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PostSubject: Re: Economics and registered marketing   Sun Jan 16, 2011 10:30 pm

Only said registered herds. Didn't say they had to be of the same breed association.
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df



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PostSubject: Re: Economics and registered marketing   Sun Jan 16, 2011 11:19 pm

Breed associations can accept data on crossbred (or straightbred) progeny of parentstock. Currently it is done in collecting and using carcass data although I am pretty sure it has been used on growth traits as well when the progeny are straightbred.

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PostSubject: Re: Economics and registered marketing   Mon Jan 17, 2011 3:49 am

MikeJ wrote:
Only half serious about this...

I've seen angus registered in the Simi association. It's the whole package: register + crossbreed = outcross EPDs! cheers

Mike
yes Mike, the Simmi evaluation looks like a future place to handle data; though the new AAA thing that all the registered breeders raised hell about could be as well; I need to build something to measure first...
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PostSubject: Re: Economics and registered marketing   Mon Jan 17, 2011 8:53 am

MKeeney wrote:
I don`t think cow size has much to do with who gets bred back; certainly, not to the extent of milk...which, btw, EPD`S define most poorly of all the traits...
so, once again...tell me the ideal cow with numbers....that is a must, beforre you can create an index...while I wait on you, mr. show-me-select heifer Smile , and others to tell me this as I have for some time now, I`m just going with avoiding exremes and fewer problems...why isn`t adjusting cow numbers to grass a far superior tool to trying to adjust genetics to grass?

Is the nucleus swine herd just avoiding extremes and few problems or are they using an index (or EPDs) on just a few traits to make them homozygous within that line? It seems they would measure some traits and give their line a name, although they may not call them Durocs.
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PostSubject: Re: Economics and registered marketing   Tue Jan 18, 2011 8:08 pm

df wrote:
MKeeney wrote:
I don`t think cow size has much to do with who gets bred back; certainly, not to the extent of milk...which, btw, EPD`S define most poorly of all the traits...
so, once again...tell me the ideal cow with numbers....that is a must, beforre you can create an index...while I wait on you, mr. show-me-select heifer Smile , and others to tell me this as I have for some time now, I`m just going with avoiding exremes and fewer problems...why isn`t adjusting cow numbers to grass a far superior tool to trying to adjust genetics to grass?

Is the nucleus swine herd just avoiding extremes and few problems or are they using an index (or EPDs) on just a few traits to make them homozygous within that line? It seems they would measure some traits and give their line a name, although they may not call them Durocs.
I don`t think so...lots of indexing; strain naming...AND controlled environment Smile

ran across some nice cows, but alas, no EPD`s...musta been luck Smile

http://www.meitlercattle.com/Cowherd.html
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PostSubject: Re: Economics and registered marketing   Tue Jan 18, 2011 8:34 pm

Hilly wrote:
We have been through this Pharo deal before, I looked into the deal about five years ago as cattle in the grain areas of Alberta tend to be larger in part due to abundant inputs and selecting the “best” performing calves. I never did buy a bull and was left with the impression.... and impressions can be useless to talk about... that I was just a Lookey Lou and more than likely going to fail farming.

I would more like to discuss the principals behind why any business model will or will not work.

For me some of the red flags in this particular deal were
1. Can you afford to sell me a bull... not if, but can you and make a profit at that price. When I am told you can’t afford not to buy a bull from me right away in know that something stinks... as dumb as I am I have half a calve crop every year that are bulls

2. If you continue to decrease inputs you will continue to decrease output, no different than the increase inputs increase output model that has been followed by many... with selection and sort based on inputs how will you stop at optimum?

3. A breeding program based on fire and ice mating would be next to imposable to be predictable without the added time it will take to bring variation down to and find out what is is. We can ague a nauseam about which cattle have more variation but natural law tells me the smaller the gene pool the smaller the variation.

4. What is the purpose of the test the bull go through is the five star bull better then the four star bull genetically? How about monetarily?

