[Po-dev] RE: Questions about associations

[Marty Sachs]

Mary,

My point was, what's the difference?  In this day of DNA sequence 
analysis, a single bp substitution difference is a scorable 
phenotypic difference (regardless of whether this occurred in nature 
or by EMS mutagenesis).  The allelic differences observed in Maize 
Diversity/Panzea project are all due to mutation.  In terms of 
morphological phenotypes, what is the difference between the D8 
allele, which is naturally occurring, and the D9 allele which was 
induced?  Both result in dwarf plants.

My point is there should be no distinction in how variant alleles are treated.

	-Marty

At 11:45 AM -0500 9/25/07, Mary (Polacco) Schaeffer wrote:
>Marty,
>If you read the association file format info they talk about MUTANTS - so I
>was assuming it did not include naturally occuring alleles - and I wished to
>be clear if  PO is making a distinction between say diversity alleles as
>from the Panzea project, and those that were induced to perturb the system.
>
>So, the question reqmains - are we? Either way works for me,
>
>     m
>
>On 9/25/07 10:27 AM, "Marty Sachs" <msachs at uiuc.edu> wrote:
>
>>  At 10:18 AM -0500 9/25/07, Schaeffer, Mary L. wrote:
>>>  I assume you mean alleles other than mutant?
>>
>>  Huh?  All alleles differ from each other due to mutation.  Many may
>>  not be induced by a researcher in a lab setting, but natural allelic
>>  variation is also due to mutation.
>>
>>  -Marty