A Database for Triticeae and Avena
Barley Genetics Newsletter (2007) 37: 100 - 104
Rules for Nomenclature
and Gene Symbolization in Barley
Jerome D. Franckowiak1 and Udda Lundqvist2
1HermitageResearch Station
Queensland Department of Primary Industries
and Fisheries
Warwick, Queensland 4370, Australia
2Nordic Gene Bank
P.O. Box 41, SE-230 53 Alnarp, Sweden
In this volume of the Barley Genetics Newsletter the recommended rules
for nomenclature and gene symbolization in barley as reported in BGN 2:11-14,
BGN 11:1-16, BGN 21:11-14, BGN 26:4-8, and BGN 31:76-79 are again reprinted.
Also, the current lists of new and revised BGS descriptions are presented by
BGS number order (Table 1) and by locus symbol in alphabetic order (Table 2) in
this issue.
1. In
naming hereditary factors, the use of languages of higher internationality
should be given preference.
2. Symbols
of hereditary factors, derived from their original names, should be written in
Roman letters of distinctive type, preferably in italics, and be as short as
possible.
AMENDMENT: The
original name should be as descriptive as possible of the phenotype. All gene
symbols should consist of three letters.
COMMENTS: All
new gene symbols should consist of three letters. Existing gene symbols of less
than three letters should be converted to the three-letter system whenever
symbols are revised. When appropriate, one or two letters should be added to
existing symbols.
For
example, add the letters "ap" to "K" to
produce the symbol "Kap" to replace "K" as
the symbol for Kapuze (hooded). As
another example, add the letters "ud" to "n"
to produce the symbol "nud" to replace "n" as
the symbol for naked seed. Similarly the letter "g" can be
added to "ms" to produce the symbol "msg" for
genetic male sterility and the letter "e" can be added to
"ds" to produce the symbol "des" for
desynapsis. When inappropriate or when conflicts arise, questions should be
referred to the Committee on Genetic Marker Stocks, Nomenclature, and
Symbolization of the International Barley Genetics Symposium for resolution.
3. Whenever
unambiguous, the name and symbol of a dominant begin with a capital letter and
those of a recessive with a small letter.
AMENDMENT: When ambiguous (co-dominance, incomplete
dominance, etc.) all symbols should consist of a capital letter followed by two
small letters that designate the character, a number that represents a
particular locus, and a letter or letters that represents a particular allele
or mutational event at that particular locus.
COMMENTS: As an example, the letters "Mdh"
can be used to designate the character malate dehydrogenase, "Mdh1"
would represent a particular locus for malate dehydrogenase and "Mdh1a",
"Mdh1b", "Mdh1c", etc. would represent
particular alleles or mutational events at the "Mdh1" locus.
Row number can be used as an example of symbolizing factors showing incomplete
dominance. At the present time, the symbol "v" is used to
represent the row number in Hordeum vulgare, "V"
is used to represent the row number in Hordeum distichum, and
"Vt" is used to represent the row number in Hordeum
deficiens. According to the amendment to Rule 3, if row number were to be
designated by the letters "Vul", the designation of the locus
on chromosome 2 would then become "Vul1" and the alleles "v",
"V", and "Vt" would be designated
"Vul1a", "Vul1b", and "Vul1c".
SUPPLEMENTARY
AMENDMENT: A period should be placed
before the allele symbol in the complete gene symbol.
COMMENTS: Since DNA sequences similar to those of the
original locus may occur at several positions in the Hordeum vulgare
genome, a three-letter symbol plus a number is inadequate to represent all
potential loci. Also, both numbers and letters have been assigned to specific
mutants and isozymes in Hordeum vulgare.
The six-rowed spike locus is used as an example although the symbol Vul1
for row number in Hordeum vulgare is not recommended because the
botanical classification of Hordeum spp has changed. The locus symbol vrs1
and the name six-rowed spike 1 are recommended for the v locus. Gene
symbols recommended for common alleles at the vrs1 locus are vrs1.a,
vrs1.b, vrs1.c, and vrs1.t for the "v",
"V", "vlr", and "Vt"
genes, respectively.
