Chapter 1.

Introduction to Animal Breeding

Introduction

Animal breeding is a branch of animal science that addresses the evaluation of the genetic
value of livestock. It is also defined as the application of the principles of animal genetics with the goals
of animal improvement. It is also defined as controlled propagation of domestic animals in order to
improve desirable qualities. In like manner, animal breeding is the study of genetic differences among
animals, it also aims to improve the quantity, efficiency and aesthetic value of farm animals and their
products. Humanity has been modifying domesticated animals to better suit human needs for centuries.

For this chapter, the process of domestication will be presented and how it plays an important
role in the early stages of animal breeding.

Learning outcomes

At the end of the module, the learner should be able to:

1. Understand the concept, process and importance of animal domestication;

2. Know the development of major domesticated animals; and
3. Understand the process of animal breeding and its importance to the society then and now.

Learning content

A. The concept of domestication

Domestication is the process of conversion of wild animals to domestic use. Domestic animals
need to live in (close) association with humans, therefore they have to become tame. Domestication
often has resulted in a type of animals that has become quite different from their wild counterparts. As
a result, domestication often also involves the development of a dependency on humans so that the
animals lose their ability to live in the wild.

Domestication should not be confused with taming. Taming is the conditioned behavioral
modification of a wild-born animal when its natural avoidance of humans is reduced and it accepts the
presence of humans, but domestication is the permanent genetic modification of a bred lineage that
leads to an inherited predisposition toward humans.
Certain animal species, and certain individuals within those species, make better candidates
for domestication than others because they exhibit certain behavioral characteristics, such as:
1. size and organization of their social structure;
2. availability and the degree of selectivity in their choice of mates;
3. ease and speed with which the parents’ bond with their young,
4. the maturity and mobility of the young at birth; and
5. degree of flexibility in diet and habitat tolerance; and
6. responses to humans and new environments, including flight responses and reactivity to
external stimuli.
It is proposed that there were three major pathways that most domesticated animals followed,
which are:
1. commensals, adapted to a human niche, such as dogs, cats, fowl, possibly pigs;
2. prey animals sought for food, such as sheep, goats, cattle, water buffalo, yak, pig,
reindeer, llama, alpaca, and turkey; and
3. targeted animals for draft and nonfood resources, such as horse, donkey, camel.

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 The figure below shows the approximate time frame of domestication based on archeological
records.

Figure courtesy of nature.com

People also domesticated animals that were easy to manage in close proximity to dwellings
and had calm temperaments. Animals were used for a guaranteed supply of meat, milk, and hides used
for clothing, storage, and shelters. The first domesticated animals were goats, followed by sheep, then
cattle, pigs, and chickens, and later larger animals such as oxen and horses that were used for plowing
and transportation. Dogs were originally domesticated to assist people when hunting but have ceased
to serve these purposes.

The domestication revolution resulted in the first successful effort by people to use social
organization to gain greater control over the production of food, and it created a dependable food supply
that led to an increased population density. The domestication of plants allowed fewer people to provide
more food and led to advances in tools such as the plow. Eventually, these effects allowed people to
trade and unleashed a chain of events that changed human societies. But how have animals evolved
during domestication?

During domestication, five main genetic processes were involved:

1. inbreeding and genetic drift (two uncontrolled processes),

2. natural selection in captivity and relaxation of natural selection (two partially controlled
processes), and
3. active selection (one controlled process).

▪ The two uncontrolled processes are due to the limited size of the population (known as
inbreeding) and the random changes in gene frequencies (genetic drift).
▪ The two partially controlled processes are natural selection in captivity that accounts
for selection imposed on captive populations that cannot be attributed to active (or
artificial) selection and relaxation of natural selection expectably accompanying the
transition from wild to captive environments.
▪ The controlled process, known as active selection, because changes are directional.

Definition of terms:

1. Inbreeding- the production of offspring from the mating or breeding of individuals or organisms
that are closely related genetically.

2. Genetic drift- is a mechanism of evolution. It refers to random fluctuations in the frequencies of

alleles from generation to generation due to chance events. Genetic drift can cause traits to be
dominant or disappear from a population. The effects of genetic drift are most pronounced in
small populations.

3. Natural selection- the process whereby organisms better adapted to their environment tend to
survive and produce more offspring. The theory of its action was first fully expounded by
Charles Darwin and is now believed to be the main process that brings about evolution.

