Principles of Animal

Breeding (MUAPS213)
Dr N. Chikumba
Overview of Genetics and Animal
Breeding
• Animal Genetics – the study of the principles of
inheritance in animals.
• Animal breeding – the application of animal
genetics principles of inheritance with the goal of
improving performance of animals.
 Animal Breeding
• Animal breeding is directed towards four main areas
of study:

Animal
breeding

Mendelian Population Quantitative Molecular

Genetics Genetics Genetics Genetics
Mendelian genetics
• It deals with the principles of transmission of
genetic material from one generation to the next.
OR RATHER
• Explores the laws of particulate inheritance as
formulated in 1865 by Austrian monk Gregor
Mendel from his experiments with the common
garden pea.
Population genetics
• Population genetics studies the genetic make-up
of populations, looking at whether genetic
material stays constant and what genetic changes
have occurred within populations over time.
• In other words, it looks at changes in the frequencies
of specific alleles of genotypes in animal
populations and the Hardy Weinberg Law.
• These changes can be caused by environmental
changes, random changes from one generation to
the next, migration or genetic mutations.
Quantitative genetics
• Quantitative genetics deals with the genetics of
continuously varying characters.
• In other words, it deals with the inheritance and
behaviour of performance traits which are controlled
by more than one pair of genes – sometimes called
polygenic traits.
• Unlike population genetics which looks at changes in
the frequencies of specific alleles of genotypes,
quantitative genetics seeks to "quantify" changes in
the frequency distribution of traits that cannot easily
be placed in discrete phenotypic classes.
Molecular genetics
• It deals with the identification of genes to the DNA
molecule level.
Mendelian Genetics

Dr N. Chikumba
Mendelian Genetics
• It deals with the principles of transmission of
genetic material from one generation to the next.
OR RATHER
• Explores the laws of particulate inheritance as
formulated in 1865 by Austrian monk Gregor
Mendel from his experiments with the common
garden pea.
Mendel’s Pea Plants
Mendel knew that:
• the male part (stamen)
of each flower
produces pollen,
containing sperm;

