Hi, I have complete genome sequences for both parents I am working with. I found P1 and P2 have chromosome rearrangement where P1's chromosome 3 maps to part of P2's chromosome 3 and chromosome 11. And P1's chromosome 11 maps to part of P2's chromosome 3 and 11 as well. I am wondering how I should construct the genetic map? For the progeny I just have partial genome sequencing from restriction enzyme based sequence.
In the progeny there are a lot of markers which are segregating differently than expected Mendelian ratio, especially on those chromosomes (90-100% of markers from one parent).
Does anyone have any experience with something like this? Should I just look at statistical association of phenotype and marker and not do the interval mapping?