5. Why is the size of sort a good thing? You can make the test as hard as you like and brag about the superiority of the few that made it through... But in my experience there are real cost to that sort.

I will stop there for now better get out in this waste deep snow and move some fence, suppose to snow for two more days...

These cows are in the June group and still have their calves on that and the -35 wind chill don’t make for nice pictures defiantly in there working cloths... they find the swath with their front feet and then start to dig, I can just about walk on top of the snow in this pic.




Speaking of home raised bulls’ competing for my dollar, the front cow in the first pic happens to be a 13 year old cow that had this bull two and a half years ago that I had kept for my use, chosen at birth but never did get use as my x- strain bulls answered the above questions better. This picture is taken at my uncles after running with 35hd of heifers... nothing special just a bull and his measurements are all wrong, but he was raised on straight forage Wink and would see use here before a $3000 bull will... He is a half brother to all first calf heifers i posted under Mob Mates on 5barx.



Here is a 15 year old March calving cow...



A bred heifer out of my 18 year old 63 cow...





The pictures have little to do with the conversation Embarassed ... but what the heck I already derailed the topic already once ...I’m on a roll cheers

I got a big kick out of showing your pics at the feed store today to a couple of KY farmers worried about SNOW Smile Is the ability to cope with this feed management scenario, a genetic or learned adaptation?
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PostSubject: Re: Economics and registered marketing   Tue Jan 18, 2011 8:46 pm

If Hilly had a lessor level of integrity he could promote his cattle as being genetically predisposed to dig thru snow for forage, thus they are breed leading "snow performance" cattle. Probably still could have pulled it off if he hadn't shown that they were "managed to perform" in that manner. Almost had a gold mine there, Hilly. Laughing
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PostSubject: Re: Economics and registered marketing   Tue Jan 18, 2011 10:09 pm

MKeeney wrote:


I got a big kick out of showing your pics at the feed store today to a couple of KY farmers worried about SNOW Smile Is the ability to cope with this feed management scenario, a genetic or learned adaptation?

Mostly learned I would say, the cows that do most of the hard work grew up in the system. Although high input/output genetics are a challenge in my system, the cow in the last picture with a yellow tag has only been here two years there are a few like her that are challenged in both ways...

Today has been a very nice day finally warmed up and the sun came out, went out to move the March cows and typically as I roll up the fence they funnel into the snow behind me... Today they just watched me roll up the fence then close their eyes and went back to sunning themselves sunny

I should mention when the snow gets that deep I move them twice a day as they only have limited time at those temps before the disturbed snow hardens and the feed will be froze down under packed snow. I mention before, but I have to have a decent size swath under there for them to go to the work of digging it out, these are 21 foot swathes and the crop would average about 5’ tall at swathing. It is interesting to watch the older cows walk out in the snow and find swath with their feet.

The day after I posted those pictures I had come to a draw in one of the fields and of course it was full of snow around 10-12’ I would say... I could walk on top to some degree so I crossed and dug out some swath to coax some cows across... not very smart pale about the time I realize there is no way they would make it and I would have to go back for the tractor... a cow headed in realized she was in trouble managed to turn around and make it back, four more took turns at it all making it a little farther before turning back the fifth made it through followed by the whole herd.. Made for a nice hallway when all was said and done but I won’t be doing that again.
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PostSubject: Re: Economics and registered marketing   Tue Jan 18, 2011 10:16 pm

dwight@steadfastbeef.com wrote:
If Hilly had a lessor level of integrity he could promote his cattle as being genetically predisposed to dig thru snow for forage, thus they are breed leading "snow performance" cattle. Probably still could have pulled it off if he hadn't shown that they were "managed to perform" in that manner. Almost had a gold mine there, Hilly. Laughing

Smile What can I say; I guess I should hire a marketer Rolling Eyes ... preferably one able to sell ice to Eskimos Cool
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PostSubject: Re: Economics and registered marketing   Tue Jan 18, 2011 10:19 pm

