Advanced intercross followed by backcrossing

[Tyler Audet]

Hello, I have an experiment that I am beginning to prepare for sequencing and analysis to map loci associated with a trait in one species by hybridising it with a sister species (that lacks the trait) for 5 generations. So I have an F5 advanced intercross, however, to narrow down out haplotype blocks, the F5 hybrids were mated back to the sister species and allowed to go to a new F2. So I have and F5 advanced intercross, stacked on to an F2 backcross. 

My current thought would be to treat it as an F7 AIL, but this seems like it may violate the assumptions of the AIL because at F5 everything is re-combining with the parental sister species genome again.

Do you think I could just treat it as an AIL, or is there another way to set this up better?

Thank you for any help.

[Karl Broman]

Treating it as an AIL should be okay. 

Alternatively, use "genail2" so that you can account for genotypes not being 50:50 between the two parents. 

See my 2022 paper on "A generic HMM for multi-parent populations", https://doi.org/10.1093/g3journal/jkab396 

karl