Genetics

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Genetics
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GENETICS DEFINITION

• The study of the means by which genetic
  information is stored, replicated, translated,
  mutated and transferred to future generations
  such that anatomical and physiological systems
  are integrated and parental characters appear in
  subsequent generations.

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KEY ELEMENTS OF THE CELL

• There are several structures and sub-cellular
  organelles in the cell, but the main ones of
  interest in genetics are the nucleus, ribosomes,
  nucleolus and centrioles.The nucleus contains
  the chromosomes, the ribosomes control RNA
  transcription, the nucleolus produces t-RNA and
  the centrioles serve as focal points for cell
  division.

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DNA

• DNA is an acronym for deoxyribonucleic acid. It
  is composed of a 5 carbon sugar, deoxyribose,
  phosphate bonds, and nitrogenous bases. These
  nitrogenous bases are adenine, thymine, cytosine
  and guanine. Chemically adenine can only bond
  with thymine and cytosine only with guanine. It
  is in the form of a double helix.

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DNA continued

• To visualize the structure of DNA, imagine a
  rubber ladder in space. The uprights of the
  ladder are composed of molecules of deoxyribose
  connected in single strands with phosphate bonds.
  The steps of the ladder are paired bases that
  join to each other and also the uprights of sugar
  and phosphate.

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DNA CONT.

• The steps then would be a pair of bases composed
  of either adenine bonded with thymine or cytosine
  bonded with guanine.
• If you were to grasp the top and bottom of this
  imaginary ladder and twist in opposite
  directions, you would form a twisted structure
  that would be in the shape of a double helix.

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The code

• Three of these bases in a row are called a codon
  or triplet. The sequence will code for a
  specific amino acid. Thus, as codons are put in
  sequence, the structure of a protein is coded.
• If we put a codon that calls for the start of a
  gene in front of the above sequence and another
  at the end to stop it we have a gene.

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Definitions

• Locus-Point on a chromosome where a specific gene
  is always found.
• Allele-Genes that are found at the same locus on
  homologous chromosome that affect the same trait
  in different ways.
• Homologous-Chromosomes of the same shape, size
  and length that carry similar genes.

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Diploid chromosomes

• Each normal animal has an even number of total
  chromosomes. These are arranged in pairs of
  homologous chromosomes one of each pair coming
  from the sire and the dam.
• Cattle60, sheep54, swine38, goats60,
  horses64, donkey62

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Homologous chromosomes

• Same length, size and shape that carry similar or
  the same genes at the same loci.
• Sex chromosomes are not homologous. In mammals
  are X and Y fowl are Z and W. Males XY, Female
  fowl are ZW.

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Mendelian genetics

• Each animal or plant has a maximum of two
  alleles.
• Each gamete will receive one gene from a locus.
• Thus the probability of a gamete receiving a
  particular gene depends upon the genotype of the
  animal or plant for that locus.

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Probabilities

• The probability of an event happening can never
  be less than zero nor more than 1.0.
• Thus the sum of all the probabilities will add to
  1.0.
• E.g. with a legal coin a toss can either result
  in a head (1/2) or a tail (1/2). And (½ ½
  1.0).

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Segregation into gametes

• Mendels first law indicates that genes are
  segregated into gametes at random based on the
  genotype of the individual.
• Thus, an animal with a genotype Aa will form
  gametes with either A or a and it will do so at
  equal probabilities.

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Example
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Segregation and meiosis

• Recall that homologous chromosomes arrive at the
  metaphase plate and line up randomly one on top
  of the other with no regard to whether the
  chromosome came from the sire or the dam.
• Thus, each pair of homologous chromosomes act
  independent of every other pair.

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Probability of two events

• The probability of two or more independent events
  happening at the same time is the product of
  their independent probabilities.
• Genes carried on nonhomologous chromosomes are
  independent events.
• In calculating, we can find each loci probability
  and then multiply them to reach the final answer.

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Two genetic loci

• If an animal were to have the genotype AaBb and
  the two loci were on different pairs of
  homologous chromosomes, then the A locus could
  produce an A or an a gamete.
• Likewise, the B locus could produce either a B or
  a b gamete.