• the female (pistil) part

of the flower produces
egg cells.
Mendel’s Peas
• During sexual reproduction, sperm and egg cells
join in a process called FERTILIZATION.
• Fertilization produces a new cell called a ZYGOTE.
• Pea flowers are self-pollinating i.e. the sperm cells
in pollen fertilize the egg cells in the same flower.
• The seeds that are produced by self-pollination
inherit all of their characteristics from the single
plant that bore them.
Mendel’s Peas
• Mendel had true-breeding pea plants that, if
allowed to self-pollinate, would produce offspring
identical to themselves.
• True-breeding plants are also called PURE LINES.
Mendel’s Peas
• Mendel wanted to produce seeds by joining male
and female reproductive cells from two different
plants.
• He cut away the pollen-bearing male parts of the
plant and dusted the plant’s flower with pollen
from another plant.
• This process is called cross-pollination.
• Mendel was able to produce seeds that had two
different parents.
Cross-pollination
Genes and dominance
• Mendel studied eight pea plant traits, each with
two contrasting characters
• A trait is a specific characteristic that varies from one
individual to another e.g., for the trait height, the two
contrasting characteristics are Tall and Short.
• He crossed plants with each of the eight contrasting
characters and studied their offspring.
Genes and dominance
• Each original pair of plants is the P (parental)
generation.
• The offspring are called the F1, or “first filial,”
generation.
• A cross between parents that differ at a single
gene pair (usually AA x aa) is called a
MONOHYBRID CROSS.
• The offspring of two parents that are homozygous
for alternate alleles of a gene pair (AA x aa) are
called MONOHYBRIDS.
Genes and dominance
• Mendel's first conclusion was that biological inheritance is
determined by factors that are passed from one generation
to the next.
• Today, scientists call the factors that determine traits GENES.
• A gene is defined as the basic unit of inheritance.
• Each of the traits Mendel studied was controlled by one
gene that occurred in two contrasting forms that produced
different characters for each trait.
• The different forms of a gene are called ALLELES.
• Mendel’s second conclusion is called the PRINCIPLE OF
DOMINANCE.
The principle of dominance
• The principle of dominance states that some alleles are
DOMINANT and others are RECESSIVE.
• Dominant allele: the allele that expresses itself at the
expense of an alternate allele OR the phenotype that is
expressed in the F1 generation from the cross of two
purelines.
• Recessive allele: an allele whose expression is suppressed
in the presence of a dominant allele OR the phenotype that
disappears in the F1 generation from the cross of two
purelines and reappears in the F2 generation.
Segregation
• Mendel crossed the F1 generation with itself to
produce the F2 (second filial) generation.
•The traits controlled by recessive alleles
reappeared in one fourth of the F2 plants.
Alleles separate during gamete formation
Segregation
• Mendel assumed that a dominant allele had
masked the corresponding recessive allele in the F1
generation.
• The trait controlled by the recessive allele showed
up in some of the F2 plants.
• The reappearance of the trait controlled by the
recessive allele indicated that at some point the
allele for shortness had been separated, or
SEGREGATED, from the allele for tallness.
Segregation
• Mendel suggested that the alleles for tallness and
shortness in the F1 plants segregated from each
other during the formation of the sex cells
(gametes).
• When each F1 plant flowers and produces gametes,
the two alleles segregate from each other so that
each gamete carries only a single copy of each
gene.
• Therefore, each F1 plant produces two types of
gametes—those with the allele for tallness, and
those with the allele for shortness.
• Mendel’s observations and conclusions led to his
1st law.
Law of Segregation
• Mendel’s 1st law is known as the law of segregation
(separation) of gene pairs.
• The law states “that genes exist in pairs
(homologous chromosomes) in the cells of the
individual, and that members of a gene pair
separate into the sex cells (gametes) formed by that
individual, such that half carry one member of the
gene pair and half carry the other.”
Law of Segregation
• The alleles for each character segregate (separate)
during gamete production (meiosis).
Punnett Squares
• The gene combinations that might result from a
genetic cross can be determined by drawing a
diagram known as a Punnett square.
• Punnett squares can be used to predict and
compare the genetic variations that will result from
a cross.
Punnett Squares
• A capital letter
represents the
dominant allele for
tall.
• A lowercase letter
represents the
recessive allele for
short.
• In this example,
T = tall
t = short
Punnett Squares
• Gametes produced by
each F1 parent are
shown along the top
and left side.

• Possible gene
combinations for the
F2 offspring appear in
the four boxes.
Punnett Squares
• Organisms that have two identical alleles for a
particular trait are said to be homozygous.
• Organisms that have two different alleles for the
same trait are heterozygous.
• Homozygous organisms are true-breeding for a
particular trait.
• Heterozygous organisms are hybrid for a particular
trait.
Punnett Squares
• All of the tall plants have the same phenotype
(physical characteristics).
• The tall plants do not have the same genotype
(genetic makeup).
• One third of the tall plants are TT, while two thirds
of the tall plants are Tt.
Punnett Squares
• The plants have
different genotypes
(TT and Tt), but they
have the same
phenotype (tall).
Probability and Segregation
• One fourth (1/4) of the F2
plants have two alleles for tallness
(TT).
• 2/4 or 1/2 have one allele
for tall (T), and one for
short (t ).
• One fourth (1/4) of the F2
have two alleles for short (tt).
Probability and Segregation
• Because the allele for tallness (T) is dominant over
the allele for shortness (t), 3/4 of the F2 plants
should be tall.

• The ratio of tall plants (TT or Tt) to short (tt) plants

is 3:1.

• The predicted ratio showed up in Mendel’s

experiments indicating that segregation did occur.
TEST CROSS
• Individuals with the dominant phenotype may be
deceptive, as some are heterozygous and will not
breed true.

