DNA Testing

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DNA Testing
Bell Ranch New Mexico
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Lecture 15
Breeding Values
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Genotype Frequency Phenotype Genetic
Value B1B1 p2 P11 V11 B1B2
2pq P12 V12 B2B2 q2 P22 V22
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Genotype Frequency Phenotype Genetic
Value B1B1 p2 P11 V11 B1B2
2pq P12 V12 B2B2 q2 P22 V22 Pij mgt
Vij
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Genotype Frequency Phenotype Genetic
Value B1B1 p2 P11 V11 B1B2
2pq P12 V12 B2B2 q2 P22 V22 Pij mgt
Vij mgt (P11 P22) / 2
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Genotype Frequency Phenotype Genetic
Value B1B1 p2 P11 V11 B1B2
2pq P12 V12 B2B2 q2 P22 V22 Pij mgt
Vij mgt (P11 P22) / 2 ? mgt (p - q) V11
2pq V12 (if equil)
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Genotype Frequency Phenotype Genetic
Value B1B1 p2 P11 V11 B1B2
2pq P12 V12 B2B2 q2 P22 V22 Pij mgt
Vij mgt (P11 P22) / 2 ? mgt (p - q) V11
2pq V12 (if equil)
AGV
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Genetic Value
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Genetic Value
The contribution of the genotype to the
expression of a characteristic
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Genetic Value
The contribution of the genotype to the
expression of a characteristic
Scenario V11 V12 (complete dominance)
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Genetic Value
The contribution of the genotype to the
expression of a characteristic
Scenario V11 V12 (complete
dominance) Performance is equal. P11 P12
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Phenotype
P11
Represent Ps
P22
A2A2
A1A2
A1A1
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Genetic Value
Two components for a single locus
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Genetic Value
Two components for a single locus 1) value of
individual alleles (B1 vs. B2 -- additive or
breeding value)
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Genetic Value
Two components for a single locus 1) value of
individual alleles (B1 vs. B2 -- additive or
breeding value) 2) value of the allele
combination in each individual (dominance value)
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ANIMAL
GENETIC VALUE
BREEDING VALUE
OWN PERFORMANCE
PROGENY
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ANIMAL
GENETIC VALUE
BREEDING VALUE
OWN PERFORMANCE
Parents can only pass on individual genes, not
combinations.
PROGENY
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To assess the value of an animal as a parent, we
evaluate the value of the genes it will
transmit.
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To assess the value of an animal as a parent, we
evaluate the value of the genes it will
transmit. Breeding Value (Additive Genetic
Value)
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To assess the value of an animal as a parent, we
evaluate the value of the genes it will
transmit. Breeding Value (Additive Genetic
Value) Transmitting Ability 1/2 BV
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To assess the value of an animal as a parent, we
evaluate the value of the genes it will
transmit. Breeding Value (Additive Genetic
Value) Transmitting Ability 1/2 BV -- average
value of gametes produced by an individual
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To assess the value of an animal as a parent, we
evaluate the value of the genes it will
transmit. Breeding Value (Additive Genetic
Value) Transmitting Ability 1/2 BV -- average
value of gametes produced by an
individual EBV -- Estimated Breeding ValueETA --
Estimated Transmitting Ability
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Questions 0.1 for being here 0.05 for every
right answer 0.25 total
Where did I get my undergraduate degree?
Where did I get my Ph.D.?
Where did I teach before Cornell?
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Answers
Where did I get my undergraduate degree? Cornell
University
Where did I get my Ph.D.? Iowa State University
Where did I teach before Cornell? UC Davis
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Example Breeding values
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Measured Phenotypes
Genotype Phenotype B1B1 P11 100 B1B2 P12
90 B2B2 P22 60
From previous lecture
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Example f(B1) p 2/3 f(B2) q 1/3 (at
equilibrium) ? 91.1 units
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Example f(B1) p 2/3 f(B2) q 1/3 (at
equilibrium) ? 91.1 units What is the mean of
progeny from a B1B1 male if mated at random to
the population?
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In the females
f(B1 B1) 4/9 f(B1 B2) 4/9 f(B2 B2) 1/9
Randomly mate these to B1 B1 male.
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Example B1B1 B1B2 B2B2 B1B1 B1B1
B1B2 B2B2
freq
male female
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Example B1B1 B1B2 B2B2 B1B1 B1B1 4/9
1 -- -- B1B2 B2B2
freq
male female
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Example B1B1 B1B2 B2B2 B1B1 B1B1 4/9
1 -- -- B1B2 4/9 1/2 1/2 -- B2B2
freq
male female
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Example B1B1 B1B2 B2B2 B1B1 B1B1 4/9
1 -- -- B1B2 4/9 1/2 1/2 --
B2B2 1/9 -- 1 --
freq
male female
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Example B1B1 B1B2 B2B2 B1B1 B1B1 4/9
1 -- -- B1B2 4/9 1/2 1/2 --
B2B2 1/9 -- 1 -- f(B1B1) 4/9 2/9
2/3 f(B1B2) 2/9 1/9 1/3
freq
male female
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Means of progeny of B1B1 male, (((((((B1B2 and
B2B2 males (not in equilibrium when looking at
progeny) ?11 f(B1B1) P11 f(B1B2) P12 f(B2B2)
P22 2/3 (100) 1/3 (90) 96.6
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Means of progeny of B1B1, B1B2 and B2B2
males ?11 f(B1B1) P11 f(B1B2) P12 f(B2B2)
P22 2/3 (100) 1/3 (90) 96.6 ?12
88.33 ?22 80.00
Calculated following same process used for the B1
B1 male but with B1 B2 and B2 B2 males.