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 Evolution- the process by which different kinds of living organisms are thought to have
developed and diversified from earlier forms during the history of the earth.

Domesticated animals have been profoundly modified during domestication. Modifications

resulting from domestication concern are the following:

1. Morphoanatomy- The study of anatomical forms and structures with emphasis on

characteristics useful in distinguishing the species.
2. Physiology- the branch of biology that deals with the normal functions of living organisms and
their part such as cells and tissues
3. Behavior- the way in which an animal acts in response to a particular situation or stimulus.
4. Genetics- is the study of heredity in general and of genes in particular.

Behavior is probably the first to have been modified during domestication. Nevertheless, behavioral
traits neither appeared nor disappeared during domestication but rather are the response thresholds
that changed. One of the most remarkable behavioral changes shared by all domesticates is their
tolerance of proximity to or complete lack of fear of people. Besides, because humans provide shelter,
food, and protection against predators, domesticated animals most often express a lower incidence of
antipredator behaviors and show lower motivation for foraging. More generally, mood, emotion,
agnostic and affiliative behavior, as well as social communication all have been modified in some way
by domestication.

Most domesticated animals are also more precocious than their wild counterparts. The activity of
their reproductive system became enhanced and relatively uncoupled from the environmental
photoperiod, and they all acquired the capacity to reproduce in any season and more often than once
a year.

Lastly, the most spectacular and obvious changes concern morphology, among which are the
animal size (dwarfs and giants), proportions (fewer vertebrae, shorter tails), color, length and texture of
coat, wavy or curly hair, rolled tails, and floppy ears or other manifestations of neoteny (the retention of
juvenile features into sexual maturity). In most domesticated species, head or brain size has decreased.
The most illustrative example of such considerable changes is the morphological variations in dogs.
These morphological changes (“domestication syndrome”) may all be linked to strong selection for
lowered reactivity to external stimuli.

At the beginning of the twentieth century, modern breeding programs were initiated, leading to
dramatic changes in productivity, such as increase laying rate for laying hens or improved feed
conservation ratio, meat yield, and growth rate in broiler chickens.

List of domesticated animals, date and location of domestication

Species Date Location

Dog >30,000 BC Eurasia
Sheep 11000-9000 BC Southwest Asia
Pig 9000 BC Near East, China, Germany
Goat 8000 BC Iran
Taurine cattle 8000 BC India, Middle East, North Africa
Zebu cattle 8000 BC India
Cat 7500 BC Cyprus and Near East
Chicken 6000 BC India and South East Asia
Llama 6000 BC Peru
Guinea pig 5000 BC Peru
Donkey 5000 BC Egypt
Domesticated duck 4000 BC China
Water buffalo 4000 BC India, China
Horse 4000 BC Eurasian Steppes
Honey bee 4000 BC Multiple places
Silkworm 3000 BC China
Rock pigeon 3000 BC Mediterranean Basin

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 Goose 3000 BC Egypt
Bactrian camel 2500 BC Central Asia
Turkey 500 BC Mexico
Rabbit 600 Europe
Japanese quail 1100-1900 Japan
Fancy rat 1800s United Kingdom
Hamster 1930s United States
Silver fox 1950s Soviet Union
Ball phyton 1960s Africa

Prerequisites for domestication

Domestication is not always successful. Despite many attempts, the zebra for example has not
been domesticated; even though it is closely related to horse ad donkey. Although several generations
in captivity and some selective breeding did not make zebra genetically tame.

Naturally, there are process that the animal needs to undergo and thus will guarantee success
in domestication. The prerequisites therefore are the following but not limited to:

1. the animals should be able to adapt to the type of the feed they are offered by humans. This
may be different (in diversity) from what were used in the wild.
2. Animals must be able to survive and reproduce in the relatively closed quarters of captivity.
Animals that need a very large territory are not suitable for domestication.
3. Animals need to be naturally calm.
4. Animals need to be willing to recognize humans as their superior, which means they must have
a flexible social hierarchy.

History of major domesticated animals

There are 40 animal species around the world that directly or indirectly contribute to agriculture are
domesticated. The brief history of domestication of the following farm animals are outlined below to
understand why are these animals were domesticated.