That's interesting about moving them twice a day - never heard that before but it makes sense. I'm more used to seeing the guys in the south that turn them into a quarter section at a time because they are too lazy to cross fence it.
It's definitely learned behavior when your herd turn into a digging herd. We found that with grazing banked grass through deep snow - cows new to the system had to learn it from a few original experienced ones but the herd got to a tipping point where most were diggers and at that point the few complainers quit looking for hay and got to work.
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PostSubject: Re: Economics and registered marketing   Tue Jan 18, 2011 11:08 pm

MKeeney wrote:
df wrote:
MKeeney wrote:
I don`t think cow size has much to do with who gets bred back; certainly, not to the extent of milk...which, btw, EPD`S define most poorly of all the traits...
so, once again...tell me the ideal cow with numbers....that is a must, beforre you can create an index...while I wait on you, mr. show-me-select heifer Smile , and others to tell me this as I have for some time now, I`m just going with avoiding exremes and fewer problems...why isn`t adjusting cow numbers to grass a far superior tool to trying to adjust genetics to grass?

Is the nucleus swine herd just avoiding extremes and few problems or are they using an index (or EPDs) on just a few traits to make them homozygous within that line? It seems they would measure some traits and give their line a name, although they may not call them Durocs.
I don`t think so...lots of indexing; strain naming...AND controlled environment Smile

ran across some nice cows, but alas, no EPD`s...musta been luck Smile

http://www.meitlercattle.com/Cowherd.html

So the difference in making progress on an economic index is a controlled environment?
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PostSubject: Re: Economics and registered marketing   Tue Jan 18, 2011 11:14 pm

df wrote:
MKeeney wrote:
df wrote:
MKeeney wrote:
I don`t think cow size has much to do with who gets bred back; certainly, not to the extent of milk...which, btw, EPD`S define most poorly of all the traits...
so, once again...tell me the ideal cow with numbers....that is a must, beforre you can create an index...while I wait on you, mr. show-me-select heifer Smile , and others to tell me this as I have for some time now, I`m just going with avoiding exremes and fewer problems...why isn`t adjusting cow numbers to grass a far superior tool to trying to adjust genetics to grass?

Is the nucleus swine herd just avoiding extremes and few problems or are they using an index (or EPDs) on just a few traits to make them homozygous within that line? It seems they would measure some traits and give their line a name, although they may not call them Durocs.
I don`t think so...lots of indexing; strain naming...AND controlled environment Smile

ran across some nice cows, but alas, no EPD`s...musta been luck Smile

http://www.meitlercattle.com/Cowherd.html

So the difference in making progress on an economic index is a controlled environment?
maternal economic index...but the first step of us making progress on an index is for you to tell me the best EPD`s for a cow...I`ve just waited a couple years; no big rush..you get that done; then we`ll work on an index...for every environment...think how many journal articles that could create Smile
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PostSubject: Re: Economics and registered marketing   Tue Jan 18, 2011 11:22 pm

The primary EPD is the Stayability EPD. You have not waited years for me to tell you this; I have told you before the Stay epd accounts for about 50% of the variation in the index. Quite simply what is needed is to account for every cow on your place as too her status; is she bred and still in the herd, bred but left the herd, open, etc.

The major reason cows leave the herd for commercial producers is open and possible followed by ornery and old. Otherwise they get to stay. If you could identify sires whose daughters stay in the herd and not cause you problems, then those sires could contribute to the entire population. However, without any data, the rest of us get to go on your ability to educate/market your product.
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PostSubject: Re: Economics and registered marketing   Wed Jan 19, 2011 4:23 am

MKeeney wrote:
df wrote:
MKeeney wrote:
I don`t think cow size has much to do with who gets bred back; certainly, not to the extent of milk...which, btw, EPD`S define most poorly of all the traits...
so, once again...tell me the ideal cow with numbers....that is a must, beforre you can create an index...while I wait on you, mr. show-me-select heifer Smile , and others to tell me this as I have for some time now, I`m just going with avoiding exremes and fewer problems...why isn`t adjusting cow numbers to grass a far superior tool to trying to adjust genetics to grass?

