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2. Guidelines for Nomenclature of Biochemical Molecular Loci
in Wheat and Related Species
2.1 Biochemical nomenclature: Biochemical nomenclature should be in accordance
with the rules of the Joint Commission of Biochemical Nomenclature (JCBN) of the
International Union of Pure and Applied Chemistry. The nomenclature recommended
by the JCBN is published periodically in major international biochemical journals,
such as the Journal of Biological Chemistry and the European Journal of Biochemistry.
Also, for enzymes, the publication Enzyme Nomenclature (035,036} may be consulted.
Enzymes and other macromolecules have both formal and trivial names. The formal
name should be given the first time a macromolecule is mentioned in a publication;
the trivial name or an abbreviated name may be used subsequently. For example,
ADH is the commonly used abbreviation for aliphatic alcohol dehydrogenase (E.C.1.1.1.1;
Alcohol: NAD+ oxidoreductase).
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 italicized.
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 catalyze 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 an homologous
set.
2.3.1 Loci that are members of an orthologous set. The basic symbol should
be followed by a hyphen (-), the accepted symbol for the genome to which
the locus belongs and an homologous 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 homologous
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 homologous
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 homologous
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 homologous 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 homologous gene loci, whether they belong
to the same or different homologous 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 homologous 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. Currently, 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.
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