Re: Estimation of additive effect?

From: <arthur.gilmour_at_DPI.NSW.GOV.AU>
Date: Thu, 28 Aug 2008 10:27:02 +1000

Dear Khandker

You wrote
This is a follow up mail of my previous email entitled "How to get
additive and dominance effect value".

Thanks Arthur for your reply and by using the commands you mentioned I
can get allele substitution effect as well as dominance effect.
(resp ~ mu SNP at(SNP,1) !r animal),
This command gives me both measurement at one single run.

However, still I can't figure out the additive effect which is
estimated as the difference between the two homozygous means divided
by two (Falconer, D. S., and T. F. C. Mackay. 1996. Introduction to
Quantitative Genetics. 4th ed. Longman Scientific and Technical, New
York, NY.). Here, I am using SNP with three genotypes
(0=homozygous,1=heterozygous,2=homozygous), so it will be the estimate
of difference between 0 and 2 divided by 2.

1) I have not reverenced Falconer, so I may have missed something.

Assuming SNP is a variable with values of 0,1 or 2
and is declared as a simple variate in ASReml (i.e. no factor
qualification appended)

the the design matrix for the fixed effects will be

mu SNP at(SNP,1)

1 0 0
1 1 1
1 2 0

and let us say the 3 fitted effects are c (for mu), a for SNP and d for

So the SNP=0 class BLUE is c
      SNP=1 class, BLUE is c+a+d
   SNP=2 class, BLUE is c+2a

So additive effect is (c+2a -c)/2 = a

So, a is the additive effect and the average allele substitution effect.

Unless I have missed something.

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 28 2008 - 10:27:02 EST

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