DNA DOUBLE HELIX ILLUSTRATION FROM WIKIPEDIA

Illustration of DNA
Double Helix from
Wikipedia.
PRINCIPLES OF ANIMAL GENETICS
ASM 391
Natural Resources Development College
Animal Science Department
By
E.Msimuko.

Illustration of DNA
Double Helix from
Wikipedia.
Introduction
• Genetics is the science of heredity and
variation
• It is the scientific discipline that deals with
the differences and similarities among
related individuals
• All animals have a predetermined genotype that
they inherit from their parents.
• However, an animal’s genotype can be
manipulated by breeding and more advanced
scientific techniques (genetic engineering and
cloning).

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• For many years, managers of agricultural
systems have manipulated the genetic makeup
of animals to:
• improve productivity,
• increase efficiency
• and adaptability.
• Successful manipulation of the genetic
composition of animals requires a depth
understanding of fundamental principles of
genetics.

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Mendelian Genetics
• Gregory Mendel is recognized
as the father of
genetics
• in the 1850’s and 1860’s, he
developed his theories
without any knowledge of cell
biology or the science of
inheritance- he failed his
teachers exams
• In later years, genes,
chromosomes, and DNA were
discovered and people began
to understand how and why
Mendel’s theories worked.
Photo courtesy of Wikipedia.

Illustration of DNA
Double Helix from
Wikipedia.
• Mendel proposed three principles to describe the
transfer of genetic material from one generation to
the next.
• The Principle of Dominance
• The Principle of Segregation
• The Principle of Independent Assortment
The Principle of Dominance – in a heterozygous
organism, one allele may conceal the presence of
another allele. Aa or Pp

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The Principle of Segregation – in a heterozygote, two
different alleles segregate from each other during the
formation of gametes. Aa individual will produce two
gametes- A-alleles and a-alleles
The Principle of Independent Assortment – the alleles
of different genes segregate, or assort, independently
of each other. PpBb x PpBb gives 9:3:3:1
Later studies have shown that there are some
important exceptions to Mendel’s Principle of
Independent Assortment, but otherwise, these
principles are recognized as the basis of inheritance.

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Knowledge of which allele has been inherited at one
locus gives no information on the allele has been
inherited at the other locus
P/p B/b
PB Pb pB pb
25% 25% 25% 25%

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• Mendel’s experiments dealt with the relationship
between an organism’s genotype and its phenotype.
• Genotype – the genetic composition of an organism.
• Phenotype – the observable or measurable
characteristics (called traits) of that organism
• Two organisms may appear to be similar, but they
can have different genotypes.
• Similarly, two animals may have the same
genotypes, but will appear to be different from each
other, if they have been exposed to different
environmental conditions throughout their lives.

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The relationship between phenotype and genotype is
expressed as the following equation:
P = G + E
P = phenotype – observed attributes (Yield, Quality)
G = genotype- A, D, E, and
E = environment- breed, Nut. A.H, Climate, housing and
research
If two individuals with identical genotypes are exposed to the
same environmental conditions, such as nutrition, climate, and
stress levels, their phenotypes (measurable and observable
characteristics) should be the same
“What you see is what you get”

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• To understand Mendel’s principles and the
relationships between phenotype and genotype, it
is necessary to understand;
• what makes up the genetic material of animals
and
• how this is transferred from one generation to
the next.

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Genetic Material
The body is made up of
millions of cells which
have a very complicated
structure.
These cells are made up
of many parts that have
specialized roles.
1. Nucleolus 5. Rough Endoplasmic Reticulum 9. Mitochondria
2. Nucleus 6. Golgi Apparatus 10. Vacuole
3. Ribosome 7. Cytoskeleton 11. Cytoplasm
4. Vesicle 8. Smooth Endoplasmic Reticulum 12. Lysosome
13. Centrioles

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The nucleus contains chromosomes that are visible
under the microscope as dark-staining, rod-like or
rounded bodies.
Chromosomes occur in pairs in the body cells.
The number of chromosomes in each cell is constant for
individual species, but it differs among species. Suis-38,
caprine-60, carnis 78, galus-78, bovine-60,

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Chromosomes are made up of tightly-coiled strands
of DNA.
DNA is a complex molecule composed of deoxyribose,
phosphoric acid, and four bases.
Individual genes are located in a fixed position
(known as the loci) on the strands of DNA.
A chromosome is made up of two chromatids and a
centromere. The chromatids are formed from tightly coiled
strands of DNA. If these strands of DNA are stretched out,
individual genes can be identified.eg DT

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A gene is made up of a specific functional sequence of nucleotides,
which code for specific proteins.
A specific protein is produced when the appropriate apparatus
of the cell (the ribosome) reads the code.
Image courtesy of Wikipedia.

Illustration of DNA
Double Helix from
Wikipedia.

Illustration of DNA
Double Helix from
Wikipedia.
• In somatic cells (body cells), chromosomes occur in
pairs, known as homologous chromosomes as a
result, genes also occur in pairs except in virus(RNA)
• Somatic cells are referred to as diploid, or 2n.
• Gametes (reproductive cells) are referred to as
haploid, or n - do not have paired chromosomes

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When discussing different generations in genetics, the
first generation is referred to as the parent or P
generation.
Their offspring are referred to as the first filial or F1
generation.
P X P = F1
When individuals from the F1generation are mated with
each other, their offspring are referred to as the F2
generation.
F1 X F1 =F2

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Principle of Dominance
• In animals, chromosomes are paired and, therefore,
genes are paired.
• These paired genes code for the same trait, but they
are not identical.
• They can have different forms, known as alleles.
• For example, sheep and cattle can be polled or horned.
• One gene codes for this trait and the two possible
forms (alleles) of the gene are polled or horned

Illustration of DNA
Double Helix from
Wikipedia.
Hereford Cattle
USDA photo from Wikipedia.
Photo from IMS.
A capital letter is used to denote the dominant form of the gene (P)
and a small letter is used to denote the recessive form of the gene
(p).
In the example, the polled allele is dominant and is, therefore,
denoted by P, while the horned allele is recessive and denoted by p.
Because genes are paired, an animal can have three different
combinations of the two alleles: PP, Pp, or pp.

