University of Florida

A message from the Managing Editor, J. W. Scott, Ph.D.:

Once upon a time there was a gene list committee associated with the Tomato Genetics Cooperative and some of its functions were to approve gene symbols and names, place genes on the chromosome map, and publish gene lists. When I took over as Managing Editor in 2002 a new committee was formed with one of the main charges to approve the naming and gene symbols of newly discovered genes. It was suggested that when tomato researchers made new gene discoveries that they write up a TGC report and get the committee to approve their name and symbol. The response to this request was underwhelming to say the least and thus the gene list committee is no more. This is another example of how times change. However, if anyone out there is thinking of naming a gene and wants to write up a TGC report about it please do so. Also, if you want advice on the name and symbol you've chosen feel free to contact myself or Roger Chetelat:

Roger Chetelat, University of California, Department of Vegetable Crops
One Shields Avenue, Davis, CA  95616  USA 

J.W. Scott, University of Florida/IFAS, Gulf Coast Research
14625 CR 672, Wimauma, FL  33598

The rules for naming genes was published in TGC
42: 6-8 in 1992.  We have provided the information below.

1.  Chromosomes.  The chromosomes are numbered according to their length measured in pachytene.  Such numbers have already been applied (Barton, 1955); chromosome 1 is the longest, chromosome 12, the shortest.  In addition to length, such features as positions of centromere and amount and distribution of heterochromatin serve to identify each chromosome.  Short arms are symbolized by "S", long ones by "L"; thus "1S" designates the short arm of chromosome 1.

2.  Linkage groups.  Linkage groups beat the same numbers as their respective chromosomes.  As soon as the arm location of a gene is known, the locus numbering shall be revised to reflect that information.  The smaller arm of each chromosome is designated as the left arm, and the zero position is the distal or left end of the small arm.

3.  Genes.  Mutant genes are designated by letter symbols.  The mutant name, an adjective or noun or a combination of both, refers to the main diagnostic feature of the phenotype.  The initial letter of the symbol should be the same as that of the name;  additional appropriate letters are added as necessary to distinguish it from other symbols already in use.

The genes c, r, s, and y do not conform to this rule, their symbols having unfortunately been derived from the normal instead of the mutant condition.  Since these symbols have been in widespread use for over 40 years, they should be retained, but all others should conform to these rules.

After obtaining reasonable evidence for the existence of a new gene for which the phenotype can be distinguished reasonably well in some or all genotypic milleux, the discoverer should select an appropriate name and symbol, taking care not to use any already reported.

Special effort should be expended to find appropriate names for new mutants.  Latin names or their English derivatives are recommended for thier international meaning.

The symbol should consist of the minimum letters or numbers necessary to distinguish it all other existing symbols.  Although lengthy symbols may have reference value to the discoverer, they are cumbersome for genetic notation and become a hindrance to other workers, who oten make greater use of the mutants than the discoverer.

4.  Alleles.  Dominance or recessiveness of a mutant gene is indicated by comparison with a "standard" or "normal" type.  The variety Marglobe is proposed as this normal type since it is widely grown and is typical of teh general concept of normal tomato morphology.

A mutant gene dominant to the normal type is written with the initial letter of the name and symbol capitalized, while a recessive is written with all letters in lower case.  The normal allele of a mutant gene is written with the symbol of the mutant gene followed by the superscript "+".  Thus the normal allele of sp is sp+ and of 1 is 1+.  A dominant allele appearing later at the sp locus would be designated as spD.  Additional alleles at teh same locus are designated by appropriate letter or number superscripts; thus for the d locus, the following alleles are known:  d, dx, dcr, and d+.  For the first member of a numbered series of alleles, which is the preferable form of notation, the "1" shall be understood but not used.  When it is clear in the text which gene is concerned, the normal allele may be designated simply by the "+" symbol.

5.  Indistinguishable alleles of independent origin.  (Supposed reoccurrence).  It is recommended that these not be given unique symbols.  If they are, however, they shall be designated by the existing gene symbol with a "series symbol" appended as a superscript.  The series symbol, which shall be enclosed in parenthesis, shall consist of an Arabic numeral corresponding to the particular reoccurrence of the allele found by any given discoverer plus a unique abbreviation derived from his name, this abbreviation to be assigned by the Gene List Committee to the discoverer and used by him for designating reoccurrences at any locus.  For example, ag(1K) and ag(2K) (formerly ag3 and ag4, respectively), the first and second reoccurrences of ag found by Knowles.  If the gene symbol already has a superscript, this shall precede the appended parenthetical superscript.

