Recombination mapping

[Marius]

I have some conceptual issues concerning the construction of a "recombination map": If I have many F2 genotyped for genome-wide SNP markers as well as their grandparents (parental generation), how would you proceed to actually find recombination? I would need to somehow infer the haplotypes of the grandparents and check whether they have recombined in the F2 I guess... Are there existing programs?

And:

- Would it be possible to let's say genotype the grandparents and the F2 without the F1 to get a higher probability for recombination (2 meiosis) and thus more resolution or would I have to also genotype the F1?
- Would it be a problem if these F2 all have the same grandparents or is it important to have different independent crosses?
- What would be a reasonable sample size for something? References?

Thanks.

[dariober]

Hi Marius,

I have some conceptual issues concerning the construction of a "recombination map": If I have many F2 genotyped for genome-wide SNP markers as well as their grandparents (parental generation), how would you proceed to actually find recombination? I would need to somehow infer the haplotypes of the grandparents and check whether they have recombined in the F2 I guess... Are there existing programs?

Try to have a look at CRIMAP (http://www.animalgenome.org/bioinfo/tools/share/crimap/), it's a program to build linkage map in general pedigrees. The function chrompic shows where recombination events occurred. (Warning: crimap is a great program, best on the marker probably. However, it's quite old and not exactly user friendly, there might be easier solutions to your problem.)

All the best
Dario