• The TEST CROSS is used to distinguish between

homozygous and heterozygous individuals sharing
the dominant phenotype.
TEST CROSS
• Definition: A cross of any INDIVIDUAL to a
homozygous recessive parent to determine if the
individual is homozygous dominant or
heterozygous.
• Recessive homozygotes are used in TEST MATINGS
because they can transmit only recessive alleles to
their offspring, thus allowing expression of all
genes transmitted by the individual with the
dominant phenotype.
• It always yields a 1:1 ratio for a cross between a
homozygous recessive parent and a heterozygous
individual..
Back-cross
• Backcross - the cross of an F1 hybrid to one of the
homozygous parents e.g Tt x TT or Tt x tt
Mendelian Genetics Definitions
• Allele – An alternative form of a given allelic pair;
tall and dwarf are the alleles for the height of a pea
plant

• Allelic pair - the combination of two alleles which

comprise the gene pair.
• Cistron: The unit of DNA carrying the information
necessary for the formation of one polypeptide
chain in protein formation or sysnthesis.
Mendelian Genetics Definitions
• Homozygote - an individual which contains only
one allele at the allelic pair eg.,
• TT is homozygous dominant and tt is homozygous
recessive;
• pure lines are homozygous for the gene of interest
• Heterozygote - an individual which contains one of
each member of the gene pair; for example the Tt
heterozygote
• Genotype - the specific allelic combination for a
certain gene or set of genes.
The Law of Independent Assortment

• Mendel also performed crosses in which he

followed the segregation of two genes controlling
separate characteristics.
• These experiments formed the basis of his
discovery of his second law, the law of
independent assortment.
The Two-Factor Cross: F1
• Mendel crossed true-breeding plants
that produced round yellow peas
(genotype RRYY) with true-breeding
plants that produced wrinkled green
peas (genotype rryy).
• All of the F1 offspring produced round
yellow peas (RrYy).
Independent Assortment
• The alleles for round (R) and yellow (Y) are
dominant over the alleles for wrinkled (r) and
green (y).
The Two-Factor Cross: F2
• Mendel crossed the heterozygous F1
plants (RrYy) with each other to
determine if the alleles would
segregate from each other in the F2
generation.
RrYy × RrYy
Independent Assortment
•.
Independent Assortment
• In Mendel’s experiment, the Punnett square
predicts a 9 : 3 : 3 :1 phenotypic ratio in the F2
generation.
•
• 9 seeds that were round and yellow
• 3 seeds that were round and green
• 3 seeds that were wrinkled and yellow
• 1 seed that was wrinkled and green

• Indicating that the alleles for seed shape segregated

independently of those for seed colour.
Independent Assortment
• The results of this experiment led Mendel to
formulate his second law:
• The law of independent assortment , which states
that, “during gamete formation the segregation of
the alleles of one allelic pair is independent of the
segregation of the alleles of another allelic pair”.
Terminology
• Dihybrid cross/ Two factor cross - a cross between
two parents that differ by two pairs of alleles
(AABB x aabb)
• Dihybrid- an individual heterozygous for two pairs
of alleles (AaBb)
Solving dihybrid problems using
the FORKED LINE METHOD
• Instead of using the Punnet square, the FLM can be
used to predict genotype and phenotype ratios in
dihybrid problems.
• The method requires knowledge of basic ratios that arise
from monohybrid crosses, assuming that in a dihybrid, the
two traits sort INDEPENDENTLY of one another.
Basic ratios from monohybrid crosses
• There are essentially only three different
genotypic ratios that can result in a monohybrid
cross namely:

1. Homozygote x Homozygote: PP x PP = 100% PP

OR pp x pp = 100% pp
2. Heterozygote x Homozygote: Pp x PP = ½ Pp; ½ PP
OR Pp x pp = ½ Pp; ½ pp.
3. Heterozyg x Heterozyg: Pp x Pp = ¼ PP; ½ Pp; ¼ pp
THE FORKED LINE METHOD
• To solve the dihybrid cross:
PpYy x PpYy
• Separate the two traits (since they assort
independently)
THE FORKED LINE METHOD
• ...
•.
•.
.
.
.
THE FORKED LINE METHOD
THE FORKED LINE METHOD
THE FORKED LINE METHOD
Calculating numbers of possible gametes

Introduction
• Locus: is the Latin word for location and denotes
the site of a particular genotype.
• At each locus is a pair of alleles, one allele on the
paternal chromosome and the one on the maternal
chromosome.
Calculating numbers of possible gametes