4. Literal
or numeral superscripts are used to represent the different members of an
allelic series.
AMENDMENT: All letters and numbers used in symbolization
should be written on one line; no superscripts or subscripts should be used.
5. Standard
or wild type alleles are designated by the gene symbols with a + as a
superscript or by a + with the gene symbol as a superscript. In formulae, the +
alone may be used.
AMENDMENT: This rule will not be used in barley
symbolization.
6. Two or
more genes having phenotypically similar effects are designated by a common
basic symbol. Non-allelic loci (mimics, polymeric genes, etc.) are distinguished
by an additional letter or Arabic numeral either on the same line after a
hyphen or as a subscript. Alleles of independent mutational origin may be
indicated by a superscript.
AMENDMENT:
Barley gene symbols should consist of three letters that designate the
character, a number that represents a particular locus, and a letter or letters
that represents a particular allele or mutational event at that particular
locus. All letters and numbers should be written on the same line without
hyphens or spaces. Alleles or mutational events that have not been assigned to
a locus should be symbolized by three letters that designate the character
followed by two commas used to reserve space for the locus number when
determined, followed by a letter or letters representing the particular allele
or mutational event. After appropriate allele testing, the correct locus number
will be substituted for the commas. Where appropriate (when assigning new
symbols or when revising existing symbols) letters representing alleles or
mutational events should be assigned consecutively without regard to locus
number or priority in discovery or publication.
COMMENTS: The use of the proposed system of
symbolization can be illustrated by the desynaptic mutants. Two loci are known:
lc on chromosome 1 (7H) and ds on chromosome 3 (3H). These will be
resymbolized as des1a and des2b. A large number of desynaptic
mutants have been collected. They will be designated des,,c, des,,d,
des,,e, etc. If allele tests show that des,,c is at a different
locus than des1 and des2, des,,c will become des3c.
If allele tests show that des,,d is at the same locus as des2, des,,d
will become des2d. In practical use, the symbol des will be used
when speaking of desynapsis in general or if only one locus was known for the
character. The symbol des2 will be used when speaking of that particular
locus, and the symbol des2b will be used only when speaking of that
particular allele or mutational event. If additional designation is needed in
particular symbolization, it can be obtained by adding numbers behind the
allele letters, and, if still further designation is needed, letters can be
added to the symbol behind the last number. Symbolization consisting of
alternation of letters and numbers written on the same line without hyphens or
spaces will allow for the expansion of the symbol as future needs arise. In any
work with large numbers of polymeric gene mutants, every mutant has to be given
a designation not shared by any other mutant of this polymeric group and this
designation should become a part of the permanent symbol representing that
particular allele or mutational event. This requirement can be met by assigning
allele designations in consecutive order without regard to locus number.
SUPPLEMENTARY AMENDMENT: A period should be used instead of two commas
in gene symbols for mutants within a polymeric group that can not be assigned
to a specific locus.
COMMENTS: The des symbol should be used when
referring to desynapsis in general; des1 and des2, for specific
loci; des1.a and des2.b for specific genes or alleles at their
respective loci; and des.c, des.d, des.e etc., for
desynaptic mutants not assigned to a specific locus.
SUPPLEMENTARY AMENDMENT:
Even if the locus in question is the only one known that affects a given
phenotype, the three-letter basic symbol is followed by a serial number.
7. Inhibitors, suppressors, and enhancers
are designated by the symbols I, Su, and En, or by i,
su, and en if they are recessive, followed by a hyphen and the
symbol of the allele affected.
AMENDMENT
This rule is no longer appicable and will not be used in barley
symbolization.
8. Whenever
convenient, lethals should be designated by the letter l or L and
sterility and incompatibility genes by s or S.
AMENDMENT: This rule will not be used in barley
symbolization.
COMMENTS: J.G. Moseman (BGN 2:145-147) proposed that
the first of the three letters for designating genes for reaction to pests
should be R. The second and third letters will be the genus and species
names of the pest.
