2. Symbols of hereditary factors, derived from their original names, should be written in italics, or in Roman letters of distinctive type.

3. Whenever unambiguous, the name and symbol of a dominant should begin with a capital letter and those of a recessive with a small letter (see also special rules for symbolizing biochemical and DNA loci and host:pathogen/pest systems).

4. All letters and numbers used in symbolization should be written on one line; as far as possible no superscripts or subscripts should be used.

5. The plus sign (+) will not be used in symbolization of hereditary factors in wheat.

6. Two or more genes having phenotypically similar effects should be designated by a common basic symbol. Non-allelic loci (mimics, polymeric genes, etc.) will be designated in accordance with two procedures:

(i) in sequential polymeric series where an Arabic numeral immediately follows the gene symbol; e.g., Sr9.

(ii) in orthologous sets where the basic symbol is followed by a hyphen ("-") followed by the locus designation taking the form of the accepted genome symbol and a orthologous set number represented by an Arabic numeral; e.g., Adh-A1 designates the A-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., Sr9a, Adh-Ala. (See also guidelines for nomenclature of biochemical and DNA loci).

6.1 Temporary symbol designations: 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 line or stock and an Arabic number referring to the gene; e.g., SrFr1, SrFr2, etc., refer to two genes for reaction to Puccinia graminis in cultivar Federation. It is recommended that official records of temporary designations be kept, but it is not essential that subsequent numbers from other laboratories (e.g., SrFr3) be checked against earlier numbers either phenotypically or genetically.

7. Inhibitors, suppressors, and enhancers are designated by the symbols I, Su, and En, or by i, su, and en if they are recessive, followed by a space and the symbol of the allele affected.

8. In wheat and related species, linkage groups and corresponding chromosomes are designated by an Arabic numeral (1-7) followed by genome designated by a capital Roman letter; i.e., for hexaploid wheat of group aestivum (Morris and Sears {737}), 1A-7D. This system supersedes the original designations using Roman numerals; i.e., I-XXI. In this Revision, the designations for homoeologous group 4 chromosomes of wheat are as agreed at Workshop I, 7th International Wheat Genetics Symposium, Cambridge, UK (see Proceedings, Miller TE & Koebner RMD eds. pp. 1205-1211); that is, the previously designated chromosome 4A was redesignated 4B and the previous 4B was redesignated 4A. Consequently, the former 4AS is now 4BS and the former 4AL is now 4BL. Likewise, the former 4BS and 4BL are now designated 4AS and 4AL, respectively. Chinese Spring is accepted as having the standard chromosome arrangement. Chromosome arms (or telocentric chromosome derivatives) are designated S (short), L (long), on the basis of relative arm length within the chromosome. In the case of equal arms, they are arbitrarily designated S or L on the basis of homoeology with the short or long arms of the other chromosomes of their homoeologous group (see Workshop I Proceedings of the 7th International Wheat Genetics Symposium).

9. Genetic formulae may be written as fractions, with the maternal alleles given first or above. Each fraction corresponds to a single linkage group.

10. Chromosomal aberrations should be indicated by the abbreviations Df for deficiency, Dp for duplication, In for inversion, T for translocation, and Tp for transposition. In wheat there are a number of genes derived from related species by introgression. Such genes in different instances reside at different locations. One location may be taken as standard. Other locations will be considered as transpositions relative to the designated standard.

When a gene does not reside in its standard chromosome position, the new chromosome designation may be given in brackets following the gene designation; e.g., Hp (Tp 6D) refers to a line carrying the introgressed "hairy neck" gene on chromosome 6D instead of 4B which is taken as standard. Alternatively, the chromosome involved may be described as a translocation. Guidelines for the description of translocated chromosomes both within wheat, and between wheat and alien chromosomes are provided in {705}.

