Linkage analysis with pseudotest cross population

Muhammad A. Lodhi mal5 at
Mon Oct 25 12:00:19 EST 1993

Dear Friends
        Does anyone have better idea about linkage analysis of test cross
populations where phase is missing (pseudotest cross).  The situation
becomes something in between test cross and F2.  Currently I have been
using MAPMAKER 3.0 but it is not easy and reliable to use this software for
such situations.  I tried JOINMAP and LINKAGE-I but both of these are based
on only pairwise analysis, as far as I understood.  With mapmaker I am able
to identify the linkage groups but it can't handle dominant markers
(segregating 1:1) and segregating 3:1 simultaneously.  Moreover, it gives
high distances between markers.  I am working on grapes and I have RAPD,
isozyme and RFLP markers from one population.  I am wondering if there is
any reliable software for such populations.  I am aware of work done by a
group in NC on forest trees and Norman Weeden on apple.  There is an
increasing demand by the geneticists working on woody plants to find
something reliable for data analysis.  I will appreciate your help and
comments.  Thanks in advance

Muhammad A. Lodhi
Cornell Univ. Geneva Campus
NYSAES, 123 Hedrick Hall
Geneva, NY 14456

Ph  :315-787-2239
Fax :315-787-2216
e-mail:mal5 at

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