Illustration of DNA
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• When both genes in a pair take the same form (PP or pp), the
animal is referred to as being homozygous for that trait.
• An animal with a PP genotype is referred to as homozygous
dominant.
• An animal with the pp genotype is referred to as homozygous
recessive.
If one gene in the pair is the dominant allele (P) and the other gene
is the recessive allele (p), the animal is referred to as being
heterozygous for that trait and its genotype is denoted as Pp.
• If an animal has the allele combination PP, it will be polled.
• If the combination is pp, the animal will be horned.
• If it is a heterozygote, the animal will have both traits (Pp), but
the animal will be polled because the polled allele (P) is the
dominant form of the gene. Mendel’s principle of dominance
states that in a heterozygote, one allele may conceal the presence
of another.

Illustration of DNA
Double Helix from
Wikipedia.
In this example, the polled allele is concealing the horned allele
and, therefore, is referred to as the dominant allele.

Illustration of DNA
Double Helix from
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Principle of Segregation
• When animals reproduce, they only pass on half of their genetic
material to their offspring
• The offspring will only receive one allele from each parent.
• The Principle of Segregation explains some of the differences that
are observed in successive generations of animals and can be used
to predict the probability of different combinations of alleles
occurring in offspring.

Illustration of DNA
Double Helix from
Wikipedia.
Considering these three types of individuals, six combinations of
the various genotypes are possible:
• PP x PP (both parents are homozygous polled),
• PP x Pp (one homozygous polled parent and one
heterozygous polled parent),
• PP x pp (one homozygous polled parent and one homozygous
horned parent),
• Pp x Pp (both parents are heterozygous polled),
• Pp x pp (one heterozygous polled parent and one homozygous
horned parent), and
• pp x pp (both parents are homozygous horned)

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The genotypes of the parents can be used to predict the
phenotypes of the offspring
Predicting the Genotypes and Phenotypes of Offspring by:
A punnett square - grid-like method that is used to display and
predict the genotypes and phenotypes of offspring from parents
with specific alleles.
The male genotype is normally indicated at the top and the
female genotype is indicated in the vertical margin.

Illustration of DNA
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When crossing homozygous dominant parents (PP x PP), all
offspring will be homozygous dominant polled individuals.
All polled

Illustration of DNA
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Wikipedia.
When crossing homozygous recessive parents (pp x pp), all of
the offspring will be horned (homozygous recessive)
individuals.

Illustration of DNA
Double Helix from
Wikipedia.
When crossing a heterozygous parent with a homozygous
dominant parent (Pp x PP), the expected offspring would occur in
a 1:1 ratio of homozygous dominant to heterozygous individuals.
Phenotypically, all offspring would be polled. When crossing a
homozygous dominant parent with a homozygous recessive
parent (PP x pp), all offspring would be heterozygous and polled.

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• If two heterozygous parents are crossed (Pp x Pp), one can
expect a genotypic ratio of 1:2:1, with one homozygous
dominant polled, two heterozygous polled, and one
homozygous recessive horned individuals.
• The expected phenotypic ratio of offspring would be 3:1 (polled
to horned).

Illustration of DNA
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. Segregation
Alleles separate during meiosis

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Considering Multiple Traits-Dihybrid Cross
Commonly, there are multiple traits that need to be considered
when mating animals.
For example, consider that cattle can be horned or polled and
white-faced or red-faced.
The horns and red-faced coloring are recessive traits.
If two individuals with two pairs of heterozygous genes (each
affecting a different trait) are mated, the expected genotypic and
phenotypic ratios would be:

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Genotypes – 1 PPWW, 2 PPWw, 2
PpWW, 4 PpWw, 1 PPww, 2 Ppww,
1 ppWW, 2 ppWw, and 1 ppww;
Phenotypes – 9 polled, white-faced; 3
polled, red-faced; 3 horned, white-
faced; and 1 horned, red-faced
offspring.

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The Law of Independent Assortment
• When considering multiple traits, Mendel hypothesized that
genes for different traits are separated and distributed to
gametes independently of one another.
• Therefore, when considering polled and white-faced traits,
Mendel assumed that there was no relationship between how
they were distributed to the next generation.
In most cases, genes do assort independently.
• However, advances in genetics have shown that an abnormal
situation, called crossing-over, can occur between genes for
different traits.
• Crossing-over is an exchange of genes by homologous
chromosomes during the synapses of meiosis prior to the
formation of the sex cells or gametes.

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10. Independent Assortment
Bb
diploid (2n)
B
b
meiosis I
B
B
b
b
sperm
haploid (n)
meiosis II
• Chromosomes separate independently of
eachother
Bb
Ff
b
F
B
f
b
f
B
F
Bb
Ff
Bb
Ff
This means all
gametes will be
different!

Illustration of DNA
Double Helix from
Wikipedia.
Other Concepts in Genetics
• Non-traditional inheritance involves alleles that are not dominant
or recessive.
• Incomplete, or partial dominance, & co-dominance are two
examples of non-traditional inheritance.
• Recent studies in sheep has indicated another form of
inheritance called POLAR DOMINANCE
• Partial, or incomplete, dominance occurs when the heterozygous
organism exhibits a trait in-between the dominant trait and the
recessive trait.
eg Homozygous mice are black (BB) or white (bb) and the
heterozygous mice will be grey (Bb).
When a pure, brown-eyed sheep is crossed with a pure, green-eyed
sheep, blue-eyed offspring are produced.