6.  Mimics.  Mutants that have different loci and are indistinguishable phenotypically from each other are known as mimics.  Members of a single mimic series are preferably designated by different names and symbols (e.g. u for uniform, ug for uniform gray-green).  If a numbered series is used, the same name and base symbol are followed by a hyphen and a distinguished number on the same type level.  The first member of such a mimic series the "1" shall be understood but not used (e.g. ms, ms-2, etc.). 

7.  Translocations are designated by the symbol "T".  The chromosome involved are designated by their respective numbers.  To distinguish between translocations involving the same chromosome, lowercase letters are used following the chromosome numbers, thus T (1-2)a, T (1-2b), etc.

8.  Inversions are designated by the symbol "In" while the chromosome in which the inversion occurs is indicated by its respective number.  Lowercase letters are used to distinguish different inversions on the same chromosome, thus In (1)a, In (1)b, etc.

9.  Deficiencies are designated by the symbol "Df" are distinguished in the same manner as inversions (rule 8).

10.  Aneuploids.  Monosomics and primary trisomics are designated according to the missing or extra chromosome; thus "triplo-1" refers to teh primary trisomic of chromosome 1 and "haplo-12" refers to the monosomic for chromosome 12.

For aneuploids possessing whole arm interchanges, the chromosomes are symbolized according to their component arms, a connective dot representing the centromere; thus "1S-12L" specifies an interchange between the short arm of chromosome 1 and the long arm of chromosome 12.  According to this system 2n + 10L•10L would be an example of a secondary trisomic, 2n + 5S•7L an example of a tertiary trisomic, 2n + 8L an example of telotrisomic, and 2n - 3S•3L + 3S•3S + 3L•3L an example of a compensating trisomic in which a normal chromosome is compensated by isochromosomes of its short arm and long arm.

11.  In order to distinguish between gene symbols and symbols of the chromosome aberrations, the former are italicized.

12.  Since chromosomes of all investigated species of Lycopersicon appear to be almost completely homologous, it is suggested that the same symbolization apply to the entire genus.  It is also proposed that the complete gene symbols not be duplicated among the species unless the genes in question are known to be identical, and that the key letters of the symbols not be duplicated unless teh genes are alleles or mimics.  Species alleles can be designated by a superscript to indicate the species, for example ah for a hypothetical allele in L. hirsutum.

13. Much confusion will be avoided by clearing names and symbols with the Chairman of either the Gene List Committee or Coordinating Committee of teh Tomato Genetics Cooperative at the earliest opportunity.  Such action will settle matters of priority and assist the investigator by assigning a reasonably permanent symbol to his mutant.  Permanence cannot be guaranteed, however, because unknown earlier or simultaneous publication  might establish priority.

14.  Modifiers.  Modifiers (mo or Mo) of specific genes shall be symbolized by the appropriate symbol followed by the symbol of the gene modified enclosed in parenthesis.  Subsequent nonallelic modifiers shall be denoted by adding a number suffix to the combined symbol.  For example, the two dominate modifiers of I and Mo(I) and Mo(I)2.  When the action of the modifying gene is known to be suppression, it is perferable to use a suppressor symbol (Sup);  likewise an enhancer symbol (Enh) for genes of enhancing action; in either case the gene whose expression is modified shall be symbolized in parentheses as specified for modifiers, thus Enh(I), Sup(I)2.

Barton, D.W. 1950.  Pachytene morphology of the tomato chromosome complement . Amer. J. Bot. 37:639-643.
Barton, D.W., L. Butler, J.A. Jenkins, C.M. Rick, and P.A. Young. 1955.  Rules for nomenclature in tomato genetics.  J. Hered. 46:22-26.
Clayberg, C.D., L. Butler, C.M. Rick, and P.A. Young.  1960.  Second list of known genes in the tomato.  J. Hered.  51:67-174.
Clayberg, C., L. Butler, E.A. Kerr, C.M. Rick, and R.W. Robinson. 1966.  Third list of known genes in the tomato.  J. Hered. 57:189-196.