DNA-Testing for single gene traits: COAT COLOUR

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DNA-Testing forsingle gene traitsCOAT
COLOUR

• Dr. Munro Marx and Joubert Oosthuizen
• Unistel Medical Laboratories (Pty) Ltd.

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From cell to genome

• CellsThe fundamental working units of a living
  organism.
• DNAFound 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).
• The GenomeThe organisms total DNA content is
  known as the genome
• Genomes sizes vary in different organisms.

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DNA, Chromosomes, Genes and Proteins

• DNA is packaged in structures known as
  chromosomes (46 in humans, 46 in Sable antelope,
  56 in Springbok, 60 in buffalo and cattle ).
• Several genes are located on each chromosome
• Genes are the functional and physical units of
  inheritance. Each genome has about 25 000 genes
• The basic structure of a gene supplies the code
  for the manufacture of Proteins.
• Proteins provide essential functions for life
  (digestion etc.) and form and structures (cells,
  hair etc.)
• Proteins consist of combinations of amino acids
  (20 different amino acids)
• The sequence of amino acids, the protein form and
  structure determines function.

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Proteins and Proteome

• The total protein content of a cell is known as
  the proteome.
• Proteome is a dynamic system and reacts to both
  the internal and external environment.
• The chemistry and behaviour of a proteome is
  determined by the total gene function and
  expression in the same cell at the same time.
• Each cell has the genetic potential to
  manufacture and express all the proteins of the
  organism.
• Gene function and expression is selective and
  cell specific.
• Genes activated in a specific cell provide that
  cell with its unique function and characteristic
  e.g. liver cells, coat colour.

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Where does coat colour fit in?

• Animals evolved different skin and coat colour
  and patterns primarily as defence against
  predators or as an aid in predation.
• An animals 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.
• Genes involved in skin and coat colour are
  amazingly similar all over the animal kingdom.

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Colour, Melanocytes and Melanin

• The pigment melanin is the primary determinant of
  colour and is found in cells called melanocytes .
• Melanin is produced in melanocytes in the eye,
  skin and hair (coat).
• Skin and coat darkness / lightness is primarily
  determined by
• 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.

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Genetic control of Skin and Coat Colour.

• The skin and coat colour (pigmentation) of an
  animal is determined by GENES that code for
  different pigments.
• Pigmentation caused by genes is constitutive
  pigmentation an intrinsic property of the
  animal.
• Two classes of genes affecting pigmentation have
  been identified
• Those affecting the pigment producing cells
  (melanocytes per se, especially on membrane).
• Those affecting pigment synthesis (the inside
  workings of melanocytes).

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Cause of colour and pattern diversity.

• As with (virtualy) all diversity in the world of
  the living, colour and pattern diversity is
  caused by genes and their mutations.
• The wide variety of colours and patterns observed
  is due to
• The number of genes involved, and
• The number of mutations per gene.
• Advantageous mutations are evolutionary retained,
  disadvantageous ones are lost.
• 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 mutations
  frequency low.

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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

• Mutations affecting the melanocyte surface result
  in qualitative changes of pheomelanine or
  eumelanine .
• These mutations influence what kind of pigment
  are produced and will influence the basic colour
  of the skin and coat.
• Mutations affecting the inner workings of
  melanocytes.
• 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.
• These mutations lead to changes in white spotting
  and MAY lead to changes in patterns

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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.
• Some are recessive the genes effect will
  only be noticed if both copies are recessive.
• Some are co-dominant if two different genes
  are present, their effect will be a combination
  of the two.
• Together with the above, a range of other
  effects may influence the inheritance and
  expression of a trait , eg
• Incomplete penetrance
• multigene vs single gene inheritance
• epistase
• epigenetic factors
• Etc, etc.

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Other factors affecting skin and coat colour

• Suplementary to genes are environmental factors
  and hormones (facultative pigmentation
  inducable property). (A topic on its own, not
  for today.)

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Colour genes illustrated the horse as
representative of the mammal (1)

• Horse colour genetics (constitutive pigmentation)
  is perhaps best understood.
• The basic coat colours Genes affecting the
  melanocyte surface (Extension and Agouti loci)
  determine the basic coat colours Chestnut, Bay,
  Black
• 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!!

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Colour genes illustrated the horse as
representative of the mammal (2)
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
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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. 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. 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. 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. 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. 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. 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. Of these 171 have been cloned and studied in detail. Of these 171 have been cloned and studied in detail. Of these 171 have been cloned and studied in detail. Of these 171 have been cloned and studied in detail. Of these 171 have been cloned and studied in detail. 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 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 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 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 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 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 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. For 149 of the 171 genes homologues have been found in the Zebra-fish. This bodes well for utilization of knowledge across species. For 149 of the 171 genes homologues have been found in the Zebra-fish. This bodes well for utilization of knowledge across species. For 149 of the 171 genes homologues have been found in the Zebra-fish. This bodes well for utilization of knowledge across species. For 149 of the 171 genes homologues have been found in the Zebra-fish. This bodes well for utilization of knowledge across species. For 149 of the 171 genes homologues have been found in the Zebra-fish. This bodes well for utilization of knowledge across species. For 149 of the 171 genes homologues have been found in the Zebra-fish. This bodes well for utilization of knowledge across species.
Coat colour - General Pattern - eg. spot, belt, stripe, toe, etc. Coat, Hair, Fur - Other effects Skin - Dark, Light, Darken, Lighten Skin - Other Effects Pigmentation - hyper, hypo, depigment. Other
22 (7 cloned) 97 (24 cloned) 52 (28 cloned) 19 (11 cloned) 7 (6 cloned) 17 (16 cloned) 88 (79 cloned)
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What about game coat colour?

• 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.
• 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.
  
• Species for which the gene sequences are known
  that are closest to the game specie in question
  should be used as starting point.
• A second phase would be the same procedure for
  the known genes that have a less dramatic effect
  (dilution, depigmentation, greying).
• 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 !!!.
• 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)
• "The question of how color patterns are
  established in vertebrates has been a black box,"
  says Marie Manceau, (Science, 2011).
• 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)

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The Beauty of Mutations

• Why mutations?
• Our environment constantly changes, the Earth and
  its ecosystems change.
• Populations must change to survive
• Evolutionary change requires variation, the raw
  material on which natural selection works
• One mechanism for variation and change is at the
  DNA level.
• Mutations can be beneficial and enable the
  organism to adapt to a changing environment.
• However, most mutations are deleterious, and
  cause varied genetic problems

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