Interactions

For a QTL with k loci, there are $k(k-1)/2$ unordered pairs of loci. We can define epistatic interactions for each of these pairs. Epistatic interactions come in four types, thus there are $2k(k-1)$ possible interactions. The abbreviations for the types are:

	Interaction	Abbrev.
1.	Additive by additive	AA
2.	Additive by dominance	AD
3.	Dominance by additive	DA
4.	Dominance by dominance	DD

If an interaction is not defined in the -interactions block, then it will be set to zero. To define the interactions, we have a block that looks similar to that defining QTL main effects. The token -interactions is followed by the -trait token with a traitname and then a repeating sequence of QTL1 QTL2 Type Value tokens. Thus, the line
1 2 AA 0.01
means that QTL 1 (chromosome 1 position 9.1) and QTL 2 (chromosome 1 position 89.1) have an additive by additive effect of 0.01. Note that the QTL with a smaller number ALWAYS comes before that with the larger number. Note that in the example file, there were no interactions between QTL 4 and any of the other QTL for the first trait. If an interaction term is missing, its value is zero.