Lecture 2 The genetic Model for Quantitative Traits

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Animal Breeding and Genetics
Instructor Dr. Jihad Abdallah Genetic Model for
Quantitative Traits
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Simply Inherited and Polygenic Traits

• Simply inherited traits traits affected by one
  or few genes (coat color, presence of horns,
  genetic defects like spider syndrome in sheep).
• Phenotypes of simply inherited traits are placed
  into categories (qualitative or categorical
  traits)
• Very little affected by the environment.

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• Polygenic traits are traits affected by many
  genes (no single gene having an overriding
  effect) like growth rate, milk production, birth
  weight, etc.
• Generally described in numbers.
• Typically quantitative or continuous in their
  expression (an exception is Dystocia which is
  affected by many genes but pohenotype is
  described in categories)
• Polygenic traits are affected by the environment.

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• Polygenic traits are traits affected by many
  genes (no single gene having an overriding
  effect) like growth rate, milk production, birth
  weight, etc.
• Generally described in numbers.
• Typically quantitative or continuous in their
  expression (an exception is Dystocia which is
  affected by many genes but pohenotype is
  described in categories)
• Polygenic traits are affected by the environment.

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The basic model for quantitative traits

• P µ G E
• P phenotypic value of an animal for a given
  trait.
• µ population mean or average phenotypic value
  for the trait of all animals in the population.
• G the genotypic value of the animal for the
  trait.
• E the effect of the environmental factors on
  the phenotype of the animal.
• G and E are expressed as deviations from the mean
  of the population. Therefore, the mean of G in
  the population and the mean of E is equal to
  zero.

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Genotypic Value

• Genotypic value is the overall effect of all the
  genes carried by the animal (singly and in
  combination) on the phenotype of the animal for
  the trait.
• Unlike the phenotypic value, G is not directly
  measurable.
• The genotypic value is the sum of two values
  breeding value (BV) and Gene Combination Value
  (GCV).
• G BV GCV

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Breeding value

• Breeding value (also called the additive genetic
  value) is the part of genotypic value that can be
  transmitted from parents to offspring. It is the
  sum of the effects of individual genes (called
  independent gene effects or additive gene
  effects) independent of the effects of dominance
  and epistasis.
• Breeding value is considered as a parental value
  (the value of an individual as a contributor of
  genes to the next generation).
• Before we select animals to be parents of the
  next generation, we first estimate their breeding
  values and choose those with the best breeding
  values.

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Example assume that a trait is affected by 5
loci and the independent (additive) gene effects
for the 10 genes (alleles) at the 5 loci are as
given in the table. The breeding value is the sum
of these effects.
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• An individual only transmits a sample composed of
  half of its genes to each of its offspring this
  half is a random half of its genes. Progeny
  difference (PD) or transmitting ability (TA) are
  used in practice by some countries to rank
  animals.
• PD TA ½ BV
• Progeny difference and transmitting ability are
  practical concepts. These are defined as the
  expected difference between the mean performance
  of the progeny of a parent and the mean
  performance of the progeny of all the parents in
  the population
• PDi TAi µ offspring of parent i µ
  offspring of all parents

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• Progeny difference and transmitting ability are
  not directly measurable but can be predicted
  using performance data.
• The predicted value for PD is called EPD
  (expected progeny difference)
• The predicted value for TA is called PTA
  (predicted transmitting ability).
• Both terms mean the same thing but EPD is used in
  beef cattle, swine and sheep breeding while PTA
  is used in dairy cattle breeding.

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• The breeding value of an offspring can be viewed
  as the sum of the additive effects of the genes
  inherited from the sire (father) and the additive
  effects of the genes inherited from the dam
  (mother).

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• For example, if the estimated BV of a sire for
  weaning weight is 2.5 kg and the estimated BV
  of the dam is 1.5 kg, then the average expected
  BV of their offspring is equal to (2.5 1.5)/2
  2 kg. That is, we expect the average of
  offspring of these sire and dam to be 2 kg
  heavier at weaning than the average of all
  offspring in the population.

Therefore, if the population mean of weaning
weight is 18 kg then the average phenotype of the
offspring of these sire and dam is 18 2 20 kg.
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Gene Combination Value (GCV)

• GCV is the part of the genotypic value that is
  due to gene combination effects (dominance and
  epistasis).
• Because individual genes and not gene
  combinations survive segregation and independent
  assortment during meiosis, GCV can not be
  transmitted from parent to offspring and
  therefore it is not important in selection.

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• Example suppose that a locus affects litter size
  in swine with two alleles T and t and T is
  completely dominant over t. The independent
  effects are 0.1 pigs for T and 0.1 pigs for t.
  

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Producing Ability (PA)

• For repeated traits (traits for which the animal
  have more than one performance record during its
  lifetime) the producing ability is very important
• Producing ability represents the performance
  potential of an animal for a repeated trait (the
  ability of the animal to repeat its performance
  in future records). Producing ability is a
  function of all those factors which permanently
  affect the performance potential of the animal
• The genotypic value and its components (BV and
  GCV) which are determined at conception and
  remain with the animal during his whole life.
• Some environmental factors which permanently
  affect the performance of the animal.

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• Examples of permanent environmental effects (Ep)
• - Nutrition at early stages of development
  affects the ability of beef and dairy cows to
  produce milk permanently.
• - A permanent problem in the udder will affect
  milk production during all productive life of the
  cow or ewe.
• The environmental effects which do not affect
  performance permanently are called temporary
  environmental effects (Et). Examples on these
  include forage quality, weather conditions and
  some management practices. These factors vary
  from season to season or year to year and so they
  do not influence different records in the same
  way.

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• The producing ability is a combination of genetic
  and permanent environmental effects
• PA G Ep ? PA BV GCV Ep
• The average of PA is 0 across the population
  because it is expressed as a deviation from the
  mean.
• The genetic model for repeated traits is
• P µ BV GCV Ep Et

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Example two records of 305-d milk production (in
lbs) for two cows
PA for cow 1 1500 1000 2500 3000 lb PA
for cow 2 1000 500 4500 -3000 lb If we
were to cull (discard) one of these cows we will
cull cow 2.
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Importance of producing ability

• It is important to commercial producers as a
  measure of productive capacity. Typically dairy
  farmers feed their cows according to their
  producing ability.
• Therefore, prediction of PA is quite useful in
  practice. The predicted value of PA is called
  Most probable Producing Ability (MPPA).
• P µ MPPA is a prediction of the animals next
  record.