SUPPLEMENTARY
COMMENT: A motion was passed during the
workshop on "Linkage Groups and Genetic Stock Collections" at the
Fifth International Barley Genetics Symposium in 1986 (Barley Genetics
V:1056-1058, BGN 17:1-4), that the International Committee for Nomenclature and
Symbolization of Barley Genes should "recommend use of Ml as the
designation of genes for resistance to powdery mildew.”
9. Linkage groups and corresponding
chromosomes are preferably designated by Arabic numerals.
SUPPLEMENTARY
AMENDMENT: The current wheat
homoeologous group numbering scheme (the Triticeae system) is recommended for Hordeum
vulgare chromosomes. Arabic numerals followed by an H will indicate
specific barley chromosomes. The H. vulgare chromosomes should be 7H, 2H,
3H, 4H, 1H, 6H, and 5H instead of 1, 2, 3, 4, 5, 6, and 7, respectively.
10. The
letter X and Y are recommended to designate sex chromosomes.
AMENDMENT: This
rule will not be used in barley symbolization.
11. Genic
formulae are written as fractions with the maternal alleles given first or
above. Each fraction corresponds to a single linkage group. Different linkage
groups written in numerical sequence are separated by semicolons. Symbols of
unlocated genes are placed within parenthesis at the end of the formula. In
euploids and aneuploids, the gene symbols are repeated as many times as there
are homologous loci.
12. Chromosomal
aberrations should be indicated by abbreviations: Df for deficiency, Dp
for duplication, In for inversion, T for translocation, Tp
for transposition.
13. The
zygotic number of chromosomes is indicated by 2n, the gametic number by n, and
basic number by x.
14. Symbols
of extra-chromosomal factors should be enclosed within brackets and precede the
genic formula.
The following
recommendations made by the International Committee for Nomenclature and
Symbolization of Barley Genes at the Fourth International Barley Genetics
Symposium in 1981 (Barley Genetics IV:959-961) on gene and mutation
designations were as follows.
AMENDMENT:
A. Present
designations for genes and mutations. - Most of the present designations should
be maintained. However, new designations may be given, when additional
information indicates that new designations would aid in the identification of
genes and mutations.
B. New
designations for genes and mutations. - New genes or mutations will be
designated by characteristic, locus, allele, and then the order of
identification or mutational event. Three letters will be used to identify new
characteristics. Consecutive numbers will be used to identify the order of
identification or mutational event. Loci will be designated by numbers and
alleles by letters when they are identified. For example, des-6
indicates that this is the sixth gene or mutation identified for the
characteristic des (desynaptic). des 1-6 and des 2-7
indicate that gene or mutational events 6 and 7 for the desynaptic
characteristic have been shown to be at different loci and those loci are then
designated 1 and 2, respectively. des 1a6 and des 1b8, indicate
that the gene or mutational events 6 and 8 for the characteristic desynaptic
have been shown to be at different alleles at locus 1 and those alleles are
then designated a and b.
SUPPLEMENTARY COMMENT:
A motion was passed during the workshop of the
"Nomenclature and Gene Symbolization Committee" at the Fifth
International Barley Genetics Symposium in 1986 (Barley Genetics V:1056-1058)
that "the recommended systems for
Nomenclature and Gene Symbolization of the International Committee be
published annually in the Barley Genetics Newsletter."
SUPPLEMENTARY COMMENT 2:
At the workshop for ”Recommendations of Barley Nomenclature”
held at Saskatoon, July 31, 1996 and adopted at the General Meeting of the
Seventh International Barley Genetics Symposium, it was recommended that a
period instead of a dash be used to designate the allele portion of the gene
symbol. Consequently, the first gene symbol for the characteristic des
(desynapsis) should be expressed as des1.a. The code des1
identifies a specific locus. The period indicates that the symbol a
identifies a specific allele or mutational event that produces a desynaptic
phenotype. (The allele symbol a will be always associated with this
specific desynaptic mutant even if the locus symbol is changed based on
subsequent research results.)