11. The zygotic number of chromosomes is indicated by 2n, the gametic number by n and the basic number by x.

12. Symbols for extra-chromosomal factors should be enclosed within brackets and precede the genetic formula.

2.2 Basic symbol: The basic symbol for a gene locus should consist of a two-, three-, or four-letter abbreviation of the trivial name of the enzyme, protein, or other macromolecule affected. The initial letter should be a capital and all characters in the symbol should be italicised.

2.3 Loci specifying the structure of similar macromolecules: Non-allelic gene loci that specify the structure of similar non-enzymatic proteins, of enzymes that catalyse the same or similar reactions, or of similar RNA molecules should be assigned the same basic symbol. The remainder of the symbol for each such locus should be formulated in accordance with one or the other of two procedures, depending upon whether or not evidence is available to assign the locus to a orthologous set.

2.3.1 Loci that are members of anorthologous set. The basis symbol should be followed by a hyphen (-), the accepted symbol for the genome to which the locus belongs and an orthologous set number in the form of an Arabic numeral. For example, Adh-A1, Adh-B1, Adh-D1, and Adh-E1 designate the A-, B-, D-, and E- genome members, respectively, of the first-designated orthologous set of aliphatic alcohol dehydrogenase structural gene loci. Identification of a minimum of two members of a set is required to use this nomenclature.

2.3.2 Other loci: In the absence of evidence to assign loci to an orthologous set, they should be designated in sequential series by a common basic symbol followed immediately by an Arabic numeral. If evidence to assign the loci to an orthologous set is obtained subsequently, the loci should be redesignated in accordance with the procedures in section 2.2.1.

Rye loci should be designated in accordance with these procedures (see {1448}). For barley loci, the procedures described in section 2.2.1 should be used when designation of a locus as a member of an orthologous set of Triticeae loci is desired; otherwise, barley genetic nomenclature should be employed. Thus, for example, Adh-H1 and Adh-R1 designate the H- and R-genome members, respectively, of the Adh-1 set of loci.

Evidence regarding phylogenetic relationships among structural genes may be obtained by comparative studies of (1) nucleotide sequences and other molecular properties of genes, (2) physical and/or biochemical properties of gene products, and (3) intra-chromosomal map positions and/or physical locations of genes in homoeologous chromosomes or segments. Criteria for determining whether or not gene loci that encode isozymes are homologous and, for orthologous gene loci, whether they belong to the same or different orthologous sets, are described in {512}. Most of the criteria are also applicable to non-enzymatic proteins. The evidence that is the basis for designating gene loci as members of an orthologous set should be stated in the publication in which symbols for the loci are proposed.

2.4 Alleles: Different alleles are designated by a lower case italic letter following the locus designation. For example, a-Amy-A1a and a-Amy-A1b are two alleles of the A genome a-Amy-1 locus. One strain should be designated the prototype strain for each allele discovered, since variation that has not been detected by the methods used may be present within each allelic class. Chinese Spring should be the prototype for allele 'a'. If an apparently identical allele in other strains is found by new methods to be different from that in the prototype strain, it should be assigned a new lower case italic letter and a prototype strain designated. This system allows the orderly assignment of symbols to newly-identified alleles and allows ready comparisons of new variants with previously reported variants.
 

Triticeae enzyme and protein gene loci are commonly initially identified and assigned designations based on studies of aneuploid strains that lack and/or contain extra copies of whole chromosomes or telosomes. Consequently, evidence may be obtained for the production of two or more similar enzyme or protein promoters by one chromosome arm without genetic evidence as to whether or not the promoters are the products of one gene, of different genes that are members of a gene complex, or of two or more genes that are not members of one gene complex. In these situations, only one locus designation for similar proteins or enzymes should be assigned to a chromosome arm until recombination evidence indicates otherwise.
 

