Barley Genetics Newsletter (2005) 35:144-149

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**Rules for Nomenclature and Gene Symbolization in Barley**

**Jerome D. Franckowiak^1^ and Udda Lundqvist^2^**

**^1^Department of Plant Sciences**

**North Dakota State University**

**Fargo, ND 58105, U.S.A.**

**^2^SvalöfWeibull AB**

**SE-268 81 Svalöv, 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 \"*V^t^*\" 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 \"*V^t^*\" 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*\",
> \"*v^lr^*\", and \"*V^t^*\" 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.)