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Codominance
• Codominance occurs when a heterozygote offspring exhibits
traits found in both associated homozygous individuals.
• An example of codominance is the feather color of chickens.
• If a homozygous black rooster is mated to a homozygous
white hen, the heterozygous offspring would have both
black feathers and white feathers
• Roan is a coat color in horses (sometimes dogs and cattle)
that is a mixture of base coat colored hairs (ex. black,
chestnut) and white hairs. Neither the base coat color or
the white hairs are dominant nor do they blend to create
an intermediate color.

Illustration of DNA
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The roan animal actually has both
colored and white hairs.
Photo courtesy of Wikipedia.
• Under these circumstances, neither allele is dominant and
neither is recessive.
• Therefore, each allele is denoted by a capital letter.

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EPISTASIS
It is possible for more than one gene to control a single trait
This type of interaction between two nonallelic genes is
referred to as epistasis.
When two or more genes influence a trait, an allele of one of
them may have an epistatic, or overriding, effect on the
phenotype.
Comb shape in chickens is an example of an epistatic
relationship.

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Mutations and Other Chromosomal
Abnormalities
Genes have the capability of duplicating themselves, but
sometimes a mistake is made in the duplication process
resulting in a mutation.
The new gene created by this mutation will cause a change
in the code sent by the gene to the protein formation
process.
Some mutations cause defects in animals, while others may
be beneficial.
Mutations are responsible for variations in coat color, size,
shape, behavior, and other traits in several species of
animals.
The beneficial mutations are helpful to breeders trying to
improve domestic animals.

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Changes in chromosomes are reflected in the phenotypes of
animals.
Some chromosomal changes will result in abnormalities, while
others are lethal and result in the death of an animal shortly after
fertilization, during prenatal development, or even after birth.
Changes that can occur in chromosomes during meiosis include:
• Changes in the chromosome number,
• Translocation or deletion – chromosome breakage, and
• Inversion and insertion – the rearrangement of genes on a
chromosome.

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Sex-Linked Traits
• Sex-linked traits involve genes that are carried only on the
X or Y chromosomes, which are involved in determining the
sex of animals.
• The female genotype is XX, while the male genotype is XY.
• The X chromosome is larger and longer than the Y
chromosome, which means a portion of the X chromosome
does not pair with genes on the Y chromosome
• Additionally, a certain portion of the Y chromosome does
not link with the X chromosome.
• The traits on this portion of the Y chromosome are
transmitted only from fathers to sons.
• Sex-linked traits are often recessive and are covered up in
the female mammal by dominant genes.

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• The expression of certain genes, which are carried on the
regular body chromosomes of animals, is also affected by the
sex of the animal.
• The sex of an animal may determine whether a gene is
dominant or recessive (Ex. Scurs in polled European cattle).
• In poultry, the male has the genotype XX, while the female
has the genotype Xw.
• An example of a sex-linked trait in poultry is the barring of
Barred Plymouth Rock chickens. If barred hens are mated to
non-barred males, all of the barred chicks from this cross are
males, and the non-barred chicks are females.

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Sex limited traits

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GENETIC OF ANIMAL BREEDING
GENETIC SELECTION
What is the “BEST” Animal?
• Permanent improvements in domestic
animals can be made by genetic
selection through natural or artificial
means.
• Natural selection occurs in wild
animals, while artificial selection is
planned and controlled by humans.

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Animals that exhibit desirable traits are
selected and mated.
Animals that exhibit undesirable traits are
not allowed to reproduce or are culled
from the herd.
Trait- measurable attributes of an individual
presence of horns; Calving easy; Growth; litter
size
Phenotype- measurable category/level for a trait in an
individua
Horned, polled, assisted, not assisted; WWT,
5,8,1

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• The goal of selection is to increase the
number of animals with optimal levels of
performance, while culling individuals
with poorer performance.
• Genetic improvement is a slow process
• Artificial insemination and embryo
transfer are breeding methods that are
commonly used to decrease the time
taken to improve a trait.
• Animals with a best set of genes may
have the best Breeding value

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• Traits are passed from parents to
offspring, but some traits are more
heritable than other traits
• Heritability is a measure of the
strength of the relationship between
BV and phenotype values for a trait
in a population
• That is, the genotype of an
individual will be expressed more
strongly and environment will be less
influential for particular traits

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Trait Sheep Swine Cattle
Weaning weight 15-25% 15-20% 15-27%
Post-weaning gain
efficiency
20-30% 20-30% 40-50%
Post-weaning rate of gain 50-60% 25-30% 50-55%
Feed efficiency 50% 12% 44%
Fertility 1.0%
Heritability of Various Traits in Livestock
High h2 Phenotypes are good indicators
Low h2 Phenotypes reveals little about BVs

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Quantitative and Qualitative Traits
Quantitative traits
• Controlled large number of genes,
• Economical traits
• Exhibit normal distribution and phenotypes
show continuous express- additive gene
effect
• Affect genes with large effect
Qualitative Traits
• Controlled by dominant or recessive genes,
• Non additive gene and non- continuous
• Single gene

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Quantitative genetics

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Measuring Heritable Variation
• The value of quantitative traits such a mohair
length or size or in dogs-running speed is
determined by their genes operating within
their environment.
• The size of how a spp grows is affected not
only by the genes inherited from their parents,
but the conditions under which they grow up.

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• For a given individual the value of its phenotype
(P) (e.g. the weight of a broiler in grams) can be
considered to consist of two parts -- the part due
to genotype (G) and the part due to environment
(E)
• P = G + E.
• G is the expected value of P for individuals with
that genotype. Any difference between P and G is
attributed to environmental effects.

