Worm Breeder's Gazette 10(3): 71

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.

Reckless Wanderings and Decomposed YAC's

Jonathan Hodgkin

Figure 1

The set of cosmids that constitute most of the physical map of the 
worm at present cover an estimated 90% or more of the genome.  
Unfortunately the residual 10% may include some important genetic loci.
One such appears to be the region including the major sex 
determining gene tra-1, on the right arm of LGIII.  As described in 
the previous issue of the Gazette, a 200 kb YAC (yeast artificial 
chromosome) Y21B3 hybridizing to the cloned Tc1 insertion eP1 also 
detected a small contig, which was found to be located in or adjacent 
to tra-1 itself.  The contig was not oriented relative to the genetic 
map, but several natural polymorphisms from the Freiburg wild strain 
RC301 were found on the contig and used to provide an orientation.  
Phage, cosmid, and YAC libraries were probed with the leftmost 
fragments of this contig.  Small extensions were obtained by phage 
walking, which were used to identify additional rearrangements in 
several tra-1 loss-of-function alleles, for example a 13 kb deletion 
in the strong (class A1) allele e1834.  An additional extension was 
obtained by probing a phage (lambda 2001) library plated on CES200, 
which is recB- recC- sbcB-.  The phage recovered did not plate on the 
standard rec+ host used here, K12.803.
Four additional large YAC's were also obtained, from the new library 
constructed by Waterston et al.  One of these, Y48A6 (300kb), was 
shown to extend only about 30 kb into the existing tra-1 contig, and 
therefore should extend 250kb leftward, probably covering the rest of 
tra-1 and extending as far as pha-1.  Mutations of pha-1 (formerly sot-
1, 'sore-throat') obtained by Heinke & Ralf Schnabel lead to a failure 
of pharyngeal differentiation during late embryogenesis (1987 Meeting 
Abstracts, p.46).   The X-ray induced mutation e1855 fails to 
complement both pha-1 and tra-1, and behaves as a deficiency with one 
breakpoint right of tra-1 and one breakpoint in pha-1 (because 
recombinants have been obtained between e1855 and other pha-1 alleles).

Y48A6 also hybridized to two new small contigs.  Cosmids from these, 
and from the tra-1 contig, were used to probe wild-type and e1855 DNA. 
These blots showed first that e1855 is indeed a deficiency (rather 
than an inversion), probably for the whole tra-1 region, because the 
right break point has not been found.  Second, one of the new contigs 
is outside this deficiency (eDf20), presumably to the left, and the 
other new contig appears to span the left breakpoint of eDf20.
Y48A6 was labelled and used to probe a genomic library plated on 
CES200.  Of 115 phage recovered, about 20% plate poorly, or not at all,
on K12.803.  Some, but not all, of these 2094 plate well on the recD 
host DB1316.  The phage have not yet been fully analyzed; it will be 
interesting to see if they cover the whole of the pha-1-tra-1 region, 
or whether there are still gaps.  Notice that of approximately 500kb 
corresponding to the sum of Y48A6 and Y21B23, only about 150kb are 
covered by cosmid contigs.
[See Figure 1]

Figure 1