Re: Maternal Genetic effects in ASReml-R

Dear Jarrod,

Let me add my thoughts.

It would appear that the design is adequate, otherwise you would generate
a singularity in the AI matrix.

However, the data set is small so it is highly likely that sampling
variation could generate the result you have observed.
If you have generated 100 samples and they all show this feature, then
maybe there is a problem with the simulation.

Just check that you have the correct number of effects fitted.

One check of coding is to export the data frame and run the job in
standalone ASReml (which uses the same license).

May Jesus Christ be gracious to you in 2008,

Arthur Gilmour, His servant .
 
Mixed model regression mapping for QTL detection in experimental crosses.
Computational Statistics and Data Analysis 51:3749-3764 at
http://dx.doi.org/10.1016/j.csda.2006.12.031

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Jarrod Hadfield <J.Hadfield_at_ED.AC.UK>
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Re: Maternal Genetic effects in ASReml-R

Dear Brian,

Thanks for the quick reply. I haven't been able to get correlated random
effects using "link" yet (I get various error messages), but I'm not sure
I've specified ASReml-R to fit the simpler model correctly.

I am using simulated data in order to test the power of different designs
for estimating maternal genetic effects, and I'm reasonably confident that
the design I have allows me to separate additive genetic, maternal
additive genetic and maternal environment effects. However when I fit the
model the maternal environment effect is constrained at zero. The
estimate of the additive genetic variance seems to be unbiased but the
estimate of the maternal genetic variance is equal to the total maternal
variance (genetic + maternal):

The model I fit is:

asreml(y~1, random=~nurse+ped(id, var=T)+ped(nurse, var=T),
ginverse(id=Gped, nurse=Gped))

but the estimates suggest that nurse and ped(nurse, var=T) are fitting the
same thing (allthough they are not).

The replicates consist of 4 pairs of sisters mated to 8 unrelated males to
form 8 parental pairs. Each of the 8 parental pairs then produce 4
offspring. The 8 parental pairs are then organised into 4 dyads where the
2 pairs making up the dyad are unrelated to each other. 1/2 of the
offspring for each pair are reared by the other parental parents within
the dyad. Offspring are therefore raised by nurses, which in 50% of cases
are also their dams. In addition the dyads are formed so that a sister
pair are not paired with individuals that are also sisters. Hence, I'm
reasonably confident the effects can be estimated since unrelated
offspring are reared by sisters (maternal genetic effects), unrelated
offspring are reared by the same nurse (maternal environmental effects)
and related offspring are reared by their mothers and unrelated nurses
(additive genetic effects).

Perhaps I'm mistaken?

Jarrod

On 30 Jan 2008, at 17:20, brian.cullis_at_DPI.NSW.GOV.AU wrote:

Dear jarrod
I have to admit that I have never fitted these but I would imagine that
you could as shown in the ASReml-R manual page 58 section 5.4. As for
correlating additive and maternal I would think this is also possible
using us(link(~ped(Calf) + ped(Dam))) but I dont think this has been
tested or requested. Hence I am ccing this to David Butler, the author of
ASReml-R to check the syntax and the use of ped() within link()

Arthur and I are in the UK at the moment and so DBs response will be in Oz
time
 

warm regards

Brian Cullis
Research Leader, Biometrics &
Senior Principal Research Scientist
NSW Department of Primary Industries
Wagga Wagga Agricultural Institute

Professor,
Faculty of Agriculture, Food & Natural Resources
The University of Sydney

Phone: 61 2 6938 1855
Fax: 61 2 6938 1809
Mobile: 0439 448 591

Jarrod Hadfield <J.Hadfield_at_ED.AC.UK>
Sent by: ASReml users discussion group <ASREML-L_at_AGRIC.NSW.GOV.AU>
31/01/2008 04:02 AM

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Maternal Genetic effects in ASReml-R

Hi Everyone,

Is it possible to fit maternal genetic effects in ASReml-R yet? If
so does any one have any example code they could show me (preferably
with the covariance between additive and maternal genetic effects
estimated)?

Thanks,

Jarrod
Received on Tue Feb 02 2008 - 06:56:18 EST