I think that the difficulties that have been pointed out with separate
designations for dominant mutations are present in every other genetic
system. Nevertheless, all the major eukaryotic systems (including mouse,
maize, Drosophila, C. elegans, S. cerevisiae, S. pombe,..) do use such
designations because the convenience of being able to follow complex
crossing schemes at a glance generally outweighs the problems that can
occur (especially when dealing with suppressor loci, where the genetics
can quickly become incomprehensible). The designations are not intended
to define relationships in an allelic series, but only in relation to
wild-type. Cases of partial phenotypes when heterozygous are also
encountered in all other systems, they are generally designated as dominant
(e.g. Kruppel in Drosophila).
In any case, if there is to be no separate designation, then I would
at least argue against using upper case to mean wild type. Otherwise we
will be writing all crosses involving dominant mutations with the upper
case to indicate the recessive phenotype. This would put us at odds with
a universal convention established by Mendel (a plant biologist), and not
reversed by any animal, plant or fungal system.
A compromise may be to use lower case for everything (as in C. elegans
and S. pombe), with + to mean wild type, as suggested by Rob Last.
Cold Spring Harbor Laboratory