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Naming the new metallic gene


Sherolyn-Basement Bettas

Excepting an interlude for the annual science fair column I have devoted the last several columns to Betta pigmentation. First, we explored the fact that some colors are caused not by pigments but by the manner in which light reflecting from the top and the bottom of a thin crystal (or film) interact and that fish exploit this physics by packing cells called iridophores with crystals of just the appropriate thickness. A subsequent column announced that a newly marketed Betta, variously called copper, platinum, or metallic, displays a new type of iridophore that reflects in the yellow to yellow-green. And finally, the last article in the series showed that the spread of yellow iridescence over the body is controlled by a single gene inherited as a simple Mendelian dominant. I continue the series now by giving the gene a name. 

The naming of genes in biology is nothing short of crazy. By precedent the person discovering the gene, either by establishing it’s mode of inheritance, as in this case, or establishing a DNA sequence corresponding to a phenotype has the right to name it. However, unlike species names, there are no universally agreed upon rules governing the naming.

Nonetheless, in some species researchers have adopted a convention that is followed by all or most researchers. These informal conventions, however, are not the same for all species. The way people working with mice name genes differs from that used by fly researchers or zebrafish researchers. Worse yet, a gene discovered and named in a worm is very likely also present in a fly, a fish or in humans. So a gene that makes a particular protein may be known by any number of unrelated names corresponding to the (often independent) discovery of those genes in different species. 
Moreover, the advent of whole genome sequencing is such that new genes are discovered far more quickly than their functions or associated phenotypes can be described. A significant fraction of the human genome codes for genes of as yet unknown function. These genes are unnamed; they are simply referred to by numbers designating their position and sequence. 
Gene Lucas was the first to face the issue of how genes in Betta would be systematized. He recommended that naming of genes should adopt the convention then in use by workers on the fruit fly Drosophila. The mode of discovery of new genes in flies was (once) largely accomplished by studying the inheritance of mutants. Mutants differ from the normal, or wild type, animal in some feature that proved to be inherited as a single gene. Since all animals have two copies of each gene, it must be the case that the gene comes in two forms: the wild type form, or allele, and the mutant allele. The first convention used in naming is that the gene is named for the mutation, not the wild type. So the gene used to create steel blue Betta is called blue, because the wild fish shows green and the mutation produces blue. 
This can be a little counter-intuitive until you get used to it. A second example might be helpful. Gene Lucas discovered a gene that has the phenotypic effect of causing yellow to appear in all locations where red would otherwise appear. The mutation causing this disrupts the production of red pigment. Since the wild-type fish produces red, he called the gene non-red. 
Other conventions apply. The name is meant to be descriptive, to capture in a shorthand fashion the manner in which the mutation changes the appearance of the animal. The final consideration in naming the mutant allele is to choose an abbreviation of the name, typically three-letters long. The first letter of the abbreviation is capitalized if the mutation is dominant, lower case if recessive. 
Now Drosophila researchers have long since abandoned any rigor in naming genes in this fashion, as the proliferation of gene names such as son-of-sevenless or sonic hedgehog might imply. And as indicated earlier the now routine identification of genes by direct DNA sequencing, without any associated phenotypic information has rendered the classical system of nomenclature obsolete. That said, there is no reason that Betta workers should not add to the chaos. Here I attempt to follow the traditional system advocated by Gene Lucas.
After having established that the ‘copper’ coloration is caused by a yellow-reflecting iridophore, the first job is to describe its distribution in the wild type. The wild type Betta splendens is considered by Lucas to be the same as Betta imbellis because the two can freely interbred and produce fertile offspring. I have examined several specimens of Betta imbellis and can confirm that the yellow-reflecting iridophore is present and is distributed on the underbelly, around the eyes, in highly reflective pinpoints on the scales, along and between the fin rays of the caudal and in the base of the dorsal fin. The wild type allele, which is always designated as +, is a fish with yellow iridophores spread across the fish. 
The next question is that of the phenotype of the mutant allele. There are two obvious possibilities: either the mutant phenotype lacks the yellow reflecting iridophore entirely or the mutant phenotype alters the abundance and distribution of this iridophore so as to limit its visual impact to the casual observer. The way to distinguish between these two alternatives is to observe fish of known pedigree that display the mutant phenotype, that is, those fish known to lack the new metallic trait.
In an earlier column I reported on a cross between a green fish that was heterozygous for the yellow iridophore spread and steel blue fish that did not carry the trait. The cross segregated in a 1:1 ratio in the offspring, with half being traditional royal blue and half were blues displaying the new metallic trait, that is, they were blue-green or teal in appearance. To establish whether the mutant phenotype is caused by a complete absence of yellow-reflecting iridophore required, then, a microscopic examination of the royal blue fish to determine whether yellow-reflecting iridophores could be detected.
The royal blue fish did indeed possess yellow-reflecting iridophores, but in very small numbers and a very restricted distribution on the body. Specifically, yellow iridophores were present at low density on the underbelly, around the eye and scattered along the lines where the dorsal fin and the anal fin meet the body. There presence in royal blue fish was a surprise to me. You would not see them at all unless you were looking for them and then only if you were using a proper microscope. 
Let’s summarize what we know so far. Betta imbellis has lots of yellow iridophores and traditional royal blue fish have some, but very few. This tells us that the mutation in the gene we are naming is a mutation that reduces the number and restricts the distribution of yellow iridophores. We can now name the gene. Since the mutation limits the spread of the yellow iridophore, I’ll name the gene ryi for reduced yellow iridophores. In an earlier column, I showed that the mutation limiting the spread was recessive (i.e., the wild type allele giving the effect is dominant), so the names ryi should be in lower case.
In an earlier column I used the abbreviation nms (for no metallic spread) to refer to this gene. The reason for this change in notation, ryi for nms, derives from a conversation with Gene Lucas. While it has become conventional for breeders and brokers to talk about fish bearing the yellow-reflecting iridophores as metallics, Gene pointed out to me that this usage deviates from that which he has used in the past. Specifically in FAMA columns appearing long before these ‘new metallic’ fish became available, Gene used the term metallic to refer to green, royal and steel blue colors. In doing so, he was making reference to the shiny appearance of iridophore colors. By implication, then, the term metallic should refer not solely to either the green/royal/steel blue colors or to yellow iridophore spread, but rather be used as a general term to describe the suite of colors derived from iridophores. In earlier columns in this series I have used the term metallic to refer strictly to pigmentation derived from yellow-reflecting iridophores, I will henceforth use the term metallic in the more general meaning that Gene has advocated. At 52 years of age, I expect to have relatively few opportunities left to defer to greater age and wisdom and so happily grasp them when they come along.

Source: FAMA Magazine
March 2006

Column Article 
BETTAS...AND MORE 
By Leo Buss, Ph.D.






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