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Combining loci

• Remember that a gamete contains only ONE of each
  gene from a locus.
• Thus, in constructing the possible gametes from
  the previous example we could have an AB, an Ab,
  an aB or an ab.

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Example
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Probabilities

• The probability of each of these gametes being
  formed is ¼. Pr (A) ½ and Pr (B) ½. ½ x ½
  ¼
• There are four possible gametes each with a
  probability of ¼, so they add to 4/4 or 1.0 and
  all the probabilities are accounted for.
• What is the probability of producing a gamete
  (abcDEf) from AaBbCcDdEEFf?

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Answer

• 1/32
• a1/2, b1/2, c1/2, D1/2, E1.0, f1/2.
• ½ x ½ x ½ x ½ x 1.0 x ½ 1/32
• Each is an independent event and so each
  probability is multiplied by all the others.
• For practice, make up genotypes and calculate the
  probability of several gametic genotypes.

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Recombining into Zygotes

• Gametic production in one sex has no influence
  over gametic production in the other. Thus,
  these too are independent events.
• If we want to know what the possibilities of
  certain genotypes resulting from known matings,
  we need only to calculate the probabilities of
  gametes and multiply.

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Aa X Aa

• The probability of the first genotype producing
  an A or an a gamete is ½ each.
• Likewise for the second genotype.
• If an A sperm fertilized an A ovum, then the
  result would be an AA zygote. The probability of
  this occurring is ½ x ½ ¼.
• The same would be true for an a sperm
  fertilizing an a ovum.

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The other result

• If an A sperm fertilized an a ovum the result
  would be an Aa zygote (also ¼).
• But, if an a sperm fertilized an A ovum the
  result would be aA. (also ¼)
• The two genotypes are equivalent, it making no
  difference which sex contributed what gene to the
  heterozygote.
• Thus, we add the two probabilities to ½.

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The result

• From any heterozygous mating, we will get 1
  homozygote, 2 heterozygotes and 1 homozygote
  (opposite).
• This is the classic 121 ratio.
• We can construct a chart known as a Punnet Square
  to illustrate this.

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Punnet Square
Genotype of Sire and dam gamete. A a
A AA Aa
a aA aa
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Two loci

• If we add another independent heterozygous locus,
  we can still treat each as an independent event.
• Thus, gametes at each locus are created in equal
  numbers.
• AaBb would yield the four gametes referred to
  earlier. If we construct a chart for their
  recombination we would get

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AaBb x AaBb
Sire/dam gametes AB Ab aB ab
AB AABB AABb AaBB AaBb
Ab AABb AAbb AaBb Aabb
aB aABB aABb aaBB aaBb
ab aAbB aAbb aabB aabb
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Same genotypes
Sire/dam gametes AB Ab aB ab
AB AABB AABb AaBB AaBb
Ab AABb AAbb AaBb Aabb
aB aABB aABb aaBB aaBb
ab aABb aAbb aabB aabb
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Same genotypes
Sire/dam gametes AB Ab aB ab
AB AABB AABb AaBB AaBb
Ab AABb AAbb AaBb Aabb
aB aABB aABb aaBB aaBb
ab aABb aAbb aabB aabb
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Same genotypes
Sire/dam gametes AB Ab aB ab
AB AABB AABb AaBB AaBb
Ab AABb AAbb AaBb Aabb
aB aABB aABb aaBB aaBb
ab aABb aAbb aabB aabb
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Same genotypes
Sire/dam gametes AB Ab aB ab
AB AABB AABb AaBB AaBb
Ab AABb AAbb AaBb Aabb
aB aABB aABb aaBB aaBb
ab aABb aAbb aabB aabb
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Same genotypes
Sire/dam gametes AB Ab aB ab
AB AABB AABb AaBB AaBb
Ab AABb AAbb AaBb Aabb
aB aABB aABb aaBB aaBb
ab aABb aAbb aabB aabb
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Different genotypes
Sire/dam gametes AB Ab aB ab
AB AABB AABb AaBB AaBb
Ab AABb AAbb AaBb Aabb
aB aABB aABb aaBB aaBb
ab aABb aAbb aabB aabb
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Phenotypic expression of genes

• Non-additive gene action-shows some type of
  dominance
• Complete or total dominance
• Incomplete or partial dominance
• Co-dominance
• Over-dominance
• Epistasis

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Complete dominance

• One allele when in the homozygous or heterozygous
  form will always be expressed in the phenotype.
  Totally covers the expression of its recessive
  allele.
• Common type first explored by Mendel.
• Aa x Aa yields AA, 2 Aa, aa
• Note heterozygotes never breed true.

