This draft is based on discussions of the draft of April 23, 1993 reviewed by the Poultry Species Committee, of the National Animal Genome Research Program (NAGRP) at its meeting in St. Louis on May 5, 1993. A revised draft (May 25,1993) was reviewed at an open meeting of the NAGRP, Poultry Committee at the 1993 Poultry Science Meetings. At the September 18, 1993 meeting of the NAGRP, Poultry Committee an International Nomenclature Committee of Bitgood, Boichard, Burt, Crittenden and Ponce de Leon was suggested, with a Resource Panel to help rename classical genes given in Somes (1988) now being revised by Bitgood.
This outline is aimed at suggesting nomenclature for use in Journal Publications and in the international chicken genome database (CHICKbase) being developed in Roslin (Edinburgh), UK by David Burt and his colleagues using G-Base developed at the Jackson Laboratory and other potential databases. The Tables appended are aimed at illustrating the use of the nomenclature and not the structure of G-Base as modified for maintenance of chicken genome data. In certain cases some aspects of the nomenclature may be different for publication in Journals, where further information cannot be readily called up from the database, and in a database where it can be readily located. For example, footnotes may be used in publications but further fields should be provided in a database. (However, memo fields for unique information may be needed in a database program.)
Some text is copied from Shows et al. (1987) with modifications to fit the Poultry Community's needs.
The human locus and allele nomenclature outlined by Shows et al. (1987) will be adopted. Thus, present standard nomenclature will be converted to the new nomenclature and the new nomenclature used for naming any new identified genes. The new terminology will be much more adaptable for use in computer databases, and will appear as entered on non-graphics screens, except for italics. The Somes nomenclature should be directly convertible to the new nomenclature in many cases by the Resource Panel appointed by the Nomenclature Committee. All new names should be reviewed for duplication and standard nomenclature.
The following is modified from Shows et al. (1987), pages 12-15 to reflect poultry-specific aspects of nomenclature and to use known genes of the chicken as examples.
In order to keep the gene and allele designations separated but together, a new character, the asterisk, has been introduced. Advantages of the asterisk are many. The asterisk is convenient, universal, and does not convey past genetic meaning such as the dash, space, or comma. The asterisk preceding a symbol indicates that it is an allele of a gene. Likewise, an asterisk following a symbol indicates that it is a gene. After the gene and allele symbols have been identified, the allele symbol preceded by an asterisk can be used separately in text.
For example: OV*A, OV*B (for alleles at the ovalbumin locus); EAA*1, EAA*7 (for haplotypes of the blood group A system).
Gene and allele symbols are underlined in manuscripts and italicized in print. Italics need not be used in catalogs. It may be convenient in manuscripts, computer printouts and in printed text to designate a gene symbol by following it with an asterisk (e.g., EAA*). When only allele symbols are displayed, they can be preceded by an asterisk. For example, for EAA*1, the allele is printed as *1.
EAA*1 ----- or EAA*1/EAA*2 or EAA*1/*2 EAA*2
EAA*1 EAB*1 EAP*1
-----; -----; -----
EAA*2 EAB*1 EAP*2
or
EAA*1/EAA*2; EAB*1/EAB*1; EAP*1/EAP*2
or
EAA*1/*2; EAB*1/*1; EAP*1/*2
Males: GHR*A
-----
GHR*B
or GHR*A/GHR*B or GHR*A/*B
Females: GHR*A
----- or GHR*A/W
W
(The W identifies the female and maintains the diploid nature of the symbol.)
Horizontal lines or slashes separate alleles and indicate chromosome location.
I*C EAJ*1 ---; ----- or I*C/I*W; EAJ*1/EAJ*2 or I*C/*W; EAJ*1/*2 I*J EAJ*2
EAJ*1 SE*N ---------- EAJ*2 SE*S
For text, the loci can be printed on a single line, with a space separating genes in phase and a slash indicating different homologs:
EAJ*1 SE*N/EAJ*2 SE*S.
EAJ*1,SE*N ---------- EAJ*2,SE*Sor printed on a single line with a separating comma:
EAJ*1/EAJ*2,SE*N/SE*S,.
EAH*1 SE*N EAJ*1
----------------
EAH*2 SE*S EAJ*2
or
EAH*1 SE*N EAJ*1/EAH*2 SE*S EAJ*2.
The linear order on chromosome 1 is pter-EAH-SE-EAJ-cen.
pter-SE-EAJ-(EV1,O,P,)-cent.
The use of DNA probes adds another level of nomenclature to the system; the probe name. Probe names cannot be used directly for locus symbols because one probe often detects polymorphisms at more than one locus, and the laboratory probe name may not even reflect the name of the cloned gene and is often long and complex. No attempt to standardize probe names will be made at this time.
Such loci have no known physiologic function and can be detected by Restriction Fragment Length Polymorpism (RFLP) using random genomic or cDNA library members as probes, or by Polymerase Chain Reaction (PCR) using arbitrary primers or primers derived from anonymous cloned sequences.
Such loci will be named by each Laboratory defining them by segregation analysis or locating them by chromosomal in-situ hybridization using a laboratory code of not more than three upper case letters and sequential Arabic numbers of not more than three digits. The naming of alleles will follow the nomenclature for classical genes as outlined by Shows et al. (1987) quoted above. Expressed genes, such as those detected by cDNA library members, that have no known function shall be followed by an uppercase E (eg. COM110E). Note that the locus symbols exceed the allele limit of five suggested for named genes. However, allele symbols should be short so that the total symbol can be less than 12 letters or digits.
