Dear Vaishali Sharma,

According to your question 

Which marker position do I have to consider for a particular marker for my study of QTL mapping?

I think that you have 8 linkage groups

So, you must first check the polymorphism between the parents for these 8 different groups and try select  the markers that have distance between each other and at least 20-25 markers per each chromosome 20 x 8= 160 markers at least and must be polymorphic in both parent first and then try to screen your mapping population individuals or plants

the more marker you have the more QTLs with high LOD score you will find

the more mapping population individuals or plants  the more QTLs with high LOD score you will find

with best regards

khaled

A correct option is to build your own map, but you got a RIL so, in this case, you got an additional difficult. You can first select MS (try khaled advices, but include more that you need in regions with no agreement between authors). Then, try to use CRIMAP with your own results (It´s an option that includes a postulate position on markers). Compare the results and try to find coincidences in close related maps. Try to use consensus positions first or those including more MS. Backcrossing is better material to build maps. Don´t forget that MS markers maps uses recombination rates, not bp, so incorrect positions are usual and you gonna deal with that often. Best wishes. SD.