• As a rule, germ cells (sperm and ova) contain half

the number of chromosomes and therefore half the
number of alleles of normal body cells (somatic
cells).
Calculating numbers of possible gametes

• Examples of gametes obtainable from two-locus genotypes:

Parental genotype Possible gametes

JJBB JB
JJBb JB and Jb
JjBb JB, Jb, jB and jb
• Note that each gamete contains only one allele from each
locus.
Calculating numbers of possible gametes

• The following examples show how to use an

estimate of the number of loci at which an
individual is heterozygous to determine
mathematically the number of unique gametes
the individual can produce.
Calculating numbers of possible gametes

• 1. An individual with the genotype AABBCC has no

heterozygous loci and produces just one kind of gamete:
ABC.

• 2. An individual heterozygous at one locus, say, AaBBCC- can

produce two different gametes: ABC and aBC .
• (Note that in this example only the heterozygous A locus
contributes to variation in gametes – the homozygous B
and C loci do not)
Calculating numbers of possible gametes

• 3. Individuals heterozygous at two loci (AaBbCC) can

produce four kinds of gametes:
• ABC aBC
• AbC abC
• How many unique gametes can be produced by an
individual heterozygous at 3 loci?
Calculating numbers of possible gametes

• There is a pattern here which can be summarized in

the following formula:
Number of unique gametes produced by an
individual = 2n
Where:
n = no. of loci at which an individual is heterozygous.
Calculating numbers of possible
ZYGOTES
• Assuming only two possible alleles per locus,
The number unique zygotes(offspring) produced by
two parents = 3n x 2m
Where:
n = the number of loci at which both parents are
heterozygous, and
m = the number of loci at which only one parent is
heterozygous.
Practice problems
• A sire’s (male) five-locus genotype is AaBBCcDdee.
A dam’s (female) genotype is AABbCcDdEe.
Considering just these five loci, how many unique
gametes can:
• (i) the sire produce?
• (ii) the dam produce?
• (iii)How many unique zygotes can be produced
from the mating of the sire and dam?
How do we decide if our data fits
any of the Mendelian ratios?
• To decide if our data fits any of the Mendelian ratios, The
Chi-Square test for goodness of fit test is used.
• Simply follow the hypothesis testing procedure:
• Null hypothesis:
• Alpha error:
• Statistic:
• Critical limits:
• Calculations:
• Results and inference:
EXAMPLE
• Linda and Pauline took plants from a pure breeding
variety with smooth seeds and crossed them with a
variety bearing wrinkled seeds. The seeds formed
as a result of this pollination were all smooth. Linda
and Pauline then planted the smooth seeds and
when they matured, they self fertilized the flowers.
The plants produced a total of 7324 seeds, of which
5474 were smooth and 1850 were wrinkled.
• Test the observations/data to determine if it fits the
3:1 ratio?
Chi- Square Monohybrid example
• Mr Nyungu took plants from a true-breeding variety with
smooth seeds and crossed them with a variety bearing
wrinkled seeds. The seeds formed as a result of this
pollination were all smooth. Mr Nyungu then planted the
smooth seeds and when the plants matured, he self-
fertilised the flowers. The plants produced a total of 7324
seeds, of which 5474 were smooth and 1850 were wrinkled.
Test the data to determine if it fits Mendel’s 3:1 ratio of
Smooth: wrinkled phenotypes.
Dihybrid example
• In Pea plants, round seeds (R) are dominant to wrinkled (r),
and yellow seeds (Y) are dominant to green (y). The cross
RrYy x RrYy, produced:
• 315 Round, Yellow seed;
• 108 Round, Green seed;
• 101 Wrinkled, Yellow seed; and
• 32 Wrinkled, Green seed.
• Test the data to determine if it fits the 9:3:3:1 ratio?
Practice problems
• Suppose that purebreeding red, belted swine,
bbWW are mated with purebreeding black, solid-
solid coloured individuals, BBww. Use the forked
line method to predict the genotypic and
phenotypic ratios of the F2 generation.
GENE ACTION
• Gene action is about allelic relationships and the
expression of genes and genotypes.
Gene actions that lead to
exceptions of Mendel’s ratios
• Codominance • Pleitropy
• Incomplete dominance • Epistasis
• Multiple alleles • Penetrance and
• Lethal genotypes expressivity
• Mutations • Phenocopies
• Chromosomal • Sex linkage
aberrations • Sex limited traits
• Sex influenced traits
 Codominance
• A phenomenon were both alleles
are expressed in the heterozygote.
• The heterozygote has its own
phenotype which is different from
either homozygote.
• For example, coat colour inheritance
in Shorthorn cattle.
• Red cows crossed with White will
generate roan cows. Roan cows have
red coats with white blotches.
Incomplete dominance
• Incomplete or partial dominance can lead to the
expression of intermediate phenotypes.

