Re: fraternity & coancestry matrices in animal model

Dear Cano,

ASReml can handle multiple relationship matrices however there are some
issues.

Additive + Dominance run
  Animal !P
  Sire
  Dam
  Sex *
  bodyweight
  fleecewt
flock.ped
dominance.giv
datafile.asd

!PART 1 # Univariate analysis
bodyweight ~ mu Sex !r Animal giv(Animal,1)

!PART 2 # Bivariate analysis
bodyweight fleecewt ~ Trait, Trait,Sex !r Tr.Animal Tr.giv(Animal,1)
1 2 2
0
Trait 0 US !GP
3*0

 Tr.Animal 2
Trait 0 US !GP
3*0
Animal 0 AINV

 Tr.giv(Animal,1) 2
Trait 0 US !GP
3*0
giv(Animal,1) 0 GIV1

1 This job asssumes the GIV file is generated assuming the same animal
order
resulting from processing the pedigree file.

2 ASReml can handle large models with an Additive matrix because the A
inverse matrix is
very sparse (a maximum of 4 nonzero values per animal). Dominance
matrices are
typically not sparse and so the models cannot be fitted for more than 2-5
thousand members.

3 Oakey and Verbyla have devised a method for plant pedigrees for a
particular dominace matrix which uses
a family level dense GIV matrix and a diagonal GIV matrix. Would you
like to comment Helena/Ari?

4 Crossa has also run models with direct and dominance matrices. Would
you like to comment Jose?

I trust this helps.

May you know Jesus Christ and His blessing in 2007,

Arthur Gilmour, His servant .

Mixed model regression mapping for QTL detection in experimental crosses.
Computational Statistics and Data Analysis 51:3749-3764 now available at
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"J. M. Cano Arias" <jose.canoarias_at_HELSINKI.FI>
Sent by: ASReml users discussion group <ASREML-L_at_AGRIC.NSW.GOV.AU>
20/04/2007 08:14 PM
Please respond to ASReml users discussion group

        To: ASREML-L_at_AGRIC.NSW.GOV.AU
        cc:
        Subject: fraternity & coancestry matrices in animal model

Dear ASreml users,

At the moment I'm running an animal model with ASreml and I would like to
estimate the dominance effects in addition the the genetic
additive ones. So far I'm running a model of pedigree data and two traits
only.

In the ASreml manual it is stated that:
"For the more general situation where the pedigree based inverse
relationship matrix is not the appropriate/required matrix, the user can
provide a particulargeneral inverse variance (GIV) matrix explicitly in a
.giv file".

I have the inverse matrix of the fraternity coefficients but from the
manual
is not clear to me if ASreml can handle in the same model the coancestry
matrix estimated from the pedigree file and the fraternity matrix for the
dominance estimates.

I would be very grateful if you could help me on that, and specially
someone
would have any example of code (or detailed reference) where such a model
has been used in ASreml.

thanks,

Cano

----------------------------------------------
J. M. Cano Arias, PhD.
Ecological Genetics Research Unit
Department of Bio- and Environmental Sciences
PO Box 65 (Biokeskus 3, Viikinkaari 1)
FIN-00014 University of Helsinki, Finland
E-mail: jose.canoarias_at_helsinki.fi
Phone: +358-9-19157707
Fax: +358-9-19157694
http://www.helsinki.fi/people/jose.canoarias

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Received on Thu Apr 22 2007 - 21:02:01 EST