"Sex" map distance differences in hemaphroditic F2 cross

[Daniel P Wood]

Dear Pasi,

I'm a little confused about sex specific mapping distances, I'm hoping you could give me some advice. I am using Lep-Map3 to analyse plant F2s resulting from a single selfed F1 individual. The parents of the F1 are also sequenced which I have used to phase the data (withgrandparentPhase=1). I've included two dummy F1 individuals in the pedigree file (please see QB.ped attached) as you've recommended elsewhere, and assigned the parents/grandparents sexes arbitrarily. For the SeparateChromosomes2 and OrderMarkers2 step I have used informativeMask=3, as "both" of the F1 individuals should have the same genotypes. So I'm a bit confused as to where the sex differences in map distances come from, especially as the chromosome lengths seem much longer in one "sex" than the other (example map from chromosome 6 also attached). I know I can generate a sex averaged mapped but I'd still like to get the bottom of these differences. Any insight you might have into what is causing these differences (perhaps it reflects different recombination rates in the grandparents?) would be very much appreciated!

Many thanks for your time and best wishes,

Daniel Wood

PS The commands I've used to generate the files are the following, in case I've just used some parameter wrongly...:
ParentCall2 data = $ped vcfFile =$vcf > parentcall
SeparateChromosomes2 data=$parentcall lodLimit=35 sizeLimit=40 distortionLod=1 informativeMask=3 grandparentPhase=1 > $parentcall.lim35
OrderMarkers2 data=$parentcall map=$parentcall.lim35 chromosome=6 outputPhasedData=1 informativeMask=3 > $parentcall.lim35.chr6

[Pasi Rastas]

Dear Daniel,

Thank you for your good question.

Firstly, you cannot find sex differences in recombination from a selfing cross. So the found difference comes from Lep-MAP3.

Maybe Lep-MAP3 will put the recombinations more often in one sex when it can put it with same likelihood to either. Also the haplotype model penalises first and additional recombination differently, separately for "maternal" and "paternal" haplotypes. This default model can also cause some difference here (setting interference parameters to 1 would reduce this effect).

Finally, I think Lep-MAP3 works correctly but you just have to ignore the found difference.

Cheers,
Pasi

Ps. I will check your attachment later.

[Daniel P Wood]

Dear Pasi,

Many thanks for your response - I will try setting those interference parameters to 1 and see what difference that makes. That's good to know, thanks!

Best wishes,

Daniel Wood