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summary of size of non-tagged, T-DNA induced mutations

Sue Gibson gibso043 at tc.umn.edu
Wed May 12 09:49:40 EST 2004


Hello,

	Several people have been kind enough to respond to my request 
for information regarding T-DNA induced mutations. Specifically, in 
cases where the locus of interest is not "tagged" by insertion of all 
or most of the T-DNA, we wanted to know what types (insertions, 
deletions or substitutions) and sizes of mutations to expect.
	We received information about a total of 13 "non-tagged" 
mutations from T-DNA mutagenized populations. A summary of these 13 
mutations is shown below and the original messages from the people 
who provided the information is also included. Thanks again to all 
who responded.

Substitutions:
4 out of the 13 mutations consisted of 1 bp substitutions

Insertions:
2 out of the 13 mutations consisted of 1 bp insertions

Deletions:
1 out of the 13 mutations consisted of a 2 bp deletion
2 out of the 13 mutations consisted of 10 bp deletions
1 out of the 13 mutations consisted of a 11 bp deletion
1 out of the 13 mutations consisted of a 30 bp deletion
1 out of the 13 mutations consisted of a 43 bp deletion
1 out of the 13 mutations consisted of a 141,115 bp deletion

-----------------------------------------------------------------------------------------------------

 From Mark Running:
You will undoubtedly get many anecdotal replies, but mine is this: 
I've seen an 11 base pair deletion and a 1 bp insertion in my limited 
experience in walking to genes that came out of a T-DNA mutagenesis.  

-----------------------------------------------------------------------------------------------------
 From Julie Lloyd:
Only one example for you, but for what it's worth I have a single 
base substitution (causing an intron splice site disruption) mutant 
which was isolated by screening the Feldmann T-DNA insertion lines 
(it had 2 unlinked insertions which we cleaned out by backcrossing).

-----------------------------------------------------------------------------------------------------
 From Thomas Kretsch:
In my lab we isolated 5 Alleles of EID1 from T-DNA tagged lines by
physiological screenings (hypersensitive toward light):

eid1-3 (Feldman): insertion of 1 nucleotide leading to a
frame shift
eid1-4 (Versaille): tag in the ORF, only right border
detectable with PCR, left border never found, most probably
re-arrangments at the left border, mRNA with increased size
detectable (duplication of sequences?)
eid1-6 (Jack): big deletion of 43 nucleotides in the ORF,
premature stop
eid1-7 (Versaille): deletion of 10 nucleotides in the ORF,
premature stop
eid1-8 (Versaille): small deletion of 2 nucleotides in the
ORF, premature stop.

-----------------------------------------------------------------------------------------------------
 From Karen Hicks:
I don't know if anyone has done a systematic study, but I do have a 
few pieces of data for you; in the three untagged alleles that I have 
sequenced, two were single basepair changes and the third was a small 
(10bp) deletion.
-----------------------------------------------------------------------------------------------------
 From Elizabeth Rogers:
the only non-tagged mutation my lab has cloned, by mapping, and sequenced
was just a point mutation, one bp to another. but I'd be curious to hear
what others say.
-----------------------------------------------------------------------------------------------------
 From Dan Riggs:
I am also interested in the answer to your question and can tell you 
what we found in one case.  My lab has been studying the BP (KNAT1) 
gene and we have 6 mutant alleles, generated by a variety of 
mutagens.  Five of the six are due to large deletions. One of the 
alleles, bp5, was generated by T-DNA insertion mutagenesis, but 
rather than harboring a T-DNA (at least at the BP locus), there has 
been a very large deletion (141,115bp, to be exact).   We've been 
mapping the breakpoints of all of these large deletion mutants and 
are trying to accumulate information on other deletions in the hopes 
of identifying  motifs that confer 'genomic instability'.
If you get any other replies could you forward them to me or post on 
the newsgroup.
-----------------------------------------------------------------------------------------------------
 From Ortrun Mittelsten Scheid :
We had a 30 bp deletion in mutant bru1-1 (Takeda et al, Genes and
Development 2004).






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