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TAS Angelfish Naming Conventions Part 1 – Genetic

Notation

A Presentation for The Angelfish Society August 19, 2007

by Tamar Stephens

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Introduction

• This presentation is the first part of a 2-part series.

• Part 1 will explain what genetic notation is, and how the TAS genetic notation for angelfish of the species Pterophyllum scalare is structured.

• Part 2 will explain how phenotype names are generated by the genetics calculator.

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Vocabulary Refresher• Chromosome – Chromosomes occur in pairs, one inherited from

each parent. Chromosomes contain the genetic information for each individual.

• DNA – DNA is a long coiled molecule that makes up a chromosome.• Gene – A segment of DNA that codes for a specific trait.• Locus – Location on a chromosome where a particular gene occurs.• Allele – Alternate form of a gene. For example, black and gold are

alleles of each other.• Genotype – The genes that create a particular phenotype.• Phenotype – The appearance of an individual, such as smokey or

zebra.• Dominant – An allele that expresses in the phenotype when present

in a single dose. • Recessive – An allele that only expresses when in double dose.• Co-dominant – An allele that partially expresses in the presence of

another allele at the same locus. For example, dark (D) and wild (+) are co-dominant, resulting in a black lace, which blends the effects of both alleles to produce the black lace phenotype.

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What is genetic notation?

• Genetic notation is a set of symbols used to represent genes on chromosomes.

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Types of Genetic Notation

• There are three principal styles of genetic notation in common use among scientists:

Plant Notation

Animal Notation

Microbial Notation

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TAS uses a Modification of Animal Genetic Notation

• Animal genetic notation is based on the concept of a “wild type” designated with the “+” symbol.

• “Wild type” means the most common phenotype.

• In TAS, “wild type” refers to the most common phenotype in wild angelfish, which we know as a wild silver, or just “wild.”

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Animal Genetic Notation Rules1. Pick a letter (or group of letters) that refers to the non-wild phenotype or the general characteristic.

For example, we can pick “D” to represent the dark or black

phenotype.

2. If the non-wild allele is recessive, use a lower case letter to symbolize it. If non wild is dominant (or co-dominant), pick an upper case letter to symbolize it.

Since the dark allele is co-dominant to the wild type, we use upper case

“D” instead of lower case “d”.

3. The wild type allele is the same symbol as the non-wild with a + superscript.

Thus conventional animal notation would show the wild allele as D+.

4. If there are more than two alleles, letter superscripts are lower case if the second allele is recessive to the initial dominant allele, and upper case if it is dominant to it.

Since gold is recessive to dark, animal notation would use lower case “g”

instead of upper case “G” for gold. A gold allele would be shown as Dg

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TAS Genetic NotationThe notation used by The Angelfish Society is a modification of animal notation. The symbols that would normally be superscripts in animal genetic notation become the actual notation for the allele.

Animal Notation

TAS Notation

Alleles at Dark Locus

D D Dark (black) allele

D+ + Wild allele

DM M Marble allele

DGm Gm Gold marble allele

Dg g Gold allele

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Animal vs. TAS notation for some dark locus phenotypes

Phenotype Animal Notation

TAS Notation

Wild silver D+/D+ +/+

Black Lace D/D+ D/+

Marble DM/DM M/M

Black Lace Angelfish

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Displaying notation for genes

• Chromosomes come in pairs. Genes therefore also come in pairs.

• Genetic notation shows the two paired genes separated by a forward slash like this: D/D.

• To show the genetic notation for more than one gene pair, each pair is separated by a hyphen like this: D/D – S/S.

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How does the TAS Genetics Calculator display the notation for a

genotype?

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TAS Genetics Calculator

• For any hypothetical cross, the calculator generates: – genotypes and the expected ratio of genotypes of the offspring,

and – phenotypes and expected ratio of phenotypes. (Phenotype

naming will be the topic of another presentation)

• When more than one locus is involved in the phenotype, the calculator shows the notation for the genotype in a specific order.

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The genetics calculator displays the alleles at each locus in this order:

1 Dark Locus (D, M, Gm, g)

2 Zebra/Stripeless Locus (Z,S)

3 Smokey (Sm)

4 Veil (V)

5 Half-black (h)

6 Pearly (p)

7 Albino (a)

8 Streaked (St)

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Let’s look at an example

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How would the calculator show the genotype for a black ghost veil tail?

1 Dark Locus (D, M, Gm, g) D/+

2 Zebra/Stripeless Locus (Z,S) S/+

3 Smokey Locus (Sm) (none)

4 Veil Locus (V) V/+

5 Half-black Locus (h) (none)

6 Pearly Locus (p) (none)

7 Albino Locus (a) (none)

8 Streaked Locus (St) (none)

When you list the alleles in order, the genotype is:

D/+ – S/+ - V/+

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You can also show the genotype to include loci with all wild alleles

1 Dark Locus (D, Gm, g) D/+

2 Zebra/Stripeless Locus (Z,S) S/+

3 Smokey Locus (Sm) +/+

4 Veil Locus (V) V/+

5 Half-black Locus (h) +/+

6 Pearly Locus (p) +/+

7 Albino Locus (a) +/+

8 Streaked Locus (St) +/+

You could display loci with all wild alleles, and show the genotype as:

D/g – S/+ - +/+ - V/+ - +/+ - +/+ - +/+ - +/+

However, this gives a cluttered look.

The genetics calculator simply omits the loci that have only wild

alleles when it displays a genotype.

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Let’s try another example

How would you show the genotype of a half-black veil tail ghost?

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Half-black veil tail ghost

1 Dark Locus (D, Gm, g) (none)

2 Zebra/Stripeless Locus (Z,S) S/+

3 Smokey Locus (Sm) (none)

4 Veil Locus (V) V/+

5 Half-black Locus (h) h/h

6 Pearly Locus (p) p/p

7 Albino Locus (a) (none)

8 Streaked Locus (St) (none)

Simply list the alleles in the order in which they

appear in the chart.

The first non-wild alleles are on the

stripeless locus (S/+), followed by the veil

locus (V/+) and then the half-black locus (h/h).

String these together in order to get:

S/+-V/+-h/h

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Does the order really matter?

• Probably not. You would probably call this fish a half-black veil tail.

• The genetics calculator would

show the genotype as V/+-h/h. • Most of us would probably list the

half-black alleles first – h/h-V/+ - because that is the dominant appearance of the angelfish.

• And anyone familiar with TAS angelfish notation will recognize the genotype and interpret it correctly in either order.

V/+-h/h or h/h-V/+?

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Wrap up

• Although you may not always list the genotype in the same order as the genetics calculator, it is useful to understand the logic that is programmed into the calculator.

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Watch for Part 2 Next Month!

• Part 2 of this presentation will show you how the calculator creates phenotype names for any genotype!

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The End

Now hurry back to the chat room for exciting

discussion!!!

(This mystery fish will be the subject of a future presentation! Can you guess why he is special?)