Is the nucleus swine herd just avoiding extremes and few problems or are they using an index (or EPDs) on just a few traits to make them homozygous within that line? It seems they would measure some traits and give their line a name, although they may not call them Durocs.
I don`t think so...lots of indexing; strain naming...AND controlled environment Smile

ran across some nice cows, but alas, no EPD`s...musta been luck Smile

http://www.meitlercattle.com/Cowherd.html

I had the privelage to see Gene Meitler's Herefords several years ago as well as hear him present on linebreeding and Bonsma. When I read your post I assumed no EPDs meant poor EPD because I remembered data on the cattle. Apparently Gene generates data somewhere other than the Hereford breed assoc. I remember one of Gene's reservation about EPDs was the manipulation of the data (cheating) and he sited on of his own bull that was co -owned where the bulls EPDs did not add up and he found out that the other owner had manipulated the data to make the bull more marketable. One of the other presenters was Dr Jim Sanders Texas A&M and he was of the opinion that there were no finer and more important Hereford cattle anywhere. I looked and it is as you post -there are no EPDs . I looked at Gene's website a month or so ago and one of the Angus bulls listed was a Shoshone Bob son who was sure a good looking bull. If Gene's cattle are any indication we would all be better off understanding and applying the Bonsma criteria than EPDs.
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PostSubject: Re: Economics and registered marketing   Wed Jan 19, 2011 5:59 am

MKeeney wrote:
http://www.meitlercattle.com/Cowherd.html

Those cattle look very nice to me. It appears this breeder paid attention to phenotype while most did not. It is a joy to see Hereford bulls with muscle.

It looks like his only use for a breed association is to keep the pedigrees.
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PostSubject: Re: Economics and registered marketing   Wed Jan 19, 2011 6:06 am

df wrote:
The primary EPD is the Stayability EPD. You have not waited years for me to tell you this; I have told you before the Stay epd accounts for about 50% of the variation in the index. Quite simply what is needed is to account for every cow on your place as too her status; is she bred and still in the herd, bred but left the herd, open, etc.

The major reason cows leave the herd for commercial producers is open and possible followed by ornery and old. Otherwise they get to stay. If you could identify sires whose daughters stay in the herd and not cause you problems, then those sires could contribute to the entire population. However, without any data, the rest of us get to go on your ability to educate/market your product.

well now, it seems you should be able by now to define the other EPD numbers that contribute to a positive stayability EPD...once again, describe me the ideal cow with EPDS...oh, one other thing, higher stayability as a stand alone EPD, might not be most profitable, eh?

now let`s apply a little common sense instead of the stuff of research papers...is not every years heifer calf crop the produce of cows that STAYED? I haven`t sold young producing cows into the industry; I just kinda wear them out, and slowly moving from 60 cows to 300, plus a 100 heifers to breed this year, while living off the proceeds uses up a fair amount of heifer replacements...like most everything universities do, stayability EPD would tell me WHAT I HAVE DONE, but with far less accuracy WHAT DO DO...

However, without any data, the rest of us get to go on your ability to educate/market your product.
until you, the academics, create a measure more meaningful than currently exists, the reputation of the breeder and his cattle will be the primary factor...in fact, in practice, when I look at the marketers with the most measures, it is usually accompanied by the most BS...the data is complied, to pile the BS higher and I would run as fast and far as I can from it to find me a cow....or a cow bull...
we`ll see how the BB heifers sell today...interestingly enough, selling them all...does that tell you something about the Stayability of the cowherd?