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Incomplete dominance

• One allele only partially covers the phenotypic
  expression of its recessive allele.
• Results in a blending type inheritance.
  Recessive allele bleeds into the phenotype.
• Example red flower crossed with white flower
  yields a pink flower.
• Yields three distinct phenotypes rather than only
  two such as complete dominance results in.

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Co-dominance

• Neither allele will cover or dominate. Both will
  be expressed completely in the phenotype.
• Red flower crossed with white flower would yield
  a red and white flower. Also the type of gene
  action in roan shorthorns and AB blood groups in
  humans.
• Three phenotypes will be expressed.

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Over dominance

• Interaction between genes that are alleles such
  that the heterozygote is superior in performance
  to either homozygote.
• Is a major factor in the phenomenon known as
  heterosis or hybrid vigor.
• Graph heterosis on blackboard.

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Heterosis

• An increase in performance in crossbred or out
  bred animals over their parents.
• Average of the F1 the average of the P1
  divided by the average of the P1 times 100 gives
  the percent heterosis.
• Note the average of the progeny only has to
  exceed the average of the parents, it does not
  have to be superior to the best parent.

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Epistasis

• Interaction between non-allelic genes such that
  there is created a new phenotype.
• Very common gene action in coat color inheritance
  in animals. The dilution gene in horses affects
  the b locus to dilute to palomino or cremelo.
• The e locus in labs will result in a yellow lab
  if the e locus is ee and the b locus is either
  BB, Bb or bb. Difference is in the nose color.

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Additive gene action

• Shows no dominance. Instead has residual genes
  and contributing genes.
• A residual gene is expressed in the phenotype as
  a particular level of performance. A1, B1 are
  examples.
• A contributing gene only adds on to the
  performance of the residual, doesnt cover. A2,
  B2 are examples.

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Additive continued

• A1A1 X A2A2 yields all A1A2 which would be
  intermediate in phenotype to the homozygotes.
• Another attribute of additive genes are that they
  are affected by environmental influences whereas
  non-additive genes are affected very little by
  environment.
• This makes it difficult to tell the genotypes
  from the phenotypes because a contributing gene
  homozygote in a poor environment might be
  confused with a heterozygote in a good environ.

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Additive cont.

• This type of gene action shows itself most often
  in what are termed economically important
  traits. These include average daily gain, feed
  efficiency, carcass traits, etc.
• Many genes and environment affect them, males are
  heavier and more efficient than females and the
  measures are continuous.

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Additive cont.

• Other characteristics of additive genes
• Involve many gene pairs-polygenic
• Shows no heterosis
• Shows sex effects
• Transgressive variation
• Medium to high heritability estimates
• Phenotypes are not distinct but instead follow a
  continuous variable format.

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Non-additive comparison

• Little environmental influence.
• Few pairs of genes involved.
• Sex effects are few.
• Heterosis and inbreeding depression expressed.
• No transgressive variation.
• Zero to low heritability estimate.
• Distinct phenotypes.

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Facts of gene expression

• Some traits affected by only non-additive or
  additive gene action.
• Some traits are affected by both types of gene
  action.
• Select differently depending on type.
• Additive identify the best and breed best to
  best.
• Non-additive easiest to outbreed or crossbreed.

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Polygenetic traits

• Most traits of economic importance are affected
  by polygenes. This means that several loci of
  genes all affect the same trait in some fashion.
  Our example of coat color inheritance in horses
  is an example of polygenes.
• Additive traits are affected by many pairs of
  polygenes each affecting the trait in a small way.

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Multiple alleles

• In a population of animals or plants there many
  times exist at a loci more than 2 alleles.
• This fact may explain differences in outcomes
  when two particular parents are mated.
• The A, B, o alleles in human blood type is an
  example. An Aa mated with a Ba could give you an
  AB, an Aa, a Ba or an aa

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Multiple alleles

• AB- Co dominance
• Aa Ba- Heterozygous
• A B blood types
• aa- O blood type