Minimum Physical Distance And Genetic Distance Required To Select Assay For Genotyping Work

Question

[blacktomato27]

Hi to all, I have data like this ASSAY MP Cm chr#
XY1723 408068 0.3 1
XY1727 463360 0.3 1
XY1708 880744 25.7 1
XY1709 900596 25.8 1
XY487 1174585 0 1
XY1641 1239146 27.3 1
XY1714 3057570 34.2 1
XY1721 3522443 34.2 1

Here i want to select assays covering all my chromosomes (12) and i want assays should be well distributed on all the chromosomes. Now i want to know is there basic criteria or rule to do that for example selecting marker after every particular basepairs or Centimorgan distances. If any one help me to improve my basic knowledge in this issues would be highly appreciated. Here i given example data on only 1st chromosome.

Thanking you very much, Regards

[Ashutosh Pandey]

Depends on your organism, how different are two lines, strains or individuals that are segregating the markers or SNPs. How big is the IBD regions that your cross has. You need to give some more detail.

Answer 1

[blacktomato27]

Dear Ashuto, Thank you very much for your reply to me. Basically my lines are not much distant you can say closely related but not much and i am sorry i am new to this field i do not know about IBD and its value for this cross. I got file like in my post containing physical position, genetic distance of segregating SNPs between lines. I have only this much information and my task is to select segregating snps which covers genome perfectly. Thanking you very much, Regards