• Andalusian blue, colour produced by CB/CW

heterozygote from Black x White chickens.
Multiple alleles
• A gene with more than two alleles per locus.
• A single diploid individual can only carry 2 alleles,
one paternal and one maternal.
• Examples
1. ABO blood types: Three alleles viz IA,IB and Ii
Lethal genotypes
• Alleles that cause an organism to die only when
present in homozygous condition are called lethal
alleles.

• The gene involved is considered an essential gene.

Lethal genotypes
• Lethal alleles arise when a mutation to a normal
allele disrupts the function of an essential gene.
Without this essential gene, the organism dies.
• Mutation: a heritable change in DNA that alters
the genetic information carried by the cell, leading
to a potential alteration of a genetically controlled
phenotype.
• Lethal alleles can be embryonic or postnatal.
Lethal genotypes
• In white horses, animals with genotype WW die.
This can be proven by mating;
Ww x Ww
• Mendelian ratio of 1WW:2Ww:1ww, is altered.
Lethal genotypes
• Postnatal lethal alleles cause abnormalities in the
progeny that cause them to die early on in
development.
• An example is parrot jaw, which is observed in
cattle.
• The phenotype results in a deformed mouth so the
calf is unable to eat correctly and eventually starves
to death.
Lethal genotypes
• Parrot jaw in cattle.
 Pleitropy
• Pleiotrophy is a phenomenon where the same gene
has different effects on different traits at the same
time.
• Pleiotropy may be the result of a single gene
product (protein) giving rise to multiple functional
characteristics.
 Pleitropy
Example:
New Zealand Drysdale sheep in which the gene N
controls both the hair and the horns. This sheep
has strong medullated fleece (a desirable trait) and
strong horns (undesirable trait).
 EPISTASIS
• It is a phenomenon where one gene masks the
expression of another genes on another loci.
• The difference between Dominance and Epistasis
is that in dominance the interaction is between
genes on the same loci (alleles) whereas in
Epistasis the interaction is between genes on
different loci (non allelic).
EPISTASIS
• Epistasis can be Recessive or Dominant.
Recessive epistasis: when the recessive allele of one
gene masks the effects of either allele of the
second gene.
• Example 1: Coat color of Labrador retriever
• Phenotypic ratios are 9:3:4 in F2.
EPISTASIS
• Dominant epistasis: when the dominant allele of
one gene masks the effects of either allele of the
second gene.
• Ratio is 12:3:1 instead of 9:3:3:1
• Example: Coat colour in sheep.
Penetrance and Expressivity
• Penetrance: the proportion of individuals of a
particular genotype that express its phenotypic
effect in a given environment.

# showing phenotype
Penetrance = ---------------------------------- %
Total of that genotype
Penetrance and Expressivity
• A genotype of a trait may not be expressed in the
phenotype at all e.g. Polydactyl (extra digit) in
chickens.
• Gene for polydactyl is dominant over that normal
feet but it has incomplete penetrance.
Penetrance and Expressivity
• Expressivity: refers to the degree to which an
individual expresses the trait.
 Piebald Spotting In Beagles

Every individual shown has the same genotype for this

gene.
 Phenocopies
• A phenocopy is an individual whose phenotype (a
specific trait) is environmentally induced to mimic
the phenotype of an organism whose phenotype
was genetically determined.
 Phenocopies
• These changes are not mutations, as the underlying
DNA sequence of the phenocopy is not altered. As
such, these changes are not heritable.

