from Gary Hart, 9 May 1994 Guidelines for Nomenclature of Biochemical/Molecular Loci in Wheat and Related Species; Revision of Section 5 and new Section 6 R.A. McIntosh, G.E. Hart and M.D. Gale The DNA-marker section (section 5) of the 'Guidelines for Nomenclature of Biochemical/Molecular Loci in Wheat and Related Species' has been revised and nomenclature for quantitative trait loci (section 6) has been added to the document. The new sections 5 and 6 are reproduced below. They will be published later this year in the Annual Wheat Newsletter and the Wheat Information Service in the 'Catalogue of Gene Symbols for Wheat: 1994 Supplement'. The complete original 'Guidelines' are contained in the Proceedings of the 7th and 8th International Wheat Genetics Symposia. NOTE REGARDING ITALICS: Italics cannot be shown on the Gopher, therefore italicized symbols and words in sections 5 and 6 of the 'Guidelines' are indicated herein by the presence of an underline (_) before and after them, e.g. _Xpsr119-7A_ and _Triticum aestivum_. 5 SYMBOLS FOR DNA MARKERS AND ALLELES This section describes nomenclature for genetic markers that are detected at the DNA level, including those detected by hybridization with DNA probes [e.g., RFLPs (restriction-fragment-length polymorphisms)] and by amplification with primers [e.g., RAPDs (random-amplified-polymorphic DNAs) and STSs (sequence-tagged sites, including loci detected with sequenced RFLP clones, sequenced RAPDs and clones containing micro- and mini-satellites]. 5.1 DNA markers of unknown function 5.1.1 Basic symbol The basic symbol for DNA markers of unknown function should be X. 5.1.2 Locus symbols The 'X' should be followed by a laboratory designator (see section 5.6), a number that identifies the probe or primer(s) used to detect the locus, a hyphen (-), and the symbol for the chromosome in which the locus is located. The laboratory designator and number should be assigned by the laboratory that produced the clone or sequenced the primer(s) or, if that laboratory chooses not to do so, then by the laboratory that mapped the locus. The number should consist of one or more Arabic numerals and should begin with a numeral other than zero, i.e., numbers such as '01,' '001,' and '002' should not be used. The number assigned to a probe need bear no relationship to the name of the clone used to produce the probe and, likewise, the number assigned to a primer(s) need bear no relationship to any name that may have been assigned to the primer(s). The letters in the laboratory designator should be lower-case and all characters in the locus symbol should be italicized. For example, _Xpsr119-7A_ designates a RFLP locus located in chromosome 7A detected with Plant Science Research probe 119 of the John Innes Centre. DNA markers detected in different chromosomes with the same probe or primer(s) should be assigned the same symbol except for the chromosome designation. For example, _Xpsr119-7D_ and _Xpsr119-4A_ designate other loci detected with probe 119. 5.1.3 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 emphasized, however, that some clones and primers are likely to detect both loci whose function is known (proven, for example, by a segregational test against allelic 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, and _Xpsr933-2A.2_ designate duplicate loci located in 2A that are detected with probe PSR933. As when two or more enzyme or protein protomers 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, _Xtam1-5A-HindIIIa_ denotes an allele detected with _Hin_dIII. 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 chromosome 2A, and _Xpsr804(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, _BamHIb_, 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 Clones, Primers and Markers". Laboratories that are investigating DNA markers in different species and/or of different types, e.g., RFLPs, STSs, 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 SYMBOLS FOR LOCI AND ALLELES CONTROLLING QUANTITATIVE CHARACTERS 6.1 Genes identified by segregational analysis Symbols for loci and alleles controlling quantitative characters that are identified by segregational analysis should be in accord with the Recommended Rules for Gene Symbolization in Wheat. 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. 6.2.1 Basic symbol The basic symbol for QTLs should be 'Q'. 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 designated by a lower-case italic letter following the locus designation.