Animal Breeding 4

QUANTITATIVE GENETICS
…study of heredity of traits that could be measured
Industry Problems
• How do we analyze and use performance records?
• Which animal is “genetically” the best?
• What is the incidence of inbreeding in our stock farm?
• Which is the “best” breed?
• Can I develop my own breed?

Quantitative Genetics…
Describing a quantitative phenotype:
P = G + E + (GxE) = (A + D + I) + E + (GxE)
…Additive genetic effects are transmitted to the

progeny
Such that, SELECTION of parents with high additive
genetic effects, will result in progenies with higher
performance.
…Dominance and Epistatic effects are not

transmitted to the progeny.
Such that, parents with high D or I do not tend
to have progenies with higher D or I. BUT, this
is important when deciding a BREEDING SYSTEM.
ANIMAL BREEDING: SELECTION
How do we determine which animals are “genetically”
the best? How does “genetic improvement” happen?
P= G + E + (GxE)
The genetic component should be isolated from the

environmental effects!
Non-genetic variables can overshadow G which

can lead to the selection of parents that are not
genetically superior
Remember: Environmental effects are also NOT

PASSED on to the progenies.
BREEDING SYSTEMS
• Selection with random mating
• Inbreeding
• Crossbreeding
Animal Breeding: SELECTION
Animal Performance Records

…adjust for non-genetic factors (age, parity of dam, etc)
…know what records to use!
Individual’s Record
Used when:
* Heritability is high!
Family Records
Sire, dam, sibs Progeny Records
Used when: Offspring’s records
* Heritability is low
* Sex limited trait Used if progeny
testing is done
Selection
…superior animals are preferred/selected for
the production of the next generation.
There must be a mechanism in place that will

permit the ranking of the tested animals
from best to worst within a contemporary group.
? ? ? ? ?
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Physical Basis for Selection
• Qualitative or “visual traits” are

evaluated.
• Positive visual traits are often

associated with favorable
performance results.
• Visual appraisal is not recommended

for traits which can be measured.
Selection based on Performance Records
• adjusting for known environmental effects

• standardize records to 30-day to have a fair
comparison!
Pig No. Age Weaning Wt.

(days) (kg)
1 30 10
2 28 7.5
3 35 12
30 day adjusted wwt = actual weight * 30

actual age
Deviations and Ratios

Boar A ADG = 2 kg/day
Ave of Contemporaries ADG = 1.5 kg/day
Deviation +0.5 kg/day
Ratio (2/1.5)*100 = 133
Interpretation: Boar A gained 0.5 kg/day MORE

or 33% FASTER than his
contemporaries
Selection based on Breeding Value
• Breeding value = genetic merit of an animal
• Selected animals transmit half of their genes

or half of their breeding value, to each offspring.
(Part of the genotypic value that is “transmittable”.)
• Superior parents will most likely produce superior

offsprings!
Estimated Breeding Value (EBV)

Expected Progeny Difference (EPDs)
EPD is a prediction of how progenies of an individual are

expected to perform relative to the group or population
average.
EPDs can be positive or negative.
Positive EPD is desired for “positive traits”, and negative

EPD is desired for “negative traits”.
Selection based on Breeding Value…
Many catalogues will showcase the superiority of their

animals via Expected Progeny Difference (EPDs).
EPD is a prediction of how progenies of an individual are

expected to perform relative to the group or population
average.
EPDs can be positive or negative.
Positive EPD is desired for “positive traits”, and negative

EPD is desired for “negative traits”.
3 Types of Selection :
1. Tandem Method
2. Independent Culling Level
3. Selection Index
Tandem Method
 One trait at a time
Trait
Trait
X2 Trait X3
X1
Improve Trait X1 first. Proceed to

Trait X2 while relaxing selection
for Trait X1; Proceed to Trait X3
while relaxing selection for Traits
X1 and X2.
INDEPENDENT CULLING
LEVEL
 Ex. You want to increase egg number

but want to maintain certain body
weight at sexual maturity
 Your predetermined level could be as
follows: egg number ≥280 eggs per
cycle; body weight at sexual maturity
≤ 1.3 kg
SELECTION INDEX
 Involves the separate determination of

the value for each of the traits selected
for, and the addition of these values to
give a total score for all traits
 More efficient than ICL and TM
 get a total score per animal before
ranking
Selection Index Method
1. Estimate adjustment factors for the known

environmental effects.
2. Adjust the phenotypic records and express

them as deviations.
3. Set up selection index equations, and solve for

b (weighting factors).
EXAMPLE OF SELECTION
INDEX FORMULA
 Swine  Beef cattle
 I = 250+110ADG-  I = 0.58W + 18.64R -
50FCR-19.5BFT 0.73F -5.87E
 ADG – ave. daily  W – weaning wt
gain  R – rate o gain
 FCR – feed  F – no. of days to
conversion ratio reach a low-choice
 BFT – backfat slaughter grade
thickness  E – amount of
feed/gain
Visible Effect of Selection: CHANGE in MEAN