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PostSubject: Re: Economics and registered marketing   Wed Jan 19, 2011 6:37 am

MKeeney wrote:
df wrote:
The primary EPD is the Stayability EPD. You have not waited years for me to tell you this; I have told you before the Stay epd accounts for about 50% of the variation in the index. Quite simply what is needed is to account for every cow on your place as too her status; is she bred and still in the herd, bred but left the herd, open, etc.

The major reason cows leave the herd for commercial producers is open and possible followed by ornery and old. Otherwise they get to stay. If you could identify sires whose daughters stay in the herd and not cause you problems, then those sires could contribute to the entire population. However, without any data, the rest of us get to go on your ability to educate/market your product.

well now, it seems you should be able by now to define the other EPD numbers that contribute to a positive stayability EPD...once again, describe me the ideal cow with EPDS...oh, one other thing, higher stayability as a stand alone EPD, might not be most profitable, eh?

now let`s apply a little common sense instead of the stuff of research papers...is not every years heifer calf crop the produce of cows that STAYED? I haven`t sold young producing cows into the industry; I just kinda wear them out, and slowly moving from 60 cows to 300, plus a 100 heifers to breed this year, while living off the proceeds uses up a fair amount of heifer replacements...like most everything universities do, stayability EPD would tell me WHAT I HAVE DONE, but with far less accuracy WHAT DO DO...

However, without any data, the rest of us get to go on your ability to educate/market your product.
until you, the academics, create a measure more meaningful than currently exists, the reputation of the breeder and his cattle will be the primary factor...in fact, in practice, when I look at the marketers with the most measures, it is usually accompanied by the most BS...the data is complied, to pile the BS higher and I would run as fast and far as I can from it to find me a cow....or a cow bull...
we`ll see how the BB heifers sell today...interestingly enough, selling them all...does that tell you something about the Stayability of the cowherd?


Actually nobody can define the perfect EPDs for you to make the most profit because each cowherd has different needs and resources. That is why I posted the CSU decision support link; they realize that making the most money might require different bulls. There is also a need, IMO, to have regional EPDs due to environmental conditions such as fescue or other major effects that could rerank bulls. Politically, that may never happen but that is not really the fault of the scientist; more an issue with breed associations. Again, the scientists need to test for this and prove if there is a need for regional epds. The use of regional epds is up to the breed associations. The breed associations would also have to supply the data to prove this need as no research facility (even all of them) have enough data to test.

HOWEVER, the Stay epd does rank the bulls by how well the females stay in the herd. Yes, on the surface it would appear the epd is given after the fact. But the (nucleus) breeders should be documenting the superiority of their lines. And accuracy of the bulls is improved by scientist who use statistics, biology and common sense to determine Stay at younger ages. Bulls that excel should be used more, bulls that are poor should be considered terminal bulls or "terminated" themselves. Certainly over time, the percentage of bulls and females that hit the benchmark should increase. If not, then the producer may be a multiplier but not what I would consider an elite breeder.

The other issue, which I brought up in the previous post, is that phenotype is also important. So my breeding program would balanced phenotype and Stay epd for the maternal line of cattle. After sorting the bulls for Stay epd, I would start at the top of the list and make sure they fit my program in terms of conformation, slick hair, etc. Certainly, I can address milk, and carcass traits as well as minor components of determining which bulls to use. If I can linebreed, which will happen if my criteria is strict enough, that is just fine.

Why would I address carcass traits? Because the cattle have to fit within the specs of the consumer and thus the packer and feeder. I don't expect the maternal line of cattle to be awesome for carcass traits, just acceptable enough that a terminal bull will sire progeny that fit their specs.

If your breed association is not supplying the correct or useful indexes and epds, it is up to the breeders to have this changed and then supply the data needed for these to be created. If the breed association is unresponsive, fire them or get somebody else to run your data.

What are BB heifers?