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• The quantitative genetics approach depends on
taking a population view and tracking variation in
phenotype and whether this variation has a
genetic basis.
• We measure variation in a sample using a
statistical measure called the variance. The
variance measures how different individuals are
from the mean and the spread of the data.
• FYI: Variance is the average squared deviation
from the mean. Standard deviation is the square
root of the variance.

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CHARACTERIZING A NORMAL DISTRIBUTION
Mean and variance are two quantities that describe a normal
distribution.
MEAN
VARIANCE

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USEFUL PARAMETERS FOR QUANTITATIVE GENETICS
 Mean: The sum of all measurements divided by the
number of measurements


 i
n
x
NN
xxx
x
1...21
 Variance: The average squared deviation of the
observations from the mean
       2
22
2
2
1 1
 

 xx
NN
xxxxxx
Variance i
n

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CORRELATIONS AMONG CHARACTERS OR RELATIVES
0 + —
Covariance:
    yyxx
N
yxCov ji  
1
,

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What is heritability?

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What is heritability?
• heritability is the proportion of the total phenotypic
variation controlled by genetic rather than
environmental factors.

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The total phenotypic variance may be decomposed:
VP = total phenotypic variance

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VG = total genetic variance

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VE = environmental variance

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VP = VG + VE

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heritability = VG/VP (broad-sense)

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The total genetic variance (VG) may be
decomposed:

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decomposed:
VA = additive genetic variance

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decomposed:
VD = dominance genetic variance

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decomposed:
VI = epistatic (interactive) genetic variance

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decomposed:
VG = VA + VD + VI

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decomposed:
heritability = h2 = VA/VP (narrow sense)

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Estimating heritability

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HERITABILITY
 The heritability (h2) of a trait is a measure of the degree
of resemblance between relatives.
h2 =
additive genetic variance (VA)/ phenotypic variance (VP)
Heritability ranges from 0 to 1
(Traits with no genetic variation have a heritability of 0)

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HERITABILITY
h2 = VA / VP = VA / (VG + VE)
 Since heritability is a function of the environment (VE),
it is a context dependent measure.
It is influenced by both,
 The environment that organisms are raised in, and
 The environment that they are measured in.

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ESTIMATING HERITABILITY FROM REGRESSION
slope = b
= Cov (x,y)/Var (x)
Method of estimation COV(x,y) h2 Slope (b)
Offspring-Single parent ½ VA 2b b = ½ h2
Half-sib ¼ VA 4b b = ¼ h2
Offspring-Grandparent ¼ VA 4b b = ¼ h2
Offspring-Midparent - b b = h2

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HERITABILITY OF BEAK DEPTH IN DARWINS’ FINCHES

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Wikipedia. IN: Falconer & Mackay. Introduction to Quantitative Genetics.1996. Longman.
HERITABILITIES FOR SOME TRAITS IN ANIMAL SPECIES
h2 (%)

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• one common approach is to compare phenotypic
scores of parents and their offspring:

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Junco tarsus length (cm)
Cross Midparent value Offspring value

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F1 x M1 4.34 4.73

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F1 x M1 4.34 4.73
F2 x M2 5.56 5.31

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F1 x M1 4.34 4.73
F2 x M2 5.56 5.31
F3 x M3 3.88 4.02

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 Slope = h2
Regress offspring value on midparent value

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Heritability estimates from other
regression analyses
Comparison Slope

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regression analyses
Comparison Slope
Midparent-offspring h2

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regression analyses
Comparison Slope
Parent-offspring 1/2h2

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regression analyses
Comparison Slope
Half-sibs 1/4h2

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regression analyses
Comparison Slope
Half-sibs 1/4h2
First cousins 1/8h2

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regression analyses
Comparison Slope
Half-sibs 1/4h2
First cousins 1/8h2
• as the groups become less related, the
precision of the h2 estimate is reduced.

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Role of reproduction in genetic
improvement
DGy = SD *
h2
GI
where
DGy= rate of genetic
progress per year (diff.
bwn.av.peformance of
superior parents selected
to parent the next
generation and the herd
improvement

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SOW 1ST
LITER
2ND
LITER
1(4) 6 4 0 -2 0 0
2 (2) 4 3 -2 -3 4 6
3 (6) 8 12 2 6 4 12
4 (5) 7 8 1 2 1 2
5 (3) 5 3 -1 -3 1 3
Σ 30 30 0 0 10 23
Mean
(4)
6 6
h2 = 2* 23/10 = 4.6

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Heritabilities vary between 0 and 1

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Cross-fostering is a common approach
Heritability of beak size in song sparrows

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Q: Why is knowing heritability important?

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A: Because it allows us to predict a trait’s
response to selection

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Let S = selection differential

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Let h2 = heritability

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Let R = response to selection

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Let R = response to selection
R = h2S

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THE UNIVARIATE BREEDERS’ EQUATION:
R = h2
S
Response to Selection Selection differential
Heritability
Where:
P
A2
V
V
h 
(Additive Genetic Variance)
(Phenotypic Variance)

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This is why it’s called
“regression”:
offspring “regress”
toward the mean!
S is the Selection
Differential

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Wikipedia.
S
RESPONSE TO SELECTION WHEN h2 = 1/3
 The selection differential
(S) = mean of selected
individuals – mean of the
base population
 The response to
selection:
R = h2S
S

Illustration of DNA
Double Helix from
Wikipedia.
VISUALIZING THE SELECTION DIFFERENTIAL

Illustration of DNA
Double Helix from
Wikipedia.
RESPONSE TO SELECTION
 For a given intensity of
selection, the response to
selection is determined by
the heritability.
High heritability
Low heritability

Illustration of DNA
Double Helix from
Wikipedia.
R = h2
S
ESTIMATING h2 USING THE BREEDER’S EQUATION
 
 PP
OO
S
R
hSlope


 *
*
2

Illustration of DNA
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Wikipedia.
Predicting the response to selection
Example: the large ground
finch, Geospiza magnirostris

