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.