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Gene Symbols

paulh

New member
What doesn't make sense here? Questions, comments, and suggestions are welcome.

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The words "heterozygous albino" contain 19 letters. That is a lot of bandwidth, particularly if it must be written over and over when diagramming a cross.

Mendel used letter symbols for several reasons. He lacked words because "heterozygous" and other genetics terms had not been invented. And symbols were simple, clear, and easy to understand. Geneticists have continued to use symbols for much the same reasons.

Various groups of geneticists have agreed on rules for genetic symbols. These rules allow a few alphanumeric characters to indicate whether the gene is normal or mutant, dominant or recessive, allelic or independent, etc. That is quite a load of information to carry, but it can be done.

So far, there is no single set of rules for gene symbols for all species. The rules for the fruit fly are not exactly the same as the rules for the mouse. And the rules for the mouse are not exactly the same as for maize, though there is considerable agreement. As uniformity is desirable, these rules follow the <A HREF="http://www.informatics.jax.org/mgihome/nomen/table.shtml">gene nomenclature for the mouse</A>.

1. Give the mutant a unique name that is reasonably descriptive of the phenotype. Examples: amelanistic, charcoal, striped.

2. Derive the unique one to four letter symbol from the unique mutant name, and italicize the symbol if possible. Alphabet books for young children often start with "a is for apple." In the same way, <I>c</I> is for charcoal. Because <I>c</I> is already used, <I>ca</I> is for caramel.

3. Use lower case letters for all letters symbolizing a recessive mutant. Again, <I>ca</I> is for caramel, a recessive mutant gene.

4. Use an upper case letter for the first letter in the symbol for a dominant or codominant mutant. The symbol <I>T</I> is for tiger, a codominant mutant in the reticulated python.

5. The locus symbol is the same as the symbol given to the first mutant discovered at that locus. The <I>a</I> locus has the <I>a</I> (amelanistic) mutant gene and all its alleles.

6. The wild type allele is symbolized by either the <I>+</I> symbol alone or by the locus symbol with the + symbol as a superscript. The wild type allele at the <I>a</I> locus can be either <I>+</I> (if the useage is obvious) or <I>a<SUP>+</SUP></I> (to make useage absolutely clear).

7. Multiple alleles are symbolized by one or two lower case letters added to the base symbol as a superscript. In the mouse, multiple alleles at the <I>c</I> locus include wild type, <I>c<SUP>+</SUP></I>; chinchilla, <I>c<SUP>ch</SUP></I>; himalayan, <I>c<SUP>h</SUP></I>; and albino, <I>c.</I>

8. If possible, use the same symbols for similar mutants in closely related species. As <I>a</I> is for amelanistic (tyrosinase negative) in the corn snake, it should also be reserved for albino (tyrosinase negative) in the black rat snake.
 
Genetic Symbols -- long post

Paul -- you know my thoughts on this subject. A set of symbols is needed. Your suggestions here follow all proper conventions of genetics symbols. Guess someone with a proper degree needs to address the issue.

But for fun, here is the list I forwarded to you a few years ago. It could serve as a basis for someone smarter, and more qualified academically, than I am.

Corn Snake Color & Pattern Shorthand
by Shannon Hiatt

Are those record blanks in your record book crammed full of color and pattern descriptions? My record books certainly were, so I decided I’d "invent" some corn snake color and pattern shorthand to allow me to unburden myself from the drudgery of writing in longhand, "normal Aztec heterozygous for lavender female."

The short abbreviations I’ve developed look suspiciously like genetic symbols but they are NOT. I do not presume that I know enough about corn snake genetics to develop symbols for its genes. Quite the opposite. It is the thinking I do about corn snake genetics, and developing these abbreviations did make me think a little, that helps me understand some of the principles involved. Here are the abbreviations I’ve developed for the basic corn snake colors and patterns; you might find them of value:

COLORS

Amelanistic = am
Anerythristic "A" = anA
Anerythristic "B" (charcoal) = anB
Blood red = br
Caramel = cr – you might use anC for caramel as some consider this morph a third form of anerythristic..
Emoryi = em+ for any locale or form, valid or not, intermontana, Brazos Island, or meahllmorum. A chocolate emoryi is ch + em+ while an albino emoryi is am + em+ and a gold emoryi is am + ch + em+.
Hypomelanistic = hy – some breeders call this type A hypo so hyA would suffice. The new hypo gene in Kathy Love’s Okeetee line could be called type B hypo or hyB. She still calls it "sunkissed" at this juncture.
Lavender = lv