Illustration of DNA
Double Helix from
Wikipedia.
Mean beak depth of survivors = 10.11 mm

Illustration of DNA
Double Helix from
Wikipedia.
Mean beak depth of initial pop = 8.82 mm

Illustration of DNA
Double Helix from
Wikipedia.
S = 10.11 – 8.82 = 1.29

Illustration of DNA
Double Helix from
Wikipedia.
S = 10.11 – 8.82 = 1.29
h2 = 0.72

Illustration of DNA
Double Helix from
Wikipedia.
S = 10.11 – 8.82 = 1.29
h2 = 0.72
R = h2S = (1.29)(0.72) = 0.93

Illustration of DNA
Double Helix from
Wikipedia.
S = 10.11 – 8.82 = 1.29
h2 = 0.72
R = h2S = (1.29)(0.72) = 0.93
Beak depth next generation = 10.11 + 0.93 = 11.04 mm

Illustration of DNA
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Wikipedia.
RESEMBLANCE BETWEEN RELATIVES
 When there is genetic variation
for a character there will be a
resemblance between relatives.
 Relatives will have more similar
trait values to each other than
to unrelated individuals.

Illustration of DNA
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Wikipedia.
offspring offspring
parents
offspring
h2 ≈ 0 h2 ≈ ½ h2 ≈ 1
h2 is the regression (slope) of offspring on parents
parents parents
Definition of the regression
coefficient (slope):
byx = cov(x,y)/var(x)

Illustration of DNA
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Wikipedia.
• Here x is the midparent value
(parental mean), y is the offspring
• The higher the slope, the better
offspring resemble their parents.
• In other words, the higher the
heritability, the better offspring trait
values are predicted by parental trait
values.

Illustration of DNA
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Wikipedia.
Evolutionary response to selection
• We want to be able to measure the effect of
selection on a population.
• This is called the Response to Selection and is
defined as the difference between the mean
trait value for the offspring generation and the
mean trait value for the parental generation i.e.
the change in trait value from one generation
to the next.

Illustration of DNA
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Wikipedia.
ARTIFICIAL SELECTION IN DOMESTIC ANIMALS
 Grey Jungle fowl

Illustration of DNA
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Wikipedia.
RESEMBLANCE BETWEEN RELATIVES DEPENDS
ON THE DEGREE OF RELATIONSHIP
Monozygotic twins
Full sibs
Parent-offspring
Half sibs
Slope of a plot of two variables (x,y) = Cov (x,y) / Var (x)
x
y

Illustration of DNA
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Wikipedia.
DEGREE OF RELATEDNESS AND THE COMPONENTS
OF PHENOTYPIC COVARIANCE
VEs = variance due to shared environment
Relationship Phenotypic covariance
Monozygotic twins: VA + VD + VEs
Parent-offspring ½ VA
Full sibs (½ VA) +(¼ VD) +VEs
Half sibs, or
Grandparent – grandchild ¼ VA

Illustration of DNA
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Wikipedia.
Modes of selection on quantitative traits

Illustration of DNA
Double Helix from
Wikipedia.
Response to Directional Selection:

Illustration of DNA
Double Helix from
Wikipedia.
FACTORS AFFECTING GENETIC
CHANGE AND PROGRESS
• Selection intensity- measures how choosy
breeders are deciding which animal to
selected
• Selection differential- variability of BVs
within a population for a trait under selection
• Generation interval- total time required to
replace one generation with the nesxt
• Accuracy of selection- measure of strength of
relationship between BV and their
predictions for a trait under question.

Illustration of DNA
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Wikipedia.
• Breeding systems aim to improve a single
trait or multiple traits.
• Single trait selection – aimed at improving
one trait in a breeding program with little or
no regard for improvement in other
(associated) traits. Determine some
economic value of a trait.
• Multiple trait selection – aims to
simultaneously improve a number of traits.
• Theoretically, multiple trait selection should
result in a faster rate of gain toward a
specific objective.

Illustration of DNA
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Wikipedia.
• Most domestic species now have a recognized
system in place that allows breeders to estimate
the genetic merit of individuals.
• In the most cattle, sheep, goat, and swine breeders
use expected progeny differences (EPDs).
• EPDs are used to compare animals from the same
species and breed.
• For EPD values to be used effectively, one needs to
know the breed averages, the accuracy of the
EPDs, and who estimated the EPDs.
• A high EPD is not necessarily good; it depends on
the trait being considered and breeding
objectives.

Illustration of DNA
Double Helix from
Wikipedia.
Dolly the Sheep
(the first mammal
cloned from adult
cells) and many
other species
have been cloned
this way.
Worldwide, the institute that has cloned the
most species is Texas A&M University, College
of Veterinary Medicine, which to date has
cloned cattle, swine, a goat, a horse, deer, and
a cat.

Illustration of DNA
Double Helix from
Wikipedia.
The possibility for selecting
desired traits at the cellular
level holds exciting implications
for the genetic improvement of
domestic animals.

Illustration of DNA
Double Helix from
Wikipedia.
Summary
• Post-genomic genetics has enormous promise
for tracking down the genes involved in
common complex diseases
• Currently our ability to exploit this potential is
limited by
– study size
– difficulty of correcting for confounding factors

Illustration of DNA
Double Helix from
Wikipedia.
Methods of Selection
• Individual and family
• Half sibs- usually sire families which are the
offspring of same bull but with different
mothers
• Full-sibs- animals sharing both parents eg
piglets
• Individual selection- on the basis of their own
performance (mass selection)

Illustration of DNA
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Wikipedia.
• Simplest method
Also called performance testing
Takes into account of all individual additive
genetic variation that exist in the population
• Family selection- based on the average value
for the family and makes no separate of
individuals
• Advantages:
i. Traits with low heritability
ii. Accounts for environmental variation
iii. Good when the family size is large
However, it tend to increase the rate of inbreeding

Illustration of DNA
Double Helix from
Wikipedia.
• Within family selection-choosing the best
individuals from each family
• Progeny testing:
• Parents/ pedigree
• Computer/ breedplan

Illustration of DNA
Double Helix from
Wikipedia.
Several genes
influence some
traits.
For example,
rate of growth
is a trait that is
influenced by
appetite,
energy expenditure,
feed efficiency, and
body composition.
Photo by Brian Prechtel courtesy of USDA Agricultural Research Service.

