Transcript How the Genetics Calculator Creates Phenotype Names

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 Rules
1. Pick a letter (or group of letters) that
refers to the non-wild phenotype or the
general characteristic.
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.
3. The wild type allele is the same
symbol as the non-wild with a +
superscript.
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.
For example, we can pick “D” to
represent the dark or black
phenotype.
Since the dark allele is co-dominant to
the wild type, we use upper case
“D” instead of lower case “d”.
Thus conventional animal notation would
show the wild allele as D+.
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 Notation
The 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+
DM
D
+
M
Dark (black) allele
Wild allele
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 TAS
Notation Notation
Wild silver
D+/D+
+/+
Black Lace
D/D+
D/+
DM/DM
M/M
Marble
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)
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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)
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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)
2
Zebra/Stripeless Locus (Z,S)
3
Smokey Locus (Sm)
4
Veil Locus (V)

V/+
5
Half-black Locus (h)

h/h
6
Pearly Locus (p)



7
Albino Locus (a)

8
Streaked Locus (St)

(none)
S/+
(none)
p/p
(none)
(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?)
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