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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 lowercase letter. For example, Xtam-5A-HindIIIa
denotes an allele detected with Hind III. 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, and Xpsr8O4(Sbp)-3A may be abbreviated
as Xpsr8O4(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, the symbols could be abbreviated as
Xtam200.1 and Xtam200.2 respectively, on a map of 1A.
Finally, Xbg1485(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.
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