Abc or abc?

[rajorgensen at UCDAVIS.EDU]

The practical difficulties noted by Carrie Schneider, Daphne Preuss, and 
Robert Robbins are valid concerns with any system of nomenclature that 
tries to indicate dominance relationships on top of allelic designations.  
The difficulties arise from the fact that dominance is a relative property, 
while nomenclatures tend to have absolute rules ("once designated Abc1-1, 
always designated Abc1-1").  Nonetheless, nearly all plant geneticists (as 
well as yeast and fly geneticists) have operated comfortably and effectively 
with this approach for many decades. Geneticists use dominance designations 
because they do in practice have great utility. The reason that they do is 
that nearly all plant genomes behave genetically as diploids. Thus, in any 
given cross, only two alleles of a gene are involved, so there is no 
confusion if one is indicated as dominant and the other as recessive. In fact 
this can be quite convenient to the reader because it saves the trouble of 
looking up or memorizing the dominance relationship between the alleles.  

Still, the disadvantages are real, so I suggest consideration of new
nomenclatural rules that adopt parts of both positions and recognize the 
inherent relativism of dominance relationships:

1)  Each allele of every gene must continue to have a unique designation, 
e.g., abc1-1, abc1-2, etc.  

2)  In "official" gene lists the lower case designation will continue to be 
used, avoiding the relativism problem.  Stock centers and databases can
continue operating exactly as they do now.

3)  Upper case designations may be used in publications whenever appropriate 
and useful, but ONLY when retaining the specific allelic designations, as in: 

Abc1-1/Abc1-1  x  abc1-1/abc1-2  --->  Abc1-1/abc1-2

(A cross between two homozygous lines to produce a heterzygous F1, where 
allele Abc1-1 is dominant over abc1-2.)

4)  All dominance designations are recognized to be relative and subject to 
change whenever dominance relationships change.  Thus, an allele designated 
as Abc1-1 in crosses with allele abc1-2 would be redesigated as abc1-1 in 
crosses with a third allele, Abc1-3, which is dominant over both abc1-1 and 
abc1-2.  

Eliminating the absolutism eliminates the practical difficulties mentioned on 
the netork. This may require some adjustment by maize geneticists coming to 
work on Arabidopsis, but little adjustment for most current Arabidopsis 
researchers. The adjustments would be in the direction of a more pragmatic 
usage that reflects biological realities.  

Comments?



Rich Jorgensen
Dept of Environmental Horticulture
UC Davis, Davis, Calif. 95616-8587
916-752-5807 (phone)
916-752-1819 (fax)
rajorgensen at ucdavis.edu