COLOR COMBINATIONS

Amber = cr + hy (but shortened to cr hy in my record book)
Amel motley = am + mt
Amel Okeetee = am + ok+
Blizzard = am + anB
Blood red amel = br + am
Blood red lavender = br + lv
Blood red Okeetee = br + ok+
Blood red (pewter) = br + anB
Butter = am + cr
Creamsicle = am + em+
Crimson = m+ + hy
Ghost = anA + hy
Hypo lavender = hy + lv
Opal = am + lv
Opal Motley = am + lv + mt
Snow = am + anA
Sunglow motley = am + mt + hy – not ALL sunglow motleys are hypo, although many can be. If you aren’t certain add a question mark next to the abbreviation (hy?) until you have proven that hypo is a gene carried by a particular Sunglow motley.

How about a hypomelanistic blood red lavender motley corn? I’d use hy br lv mt to speed up my record keeping. Or an amelanistic hypomelanistic lavender Okeetee zig zig corn? The abbreviation am hy ok+ lv zz is much more economical.



WILD TYPE CORNS

Normal, wild type = + -- not associated with a locale (or morphology) as noted below.
Okeetee = ok+ -- any corn with the characteristics of an Okeetee phase no matter the true origin.
Keys corns = k+ -- indicates any Keys corn locale—Upper Keys, Marathon Key, or Big Pine keys.
Miami = m+ -- the Miami phase look corn no matter its origin.
Kisatchie = k+ -- although originally I considered +/em+ for this corn (suggesting it is a guttata X emoryi intergrade), now that it is a NEW species, I’d use sl+ to placate those who agree with that distinction.

PATTERNS

Banded = bd -- I’m not sure this abbreviation is valid due to the selective breeding involved, but if you have banded corns of any type, use this abbreviation as a matter of convenience.
Motley = mt – I use this abbreviation for ALL forms of the highly variable motley morph; when I see a motley influence in a striped corn I use BOTH symbols in the record book. So striped motleys would be indicated by st mt.
Striped = st no matter the width or extent of striping. This is a highly variable morph as are ALL pattern genes. Those with vanishing striped corns in their collection could use stV for snakes carrying that gene.
Zig Zag = zz – what others indicate as a separate gene, Aztec, might be abbreviated az if you prefer that term. Zipper is another term (or look) and you may use zi if that is more descriptive of the corns you breed. This polygene is as variable as the striped or motley gene.

Good effort and my condolences for the loss of our father Willard.
 
Hi, Shannon! Glad to see you here on the forum!

I agree that a set of symbols is needed. Shawn Lockhard (in Iowa City) has made a set, but it was supposed to see print in the genetics chapter in The Biology of the Corn Snake, which has been stalled for several years. When I saw Shawn last year, he thought that the book would be published Real Soon Now. So I figure that I can go on saving up my pennies for another couple of years at least. :)

In the meantime, Bern Bechtel assigned <i>a</i> to amelanistic and <i>ax</i> (for axanthic) to anerythristic. Those appeared in the Journal of Heredity back in 1989, so they are official.

I'd just as soon kill off use of Anerythristic A and B and hypo A, B, and C. They don't use that sort of terminology in either mice or pigeons.

I like br for blood red and hy for hypomelanistic. They are certainly appropriate genetic symbols. I was thinking ca for caramel and la for lavender, but I could go for cr and lv as well.

Motley is a tough one. Either m, mo, or mt would be acceptable. However, Bechtel used striped for the name of what we now call motley. This was way back in the 1960s. So I'm thinking about s for motley and s<sup>st</sup> for striped. But when Shawn's list is published, I'll go with whatever he uses.
 
Yes, we need to adopt the accepted symbols and add more when a color has been worked out definitively. Too many corn colors are pure conjecture at this point or poorly understood. Of course, I knew Shawn was working on a chapter in that book but haven't seen it in print yet. Now I understand why!

But as I noted, my symbols are shorthand for MY records. I'll adapt the records with the currently accepted symbols to make sure I don't muddy corn snake inheritance up further with heretical notations. LOL.

And I see the "our" in my last post should have been "your." A slight Freudian slip, thinking of Willard as "the father" of pigeon genetics.
 
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