From lfreebortulane.edu  Tue Apr  2 02:24:11 2013
From: "Freeborn, Layla" <lfreebortulane.edu>
To: Multiple Recipients of <crimap-usersanimalgenome.org>
Subject: CRI-MAP for multiple, small families?
Date: Tue, 02 Apr 2013 02:24:11 -0500

Hello,

I'm attempting to construct a genetic linkage map from 3 families with 10
F1 each. I am working with SNP data generated from RAD sequencing of a
species with a very large genome (9Gb; with presumably a lot of duplication
and junk). I'm currently working with JoinMap 3.0, but the program isn't
able to form more than a couple of linkage groups containing ~100 loci,
when I should have 10 linkage groups with thousands of loci. The other
~2,000 loci are never paired with any significance. I have tried doing this
for each family separately and for all three families combined but never
get more than a couple of linkage groups. Also, when I input files
containing loci of multiple segregation types, it seems like the program
always groups loci according to segregation type rather than recombination
frequency. Unfortunately, I'm not sure if I'm dealing with a computational
problem, something having to do with the species' genome, or a combination
of the two. The crosses are of two heterogenously homozygous and
heterozygous diploid parents (recombination in both). I'm hoping to make
one map using male-informative loci, another map using female-informative
loci, then use abxab or abxcd markers to link the two maps together. Do you
think that CRI-MAP is suited for my purpose? Beldade et al. 2009
(http://www.plosgenetics.org/...oi%2F10.1371%2Fjournal.pgen.10
00 366#s3) use a similar strategy of multiple small families and were
successful with CRI-Map. Any suggestions would be greatly appreciated.

Thank you, Layla