Re: fraternity & coancestry matrices in animal model

From: <arthur.gilmour_at_DPI.NSW.GOV.AU>
Date: Sun, 22 Apr 2007 21:02:01 +1000

Dear Cano,

ASReml can handle multiple relationship matrices however there are some

Additive + Dominance run
  Animal !P
  Sex *

!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
Trait 0 US !GP

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

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

1 This job asssumes the GIV file is generated assuming the same animal
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

Personal website:,
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; mobile: 0438 251 426

ASREML 2 is now available from
The ASReml discussion group is at
To join it,

Proposed travel:
ASReml workshop (Forestry) 16-18 April Tasmania
Rec leave 19-20 April
ASReml planning at Tumut 23-27 April
Biom Brch meet 2-4 May
ASReml workshop (Animal Breeding) 8-26 May South Africa
AAABG 24-26 September Armidale

"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

        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

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
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
would have any example of code (or detailed reference) where such a model
has been used in ASreml.



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
Phone: +358-9-19157707
Fax: +358-9-19157694

This message is intended for the addressee named and may contain
confidential information. If you are not the intended recipient or
received it in error, please delete the message and notify sender. Views
expressed are those of the individual sender and are not necessarily the
views of their organisation.
Received on Thu Apr 22 2007 - 21:02:01 EST

This webpage is part of the ASReml-l discussion list archives 2004-2010. More information on ASReml can be found at the VSN website. This discussion list is now deprecated - please use the VSN forum for discussion on ASReml. (These online archives were generated using the hypermail package.)