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In a paper, Berkley, C. A., and C. Lexer. 2008. Admixture as the basis for genetic mapping. Trends in Ecology & Evolution 23:686–694, the definition of Genetic architecture is given. It says:

Genetic architecture: the number and genomic location of loci that contribute to variation in a trait, as well as the allelic effect sizes and direction, the genotypic effects (additivity and dominance) and the extent of epistatic interactions among loci.

What is the allelic effect sizes and direction?

I found that allelic effect sizes is the same thing as penetrance. But the direction?

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These two concepts are different from penetrance.

Allelic effect size

An allelic effect size is the magnitude of the effect of an allele on a phenotype.

The detailed definition seems a little bit trickier than it sounds I think (and I would love confirmation by other users on what follows and or a reference). For example, a phenotypic trait might be influenced by 20 QTL. At one such QTL (say QTL8), you may observe two alleles in the population: QTL8_A and QTL8_B. The effect size is the absolute phenotypic difference between two individuals differing exclusively at QTL8. I suppose it is also possible to define an allelic effect size as the average difference between the phenotype of QTL8_A and QTL8_B over all possible genetic background (eventually weighted by the average frequency of each background in the population at a given instant). In the case of a QTL that contains more than two alleles, then the allelic effect size can be defined either between each pair of alleles or between one allele and the average effects of all the others. Strong epistasis make the whole thing more complicated if one wants to average over all possible genetic backgrounds.

Direction of an allelic effect

The direction of an allelic effect is the direction (add or subtract) that an allele has on a phenotype.

Talking about direction makes sense only in the absence of sign epistasis.

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    $\begingroup$ Do you have a reference that talks about this? $\endgroup$
    – M. Beausoleil
    Commented Jan 13, 2016 at 13:46
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    $\begingroup$ Nope! The term is often encountered but I am not I ever saw a nice and complete definition of it (although it probably exists). This is the reason why I am asking for confirmation from other users. Sorry, cannot do better! $\endgroup$
    – Remi.b
    Commented Jan 13, 2016 at 15:03

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