Designate them as RFLP's would be designated see Section 8 , but follow the institutional symbol and number with a double colon and the symbol of the transposable element e.
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This has the definite advantage in maintaining data bases and indices that no retrospective correction would be necessary if a second gene locus receives the same designation.
Where a mutant allele is recessive, it should be designated by an italicized symbol lower case as dek12 , which is the same as the symbol of the locus. Since it is unlikely that any two mutant or nonmutant alleles in a highly polymorphic species such as maize have identical sequences, maize geneticists are encouraged to specify the particular allele with which they are working see in this Section, Alleles of Independent Mutational Origin and Designation of Nonmutant Alleles.
The symbol for dominant, nonmutant i. The symbol of the gene product should not be italicized and should be written with all letters capitalized e. The name of the gene product alcohol dehydrogenase should neither be capitalized nor italicized.
When the mutant alleles of a gene are dominant, the first letter of the mutant symbol is capitalized. The nonmutant symbol has all the letters lower case. For example, the corn grass1 cg1 gene locus has several dominant mutant Cg1 alleles as well as nonmutant cg1 alleles. The reference mutant allele is designated as Cg1-R or Codominant alleles such as isozymes where the variants are functional and distinguished from each other by electrophoretic mobility, should be designated by symbols with the first letter capitalized and identified by allelic specifications as Pgm or Pgm The unambiguous designation of mutant alleles that have arisen as independent mutational events is increasingly important.
It is generally understood that a gene symbol followed by a hyphen plus a letter or number s specifies a particular recessive allele at that gene locus. We have referred to the mutation by which the gene was identified as the reference allele; e. It is equally appropriate to refer to that allele as bz The mutations in any gene that were identified subsequently have been categorized in various idiosyncratic ways. Alleles that have arisen by independent mutational events have been designated by letters, numbers, a letter plus numbers, the name of the inbred in which the mutation occurred, and sometimes all of these applied to a group of alleles at a gene locus.
While all of these designations served the purpose of indicating that these alleles had independent mutational origins, there is a clear advantage to greater standardization.
As in the Nomenclature Standard, it is recommended that new alleles be identified by a laboratory number that might indicate the year of isolation as sh This has the definite advantage that two laboratories are unlikely to designate two new mutations of the same gene by the same number. However, if two laboratories are targeting the same locus in mutagenesis experiments, they should consult before naming their new alleles to avoid giving the same designation to different alleles.
In the second instance a previously unidentified locus , a new gene name and symbol would be selected, and this mutant would become the reference allele -R or When mutant alleles are referred to in the generic sense without specification of their origin, a hyphen without further designation e.
Since it is now apparent that in a species as polymorphic as maize, nonmutant alleles from different sources are apt to have a number of sequence differences one from the other, and these differences can be reflected in gene action nonmutant isoalleles , it is desirable to specify the nonmutant allele being investigated or used as a control.
Incorporating the name of the inbred as part of the allelic designation, Bz1-W22 , is an appropriate method of doing this. However, mutant alleles should not be designated by the inbred in which they arose e. Also, there may eventually be numerous mutant alleles of a particular gene isolated in that inbred if a researcher uses that inbred in a mutagenesis experiment.
A particular nonmutant allele may be found in an exotic race or other accession that is not an inbred. A unique designator e. The presence or absence of a restriction site or a primer-amplifiable sequence at a particular locus represent Mendelian alternatives. They fall under the broadest definition of an allele, and it is appropriate to refer to these alternatives as alleles as has already been done in some reports.
When it is clear that a mutation results from a deletion that has removed all or part of two gene loci, it would be appropriate to indicate this in the following manner. When molecular evidence indicates that a deletion has removed all of the structural portion of a gene as is true of wx1-C34 , it should be indicated in the same manner; i. There is one further point concerning allelic specification. Maize in particular has many mutable alleles resulting from the insertion of a transposable element.
These have been designated by the mutant symbol, a hyphen, a lower case "m", and an isolation number; e. Further, mutable alleles generate both stable nonmutant and stable mutant alleles when the transposable element excises from the gene locus. Since the mutant derivatives are certain to differ in sequence from the nonmutant progenitor allele around the site of the transposable element insertion and the nonmutant derivatives are very likely to differ at that site, researchers should be certain to indicate the origin of such alleles in their reports.
The specifics of its origin including the transposable element involved could then be included in the text and entered in the Maize Genome Data Base.
Since transpositions of a transposable element from a site within a gene often insert in locations where they have no phenotypic effect but can be useful markers, it is desirable to have a standard to refer to such insertions. Designate them as RFLP's would be designated see Section 8 , but follow the institutional symbol and number with a double colon and the symbol of the transposable element e.
In naming RFLPs and RAPDs, use a lower case three or four letter code designating the originating university or company followed by a laboratory number no space between the code and the number. When the probe used is a cDNA or a subclone of a gene, the gene symbol should be added in parentheses after the RFLP locus designation, as umc a1.
Since a probe not infrequently recognizes RFLPs on two or more chromosomes, these should be designated by the same institutional code, number, and probe followed immediately by A, or B, or C. In so far as possible, the locus with the strongest hybridization should be designated A and the more weakly hybridizing loci be designated B, C etc. Help you understand what going on in my language.
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