Keeney`s Corner

A current and reflective discussion of cattle breeding from outside the registered mainstream
 
HomeUsergroupsRegisterLog in

Share | 
 

 Economics and registered marketing

View previous topic View next topic Go down 
Go to page : Previous  1, 2, 3, 4, 5
AuthorMessage
df



Posts : 613
Join date : 2010-09-28

PostSubject: Re: Economics and registered marketing   Wed Jan 19, 2011 7:45 pm

MKeeney wrote:
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.

It means there is an Angus "population" that is different than the other population because it has been an isolated population longer than other US Angus herds. The other Angus herds have used similar genetics in the not to distant past. Even herds that are considered "isolated" are not really as isolated as this one.
Back to top Go down
MKeeney
Admin


Posts : 4625
Join date : 2010-09-21

PostSubject: Re: Economics and registered marketing   Thu Jan 20, 2011 2:10 am

df wrote:
MKeeney wrote:
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.

It means there is an Angus "population" that is different than the other population because it has been an isolated population longer than other US Angus herds. The other Angus herds have used similar genetics in the not to distant past. Even herds that are considered "isolated" are not really as isolated as this one.

hmmm...I was kinda thinking it was the ones who had infused crossbreeding into their registered Angus, versus those who avoided it...could that be a close reason?
Back to top Go down
http://www.keeneyscorner.com
Mean Spirit



Posts : 321
Join date : 2010-09-26

PostSubject: Re: Economics and registered marketing   Thu Jan 20, 2011 7:12 am

I think it depends on what one means by "isolated"...

I wonder if the ones who were less isolated could speak a little bit of Italian, a little bit of german, maybe some Dutch, some Japanese?

Of course I'm kidding. I have Tom Burke's book, which seems to prove that all the sire lines trace back to Scotland. I'm sure "isolated" just means they didn't hang out together.
Back to top Go down
MKeeney
Admin


Posts : 4625
Join date : 2010-09-21

PostSubject: Re: Economics and registered marketing   Thu Jan 20, 2011 7:26 am

Mean Spirit wrote:
I think it depends on what one means by "isolated"...

I wonder if the ones who were less isolated could speak a little bit of Italian, a little bit of german, maybe some Dutch, some Japanese?

Of course I'm kidding. I have Tom Burke's book, which seems to prove that all the sire lines trace back to Scotland. I'm sure "isolated" just means they didn't hang out together.

yeah, right... Smile I need to buy that Angus bible for handy reference Smile
Back to top Go down
http://www.keeneyscorner.com
df



Posts : 613
Join date : 2010-09-28

PostSubject: Re: Economics and registered marketing   Thu Jan 20, 2011 10:59 am

MikeK,

I'll see if I can get more details but the answer is no, the two populations in question are not "used pure angus" vs "used other breeds and register them unethically as Angus".
Back to top Go down
MKeeney
Admin


Posts : 4625
Join date : 2010-09-21

PostSubject: Re: Economics and registered marketing   Thu Jan 20, 2011 11:57 am

df wrote:
MikeK,

I'll see if I can get more details but the answer is no, the two populations in question are not "used pure angus" vs "used other breeds and register them unethically as Angus".
I`ll buy that..otherwise, there would be more than two populations as MS purposed as well..
Back to top Go down
http://www.keeneyscorner.com
Oldtimer

avatar

Posts : 308
Join date : 2010-10-04
Location : Northeast Montana

PostSubject: Re: Economics and registered marketing   Sat Feb 19, 2011 12:09 pm

Quote :
Monarch Farms
Seventh Metamorphosis Angus Bull & Female Sale

180 Head Sell

THIS SATURDAY,
February 19, 2011
Folsom, LA



Lot 26 - Monarch Blackcap R591
GAR Retail Product x 6I6

Lot 44 - Monarch Blackbird 0015
GAR Predestined x BR Midland

Lot 55 - Monarch Rita T427
SAV Net Worth 4200 x N Bar Emulation EXT

Lot 77 - Monarch Miss Countess T316
GAR Predestined x BR Midland

I received this in an e-mail this morning from one of the sale manager outfits... So if anyone wants to buy a "Metamorphosized" angus bull, the sale is on Liveauctions today... Wink Razz Laughing
Back to top Go down
Sponsored content




PostSubject: Re: Economics and registered marketing   

Back to top Go down
 
Economics and registered marketing
View previous topic View next topic Back to top 
Page 5 of 5Go to page : Previous  1, 2, 3, 4, 5
 Similar topics
-
» Registered Breeder Birman Kittens
» MARKETING TERMS
» Internet Book Marketing
» Parliamentary Legal: the registered object to the approval of the draft parties On: Wednesday 02/22/2012 10:55
» REGISTERED OFFICE OF A COMPANY

Permissions in this forum:You cannot reply to topics in this forum
Keeney`s Corner :: Breeding Philosophies :: Breeding Philosophies-
Jump to: