Re: How to get additve and dominance effect value?

From: <arthur.gilmour_at_DPI.NSW.GOV.AU>
Date: Thu, 14 Aug 2008 14:45:44 +1000

Dear Khandker

I was trying to analyze my data using ASReml, to find out association
of single nucleotide polymorphism (SNP) with phenotypic trait (in
animal data). For three different genotypes (0,1,2 in data set) of a
single SNP, I can get predicted trait values for individual genotype
and also can get allele substitution effect for a SNP. However, I am
unable to calculate the additive and dominance effect of a single SNP.
How can I get those values? [I use animal model and univariate analysis]

Let me assume you have a variable in the data coded 0,1 2 and we will call
it SNP
[You may in fact have many of these but I assume you are just looking at
them one at a time.]

If you leave SNP as a variable and fit it as a fixed effect, you will just
have the additive (substitution) effect.

resp ~ mu SNP !r animal

If you add the term
resp ~ mu SNP at(SNP,1) !r animal

then the at(SNP,1) effect will reflect the dominance, being the
deviation of the SNP=1 class
from the average of the SNP=0 and SNP=2 classes. This gives the basic

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May Jesus Christ continue to be gracious to you,

Arthur Gilmour, His servant .
Mixed model regression mapping for QTL detection in experimental crosses.
Computational Statistics and Data Analysis 51:3749-3764 at

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Received on Sat Aug 14 2008 - 14:45:44 EST

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