Gen 2
Genetic Improvement
Genetic Lift
Genetic change
Gen 1 Response to Selection
Mathematically,
R = h2 Sd Where h2 is the heritability
Sd is the selection differential
Sd = Ps - P Ps is the average of the selected
parents
P is the average for their
population
In a swine herd, 100 growing pigs had an ADG of

0.60kg/day. Selection was applied, and only the top
25 fastest growing boars and gilts were selected.
The selected parents averaged 0.85 kg.
Heritability for ADG is 0.30.
What is the expected response due to selection?
R = h2Sd
= 0.30 (0.85-0.60)
= 0.075 kg/day
New herd average after one generation of selection:

0.60 + 0.075 = 0.675 kg/day
Which is the “best” animal?
SELECTION – is a process where SOME

individuals are chosen to be
parents of the next generation.
CULLING
• voluntary selection, individuals are
selected on the basis of production &
reproduction
• Non-voluntary selection – culling animals
that are abnormal reproductively
• Does not create new genes
AIM : to increase f (desirable genes)
to decrease f ( undesirable genes)
CULLING….
FORMS : on the basis of phenotype
- on the basis of BREEDING VALUE,
transmitted from parent to offspring
BASIC EFFECT : change the array of gene
frequencies (although most completely
hidden)
- Can be observed thru change in gene
frequencies
Bases for selection
Molecular
DNA markers
EBVs Actual genetic merit
of the animal
Performance
Reproduction and Production
Physical performance records
Reproductive and
skeletal soundness
BASIC EFFECT OF
SELECTION
• Change the array of gene frequencies
• Can be observed by changes in the MEAN
How to describe change?

Compare successive generations at the
same point in the life cycle of the individual
Genetic change/progress as response to
selection
Approach to GIP
The selection
system
Selection is a process
where certain individuals
contribute more progeny
to the next generation
than other individuals in
the population.
 Natural vs Artificial Effectiveness of selection depends on
selection how much genetic variability the breeding
 Different populations population carries
characterized by wide
degree of variability
Organizing a National GIP: Key to 27
Sustainable Livestock Sector
Approach to GIP
Effective population
size
• The larger the population

size the more is the
opportunity for obtaining
more of the superior
individuals to be selected as
parents.
• Effective population size is
defined by the number of the
males and females in the
population as
Ne = (4NmNf)/(Nm + Nf)
For a herd of 500 males and
500 females, Ne = 1000 Selection differential
For a population of 5 males
and 995 females, Ne = 20
Organizing a National GIP: Key to 28

Sustainable Livestock Sector
METHODS OF ARTIFICIAL
SELECTION
1. Individual selection or mass selection
2. Family selection
3. Within family selection
4. Combinations of 1, 2 and 3
INDIVIDUAL SELECTION
• Based on individual’s own performance
record or phenotype
• Higher the h2,higher potential for
improving genetic quality of the selected
individuals
FAMILY SELECTION
• Based on family’s average performance as
s deviation from population mean
• Useful when h2 is low, sex limited and
carcass traits
• Environmental variance and family >
genetic variance and family members
resemble one another because of their
genetic relationship
RECOMMENDATIONS
1. Reduce environmental variance by
improving farming and husbandry
practices BEFORE initiating selection
breeding programs
2. Save all members of families for breeding
purposes although some members have
relatively poor phenotypes
Variations: family selection
sib selection
selection by progeny test
Ancestors (pedigree) family tree
Collateral individual
relatives (sibs)
offspring(progeny)
-testing the progeny not
because you’re using them for future
breeding but testing the parents to be used
for future breeding
WITHIN FAMILY SELECTION
• Based on individual performance as a
deviation from family mean
• COMBINATIONS OF 1, 2, & 3
- Complicated but accurate predictions of
EBV’s
Eg. Best Linear Unbiased Prediction (BLUP)
Breeders catalogue
Sire proofs : EBV’s of sires
Cow indices : EBV of females
Selection based on Breeding Value…
TAKE OUT:
P = A + D + I + E + (GxE)
Phenotypic record
Selection
BLUP
Index
(Mixed models)
Method
Parameters to be considered
heritability
additive genetic relationships
correlations
Selection Index Method
1. Estimate adjustment factors for the known

