linkage analysis with mixed markers

Kevin Livingstone kdl3 at
Sat Aug 16 10:59:47 EST 1997

I am working on constructing a genetic map of pepper.  I have a framework
of RFLP-based dominant and codominant markers, and I recently received a
large set of AFLP markers to try and add to the existing framework.  While
attempting to do this however, I ran into an interesting problem that has
stumped me.

I started out grouping the AFLP markers (by the way, I am using Mapmaker
3) and then established a separate framework for them, my thought being
that I could then take the representative frameworks for each of the AFLP
groups and build them into the RFLP framework to get an initial indication
of where markers placed, etc.  I used the 'assign' command to match up the
AFLP groups with the RFLP groups, and then used the 'build' command to
integrate the respective groups.  All of the frameworks that I am using
look good when I look at the lod tables (values all >6 along the diagonal
and properly descending down a column and reversed along the rows) and
hold up to a 'ripple' of 3 markers at Lod 3.  The problem I am seeing is
that for one of the pairs of frameworks, Mapmaker wants to take the 15 cM
interval between the two terminal markers (lod=6.73, 15.8 cM) and expand
it by placing all 70 cM of an AFLP framework between them.  I can come up
with no rational explanation for this.  My only guess is that it has to do
with the structure of the data.  All the RFLPs are scored as dominant or
codominant, but the AFLPs were scored so that they are mixed markers, i.e.
they contain A, B, H, C, and D individuals in the Mapmaker parlance.  

Can anyone help with this problem?  Would these data cause Mapmaker to
have problems?  Any help that can be offered would be appreciated-

Kevin Livingstone
KDL3 at

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