox wrote: I am referring to the building/maintaining of brood stock lines that indeed are more narrow in their genetic makeup. If one selects from the more average/center of the herd/flock the variability will be reduced significantly...and I am talking about culling the outliers from both ends of the bell-curve.


If one has the power to manipulate the bell curve (and I would argue that that power is limited if one avoids using math in their selection criteria), why would one not strive to move the entire population (i.e., shift the bell curve) in a desired direction? As Janet wrote, reducing variation lessens the ability to change the mean. It is a pretty bold statement to say a line is so perfect that no improvement is necessary. In general, most who take such a position fade into history as times change.

outsidethebox wrote: EBVs and EPDs simply informs one of the expected average. They do not inform one of anything about variability...please explain this otherwise.


For an individual:
Most BLUP evaluation also reports some form of accuracy, which provides a measure of the reliability of the estimate of the mean (EBV). Among many other things, accuracy takes into account the variation in the records for an animal and its relatives.

For a population:
1. Take a list of numeric EBVs for all individuals.
2. Compute variance for trait within population.
3. Hard to do without a list of numbers.
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Re: beef and sheep business

Postby woolpuller » Wed Jul 18, 2012 2:29 pm

I prefer to try to move the bell curve to the right.
high performance, high health, high biosecurity, a truly closed Suffolk Flock
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Re: beef and sheep business

Postby Lana Rowley » Wed Jul 18, 2012 6:47 pm

outsidethebox wrote:Janet, you clearly do not understand what I have presented. The expectations, belief and confidence in EBVs is seriously flawed. When I have time I will consider how I might restate the value of close breeding.



Add your real name when you do.
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Re: beef and sheep business

Postby Ebenezer » Thu Jul 19, 2012 8:40 am

Joe Emenheiser wrote:
Ebenezer wrote:So, the question comes down to the EBVs in sheep and EPDs in Angus cattle. .....How is the easiest way to increase them? Either outcross lines or use the growthest parents or both.


EPDs are adjusted for known inbreeding. Linecrossing is detected, even within breeds.


Joe, can you provide me with a reference that shows AAA EPDs have an inbreeding and outcrossing calculator? Thanks.
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Re: beef and sheep business

Postby Ebenezer » Thu Jul 19, 2012 8:44 am

woolpuller wrote:I prefer to try to move the bell curve to the right.


Let me know how it works out on birth weight!
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