5.1 Basic symbol: The basic symbol for DNA markers of unknown function should be 'X'

5.1.2 Locus symbols for DNA markers detected with ‘known-function’ probes or with primers that amplify genes: The locus symbols for RFLP markers of unknown function that are detected with ‘known-function’ probes may include, in parentheses following the probe number, a symbol for the gene from which the probe was obtained. For example, Xpsr804(Sbp)-3A designates a chromosome 3A locus detected with a sedoheptulose-1,7-bisphosphatase gene probe. Likewise, when the primers used to amplify a DNA marker of unknown-function are of sufficient length and similarity to a known gene to amplify the gene, the DNA-marker symbol may include the gene symbol in parentheses following the number assigned to the primers. For genes for which the Commission on Plant Gene Nomenclature has assigned mnemonic designations, the set number and other numbers assigned by the Commission may also be included inside the parentheses immediately after the gene symbol.

5.2 'Known-function' DNA Markers: Loci that are detected with a DNA probe or DNA primers and whose function has been demonstrated should be designated with a symbol that indicates the function of the locus, as described in either Section 2 or in the Recommended Rules for Gene Symbolization in Wheat. It must be emphasised, however, that some clones and primers are likely to detect both loci whose function is known (proven, for example, by a segregational test against allelelic forms of a gene encoding a protein) and additional loci of unknown (i.e. unproven) function (either pseudogenes or unrelated loci whose sequence homology to the probe or primers is sufficient to allow detection by it). In this case, the two types of loci require different nomenclature, namely, that described in section 2 or in the Recommended Rules for Gene Symbolization in Wheat and in Section 5.1, respectively.

5.3 Duplicate DNA-marker loci: DNA markers located in the same chromosome that hybridize with the same probe or that are amplified with the same primer(s) should be assigned the same symbol except for the addition of a period and an Arabic numeral immediately after the chromosome designation. For example, Xpsr933-2A.1 and Xpsr933-2A.2 designate duplicate loci located in 2A that are detected with probe PSR933. As when two or more enzyme or protein promoters are produced by one chromosome arm, multiple DNA fragments from one chromosome arm that hybridize to one probe or that are amplified by one pair of primers (or by one primer) should be assigned to only one locus until recombination evidence indicates otherwise. As noted in Section 5.1, DNA markers located in different chromosomes that hybridize with the same probe or that are amplified with the same primer(s) should be assigned the same symbol except for the chromosome designation.

5.4 Allele symbols: Alleles should be designated as outlined in Section 2.3 with the exception that restriction-enzyme-specific alleles, e.g. RFLP- and indirect-STS alleles, should be designated with the name of the restriction enzyme followed by a lower-case letter. For example, Xtam-5A-HindIIIa denotes an allele detected with HindIII. Where possible, Chinese Spring should be the prototype for allele ‘a’. When a double-digest is used to detect an allele, both restriction enzymes should be listed, separated by a slash. The name and source of the probe or primer(s) and the length(s) of the DNA fragment(s) detected normally should be stated in the first publication describing an allele.

5.5 Abbreviation of locus and allele symbols: The chromosome designation is an integral part of the locus symbol for DNA markers. Nevertheless, on chromosome maps and in a limited number of other contexts, the chromosome designation and the hyphen preceding it may be omitted. For example, Xpsr35-3A may be abbreviated as Xpsr35 on a map of chromosome 3A, Xpsr933-2A.1 and Xpsr933-2A.2 may be abbreviated as Xpsr933.1 and Xpsr933.2, respectively, on a map of 2A,andXpsr804(Sbp)-3A may be abbreviated as Xpsr804(Sbp) on a map of 3A. Also, the chromosome designation and the hyphen preceding it may be omitted on chromosome maps from the symbols for intra-chromosomally duplicated loci that are detected with a ‘known-function’ probe (or with primers that amplify a gene) but that do not include a gene symbol. For example, if Xtam200-1A.1 and Xtam200-1A.2 were the symbols for duplicated loci detected with a ‘known-function’ clone designated TAM200, then the symbols could be abbreviated as Xtam200.1 and Xtam200.2 respectively, on a map of 1A.

