Question: Haldane Map Function And Genetic Linkage
2
gravatar for User 9334
7.5 years ago by
User 933460
User 933460 wrote:

if i have two markers that are 100 Mb apart on the same chromosome, and i know that for my chromosome, centiMorgan to megaBase ratio is .9, then how many offspring in a generation can i expect to recombine between A and B?

since 1 centiMorgan is roughly 1 megaBase in this case, and 1 centiMorgan is 1% of the generation, then it would not make sense to say that 100% of the offspring would have recombined. The recombination frequency is bounded at 0.5.

so how can this be estimated? must i use haldane's function? what is a good way to think of this? thanks.

linkage genetics snp • 6.6k views
ADD COMMENTlink written 7.5 years ago by User 933460
4
gravatar for Haibao Tang
7.5 years ago by
Haibao Tang3.0k
Mountain View, CA
Haibao Tang3.0k wrote:

You are right about using a map function. See a derivation here. The relationship between map unit and recombination frequency is:

alt text

When r is small, r and m is roughly equal - so you are right about 1cM ~ 1% of the generation. It does not hold when r is approaching 0.5.

alt text

ADD COMMENTlink written 7.5 years ago by Haibao Tang3.0k
1

if I plug in 100 cM into the equation for r from http://statgen.ncsu.edu/qtlcart/manual/node46.html i still get that r = 0.5, which cannot be right. if snp A and snp B are 100 Mb apart on the same chromosome, they will not segregate independently

ADD REPLYlink written 7.5 years ago by User 933460
1

@unknown (google): see the plot above (x-axis is r, y-axis is m), remember 100cM = 1 morgan, and when you look at m = 1, r is somewhere between 0.4 and 0.5. Sean gave an exact calculation.

ADD REPLYlink written 7.4 years ago by Haibao Tang3.0k
1

@unknown (google): it is not clear to me where your intuition comes from. 100Mb is a very large distance, it could be the two ends of a chromosome in human. I wouldn't expect strong linkage across that distance. Unless you really meant 100Kb rather than 100Mb - for example if snp A is 100Kb away from snp B, then that's 0.1cM and roughly 0.1% recombination frequency.

ADD REPLYlink written 7.4 years ago by Haibao Tang3.0k

so what would it be in this case? i am not sure i see the answer

ADD REPLYlink written 7.5 years ago by User 933460

0.5(1-exp(-21)) = 0.4323324

ADD REPLYlink written 7.5 years ago by Sean Davis25k

This makes no sense, since if you have something that's roughly 100 Mb away, it can't be that the recombination frequency is around 40%. It should be far less. if snp A is 100 Mb away from snp B, what is their predicted recombination frequency?

ADD REPLYlink written 7.4 years ago by User 933460
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