Transcript DNA-TOETSING - Stud Game Breeders

DNA-Testing for
single gene traits:
COAT COLOUR
Dr. Munro Marx and Joubert Oosthuizen
Unistel Medical Laboratories (Pty) Ltd.
From cell to genome
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Cells:
The fundamental working units of a
living organism.
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DNA:
Found in the nucleus of cells
All instructions to regulate the
activities of cells are tucked up in
the DNA.
The DNA molecule is a side by side
arrangement of nucleotides (e.g.
ATTCCGGA).
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The Genome;
The organism’s total DNA content is
known as the genome
Genomes sizes vary in different
organisms.
DNA, Chromosomes, Genes and Proteins
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DNA is packaged in structures known as
chromosomes (46 in humans, 46 in Sable
antelope, 56 in Springbok, 60 in buffalo and
cattle ).
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Several genes are located on each
chromosome
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Genes are the functional and physical units of
inheritance. Each genome has about 25 000
genes
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The basic structure of a gene supplies the
code for the manufacture of Proteins.
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Proteins provide essential functions for life
(digestion etc.) and form and structures (cells,
hair etc.)
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Proteins consist of combinations of amino
acids (20 different amino acids)
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The sequence of amino acids, the protein form
and structure determines function.
Proteins and Proteome
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The total protein content of a cell is known as the
proteome.
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Proteome is a dynamic system and reacts to both
the internal and external environment.
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The chemistry and behaviour of a proteome is
determined by the total gene function and
expression in the same cell at the same time.
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Each cell has the genetic potential to manufacture
and express all the proteins of the organism.
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Gene function and expression is selective and cell
specific.
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Genes activated in a specific cell provide that cell
with its unique function and characteristic e.g.
liver cells, coat colour.
Where does coat colour fit in?
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Animals evolved different skin and coat
colour and patterns primarily as defence
against predators or as an aid in predation.
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An animal’s phenotype (what it looks like),
is a result of a complex interaction between
its inherited genetic makeup (genotype)
and the environment in which it lives.
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Genes involved in skin and coat colour are
amazingly similar all over the animal
kingdom.
Colour, Melanocytes and Melanin
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The pigment melanin is the primary determinant of
colour and is found in cells called melanocytes .
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Melanin is produced in melanocytes in the eye, skin and
hair (coat).
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Skin and coat darkness / lightness is primarily
determined by:
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the amount of melanin in the melanocytes
the ratio between eumelamin (Black/Brown pigment) and
pheomelamin (Red/Yellow).
Melanocytes originate in the neural crest and migrate
during embryogenesis. This migration plays a role in
colour patterning.
Genetic control of Skin and Coat Colour.
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The skin and coat colour (pigmentation) of an
animal is determined by GENES that code for
different pigments.
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Pigmentation caused by genes is constitutive
pigmentation – an intrinsic property of the animal.
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Two classes of genes affecting pigmentation have
been identified:
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Those affecting the pigment producing cells
(melanocytes per se, especially on membrane).
Those affecting pigment synthesis (the inside
workings of melanocytes).
Cause of colour and pattern
diversity.
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As with (virtualy) all diversity in the world of the living, colour and
pattern diversity is caused by genes and their mutations.
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The wide variety of colours and patterns observed is due to:
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The number of genes involved, and
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The number of mutations per gene.
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Advantageous mutations are evolutionary retained,
disadvantageous ones are lost.
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In the wild disadvantageous mutations that inherit recessively may
be retained for generations. Loss of the properties assisting
survival prevent the recessive phenotype from surviving, thereby
keeping the mutation’s frequency low.
Mutations that affect melanocytes.
Melanocytes are responsible for eye, skin and coat colour, as
well as patterning. Mutations may affect the following areas
of melanocyte function:
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Mutations affecting the melanocyte surface result in
qualitative changes of pheomelanine or eumelanine .
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Mutations affecting the inner workings of
melanocytes.
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These mutations influence what kind of pigment are
produced and will influence the basic colour of the skin
and coat.
These mutations result in quantitave changes in pigment
production and may lead to changes in the basic colours
(colour dilution).
Mutations affecting differentiation, proliferation and
migration of melanocytes.
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These mutations lead to changes in white spotting and
MAY lead to changes in patterns
How do genes work to have the effect they have?
Genes operate in pairs, with one of
each inherited from each parent.
Some genes are dominant – if an animal have
one of those genes, it will totally cancel the
effect of the other gene.
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Some are recessive – the gene’s effect will
only be noticed if both copies are recessive.
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Some are co-dominant – if two different genes
are present, their effect will be a combination of
the two.
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Together with the above, a range of other
effects may influence the inheritance and
expression of a trait , eg:
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Incomplete penetrance
multigene vs single gene inheritance
epistase
epigenetic factors
Etc, etc.
