The direction of effect is based on the coding of the genotypes, and as such depends on the reference allele (or the parental allele) coding.

In crosses from inbred parents (e.g. Arabidopsis RIL) the direction of effect will tell you which parental strain supplied the "increasing allele". If this increase is positive or negative depends on the trait in question... e.g. higher yield might be positive, while higher flowering time might be seen as a negative trait.

If you know that the LER allele is increasing yield, you might want to breed this allele on another background, to increase yield.

Thank you Danny. I understood your point. I will appreciate if you can put forward your insight on the following example...Four QTLs are identified for sugar content in strawberry (octoploid) using a CP (F1) population of which the additive effect of three QTLs are positive (3.328, 4.244 & 2.169) and one is negative (-2.03). So what possibly could this opposite direction mean in terms of practical breeding sense. Thank you

Well it depends on what phenotype you're looking at. Assuming yield, and parental strains coded as AAAA and BBBB (this is important since it flips around if you map the other way around). Optimizing your strawberries yield means, creating a strain which has:

BBBB for the positive effect QTLs (since every B allele increases by 3.3, 4.2 and 2.1)

AAAA for the negative effect QTL (since every A allele increases by 2)

The theoretical yield (ignoring dominance and interactions ) would then be: 3x 3.3 + 3 x 4.2 + 3x 2.2 + 3x 2.0 = 35.1

If you are looking at a phenotype you want to minimize it's the other way around (e.e. growth time), then you'd create a strain having AAAA for the positive QTLs, and BBBB for the negative QTL effect

Hope this helps,

Danny

Dear Danny thank you very much. I appreciate your effort. Best wishes.