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rohan-shah / mpMap2

New version of mpMap
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Can mpMap2 construct a map for the MAGIC population generated by DH (not selfing)? #7

Open Zhutn opened 1 year ago

Zhutn commented 1 year ago

Dear developers,

I would like to express my gratitude for providing such a useful tool, mpMap2. I am currently working on constructing a linkage map for a 16-parents MAGIC population that was generated using double haploidization (DH) to form inbred lines, typically through selfing, similar to RILs.

In the pedigree() function provided by mpMap2, there is a parameter called selfing, which implies that we can only import the pedigree for the MAGIC population generated by selfing. However, I am unsure if this is the case for the DH-generated inbred lines.

I would appreciate any help or guidance you can provide on how to properly use the pedigree() function in mpMap2 for constructing a linkage map for a DH-generated inbred line MAGIC population.

Thank you for your time and assistance.

rohan-shah-nearmap commented 1 year ago

I don't think there is any functionality for double haploidization. Correct me if I'm wrong, but isn't that not equivalent to any kind of selfing?

I no longer work in this space, so while I might one day get a chance to come back and try and help you with this....it's going to take a long time.

Zhutn commented 1 year ago

Dear developers,

I would like to express my gratitude for providing such a useful tool, mpMap2. I wanted to share my thoughts on the difference between double haploidization (DH) and recombinant inbred lines (RILs). While RILs are usually calculated based on the accumulated recombination rate, DH only occurs once, and the recombination rate of DH is different from that of a single self-cross.For instance, in conventional biparental populations, the cumulative recombination rate of RILs can be calculated as R=2r/(1+2r) (Haldane and Waddington, 1931), where r represents the recombination rate of double haploidization (DH) populations.

Regarding the pedigree() function in mpMap2, I understand that it does not currently support DH-generated inbred lines. However, I would like to express my willingness to modify the code myself to enable the construction of linkage maps for DH-generated multi-parent populations, provided it is feasible to do so.

Thank you for your time and assistance. I appreciate your response and understand that you are no longer working in this area.

Best regards