Your question should be framed differently. Each QTL is important, whether it has an overall negative or positive effect. You have to select the desirable allele of each QTL, whether it comes from parent A (poor) or B (superior). The poor parent may also carry a desirable allele for a QTL. It is not the QTL, but its desirable allele, which needs to be selected. Each QTL will have one desirable and the other undesirable allele. Sometimes the desirable allele of a QTL may be present in poor parent. I hope I have answered your question. 

Dear Raman

I would imagine that the epistatic loci with homozygous alleles (from the same parent), say AA)  could increase the trait value. Considering the fact that you have three QTLs with positive effects, you could try to see if it increases the phenotype. 

To me, it would be a challenge to see if it were the favorable allele and at the end of the day what matters is that you have a marker that you could develop in less time. 

That said, I was wondering if you have data for genotype by environment interactions (GEI) to have more rigorous selection?

Best regards

Prash 

Dear R Dhariwal

Would you please try it in opposite way, i mean, lets take A for the superior parental type and B for the poor parental type and go for analysis again....& check the results. By the way, which software you are using? Write you again. Thanks

QTL with a positive effect shows how much protein is increased by alleles coming from the first parent and on the other hand,  QTL with negative values shows how much protein content is increased by alleles coming from the second parent. Therefore in your case regardless of the sign of values look at QTLs with the largest effects then look at the sign if is + means flanking markers are linked to the chromosome regions of Parent A and if is -  indicates flanking markers are linked to the chromosome region of parent B.

How would you decide which is your first parent and which is second parent? Do you mean that female parent is the first parent which I score as A and second parent, the male parent score as B? In this case does it mean that for QTLs with +additive effects, favorable alleles from first parent (A) contributed and for QTLs with -ve additive effects, favorable alleles from second parent  (B) contributed? Am I correct? Please let me know...  How can we determine from which parent the favorable alleles came? 

Read the exact answer given by M. Ghanbari. You will also find other answers (by Prof Gupta and Dr. Prashanth) very useful for understanding this. 

In a case where the superior parent is coded as A and the poor parent as B (for example in protein content, seed weight, yield traits..) + would indicate that at the particular locus the favorable allele is contributed by the superior parent and vice versa. Additive effect is the difference in the average performance of the RILs/DH carrying A allele wrt  those carrying the B allele at the particular locus (QTL). If A is more, one would see a positive value and negative would indicate that the RILs carrying the B allele at that locus are showing higher trait value. 

I would like to remember the following things while interpreting these results-

1. Our tendency is to score the superior parent as A and poor parent as B. In case the poor parent is scored as A, one would interpret the additive effect values in the reverse manner – negative values would indicate that the superior parent (alleles contributed by it scored as B) contributed the better allele at that locus.

2. If one is focusing on traits where high trait value is undesirable - as in seed phytic acid content or any adverse phytochemical levels (ex. cyanogenic glycosides) the superior parent is the one that is carrying lower trait value.

i think it depends upon your research objective . if increase in the trait value is your objective then +ive allele effect is favorable... While in other case i.e. (decrease in trait value is of interest) negative is favorable, with the condition that your mapping analysis follows the logic that positive alleles increased the trait value.

what if I am studying disease resistance where the less lesion length is favorable,,, still the negative value means the favorable allele (causing resistance) is from parent B, where parent B is susceptible one and not resistant? Pushpendra Gupta

it is really not clear that positive and negative additive effect value is either contributed from superior parent or poor parent. as i have tried analysis by scoring both the way i.e, first superior parent as B and poor parent as A and in reverse also, the result shows there is change in positive and negative sign of additive effect, while values are same.

a research paper by Qiao et al 2016 entailed "Development and characterization of chromosome segment substitution lines derived from oryza rufipogon in the genetic background of 0.sativa spp. indica cultivar 9311" interpret that

additive effect value ither positive or negative will contributed by donor parent only. positive value means increase in particular trait , while negative value means decrease in particular trait.

even in user manual of QTL IciMapping and user manual of WinQTL cartographer 2.5 also they have not mentioned about positive and negative additive effect value, they have just given the scoring method.

hope to get answer positively and satisfactory