The rules of gene symbolization were adapted from the International Rules of Genetic Nomenclature,
from the recommended rules in wheat (178, 179), and from the Recommendation of the 1st International Workshop on Rye Chromosome Nomenclature and Homoeology Relationships (356) and the 3rd Workshop of Rye Genetics, Cytogenetics – Revision and Completion of the Genetic Map of Rye (222), and Internat. Symp. on Rye Breeding and Genetics (397) .
1. In naming hereditary factors, the use of languages of higher internationality is given preference.
2. Symbols of hereditary factors, derived from their original names, are written in italics.
3. Whenever unambiguous, the name and symbol of a dominant allele begins with a capital letter and those of a
recessive with a small letter.
4. Two-letter or three-letter symbols are given preference.
5. All letters and numbers used in symbolization are written on one line.
6. Two or more genes having phenotypically similar effects are designated by a common basic symbol. Non-allelic
loci (mimics, polymeric genes etc.) are designated in accordance with three procedures:
- In sequential polymeric series, an Arabic numeral immediately follows the gene symbol, for example, ct2.
- In homologous chromosomes, the basic symbol is followed by a hyphen (-) followed by the locus designation taking the form of the accepted genome symbol of rye ‘R’ and a homoeologous set number represented by an Arabic numeral; e. g. Adh-R1 designates the R-genome member of the first Adh set. Different alleles, or alleles of independent mutational origin, are designated by a lower-case Roman letter following the locus number designation; e. g., Pm1a.
- Temporary symbol designation. Where linkage data are not available, provision has been made for temporary
symbols. These shall consist of the basic symbol followed by an abbreviation for the genotype or stock and an Arabic number referring to the gene; e. g., YrKi2, YrKi3 refer to two genes for reaction with yellow rust in genotype ‘King II’.
It is recommended that official records of temporary designations be kept, but it is not essential that subsequent
number from other laboratories be checked against earlier numbers either phenotypically or genetically.
7. Inhibitors, suppressors, transporters, and enhancers are designated by the symbols I, Su, Ta, and En if they are dominant alleles or i, su, and en if they are recessive alleles, followed by the symbol of the allele affected (in brackets).
8. Whenever convenient, lethals are designated by the letter l or L, and sterility and incompatibility genes by s or S.
9. In rye and related wilds, linkage groups and corresponding chromosomes are designated by an Arabic numeral (1...7)
followed by genome designated by a capital Roman ‘R’. Whenever in context it appears necessary to indicate from which Secale species a certain chromosome (or chromosome arm) is derived, a superscript of three letters is added. Thus, 1RLmon indicates the long arm of chromosome 1 of the species S. montanum. Telocentric chromosomes are designated S (short) and L (long), respectively.
10. Genetic formulae are
written as fractions, with the maternal alleles given first or as numerator. Each fraction corresponds to a single linkage group.
11. Chromosomal aberrations are indicated by the abbreviations Tr for translocation and Tp for transposition.
12. The zygotic number of chromosomes is indicated by 2n the gametic number by n and the basic number by x.
13. Symbols for extra-chromosomal factors are enclosed within brackets and precede the genetic formula.
14. All molecular markers including SSRs, RAPDs, AFLPs etc. are described with the basic symbol ‘X’.
- 14.1. The ‘X’ is followed by a laboratory designator written in small letters, except a
capital letter is specifically needed, for example Xlprm2-4R. The laboratory designator is given in a separate list of marker abbreviations.
- 14.2. Anonymous loci: The ‘X’ is followed by a laboratory designator, a probe number, a
hyphen (-) and, in case of doubt, the symbol of the chromosome in which the locus is located.
- 14.3. For example, RFLP loci detected in different chromosomes with the same probe is assigned the same symbol
except for the chromosome designation (Xpsr161-R1 and Xpsr161-R5).
- 14.4. Duplicate DNA loci located in the same chromosome are assigned the same symbol except for the addition
of an Arabic numeral in parentheses immediately after the chromosome designation (Xpsr158-R1(1) and Xpsr158-R1(2).
- 14.5. DNA loci for which no product is described or for which ‘allelism’ with known loci are not
demonstrated, the locus symbol consists of the basic symbol ‘X’ followed by an abbreviation of the function, a hyphen, and symbol of the chromosome in which the locus is located (XNar-R2).
- 14.6. DNA loci that are ‘allelic’ with named protein loci are designated with the protein locus symbol.
- 14.7. Clone designations should identify the type of vector, the species from which the cloned DNA was
obtained and the cloned DNA and source laboratory, in that order (p = plasmid; l = lambda; c = cosmid; m = M13 should be used to identify the vector). Initials of the species name (i.e. Sc = Secale cereale; Ta = Triticum aestivum;
...) should be applied to designate the source of the cloned DNA and a unique number-letter combination chosen by the source laboratory should be used to designate the cloned DNA and the laboratory
- 15. Defined regions and more precisely localized genes are given together with the appropriate
nomenclature of the C- and N-bands57 of the chromosome(357).
- 16. Naming quantitative trait loci (QTLs): a QTL name should reflect the trait,
the cross and the chromosome, instead to the standardized wheat QTL naming scheme in which an acronym for the institution that described the QTL. The basic symbol is ‘QTL’ written in
capital letters. Since trait or trait complex descriptions can be extensive, in the present compilation the acronym only includes a number and the chromosome or chromosome region designation, for example QTL14-1RL. The
details are given in a separate list of marker abbreviations.