Re: G*E in animal model

From: Sonja Dominik <Sonja.Dominik_at_CSIRO.AU>
Date: Thu, 21 Jul 2005 12:00:46 +1000

Dear Rob,
Falconer describes the approach to GxE by correlations between
environments in
Falconer, D.S. (1952) The problem of environment and selection. The
American Naturalist 86: 293 - 298.
The question you might have to ask yourself in finding the right
analysis approach is what outcome you require and what you would like to
do with it. Correlations for the same trait between environments are
descriptive and can easily be applied in further studies to look at e.g.
effects on breeding programs. In plant genetics the regression approach
is widely used to describe the performance over multiple environments
and give some description of adaptation.

Regards, Sonja

Sonja Dominik
Postdoctoral Fellow, Quantitative Genetics
CSIRO Livestock Industries
Locked Bag 1
NSW 2350
Phone 61-2-67761376
Fax 61-2-67761333

-----Original Message-----
From: ASReml users discussion group [mailto:ASREML-L_at_AGRIC.NSW.GOV.AU]
On Behalf Of Rob Brooks
Sent: Thursday, 21 July 2005 11:11 AM
Subject: Re: G*E in animal model

Thanks Alastair,

I had a similar idea, but didn't know if it would be an acceptable test
G*E. Your suggestion has encouraged me to plough ahead with this

Allt he best,


At 10:04 AM 20/07/2005 +0100, you wrote:
>Since it looks like you have 2 environments another way to do it would
be to
>set it up as a two trait model with CE_PN_env1 and CE_PN_env2 as
>traits. Adjust the data file accordingly and then the rest could look
>something like...
>CE_PN_env1 CE_PN_env2 ~ Trait !r Trait.Anim
>1 2 1
>Trait 0 US
>0.01 0.1 #or better starting values
>Trait.Anim 2
>Trait 0 US
>0.1 1 #or better starting values
>This would give you a residual and additive variance for the trait in
>environmnet, plus the covariances across environments. Scaling the COVa
to a
>genetic correlation would let you see if rG was significantly les sthan
>(one way to define GxE). If each animal is only measured in one
>or the other then the residual covariance will be 0 but you should
>estimate the additive covariance.
>Alastair J Wilson PhD
>Postdoctoral Research Fellow
>tel. 0131 6507287
>Institute of Evolutionary Biology
>School of Biological Sciences
>The University of Edinburgh
>Ashworth Laboratories
>The King's Buildings
>West Mains Road
>Edinburgh EH9 3JT, UK
>----- Original Message -----
>From: "Rob Brooks" <rob.brooks_at_UNSW.EDU.AU>
>Sent: Wednesday, July 20, 2005 2:05 AM
>Subject: G*E in animal model
>>Dear ASREMLers
>>I have a general and a specific query. Generally, I have enormous
>>designing the G and R structure lines of my ASREML jobs. Unfortunately
>>just not well enough schooled in thinking about these problems, but I
>>I have to really bang my head agains the wall to figure out how to
>>these bits of my jobs. Apart from teh AREML help, Asreml cookbook and
>>various web nortes from workshops, does anyone know of a good starting
>>place to learn about how to set these things up properly, from first
>>More specifically the problem I have been grappling with for the last
>>is how to test for G*E interactions in a univariate animal model. I
>>the animal model going fine, as per the below .as file, but I cannot
>>the Anim.ENV term. Does one specify Anim.ENV as a random effect, or is
>>there another way of doing it. Irrespective, if anyone has any
insights on
>>how to specify the G and R structure lines in the job file, they would
>>much appreciated.
>>Many thnaks,
>>Single Trait Animal Model
>> Anim * !P
>> Sire * !P
>> Dam * !P
>> SEX !A 2
>> ENV 2
>> CE_PN
>>am_tfd.txt !SKIP1 !ALPHA !MAKE #pedigree file
>>am_tfd.txt !SKIP1
>>CE_PN ~ mu ENV !r Anim
>>0 0 1
>>Anim 1
>>0 0 AINV
>>School of Biological, Earth and Environmental Sciences
>>The University of New South Wales
>>Kensington, Sydney 2052
>>NSW, Australia
>>PH: +61-2-9385-2587 FAUX: +61-2-9385-1558

School of Biological, Earth and Environmental Sciences
The University of New South Wales
Kensington, Sydney 2052
NSW, Australia
PH: +61-2-9385-2587 FAUX: +61-2-9385-1558
Received on Wed Jul 21 2005 - 12:00:46 EST

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