This system does not contain an embedded chromosome number or other information on the type of probe as does the Human system. However, the advantages are that a unique name can be assigned to the locus by the typing laboratory which does not have to be changed with chromosome assignment, or assigned by the database manager or a committee. However, the probe should be renamed once it is shown to contain coding sequences for a named gene product (See the next section). Further information about each probe will be available in the original publication and in supplementary Tables that can be called up in a database.
The locus name can be clarified in publications by adding a code for the type of probe in upper case letters in parentheses. F for RFLP, A for RAPD, R for CR1, M for microsatellite, and V for minisatellites are suggested. These letters will not be considered part of the official name and will not be included in the database, but are optional in Journal publication for clarity and should be footnoted.
These loci should be named in uppercase letters and numbers that reflect the name of the gene product. Three letters or numbers are preferred but five should be maximum. The name should begin with a letter that reflects the first letter of the gene product and numbers should be used when necessary. The general rules for naming loci and alleles should follow Shows et al. (1987) as modified above. All names should be reviewed against a central list for standard nomenclature and duplication maintained by the nomenclature committee. When genes are homologous to human genes, or have strong evidence for homology, the gene name should be the same as the human gene listed in the latest "Catalog of Mapped Genes", (Mc Alpine et al., 1993).
A gene can consist of coding and non-coding regulatory and intron sequences. The general location of a specific gene on the genetic map can be found using probes representing coding or non-coding sequences. Thus, the gene can be considered a haplotype. Therefore, the gene name should be used for the locus symbol on genetic maps whether the probe represents a coding sequence or not. However, the anonymous nature of the probe should be clearly retained in publications and databases, and its anonymous locus name should be used in fine structure mapping. This is a rather confusing distinction and further discussion can be found in the attached excerpt from the 8/30/93 version of mouse "Rules and Guidelines for Gene Nomenclature".
Autosomes will be numbered in descending order by size. The sex chromosomes will not be numbered but called Z and W. Ideally, all mapped loci should be assigned to chromosomes, but very few linkage groups are now assigned to chromosomes. Therefore, the classical linkage groups should be designated in Roman numerals as assigned by Bitgood and Somes (1990, 1993). The linkage groups assigned in the Compton and East Lansing reference populations are not associated in many cases and will be called C01-nn and E01-nn until chromosomal assignments can be achieved. It may be necessary, before all linkage groups are assigned to chromosomes, to develop a distinct system of naming common linkage groups between the East Lansing and Compton maps that have not been assigned to chromosomes.
Microchromosomes, defined as chromosomes smaller than chromosome 8, Z and W, will be temporarily named for the first gene that is assigned to them by in-situ hybridization. Any gene linked to that locus by physical or genetic means, will be considered to be on that microchromosome.
A standard banding nomenclature was discussed at the North American Colloquium on Domestic Animal Cytogenetics and Gene Mapping held in Guelph, Ontario, July 13-16, 1993. Standard banding nomenclature for the Z, W and the eight largest autosomes was agreed upon and a publication should be submitted within the next few months. Such standardization is necessary for the integration of physical and genetic maps. Genes that are assigned to a unique location in the genome can be named as outlined above even though Mendelian segregation has not yet been detected. As physical mapping progresses nomenclature for expanded DNA fragments or contigs will need to be addressed.
Loci will be named by the Laboratory that first conducts the genetic segregation analysis or assigns a gene to a specific chromosomal location by in-situ hybridization. Alleles will be named by the Laboratory that first conducts the segregation analysis defining that allele. The allele symbol should be confined to four characters. The alleles may be arbitrary numbers or letters or may convey some meaning. Numbers or letters can be added for multiple alleles. In cases where classical allele symbols have specific meaning they can be retained if they do not exceed four sysbols and adhere to the rules stated above. The population in which the allele was found should be stated. This is particularly important for alleles defined by molecular probes which may have large numbers of detectable alleles.
Mc Alpine, P. J., 1993. The 1992 calalog of mapped genes and report of the nomenclature committee. Genome Priority Reports 1: 11-142. (Alphabetical lists of human gene symbols and names)
Bitgood, J.J., and R.G. Somes Jr., 1990. Linkage relationships and gene mapping. Pages 469 495 in: Poultry Breeding and Genetics. Crawford, R.D., ed. Elsevier, Amsterdam. (Classical Map summary)
Bitgood, J.J., and R.G. Somes Jr., 1993. Gene map of the chicken (Gallus Gallus or G. domesticus). Pages 4,333-4,342 in Genetic Maps, 6th ed., S.J. O'Bren, ed. Cold Spring Harbor Laboratory Press, Plainview, NY.
Shows, T.B., P.J. McAlpine, C. Boucheix, F.S. Collins, P.M. Conneally, J. Frezal, H. Gershowitz, P.N. Goodfellow, J.G. Hall, P. Issitt, C.A. Jones, B.B. Knowles, M. Lewis, V.A. McKusick, M. Meisler, N.E. Morton, P. Rubenstein, M.S. Schanfield, R.D. Schmickel, M.H. Skolnick, M.A. Spence, G.R. Sutherland, M. Traver, N. Van Cong, and H.F. Willard, 1987. Guidelines for human gene nomenclature: An international system for human gene nomenclature (ISGN, 1987). Cytogenet Cell Genet 46: 11 28. (Human Gene Nomenclature)
Somes, R.G.Jr., 1980. Alphabetical list of the genes of domestic fowl. J Hered 71: 168 174.
Somes, R.G.Jr., 1988. International registry of poultry genetic stocks. Bulletin 476, Storrs Agricultural Experiment Station. (Updated gene list and maps)
This page was last modifed on 26 November 1999 By Irene Black
Converted to HTML by Andy Law from an original Draft by Lymen B. Crittenden
This page is maintained at Roslin by Irene Black