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Difference in Means ?11 - ?12 96.66 - 88.33
8.33 ?12 - ?22 88.33 - 80.00 8.33
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Difference in Means ?11 - ?12 96.66 - 88.33
8.33 ?12 - ?22 88.33 - 80.00
8.33 parent B2B2 gt B1B2 gt B1B1
B1
B1
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Difference in Means ?11 - ?12 96.66 - 88.33
8.33 ?12 - ?22 88.33 - 80.00
8.33 parent B2B2 gt B1B2 gt B1B1
B1
B1
?22 ?12 ?11
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Difference in Means ?11 - ?12 96.66 - 88.33
8.33 ?12 - ?22 88.33 - 80.00
8.33 parent B2B2 gt B1B2 gt B1B1 8.3
8.3
B1
B1
?22 ?12 ?11
?
?
-- This implies value to the B1 allele. --
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For a single locus TA progeny mean minus
population mean
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For a single locus TA progeny mean minus
population mean Genotype ETA BV 2
ETA B1B1 ?11 - ? 96.66 - 91.11
5.55 11.10 B1B2 ?12 - ? 88.33 - 91.11
-3.78 -5.56 B2B2 ?12 - ?
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For a single locus TA progeny mean minus
population mean Genotype ETA BV 2
ETA B1B1 ?11 - ? 96.66 - 91.11
5.55 11.10 B1B2 ?12 - ? 88.33 - 91.11
-3.78 -5.56 B2B2 ?12 - ?
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For a single locus TA progeny mean minus
population mean Genotype ETA BV 2
ETA B1B1 ?11 - ? 96.66 - 91.11
5.55 11.10 B1B2 ?12 - ? 88.33 - 91.11
-2.78 -5.56 B2B2 ?12 - ?
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For a single locus TA progeny mean minus
population mean Genotype ETA BV 2
ETA B1B1 ?11 - ? 96.66 - 91.11
5.55 11.10 B1B2 ?12 - ? 88.33 - 91.11
-2.78 -5.56 B2B2 ?12 - ? 80.00 - 91.11
-11.11 -22.22
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For a single locus TA progeny mean minus
population mean Genotype ETA BV 2
ETA B1B1 ?11 - ? 96.66 - 91.11
5.55 11.10 B1B2 ?12 - ? 16.66 88.33 -
91.11 -2.78 -5.56 B2B2 ?12 - ?
16.66 80.00 - 91.11 -11.11 -22.22
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More Formulas
? average effect of a gene substitution
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More Formulas
? average effect of a gene substitution V11
V12 (q - p) 16.66
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More Formulas
? average effect of a gene substitution V11
V12 (q - p) 16.66 -- the difference in BVs
of individuals who differ in genotype by one
B1 allele
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More Formulas
? average effect of a gene substitution V11
V12 (q - p) 16.66 -- the difference in BVs
of individuals who differ in genotype by one
B1 allele
BV11 2 q ? BV12 (q- p) ? BV22 -2 p ?
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Phenotype
Represent BVs
Represent Ps
A2A2
A1A2
A1A1
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Basic Model Pij mgt Vij
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Basic Model Pij mgt Vij Pij mgt Vij
(AGV - AGV)
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Basic Model Pij mgt Vij Pij mgt Vij
(AGV - AGV) (mgt AGV) (Vij - AGV)

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Basic Model Pij mgt Vij Pij mgt Vij
(AGV - AGV) (mgt AGV) (Vij - AGV)
? (Vij - AGV)
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Basic Model Pij mgt Vij Pij mgt Vij
(AGV - AGV) (mgt AGV) (Vij - AGV)
? (Vij - AGV) Vij - AGV BVij Dij (Dij
value of combination)
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Basic Model Pij mgt Vij Pij mgt Vij
(AGV - AGV) (mgt AGV) (Vij - AGV)
? (Vij - AGV) Vij - AGV BVij Dij Pij
? BVij Dij (for a single locus)
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Phenotype
Represent BVs
Represent Ps
A2A2
A1A2
A1A1
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Basic Model, Single Locus
Estimating Dominance effect for an animal Dij
Pij - ? - BVij
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Basic Model, Single Locus
Own performance Pij ? BVij Dij
Progenys performance Pij ? BVij Dij
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Have a good break!