Pea gene symbols – a time for change
Murfet, I.C. Dept.
of Plant Science
Univ.
of Tas., Hobart 7001, Australia
The pea has been among the leading model plant species since the time of Mendel. Pea mutants have particular advantages for use in work on the physiological and biochemical control of plant development. However, no one species holds all the advantages and to facilitate progress it is important to capitalise on the complementary advantages of the several model species. To that end, it is desirable that literature on one species is easily accessible by those working on other species. In this molecular age, the literature on the model species Arabidopsis now dominates the world of plant genetics. Arabidopsis symbols differ significantly from those of pea in several ways. The most confusing concerns the use of the hyphen and symbolisation of multiple alleles.
To avoid the hyphen problem, the Hobart pea group has used the Arabidopsis system in recent publications. What this means, for example, is that the third rms locus is specified rms3 not rms-3 and mutant alleles at this locus are symbolised as rms3-1, rms3-2, etc, with each allele assigned a type line as exemplified in the paper by Symons and Murfet (3). The Arabidopsis system has proved simple and convenient and it avoids the use of cumbersome superscripts. For new alleles, numbers are desirable, but for certain well known cases such as cryc and tlw the superscript letter can be dropped to the line following a hyphen, e.g. cry-c, tl-w. Mutant alleles with complex superscripts need further consideration.
The Arabidopsis system of using capitals for the wild-type allele and lower case letters for all mutant alleles regardless of whether they are dominant or recessive can be supported by strong argument. In the molecular age it is important to identify the allele with the normal or wild-type DNA sequence. Moreover, dominance is not as simple as it might first appear. This is nicely illustrated in the paper by Rozov et al. (2) introducing new mutant alleles at the am1 locus. The new mutations influence anthocyanin coloration at several different sites. The dominance relationships between the new alleles and the original mutant allele am1-1 depend on which site or trait is being considered. In some cases the dominance relationship between two alleles can be reversed by changing the background. In other cases two alleles influencing a quantitative trait may show no dominance with the heterozygotes essentially intermediate in phenotype. Of course in some cases an arbitrary decision may be necessary to choose the wild-type allele.
The merits of the Arabidopsis system of writing the wild-type allele with all capital letters are not so obvious but certainly allow that allele to be clearly recognizable.
It has been said (1) that academicians are more likely to share each other’s toothbrush than each other’s nomenclature. Let us prove the exception to that generalisation and have the grace and wisdom to adopt the Arabidopsis system for pea. That move will make our literature more accessible to others, make the editors of some top journals happy, and undoubtedly enhance the role of pea as a model plant species.
________________
* * * * *