Finally, Xbgl485(Ger)-4D.2 may be abbreviated on a map of 4D by omission of the hyphen, the chromosome designation and the period, i.e. as Xbgl485(Ger)2. In some contexts it will also be possible to abbreviate the symbols for alleles as, for example, BamH1b, or even simply b.

5.6 Laboratory designators: Laboratory designators should consist of from two to four and preferably three letters. When used in locus symbols, all of the letters should be lower-case and italicized (see Section 5.1.2).

Laboratory designators should be chosen carefully to insure that they differ both from those used by other laboratories and from those that compose gene symbols. As an aid in this regard, a list of laboratory designators that have appeared in the literature is available electronically via the Internet Gopher from host greengenes.cit.cornell.edu, port 70, menu "Grains files to browse" / "Reserved Laboratory Designators for DNA Probes, Primers and Markers".

Laboratories that are investigating DNA markers in different species and/or of different types, e.g., RFLPs, STS, and RAPDs, may choose to use more than one designator. For example, oat and barley cDNA clones isolated at Cornell University have been designated with the prefixes CDO and BCD, respectively, and cdo and bcd, respectively, are appropriately used as laboratory designators in symbols for loci detected with these clones. Likewise, tam and txs, respectively, are being used as laboratory designators in symbols for loci detected with wheat and sorghum DNA clones isolated at Texas A&M University, and the John Innes Centre is using psr and psm as laboratory designators in the symbols for DNA markers detected with wheat and millet probes, respectively, and psp for wheat PCR markers.

5.7 Clone designations: Clone designations should minimally identify the type of vector, the species from which the cloned DNA was obtained, and the source laboratory and cloned DNA, in that order. p = plasmid, l = lambda, c = cosmid, and m = M13 should be used to identify vectors. Initials of the species name, e.g., TA = Triticum aestivum and SC = Secale cereale, should be used to designate the source of the cloned DNA and a unique letter-number combination chosen by the source laboratory should be used to designate the source laboratory and the cloned DNA.

6.2 Quantitative trait loci (QTLs): QTLs are loci controlling quantitative characters whose allelic classes do not exhibit discontinuous variation or clear segregational patterns. They are identified by association with one or more linked markers.

6.2.2. Locus symbols: The ‘Q’ should be followed by a trait designator, a period, a laboratory designator (see Section 5.6), a hyphen (-) and the symbol for the chromosome in which the QTL is located. The trait designator should consist of no more than four and preferably three letters, the first of which is capitalized. Different QTLs for the same trait that are identified in one chromosome should be assigned the same symbol except for the addition of a period and an Arabic numeral after the chromosome designation. All characters in the locus symbol should be italicized. For example, QYld.psr-7B.1 and QYld.psr-7B.2 would designate two yield QTLs identified in chromosome 7B by the John Innes Centre. On a map of 7B, these could be abbreviated as QYld.psr.1 and QYld.psr.2.

6.2.3 Allele symbols: Alleles at QTL loci should be designatedby a lower-case italic letter following the locus designation.
 

The foregoing should be considered only as a proposal at this time as no AFLPs are listed in the catalogue. Comments regarding the proposal are welcomed and should be sent to the authors.

Update 20March2000: The Standard List for AFLP® Primer Nomenclature is Now Available. This list was generously provided by KeyGene. AFLP® is a registered trademark of Keygene N.V.

2. Where no recombination occurs between genes conferring resistance to more than one pathogen, the gene(s) segment shall be designated separately for each disease; e.g. Pm1, Sr15 and Lr20.

3. Where recombination occurs between two closely linked factors for reaction to a pathogen, the recombined ‘allele’ may be designated as a combination of the separate alleles; e.g. the recombined ‘allele’ obtained by combining Lr14a and Lr14b was designated as Lr14ab. The decision as to whether a designation should be as a combination or as separate genes shall be at the discretion of particular workers. A maximum value of 1 crossover unit for designation as an ‘allele’ is suggested.
Although the need to consider uniform symbolization of corresponding genes in pathogens is recognized, no recommendations are proposed.