Segregation distortion analysis

[Yuqing Jin]

Hi Pasi,
Can LEPMAP3 do the analysis on the Segregation distortion ?
And can i use this software add the segregation distortion loci to the pre-existing linkage map?
Best regards, yuqing

[Pasi Rastas]

Dear Yuqing,

Thank you for your question.

Typical segregation distortion should not a major problem with Lep-MAP3 (however, very extreme distortion reduces the information in the data so mapping could become impossible). The marker ordering (OrderMarkers2) does not care about distortion, but getting markers into chromosomes might be more difficult with distortion. This is because of genomic repeats in sequencing data cause markers to look like distorted and join markers in different chromosomes. This is why some sort of filtering based on distortion makes sense.

You can handle distorted markers in two different ways in LM3, either filter out too extremely distorted markers (with Filtering2, paramater dataTolerance) or use distortionLod=1 parameter (single family data) in SeparateChromosomes2. You can also use JoinSingles2All module to try to add distorted markers back to linkage groups (after Filtering2).

Cheers,
Pasi