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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 Basic symbol: The basic symbol for DNA markers of
unknown function should be 'X'
5.1.1 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
an 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.
5.1.2 Locus symbols for DNA markers detected with 'known-functixaon'
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, Xpsr8O4(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 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 xasame 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.
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