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.
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.
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