Cattle

The wild ancestor of cattle is a group of races of the now extinct aurochs Bos primigenius which
had a very wide geographic distribution, which extended from East Asia to Europe and North Africa.
Traditionally, two major types of domestic cattle are considered:

a. zebu (Bos indicus) which have a prominent thoracic hump and

b. taurine (Bos taurus), which do not have thoracic hump

Pigs

The wild ancestor of domestic pigs is boar Sis scrofa.

▪ Wild boars occurred throughout Eurasia and North Africa. Multiple independent domestication
events, mainly in Asia Minor, Europe, and East Asia, have probably occurred, starting
approximately 9000 years ago.
▪ Chinese breeds originated in East Asia, whereas European believed to have originated in
Southwest Asia.
▪ By the late 18th to early 19th century, strict organized breeding was adopted to improve and
develop livestock breeds, particularly in Britain, as a reaction to increasing demand for meat in
the wake of industrial revolution.
▪ From the 18th century, pig breeds were selectively bred for specific production traits such as:

- early maturation,
- rapid growth and

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 - increased prolificacy.

▪ From the 20th century, with the recognition of the benefits of genetic improvement and changing
consumer preferences, certain pig breeds experienced further strong selection for lean meat
content, masculinity and enhanced reproduction.
▪ To date, there are likely over 730 pig breeds or lines globally of which two-thirds are in China
and Europe and over 270 are considered as endangered or critical.
▪ Currently, 58 pig breeds are recorded as “transboundary” which means that the breeds
occur in more than one country. The worldwide distribution of pigs is dominated by five
transboundary pig breeds from United States or Europe to include:

1. Large white- 117 countries

2. Duroc- 93 countries
3. Landrace- 91 countries
4. Hampshire- 54 countries
5. Pietrain- 35 countries.

Sheep

The wild ancestors of the domestic sheep are probably the mouflon (Ovis musimon) and the
urial (Ovis orientalis). Both archaeological and genetic data spot the domestication center of sheep in
eastern Anatolia and North-West Iran between 8500 and 12,000 years ago.

Goat

The wild ancestor of goat is the bezoar Capra aegagrus. The first archeological evidence of
goat domestication traces back in the Fertile Crescent about 10,000 years ago.

▪ The extraordinary adaptability and hardiness of goats favored their rapid spread over the Old
world.
▪ Goats have successfully adapted to desert, mountainous and tropical areas where other
livestock species would not thrive.
▪ Between the 15th and 18th centuries, goats were transported to America and Oceania.
▪ Over the course of domestication, several morphological traits were modified to include:

1. horn and ear shapes,

2. the presence of wattle,
3. long hair, and
4. coat colors which were driven probably by intentional selection as well as by genetic
drift, isolation, and founder effects.

▪ Throughout the ages, goats have been raised for milk production and cheese, meat and skin
and fiber commodities such as leather, mohair wool and cashmere hair.
▪ Breeds also show strong differences in their physiological capacity of adaptation to extreme
conditions of temperature and humidity and differ in feed efficiency, behavior and resistance to
infectious and parasitic diseases.
▪ At present, there are 1 billion goats worldwide, in which Asa contains 58.2% and Africa shares
36.2%. The top five goat producers are the following:

1. China- 187.8 million hds

2. India- 133 milion hds
3. Nigeria- 71 million hds
4. Pakistan- 66.6 million hds
5. Bangladesh- 55.9 million hds

Chicken

Domestication of the chicken dates back to at least 2000 B.C. and their ancestry can
be traced back to four species of wild jungle fowl from Southeast Asia. However, the Red jungle

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fowl (Gallus gallus or Gallus bankiva) is the most commonly found wild species in the world today
and is considered the main ancestor of the domestic chicken. The chicken belongs to the genus
Gallus of the family Phasianidae. Domestic chickens are simply classified as Gallus domesticus.

▪ The sport of cockfighting had tremendous influence not only in the domestication of the
chicken but also on the distribution of fowl throughout the world.
▪ After centuries of selection and breeding for numerous extremes, chickens now exist in
many colors, sizes and shapes.
▪ There are more than 350 combinations of physical features known today.
▪ In 1873, the American Poultry Association was organized for the purposes of adopting
standards of excellence and establishing a way of classifying the various breeds.
▪ Today, the two industries are very different:

1. The purebred fowl of today are basically the same as they were 100 years ago
and are mainly raised as a hobby;
2. The commercial poultry industry has developed into a science, which produces
highly nutritious meat and eggs with extreme efficiency.

