AIL genetic map construction

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Xinghua Li

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Jul 16, 2024, 11:30:15 AM7/16/24

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AIL can provide much higher mapping resolution. Is R/qtl2 capable of make genetic maps using the AIL population? Or can we treat the AIL as F2 and use qtl1 to make a map, then use it in qtl2?

Karl Broman

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Jul 16, 2024, 11:35:23 AM7/16/24

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Genetic map estimation has not been implemented for AILs in R/qtl2.

I agree that you could treat it as an F2 and estimate the map, either in R/qtl1 or R/qtl2, but you'd need to rescale it, as the intervals would be expanded due to the multiple generations of recombination.