environmental effects.
2. Adjust the phenotypic records and express

them as deviations.
3. Set up selection index equations, and solve for

b (weighting factors).
Multiple Trait Selection Index
SI = 240 + 110 (ADG, kg)-50 (FE) – 19.7 (BFT,cm)
NATIONAL SWINE PERFORMANCE TESTING PROGRAM

(16th Boar Auction)
Breed BFT ADG FE SI
Duroc 8 1.37 0.939 2.4 221

Duroc 23 1.07 0.770 2.72 168
Landrace 1.40 1.041 2.38 208

Landrace 1.43 0.813 2.70 166
Ranking via
Animal Performance Records Selection index
Best Linear Unbiased Prediction “BLUP”
FIXED effects GENETIC effects

PHENOTYPIC RECORD
HERD
ANIMAL effect
YEAR
SIRE effect
SEASON
MEAN
AGE
BLUP
1. Describe phenotypic records with a statistical

model, where the mean, genetic and
environmental effects are included.
2. Set up mixed model equations and solve for

genetic effects which are estimated
simultaneously with the fixed effects.
BLUP
Y = Xb +Za+e
(n x r) vector with estimates
incidence matrix for the additive g.e.
for fixed effects (n x s)
incidence matrix
vector with estimates for additive genetic effects.
for the fixed effects.
k1 235
^b 250
k2
a1
= -10.5 Worst animal
^a
a2 0 EBVs
a3 10.5
Best Animal
EPDs
Animal 1’s progenies will have 5.25 less

growth than the average of the herd.
Animal 3’s progenies will have 5.25 more growth
than the average of the herd.

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QUANTITATIVE GENETICS

…study of heredity of traits that could be measured

• How do we analyze and use performance records?

• Which animal is “genetically” the best?

• What is the incidence of inbreeding in our stock farm?

• Which is the “best” breed?

• Can I develop my own breed?

…Additive genetic effects are transmitted to the

…Dominance and Epistatic effects are not

The genetic component should be isolated from the

Non-genetic variables can overshadow G which

Remember: Environmental effects are also NOT

Animal Performance Records

There must be a mechanism in place that will

• Qualitative or “visual traits” are

• Positive visual traits are often

• Visual appraisal is not recommended

• adjusting for known environmental effects

Pig No. Age Weaning Wt.

30 day adjusted wwt = actual weight * 30

Deviations and Ratios

Interpretation: Boar A gained 0.5 kg/day MORE

• Breeding value = genetic merit of an animal

• Selected animals transmit half of their genes

• Superior parents will most likely produce superior

Estimated Breeding Value (EBV)

Expected Progeny Difference (EPDs)

EPD is a prediction of how progenies of an individual are

EPDs can be positive or negative.

Positive EPD is desired for “positive traits”, and negative

Many catalogues will showcase the superiority of their

EPD is a prediction of how progenies of an individual are

EPDs can be positive or negative.

Positive EPD is desired for “positive traits”, and negative

Improve Trait X1 first. Proceed to

 Ex. You want to increase egg number

 Involves the separate determination of

1. Estimate adjustment factors for the known

2. Adjust the phenotypic records and express

3. Set up selection index equations, and solve for

Visible Effect of Selection: CHANGE in MEAN

In a swine herd, 100 growing pigs had an ADG of

New herd average after one generation of selection:

SELECTION – is a process where SOME

How to describe change?

• The larger the population

Organizing a National GIP: Key to 28

1. Estimate adjustment factors for the known

2. Adjust the phenotypic records and express

3. Set up selection index equations, and solve for

NATIONAL SWINE PERFORMANCE TESTING PROGRAM

Breed BFT ADG FE SI

Duroc 8 1.37 0.939 2.4 221

Landrace 1.40 1.041 2.38 208

FIXED effects GENETIC effects

1. Describe phenotypic records with a statistical

2. Set up mixed model equations and solve for

Animal 1’s progenies will have 5.25 less

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