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PostSubject: Re: Economics and registered marketing   Wed Jan 19, 2011 6:42 am

Your reputation can set you apart from other breeders by meeting their (genetic) needs with a personal relationship and customer service. You will always have to combat other breeders who may have similar or possibly better genetics with more money allocated to customer service. And for those commercial cattlemen that go to another breeder, according to you, the within breed hybrid vigor will make his calves look better than your calves. Always need to do more education than the next guy.
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PostSubject: Re: Economics and registered marketing   Wed Jan 19, 2011 6:51 am

bill bolin..a user of Shoshone bulls...
We, as most always, after debating the possibilities, agree in principle Smile I just ain`t going to do it your way, recording everything; because the extra benefit is not commensurate with the extra trouble...the "herd effect" takes care of everything in due time; but it doesn`t define it with math, except in commercial dollars...the marketing program is simple, here it is, it ain`t great, what you see is pretty much what you get, and one piece of advice...be damn cautious buying from someone promising more than you see...
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PostSubject: Re: Economics and registered marketing   Wed Jan 19, 2011 6:59 am

MKeeney wrote:
bill bolin..a user of Shoshone bulls...
We, as most always, after debating the possibilities, agree in principle Smile I just ain`t going to do it your way, recording everything; because the extra benefit is not commensurate with the extra trouble...the "herd effect" takes care of everything in due time; but it doesn`t define it with math, except in commercial dollars...the marketing program is simple, here it is, it ain`t great, what you see is pretty much what you get, and one piece of advice...be damn cautious buying from someone promising more than you see...

I assume he is selling them all because prices have never been this high!!!

But do you fault those who say the same thing as you, only in color?
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PostSubject: Re: Economics and registered marketing   Wed Jan 19, 2011 7:03 am

df wrote:
MKeeney wrote:
bill bolin..a user of Shoshone bulls...
We, as most always, after debating the possibilities, agree in principle Smile I just ain`t going to do it your way, recording everything; because the extra benefit is not commensurate with the extra trouble...the "herd effect" takes care of everything in due time; but it doesn`t define it with math, except in commercial dollars...the marketing program is simple, here it is, it ain`t great, what you see is pretty much what you get, and one piece of advice...be damn cautious buying from someone promising more than you see...

I assume he is selling them all because prices have never been this high!!!

But do you fault those who say the same thing as you, only in color?

??? color? probably Smile clarify

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PostSubject: Re: Economics and registered marketing   Wed Jan 19, 2011 7:14 am

MKeeney wrote:
df wrote:
MKeeney wrote:
bill bolin..a user of Shoshone bulls...
We, as most always, after debating the possibilities, agree in principle Smile I just ain`t going to do it your way, recording everything; because the extra benefit is not commensurate with the extra trouble...the "herd effect" takes care of everything in due time; but it doesn`t define it with math, except in commercial dollars...the marketing program is simple, here it is, it ain`t great, what you see is pretty much what you get, and one piece of advice...be damn cautious buying from someone promising more than you see...

I assume he is selling them all because prices have never been this high!!!

But do you fault those who say the same thing as you, only in color?

??? color? probably Smile clarify


Well, an ad with color (instead of black and white) typically gets more attention. Without embelishing, the color ad may sell more bulls.
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PostSubject: Re: Economics and registered marketing   Wed Jan 19, 2011 7:18 am

df wrote:
MKeeney wrote:
df wrote:
MKeeney wrote:
bill bolin..a user of Shoshone bulls...
We, as most always, after debating the possibilities, agree in principle Smile I just ain`t going to do it your way, recording everything; because the extra benefit is not commensurate with the extra trouble...the "herd effect" takes care of everything in due time; but it doesn`t define it with math, except in commercial dollars...the marketing program is simple, here it is, it ain`t great, what you see is pretty much what you get, and one piece of advice...be damn cautious buying from someone promising more than you see...

I assume he is selling them all because prices have never been this high!!!

But do you fault those who say the same thing as you, only in color?