Illustration of DNA
Double Helix from
Wikipedia.
• Reproduction plays a major role in the
genetic improvement of farm animals
through the application of artificial
insemination (AI) and multiple ovulation
& embryo transfer (MOET). These help to
increase selection differentials on the male
and female sides respectively, leading to
significant increase in the rate of genetic
progress per year, as apparent from the
equation below:
improvement

Illustration of DNA
Double Helix from
Wikipedia.
DGy = SD * h2
GI
where
DGy= rate of genetic progress per
year (diff. bwn.av.peformance of superior
parents selected to parent the next
generation and the herd average)
SD = selection differential
h2 = heritability estimate, and
GI = generation interval in years.
improvement

Illustration of DNA
Double Helix from
Wikipedia.
improvement

Illustration of DNA
Double Helix from
Wikipedia.
FACTORS THAT AFFECT GENETIC
PROPERTIES OF A POPULATION
• Hardy-Weinberg Law:
• Population size
• Fertility and viability
• Mutation
• Immigration/migration
• Mating system
• selection

Illustration of DNA
Double Helix from
Wikipedia.
Modern Genetics
• In recent years, traditional methods of
improvement through selection and breeding
have been superseded by genetic
manipulation.
• A substantial amount of research has focused
on direct manipulation of genes and DNA.
• transferring a gene from one individual to
another
• This area of genetic manipulation makes important contributions
to domesticated animals in relation to immunology, vaccines,
aging, and cancer.eg bioengineered to have a gene for
mastitis resistance

Illustration of DNA
Double Helix from
Wikipedia.
The implications for introducing superior
production, conformation, and disease-
resistant traits into domestic animals through
gene transfer hold considerable promise in
the genetic improvement of animals.
Cloning
Embryonic cloning of animals involves the
chemical or surgical splitting of developing
embryos shortly after fertilization and,
consequently, developing two identical
individuals.
It has been performed successfully in several species of animals

Illustration of DNA
Double Helix from
Wikipedia.
Animal Breeding Systems
UNIT 4

Illustration of DNA
Double Helix from
Wikipedia.
• Name and explain common breeding systems
used in livestock production
• Explain the effects, advantages and
disadvantages of using various breeding
systems
• Indentify the factors involved in selecting a
breeding system
• Calculate the percentage of parental stock in
offspring using various breeding systems
Objectives

Illustration of DNA
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Wikipedia.
• Breed for environment- to increase
performance
• Increase animal yield
• Improve animal products
• Develop methods of disease control
• Extend range of animal products
• Conservation of genetic resources
• Develop new animals
• Scientific
• Ornaments, sports, and show purpose
Roles of animal breeding

Illustration of DNA
Double Helix from
Wikipedia.
• 2 basic Breeding systems
– Straight breeding
• Mating animals of the same breed
purebred, inbreeding, outcrossing, grading up
– Cross breeding
• Mating animals of different breeds
two-breed cross, three-breed cross, rotation
Systems of Breeding

Illustration of DNA
Double Helix from
Wikipedia.
• An animal of a particular breed
• Both parents are purebred
Purebred Breeding

Illustration of DNA
Double Helix from
Wikipedia.
Characteristics of the breed
1. Eligible for registry in breed
association
2. Tend to be genetically homozygous
3. Specialized business

Illustration of DNA
Double Helix from
Wikipedia.
• Mating related animals
• Linebreeding and Closebreeding refer to how
closely related the animals are
• Requires a careful program of selection and
culling
• Expensive
• Used most often by Universities for
experimental work and Seedstock producers
that provide animals for crossbreeding herds
Inbreeding

Illustration of DNA
Double Helix from
Wikipedia.
• Animals are very closely related and can
be traced back to more than 1 common
ancestor
• Examples:
– Sire to daughter
– Son to dam
– Brother to sister

Illustration of DNA
Double Helix from
Wikipedia.
1st Mating
• A (Male) X B (Female)
F1
• ½ A ½ B
2nd Mating
• A
• 1/2A 1/2B
F2
• 3/4A 1/4B
Example

Illustration of DNA
Double Helix from
Wikipedia.
• Mating animals that are more distantly related
• Can be traced back to 1 common ancestor
• Examples
– Cousins
– Grandparents to grand offspring
– Half-brother to half-sister
• Increases genetic purity
• Several generations results in desirable and
undesirable genes to become grouped together
with greater frequency—making culling easier
Linebreeding

Illustration of DNA
Double Helix from
Wikipedia.
1st
Mating
• A x B
• A x C
F1
• ½ A ½ B
• ½ A ½ C
2nd
Mating
• 1/2A1/2 B x 1/2A/2C
F2
• ½ A ¼ B ¼ C
Example

Illustration of DNA
Double Helix from
Wikipedia.
• Mating animals from two different lines of
breeding within a breed
• Purpose is to bring together desirable traits
from different lines
• Experience is the best guide to use when
line crossing
Linecrossing

Illustration of DNA
Double Helix from
Wikipedia.
• Mating of animals of different families within the
same breed
• Animals are not closely related
• Purpose is to bring into the breeding program traits
that are desirable but not present in the original
animals
• Used most by purebred breeders
• Popular because it reduces the chances of
undeniable traits are still present
• Sometimes used in inbreeding programs to bring in
needed traits
Outcrossing

