Re: Maternal Genetic effects in ASReml-R

From: Bruce Southey <southey_at_UIUC.EDU>
Date: Fri, 1 Feb 2008 20:00:51 -0600

You might find Chapter 7 (especially figure 7.8) of Lynch and Walsh's book informative.

I don't know R-ASREML so I have to assume that you are actually fitting the model correctly. But I don't see any covariance between additive genetic and maternal effects. If it is actually correct, as indicated by Arthur, it could be lack of power so pump up the parameters so you can estimate them AND increase the number of observations. If that does not work then it should be clear that you need to rethink your logic.


---- Original message ----
>Date: Thu, 31 Jan 2008 19:52:30 +0000
>From: Jarrod Hadfield <J.Hadfield_at_ED.AC.UK>
>Subject: 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 To ASREML-L_at_AGRIC.NSW.GOV.AU
> <J.Hadfield_at_ED.AC.UK> cc
> Sent by: ASReml users Subject Maternal Genetic effects in
> discussion group ASReml-R
> 31/01/2008 04:02 AM
> +-----------------------------+
> | Please respond to |
> | ASReml users discussion |
> | group |
> +-----------------------------+
> 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 Mon Feb 01 2008 - 20:00:51 EST

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