??? color? probably Smile clarify


Well, an ad with color (instead of black and white) typically gets more attention. Without embelishing, the color ad may sell more bulls.
I read the message, but color sends a message...me, the customer, must pay for it Smile are the jans articles in color? Smile
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PostSubject: Re: Economics and registered marketing   Wed Jan 19, 2011 10:08 am

MKeeney wrote:
df wrote:
MKeeney wrote:
df wrote:
MKeeney wrote:
bill bolin..a user of Shoshone bulls...
We, as most always, after debating the possibilities, agree in principle Smile I just ain`t going to do it your way, recording everything; because the extra benefit is not commensurate with the extra trouble...the "herd effect" takes care of everything in due time; but it doesn`t define it with math, except in commercial dollars...the marketing program is simple, here it is, it ain`t great, what you see is pretty much what you get, and one piece of advice...be damn cautious buying from someone promising more than you see...

I assume he is selling them all because prices have never been this high!!!

But do you fault those who say the same thing as you, only in color?

??? color? probably Smile clarify


Well, an ad with color (instead of black and white) typically gets more attention. Without embelishing, the color ad may sell more bulls.
I read the message, but color sends a message...me, the customer, must pay for it Smile are the jans articles in color? Smile

The Journal of Animal Science has facts of a study with >1 treatment. They don't sell anything and only "geeks" read them! Smile
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PostSubject: Re: Economics and registered marketing   Wed Jan 19, 2011 6:33 pm

are you geekish enough to tell me what this means? Smile


Here's an interesting abstract report from the 2010 Plant & Animal Genomics Conference by the U of Mo group that has done a lot of the development in Angus genomics.

Having come from a Shorthorn background, it's very easy for me to understand their finding that stratified that breed into 5 distinct genomic subpopulations.

The Angus finding is much more interesting, and it would be useful to know whether one of the two Angus groups found is of recent origin. Notice that the group of AI bulls studied went back to 1956, very early in the frozen semen era and long before the late 60s type transition.

The good news in this is that the scientists have been doing the right homework before the genomic EPDs are released.
_______________________
Effects Of Population Stratification On GWAS In Livestock Populations Assumed To Be Homogenous

Jared E Decker, Daniel A Vasco, Stephanie D McKay, Megan M Rolf, Tasia M Taxis, Richard H Chapple, Sarah J Gregg, JaeWoo Kim, Robert D Schnabel, Jeremy F Taylor

Division of Animal Sciences, University of Missouri, 920 E Campus Dr, Columbia, MO 65211 USA

Biases induced by the inappropriate modeling of data are of concern in all statistical analyses. Human genome-wide association studies (GWAS) have increasingly demonstrated that population stratification leads to an increase in the rate of false positive associations. In its simplest form, population stratification within the context of GWAS occurs when cases and controls differ, due to ancestry, in allele frequency at many loci in addition to the disease-associated loci. Human populations which were once thought to be homogenous have now been shown to possess significant levels of stratification. Here, we investigate this phenomenon in bovine populations, and find that breeds, often presumed to be homogenous, can possess significant levels of stratification. In Shorthorn and ShorthornPlus (composite Shorthorn recognized by the American Shorthorn Association) cattle, we found significant population stratification between 5 hypothesized subpopulations (largest P-value = 1.53e-36) using BovineSNP50 genotypes. Using the ADMIXTURE and DISTRUCT software, the extent of admixture of ancestral populations present in modern Shorthorn populations can be visualized. To investigate the effects of population stratification on GWAS, we analyzed BovineSNP50 genotypes scored in a population of 1,983 registered Angus sires used in artificial insemination since 1956. Using SMARTPCA, we surprisingly identified two discrete populations (Chi-squared value=3,880.729) of sires based upon their ancestry. This stratification significantly inflated GWAS log10P-values for traits for which the two populations have distinct mean phenotypes. We conclude that ancestry should either be explicitly modeled using pedigree information or implicitly modeled as in software such as EIGENSOFT in GWAS studies performed in livestock.
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