Illustration of DNA
Double Helix from
Wikipedia.
• Mating purebred males to grade females
• Good way to improve quality
• Less expensive
• Use of purebred sires long enough will
eventually lead to the amount of grade
breeding left in the offspring being less
than 1%
Grading Up

Illustration of DNA
Double Helix from
Wikipedia.
1st Mating
• A1 x G
F1
• 1/2A:1/2G
• 50% Pure 50% Grade
2nd Mating
• A2 x ½ A1 ½ G
F2
• ½ A2 ¼ A1 ¼ G
• 75% Purebred 25% Grade
3rd Mating
• A3 x ½ A2 ¼ A1 ¼ G
F3
• ½A3 ¼A2 1/8A1 1/8G
• 87.5% Purebred, 12.5% Grade
Example

Illustration of DNA
Double Helix from
Wikipedia.
• Mating two animals of different breeds
• Offspring is a Hybrid
• Usually results in improved traits because
dominant genes mask undesirable
recessive genes
• Superior traits that MAY result from
crossbreeding are called heterosis
Crossbreeding (X)

Illustration of DNA
Double Helix from
Wikipedia.
• Good record keeping is essential
• Calving difficulties may increase when crossing
large breed sires with small breed dams
• Fewer calving problems if large breed dams are
used
• Large breed dams have higher maintenance costs
• Artificial insemination allows access to better
bulls
• To avoid inbreeding more than 1 breeding pasture
may be required
General Considerations Regarding
Beef Crossbreeding Systems

Illustration of DNA
Double Helix from
Wikipedia.
• Terminal Sire Crossed with F1 Females
• Rotate Herd Bull every 3-4 years
• Two Breed Rotation
• Three Breed Rotation
• Four and Five Breed Rotation
• Static Terminal Sire
• Rotational Terminal Sire
• Composite Systems
Beef Crossbreeding Systems

Illustration of DNA
Double Helix from
Wikipedia.
• Replacement crossbred (F1) females in the herd
are purchased and crossed with a terminal bull.
• All offspring are sold.
Rotate Herd Bull Every 3-4 Years
• Same breed of bull is used for years and then
replaced with a bull of a different breed.
• Replacement females are selected from the
herd.
Terminal Sire Crossed with F1
Females

Illustration of DNA
Double Helix from
Wikipedia.
• Bulls from Breed A are crossed with cows
from Breed B.
• Resulting heifers are bred to bulls from breed
B for the duration of their productive life.
• Replacement heifers from that cross are bred
to bulls from breed A.
• Each succeeding generation of replacement
heifers is bred to a bull from the opposite
breed used to sire the replacement heifer.
Two-Breed Rotation

Illustration of DNA
Double Helix from
Wikipedia.
F Parents Offspring Genes Heterosis
(approx. %)
L E
female male
1 L E LE 50 50 100
2 LE L L/LE 75 25 50
3 L/LE E E/(L/LE) 37 63 75
4 E/(L/LE) L L/[E/(L/LE) 69 31 62
5 EL E EEL 34 66 63
Rotational crossing using two breeds

Illustration of DNA
Double Helix from
Wikipedia.
• Same pattern of breeding as the 2 breed
rotation except that a bull from a 3rd
breed is used in the sire rotation.
3 Breed Rotation

Illustration of DNA
Double Helix from
Wikipedia.
• Larger herds
• Bulls from a 4th or 5th breed may be used in
the rotation of sires
• This system requires a higher level of
management and record keeping than 2 and
3 breed systems.
4 and 5 Breed Rotations

Illustration of DNA
Double Helix from
Wikipedia.
Genera
tions
Parents
Off-spring Genes
Heterosis
Female Male L A B
1 L A LA 50 50 100
2 LA B B/LA 25 25 50 50
3 B/LA L L/(B/LA) 63 12 25 75
4 L/B/LA A A/{L/(B/LA)} 32 56 12 62
5 ETC B ETC 16 28 56 32
6 ETC L ETC 58 14 28 84
Heterosis-in three crossbreeding
After many generations, the breed will settle down
to ratio of 4:2:1

Illustration of DNA
Double Helix from
Wikipedia.
• 4 breeding groups
• Group 1 (25% of the herd) mates breed A bulls to
breed A cows to produce replacement heifers for
group 1 and group 2.
• Group 2 (25% of the herd) breeds the AA heifers
to a bull (breed B) to a different breed, producing
crossbred heifers (breed AB)
• Group 3 (50% of the herd) breeds the AB heifers
to a terminal (T) bull selected for its ability to
transmit a high rate of gain.
Static Terminal Sire System

Illustration of DNA
Double Helix from
Wikipedia.
• A subgroup (Group 4, 10% of the herd) of
the 3rd group is composed of AB heifers
being bred for the first time. These AB
heifers are bred to a smaller breed (breed C)
bull to reduce 1st time calving problems.
• All the male offspring of groups 1 and 2 and
all offspring of groups 3 and 4 are sold.
• Any heifers from groups 1 and 2 that are not
kept for breeding are also sold.

