Worm Breeder's Gazette 14(5): 32 (February 1, 1997)

These abstracts should not be cited in bibliographies. Material contained herein should be treated as personal communication and should be cited as such only with the consent of the author.

Polymorphisms between strains N2 and DP13 associated with satellite-like repeats

Andrew Hahn, Scott Emmons

Albert Einstein College of Medicine, Department of Molecular Genetics Ullmann 703, 1300 Morris Park Ave. Bronx NY 10461

In the process of genetic mapping we learned that the left arm of LG IV
contains restriction fragment length polymorphisms between the strains
N2 and DP13 (a Bergerac RW7000 subclone).  These were detectable by
Southern hybridization with cosmid probes (G. Beitel, personal
communication).  This region happens to be the target of current
sequencing efforts.  Visual inspection of cosmid sequences revealed the
frequent occurrence of repetitive DNA, leading us to wonder whether the
RFLPs arise from differences in lengths of these repetitive sequences in
the two strains.
   The repetitive sequences are similar to satellite repeats in that
they consist of tandem repeats of short units flanked by nonrepetitive
sequence.  We analyzed 12 such repetitive regions, with repeat unit
lengths varying between 6 and 30 bp, and between 300 and 1800 bp in
total length.  PCR was performed on single N2 and DP13 worms as
described by Williams (Epstein & Shakes, Methods in Cell Biology volume
48) using primers based in nonrepetitive flanking DNA.  Analysis of PCR
products by 1% agarose gel electrophoresis showed length differences
between N2 and DP13 for 7 of the 12 regions.  In each case the length of
the fragment amplified from N2 was consistent with sequence data.  DP13
PCR products were longer or shorter than the corresponding N2 PCR
products by a few hundred base pairs.  It seems likely that the length
differences are due to differences in the number of unit repetitions. 
We plan to test other strains for these polymorphisms.
   PCR analysis of polymorphisms is a simple and quick way to determine
the genotype of a single worm at a physically defined location.  This
method can be useful for gene mapping through analysis of F2 progeny
from a cross between a worm homozygous for the gene of interest and a
wild-type worm of a different strain (Korswagen et al., PNAS 93,
14680-14685, 1996).  The distance between a repeat region and the gene
of interest should be inversely proportional to the frequency of
coincidence of the mutant phenotype and homozygosity for the repeat
length of the strain of the mutant parent.