what to screen-answers

RATCLIFF FRANK.RATCLIFF at bbsrc.ac.uk
Thu Apr 6 07:33:23 EST 1995


Several people have written to me asking for the answers to yesterdays 
question to be networked, so here they are. For those who dont want to read 
it all; Col or Ler.

Thank you to all those who replied


We screen Ler for two primary reasons.  1) There are a lot of
polymorphisms between Col 0 and Ler and 2) Ler plants are shorter and
less apt to get tangled up (that's the "er"ecta part) and also it
flowers a bit more quickly than the others.  Because of the nature of
the er mutant in Ler, the siliques are shorter and fatter.  It turns
out that the buds are easier to work with (as fas as crossing goes) in
our hands.

Ws also has many polymorphisms (probably with Ler and Col - but I'm not
sure). I'm not so sure about RLD and dijon - it might be trouble
mapping with these two.  If you want to use RAPDs for mapping, I think
you'll need Ws.

As a final note, it seems that most (non-tagged) mutants are in the Ler
background.  Because there are differences (and because this is a
mutant), this background MAY affect the mutants you are looking for.
Certainly cell elongation mutants could be somewhat complicated in this
background.
Well, I hope my ramblings have helped.

--
Shawn C. Baker              Division of Biological Sciences
scbaker at ucdavis.edu         Section of MCB (Gasser Lab)
(916) 752-3111              University of California - Davis
                            Davis, CA  95616


Dear Frank,

The Lister-Dean RI population (Lister and Dean, 1993) is based on a 
Col x La-er cross and provides a high density map from 1 mapping population 
(not the integration of many populations [Hauge et al., 1993]). Im addition, 
most of the YAC libraries are derived from Col DNA. 

Cheers,
pat


Frank--
You are probably getting lots of mail on this so I"ll keep it short. Col-O
or Ler are probably the best for cloning & other studies. We use Col because
the largest number of useful molecular markers detect differences between
Col and Ler and there are lots of useful visible markers in Ler which one 
can
use to map and identify flanking recombinants for one's mutation.
Good luck.
Lawrence Hobbie (Estelle lab0


Frank-

Hi, I just read your posting to the Arabidopsis net and I figured I'd make 
my
suggestion.  You're going to have to chromosome walk to any loci you want to
clone so you'll being doing alot of RFLP analysis.  Most of the RFLP clones
have known polymorphisms between Ler and Col so I'd use one of those 
ecotypes
and not RLD, WS or Dijon.  I would suggest Ler because the plants are 
smaller
and easier to deal with than Col plants.  Also, once you have a mutant that
you'd like to clone, the best way to generate recombinants near your gene is
to make double mutants with your mutant and linked visible markers (also in
Ler) than cross each double to Col.  In the F2, any plants that are single
mutant (i.e. either your mutant or the flanking visible marker but not both)
have recombinants in that region near your gene.  Most visible markers are 
in
Ler so that's why I'd suggest buying the mutagenized Ler seed.

Good Luck,
Bobby Williams


Col (or Col gl1) and Landsberg are the best because most of the 
molecular markers used for mapping have been developed for crosses 
between these races. 

Most of the RFLPs and PCR markers have been generated between Ler and Col--
choosing one of these can simplify the work down the line if you have to
turn to positional cloning techniques (quite likely for an EMS mutation). 
Many researchers prefer Ler because it grows very quickly and produces lots
of pollen; Col, on the other hand has more reliable root phenotypes.

  
Robert Rutherford
Laboratory of Genetics- Masson group
University of Wisconsin-- Madison
Madison, WI 53706  
USA
(608) 256-0243
rrutherf at students.wisc.edu



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