Generate Mapping/Genetic Map Positions From Physical Position In Case Of Soybena Snps

Question

[k2bhide]

Dear all,

I would like to get the genetic/mapping position from physical position of small set of Soybean SNPs. What I have is:

• list of SNPs with their physical position in Hapmap file format

My aim is generate genetic map of Soybean using SNPs. I would appreciate if anyone would let me know the formula to calculate mapping position of SNPs from physical positions. It would be great if anyone knows any software or tools which can be used to obtain these positions.

Thanks for your help.

Ketaki

[Neilfws]

It would help to show a small example of the data. Your question is also somewhat ambiguous and confusing. What do you mean by "physical position"? To most people, "physical mapping" is a form of "genetic mapping", i.e. the map you use in the absence of genome sequence. If by "physical position" you mean chromosome + coordinates, then why would you want to take a backwards step to a genetic map?

[ice4prince]

Hi k2bhide,

Did you solve this problem finally?

Yours,
Sunny

Answer 1

[Bioch'Ti]

As the relationship between physical (bp) and genetic (cM) maps is not linear at all (across and along chromosomes), it is not possible (to my mind) to get the genetic map from the physical position of your SNP. You have to understand that the genetic map relies on the recombination rate (measured between two generations i.e. F1=>F2) that vary according to the cross you are working on (I mean, intra/inter species cross for example and its type F1, BC, F2). So you have to study the recombination pattern in a pedigree to get the genetic map. Maybe, there are already available genetic maps for your species you can base your work on. Then, there are plenty of linkage mapping software such as Crimap, JoinMap, etc... Cheers.