Pedigree x GXE analysis

From: Arthur Gilmour <arthur.gilmour_at_AGRIC.NSW.GOV.AU>
Date: Mon, 10 Jan 2005 09:44:34 +1100

I'm using pedigree information in the form of a generalised inverse
relationship matrix (coefficient of parentage matrix in crop terminology)
in a genotype by environment model.

The model I'm using with BLUEs and weights from single site analysis is:

yld !WT yldwt ~ mu site !r site.giv(gen),
!f mv
1 1 0
2922 0 IDEN !S2==0.3118207 #yld
predict site gen

This model works and the values seem sensible however I'm having trouble
finding examples of others doing this, although there is a example of how
to set up the code in the latest ASREML manual using site and variety
Has anyone done something similar and investigated how the site.gen
variance component changes with the inclusion of the pedigree infromation?
And/or described the theory?

Dear Ky,
This is not the way I would fit the model.
First, I doubt ASReml will actually use the GIV matrix in this case.
You need to add a G structure for the random term
yld !WT yldwt ~ mu site !r site.giv(gen),
!f mv
1 1 0
2922 0 IDEN !S2==0.3118207 #yld
site.giv(gen) 2
site ...
giv(gen) 0 GIV1

Second, you need to think about what to put in place of ...

I expect you need some kind of correlation model. Assuming equal
genetic variance for each site
site 0 CORUV .4 .1

might be an appropriate place to start.

There are possibly other problems depending on the actual structure of the
and whatever variance assumptions need to be made.

Peace to you 2005 in the Name of Jesus Christ

Arthur Gilmour PhD
Principal Research Scientist (Biometrics)
NSW Department of Primary Industries
Orange Agricultural Institute, Forest Rd, ORANGE, 2800, AUSTRALIA
fax: 02 6391 3899; 02 6391 3922 Australia +61
telephone work: 02 6391 3815; home: 02 6364 3288;
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Received on Sun Jan 10 2005 - 09:44:34 EST

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