Toward unambiguous designations for loci defined by restriction fragment polymorphisms

The definition of polymorphisms with probes, rapidly becoming a major tool for mapping and other purposes, raises some potential ambiguities in terminology for the gene as a functional unit. We would like to propose a conservative, yet efficient and informative, symbolization of RFP loci that is consistent with current nomenclatural standards and that will minimize ambiguities, especially for probes derived from functionally defined units. We hope this proposal responds to some of the other concerns raised in the 1986 Maize Conference and reflects to a suitable degree the suggestions and comments of Cooperators who have discussed the need for a systematic nomenclature.

The ambiguity to be avoided is that of specifying a polymorphic locus as the structural gene or coding sequence when it is not. Probes are rapidly being obtained for functional products, e.g., enzymes for which no "Mendelizing" variation in the product has been established. For example, a genomic clone for the second sucrose synthase gene has been used to map a new locus through polymorphisms probed by the clone (D.R. McCarty et al., PNAS, 1986); an impressive number of other loci, probed by homologous or heterologous probes, is presented by T. Helentjaris and collaborators in a new report in this issue of the News Letter. Taken at face value, the assumption is easily made that the polymorphism (which is the genetically mapped property) is co-sequential with the functional gene; but it is much more probable that the polymorphism is actually in an intron or in an adjacent, noncoding sequence. While current mapping resolution makes the distinction moot for the time being, we suggest that, in the interest of accuracy, the polymorphism be defined separately from the functional unit.

Our nomenclatural suggestion is that, following the practice of T. Helentjaris in the maps to date, a polymorphic locus be defined by a number that is uniquely applied to the segregating variation, specifically mapped relative to other factors.

For the 3-letter designator, a reconsideration is in order. In MNL 60 the interim symbol RFP, with the number appended to it, was used for purposes of indexing, especially toward consolidating the loci under one source symbol. Unfortunately the use of one 3-letter symbol for all polymorphisms may lead to overlapping numbers, and would require a clearing-house system. A simple alternative is for each laboratory to choose a distinctive 3-letter symbol for the source of the mapping study, e.g., NPI, UMC, PIO, etc. Thus the loci will be NPI1, NPI2, etc., UMC1, UMC2, etc., with the number immediately following the 3-letter symbol without a hyphen, consistently with the current standards of nomenclature.

For loci that are defined by a probe for a functional product, a unique number for the locus should again be chosen by the lab that defines and maps the polymorphism. The product may, if desired, be specified by a hyphenated addition to the numbered symbol. Thus, the polymorphic locus defined by a probe for the small subunit of rubisco could be, for example, NPI227-ssu. In our current standards of nomenclature a hyphenated addition specifies allelic variations at a locus, and the particular RFP morph could be specified efficiently by numbers or letters, as with isozymes, with or without the functional specification.

This proposal is used in the working maps presented with this issue of the News Letter, and we invite comments, suggestions or critiques.

Ed Coe and Dave Hoisington
 
 


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