• Example: The Vanessa genus of butterflies, who

may adopt the phenotype of butterflies living in
either Lapland or Syria, depending on which region
to which they are introduced.
 Modifier genes
• Modifier Genes: A gene that alters the phenotypic
expression of another gene.
Example
• The spotting pattern in Holstein cattle is determined by a
recessive allele, and the allele is fixed in the Holstein breed
i.e all Holsteins are spotted.
•
 Modifier genes
• However, the spotting patterns of all Holsteins are
not alike.
• Holsteins exhibit coat colours ranging from almost
white, some almost all black, with the majority in
between.
• Variation in white spotting is an example of genes
at additional loci MODIFYING the effect of genes at
the first locus.
Modifier genes
• One locus determines whether there will be spots
or not; and this is called the MAJOR GENE.

• Other loci determine how many and where on the

body these spots will be; and these are known as
the MODIFYING genes.
LINKAGE
• Enormous
 Sex-linked Traits

• Traits (genes) located on the sex chromosomes

• Sex chromosomes are X and Y

XX genotype for females (homogametic sex)
XY genotype for males (heterogametic sex)

Many sex-linked traits carried on X chromosome

copyright cmassengale 98
 Sex-linked Traits
Example: Eye color in fruit flies

Sex Chromosomes

fruit fly
eye color

XX chromosome - female Xy chromosome - male

copyright cmassengale 99
Sex-linked Trait Problem
Example: Eye color in fruit flies
(red-eyed male) x (white-eyed female)
XRY x XrXr
• The Y chromosome in males does not carry traits.
Xr Xr

XR

copyright cmassengale 100

 Sex-linked Trait Solution:

50% red eyed

Xr Xr female
50% white eyed
male
X R XR Xr XR Xr

Y Xr Y Xr Y

copyright cmassengale 101

Sex- influenced Traits
• A phenotypic characteristic or trait such as male pattern
baldness, that is expressed differently in males and females,
usually because its expression depends on androgens or
oestrogens, and that is controlled by a single gene that is
dominant in males but recessive in females.
• For example, men who inherit the gene from either parent
lose hair as they age, whereas women do so only if they
inherit it from both parents and are thus homozygotes.
• Other examples: Horns in sheep, growth rate and body
composition.
Chromosomal aberrations
• Chromosomal aberrations: Deviations from the normal
number of chromosomes and morphology (karyotype).
• As a result the expected Mendelian ratios are disturbed and in
addition, linkage relationships are changed.
• The abnormal chromosome number will lead to errors during
replication.
• These abnormalities also reduce the reproductive performance
due to:
I. Failure to produce functional gametes; and
II. Death of embryo
Chromosomal aberrations
• Types of abnormalities
1. Heteroploidy: having an abnormal chromosome number
that deviates from the normal diploid number of a given
species.
2. Euploidy: having a chromosome number that is an exact
multiple of the haploid number (excess).
3. Aneuploidy: is the presence of an abnormal number of
chromosomes in a cell, for example when having 45 or 47
chromosomes when 46 is expected in a human cell. It
does not include a difference of one or more complete
sets of chromosomes, which is called euploidy.
Chromosomal aberrations
• Types of chromosomal aberrations
1. Inversion: where a portion of the chromosome has
become reversed. A section of the chromosome becomes
changed by rotation at 180° and the order of the genes in
it are reversed.
2. Duplication: where a break in a chromosome, become
attached to the other member of a homologous pair. This
occurs as a result of unequal crossing over between
homologous chromosomes.
Chromosomal aberrations
III. Deletion/Deficiency: where a break in a chromosome
occurs and the part breaking off is lost and creates a
deficiency.
IV. Translocation: where a chromosome becomes broken
and one of the pieces is attached to some other
chromosome.
• Centric-fusion or Robertsonian translocation: A type
of chromosome rearrangement, in which there is
fusion of an entire long arm of one acrocentric
chromosome with a similarly intact long arm of
another acrocentric chromosome.
Chromosomal aberrations
• The short arms of the chromosomes participating in
the translocation are usually lost.
• Acrocentric chromosomes have their centromere near
but not at the very end of the chromosome