David Smyth pointed out that because transgenes are (meant to be) functional
genes, they could be considered as wild type and if so should be upper case.
At the risk of confusing this discussion with the one on dominance, the
proposal could be amended as follows:
1) Transgene loci are identified as such by the prefix "t" (or "T"?) (by
analogy to the bacterial plasmid "p" designation).
Example: a chalcone synthase transgene would be T-CHS (or TCHS or
2) Because transgenes can insert at many loci, each is distinguished
numerically as T-CHS1 through T-CHS1000 - and beyond.
3) Because one can construct an infinite number of chs transgene variations
(different promoters, different linked drug markers, etc), there has to be a
mechanism to avoid two labs using the same designation. Thus, symbols and
blocks of numbers would be registered with the database (i.e., applied for
and assigned). Thus, Fred Ausebel might be assigned T-CHS1-100 and Joe
Schmo, T-CHS101-110. (Note: This is exactly what was adopted by bacterial
geneticists in 1976 for plasmid nomenclature. Unfortunately, e-mail was not
available to "spread the word" and to make the process of registering symbols
painless. As the field exploded, the system was overrun; hence many
constructs were called things such as, p12X/lac-4bnptII#1, and that sort of
nonsense (which looks a lot like many transgene designations in plants).)
4) Transgene loci should be assigned symbols only when genetically
characterized as single Mendelian loci.
5) Transgene alleles can be designated by the same rules as for endogenous
genes, e.g., T-CHS210-4.
6) Symbols can be any three letter combination followed by one or more
numerals. (Note: symbols would not have to have any relationship to genes
carried by the transferred insert, and often should not. For instance, a
T-DNA might carry a nos/npt gene and a 35S-driven AGAMOUS cDNA, as well as a
2'/GUS gene. Perhaps the construct is called pNAG101. At first thought, the
researcher might want to register the name T-NAG101 for a transgene locus
carrying this T-DNA. But what of the next ten loci? T-NAG102, etc might
appear to correspond to plasmids pNAG102, etc, but would in reality be
different loci with the pNAG101 T-DNA. For this reason, it would be less
confusing to choose three letter codes that are different than the T-DNA