Illustration of DNA
Double Helix from
Wikipedia.
• Two breeding groups needed
• Bulls from breeds A and B are used on a
rotating basis on 50% of the herd providing
crossbred females for the entire herd
• Mature cows in the herd are mated with a
terminal bull to produce offspring, all of
which are sold.
• Replacement females come from mating of
bulls A and B with younger cows in the herd.
Rotational –Terminal Sire System

Illustration of DNA
Double Helix from
Wikipedia.
• Developing a new breed based on
crossbreeding 4 or more existing breeds of
cattle to avoid inbreeding problems
• After development the composite breed is
not crossbreed with other breeds
Composite Breeds

Illustration of DNA
Double Helix from
Wikipedia.
Livestock Breed Composition
Dairy cattle Australian Milking Zebu
Jamaica Hope
Karen
0.33 Sahiwal + red Sindi/0.67 Jersey
o.8 Jersey/0.05 Friesian/0.15 Sahiwal
Brown Swiss/Sahiwal
Beef cattle Bonsmara
Chabray
Santa Gertrudis
Renitole (of madagascar)
0.62 afrikander/0.19 hereford + 0.19
Shorthorn
0.6Charolais/0.38 brahman
0.62 Shortorn/0.38 Brahman
3-breed cross malagasy zebu+
Limousin + Afrikander
Sheep Dorper
Katahdin
Perendale
Dorset Horn/Blackhead Persain
Virgin Island/ Wiltshire Horn +
Suffolk
Goats Boer Local with European, Angora and
Indian blood

Illustration of DNA
Double Helix from
Wikipedia.
Breed
Wt, 2.5
years kg
Weaning
%
Weaning weight (Kg)
Calf Per Cow*
Afrikander(AF) 339 51.4 174 89.4
Angoni (AN) 285 65.1 149 97.0
Barotse (BA) 311 53.8 163 87.0
Boran (BO) 329 64.5 169 109.0
AVERAGE OF CROSSES
AN X BA 302 61.8 158 97.6
AN X BO 312 69.1 160 110.6
BA X BO 340 65.9 173 114.0
Breed and crossbred means (reciprocal
crosses) for Various traits of cattle in Zambia

Illustration of DNA
Double Helix from
Wikipedia.
• 2 basic breeding systems—straight and
crossbreeding
• The type of system used depends on: the size of the
operation, the amount of money available and the
goal of the producer
• Purebred animal are eligible for registry and tend to
be genetically homozygous
• Inbreeding increases the genetic purity of livestock
but generally reduces performance. It is not
generally used by the average producer but rather by
those that do experimental work to improve the
breed.
Summary

Illustration of DNA
Double Helix from
Wikipedia.
• Outcrossing brings genetic traits into the
breeding program that tend to hide
undesirable traits
• Crossbreeding is the mating of animals
from two different breeds, it is used by
many commercial producers and usually
results in hybrid vigor. This improves
some traits but all little effect on feed
efficiency and carcass traits.

Illustration of DNA
Double Helix from
Wikipedia.
• Occurs when two individuals share the
common ancestor or ancestors;
• Mating of close related animal can either
deliberate or accidental
• More likely to occur
i. in small, self-contained herds flock than
in large population
ii. Small numbers of males
Inbreeding

Illustration of DNA
Double Helix from
Wikipedia.
Systems of Mating:
the rules by which pairs of
gametes are chosen from the
local gene pool to be united in a
zygote with respect to a particular
locus or genetic system.

Illustration of DNA
Double Helix from
Wikipedia.
Systems of Mating:
A deme is not defined by geography but
rather by a shared system of mating.
Depending upon the geographical scale
involved and the individuals’ dispersal and
mating abilities, a deme may correspond to
the entire species or to a subpopulation
restricted to a small local region. The Hardy-
Weinberg model assumes one particular
system of mating – random mating – but
many other systems of mating exist.

Illustration of DNA
Double Helix from
Wikipedia.
Some Common Systems of
Mating:
• Random Mating
• Inbreeding (mating between biological
relatives)
• Assortative Mating (preferential mating
between phenotypically similar individuals)
• Disassortative Mating (preferential mating
between phenotypically dissimilar
individuals)

Illustration of DNA
Double Helix from
Wikipedia.
Inbreeding: One Word, Several
Meanings
Inbreeding is mating between biological
relatives. Two individuals are related if
among the ancestors of the first individual
are one or more ancestors of the second
individual.

Illustration of DNA
Double Helix from
Wikipedia.
• Inbreeding Can Be Measured by Identity by
Descent, Either for Individuals or for a Population
(Because of shared common ancestors, two
individuals could share genes at a locus that are
identical copies of a single ancestral gene)
• Inbreeding Can Be Measured by Deviations from
Random Mating in a Deme (either the tendency to
preferentially mate with relatives or to
preferentially avoid mating with relatives relative
to random mating)

Illustration of DNA
Double Helix from
Wikipedia.
Identity by Descent
Some alleles are identical because they are replicated
descendants of a single ancestral allele

Illustration of DNA
Double Helix from
Wikipedia.
Properties of Assortative Mating
• Increases the Frequency of Homozygotes Relative to
Hardy-Weinberg For Loci Contributing to the
Phenotype Or For Loci Correlated For Any Reason to
the Phenotype
• Does Not Change Allele Frequencies –
• Assortative Mating Creates Disequilibrium Among
Loci that Contribute to the Phenotype and Is A
Powerful Evolutionary Force at the Multi-Locus Level
• Multiple Equilibria Exist at the Multi-Locus Level
And The Course of Evolution Is Constrained By the
Initial Gene Pool: historical factors are a Determinant
of the course of evolution

Illustration of DNA
Double Helix from
Wikipedia.
Disassortative Mating
occurs when individuals with
dissimilar phenotypes are more likely
to mate than expected under random
pairing in the population

Illustration of DNA
Double Helix from
Wikipedia.
Disassortative Mating as an
Evolutionary Force
• Is a powerful evolutionary force at the single locus
level, generally resulting in stable equilibrium
populations with intermediate allele frequencies
and f<0
• It is less powerful as an evolutionary force at the
multi-locus level because it produces a
heterozygote excess, which allows linkage
disequilibrium to break down more rapidly
• Mimics the heterozygote excess of avoidance of
inbreeding, but unlike avoidance of inbreeding, it
affects only those loci correlated with the relevant
phenotype, and it causes allele frequency change.

Illustration of DNA
Double Helix from
Wikipedia.
And now it’s time for….
• Spongebob
Genetics!!!!!

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