Other factors affecting
skin and coat colour
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Suplementary to genes are environmental factors
and hormones (facultative pigmentation – inducable
property). (A topic on it’s own, not for today.)
Colour genes illustrated – the horse
as representative of the mammal (1)
Horse colour genetics (constitutive pigmentation)
is perhaps best understood.
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The basic coat colours: Genes affecting the melanocyte
surface (Extension and Agouti loci) determine the basic coat
colours – Chestnut, Bay, Black
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Chestnut: eumelanine (black/brown) in the skin, pheomelamine
(red/yellow) in the hair, including mane and tail.
Black: eumelanine (black). In skin and hair (entire body).
Bay: pheomelanine (body) and eumelanine (mane and tail and
lower leg) patterns.
So far, so good, so simple!!
Colour genes illustrated – the horse
as representative of the mammal (2)
Phenotype
Dilution
coat colours
Locus (symbol)
gene abbrev
Cream (CR)
MATP
Cream (CR)
MATP
PalominolBuckskin
Cremello/Perlino - creamy white coat
colour with blue eyes
Dun - diluted basic colours and primitive
markings (c.g dorsal stripe, zebra stripes Dun (D) Not
on legs)
known
Silver dapple - chocolate-to-reddish body
with whitelgrey mane and tail
Champagne - metallic sheen (eye and
skin colour may change with age)
Progressive greying with age; associated
Greying
with melanoma
Roan - interspersed white hairs in basic
colour
Depigmen- Overo-spotting - irregular white spotting,
tation
often horizontal distribution
Tobiano-spotting - regular white spotting,
often vertical distribution
Silver (Z) PMEL
17
Champagne (CH)
SLC36Al
Grey (G) STX17
Roan (RN)
Associated to KIT
Overo (0) EDNRB
Tobiano (TO) KIT
16 Genes influencing
coat colour has so far
been found. Two are
responsible for
primary colour, while
the rest, some singly,
some in combination,
modify the basic
colour a varying
degree.
For each of these
genes, mutations
have been described.
Mutations within
these genes can
multiply the effects
on colour
Colour and pattern genes – the mouse
The mouse is the most studied mammal, also as far as pigmentation
is concerned. Some sobering data is given in the table below. It also
give us hope that coat pattern will soon be as well understood as
colour.
302 Mouse genes and variants involved in pigmentation have been identified. The variants
are mutated genes - the total number of genes is less than 302, but still many times the 16 of
the horse.
Of these 171 have been cloned and studied in detail.
For each of these171 genes a human homologue has been found. There seems to be a
large degree of similarity in mammalian pigmentation genetics over species.
For 149 of the 171 genes homologues have been found in the Zebra-fish. This bodes well for
utilization of knowledge across species.
Pattern - eg.
Skin - Dark,
Coat colour Coat, Hair, Fur spot, belt, stripe,
Light, Darken,
General
Other effects
toe, etc.
Lighten
Skin - Other
Effects
Pigmentation hyper, hypo,
depigment.
Other
22 (7 cloned)
7 (6 cloned)
17 (16 cloned)
88 (79 cloned)
97 (24 cloned)
52 (28 cloned)
19 (11 cloned)
What about game coat colour?
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These same genes have been found in many mammals, even though they may
not have exactly the same effect. Most will be present in most game species,
but with slight sequence differences.
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A starting point would be to determine the DNA sequences of the known primary
colour genes (Extension and Agouti loci) of both standard and other phenotypes,
analyse for differences and investigate the genetic effect, if any, of each.
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Species for which the gene sequences are known that are closest to the game
specie in question should be used as starting point.
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A second phase would be the same procedure for the known genes that have a
less dramatic effect (dilution, depigmentation, greying).
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Literature should be carefully monitored for any new developments.
Finally breeding and breeding experiments might be required.
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What about coat colour patterns?
Is the basis for variation in coat colour
pattern known?
Hardly !!!.
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Mammalian coat patterns (e.g., spots, stripes) are hypothesized to
play important roles in camouflage and other relevant processes,
yet the genetic and developmental bases for these phenotypes
are completely unknown. (Eizirik, E. January 2010)
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"The question of how color patterns are established in vertebrates
has been a black box," says Marie Manceau, (Science, 2011).
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They found that subtle changes in the Agouti gene's embryonic
activity can also make a profound difference in the distribution of
pigments across the entire body. Mary Manceau, Hopi E. Hoekstra
et al: 2011)
The Beauty of Mutations
Why mutations?
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Our environment constantly changes, the
Earth and its ecosystems change.
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Populations must change to survive
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Evolutionary change requires variation, the
raw material on which natural selection
works
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One mechanism for variation and change is
at the DNA level.
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Mutations can be beneficial and enable the
organism
to
adapt
to
a
changing
environment.
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However, most mutations are deleterious,
and cause varied genetic problems
BAIE DANKIE
THANK YOU
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