Ducks

Mallard ducks were first domesticated in Southeast Asia at least 4000 years ago, during
the Neolithic Age, and were also farmed by the Romans in Europe, and the Malays in Asia. In ancient
Egypt, ducks were captured in nets and then bred in captivity. During the Ming Dynasty, the Peking
duck—mallards force-fed on grains, making them larger— was known to have good genetic
characteristics. Almost all varieties of domestic duck except the muscovy have been derived from
the mallard.

Domestication has greatly altered their characteristics. Domestic ducks are

mostly polygamous, where wild mallards are monogamous. Domestic ducks have lost the mallard's
territorial behaviour, and are less aggressive than mallards. Despite these differences, domestic ducks
frequently mate with wild mallard, producing fully fertile hybrid offspring.

Horses

The wild ancestors of domestic horse are now extinct, Equus ferus from Central Asia. The Asian
wild horse, Equus przewalskii is also significantly contributed to the genetic makeup of domestic horses.
The species has been maintained in captivity for the last 90 years. Both archeological and genetic
evidence strongly support the onset of domestication of the horse in the western Eurasian steppes of
Ukraine dating to 5500 years ago. Over the course of domestication, it has been argued that difficulties
in maintaining domestic horse herd sizes during pastoral migrations led directly to restocking through
the capture of wild females.

Horses were not only used as a source of meat and milk; their stamina and quickness provide
humans with rapid transportation, which has considerably changed the speed and magnitude of the
circulation of goods and people, as well as cultural exchange, including the spread of Indo-European
languages, religious, science and art and diseases.

With the introduction of the horse collar and horseshoes in agriculture, the horse was
increasingly used for tilling oils, incrementing farmland productivity in medieval Europe, and remains
today a crucial asset to the agriculture of the least-developed countries.

The earliest horse studbook, that of the Thoroughbred racing horses, was created in 1791. The
population structure resulting from selective breeding is characterized by high interbred and low
intrabreed genetic diversity. Domestic horses exhibit remarkable variation in coat coloration, including
the bay or bay-dun wild type phenotypes, other basic colors like chestnut and black, as well as dilution,

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and spotting patterns. Horse locomotion has also been recurrently selected, including their ability to
perform alternate gaits, such as four-beat, lateral or diagonal ambling. Although some horse breeds,
such as the Thoroughbred racing horses, are still extremely popular, a significant part of this great
diversity is currently endangered: 87 horse breeds are already extinct, and among the remaining 905,
almost a quarter are categorized as at risk.

B. History of Animal Breeding

The history of animal breeding started even before the domestication of animals. The
following are the works of scientist who worked to establish animal breeding:

Robert Blakewell (1725-1795)

- A British agriculturist and considered as father of animal breeding.

- He developed several breeds of animals such as Shire breed of horses, old Longhorn cattle
and Leicester sheep
- R Blakewell concluded that “like begets like” since superior parents were more likely produce
superior progeny than were inferior parents. He therefore recommended to “breed the best to
best”.

Jay Laurence Lush (1896-1892)

- An American animal breeder and consider as father of modern animal breeding

- 1930, Lush established the foundation of modern methods estimating breeding values.
- He asserted that “like does not always begets like”

RA Fisher (1890-1962)

- Showed that the diversity of expression of trait could depend on the involvement of large
number of genes

Charles Roy Henderson (1911-1989)

- An animal geneticist
- Computer-based evaluations

Lanoy Nelson Hazel (1911- 1992)

- Developed the selection index theory → determine the value that can be put on the different
traits under selection
- Also developed the concept on how to estimate genetic correlations

CR Henderson (1911-1989)

- Developed and further improved the accuracy of estimated breeding values (EBV)
- Developed the method to derive on best linear unbiased prediction or BLUP

Alan Robertson (1920-1989)

- A British geneticist
- Also famous for developing computer evaluations

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 Chapter 2. Genetic basis of animal differences

A. Gametogenesis and Fertilization

Characteristics of domestic animals are inherited through the random combination of certain
factors (genes) in the parents’ gametes as they are transmitted into their offspring.

▪ Genes are the carrier of hereditary materials. Genes are composed of half-pairs of
chromosomes.
▪ James Watson and Francis Crick described the gene as deoxyribonucleic acid (DNA).
▪ DNA is composed of linear sequence of nucleotides composed of an organic base, a
pentose sugar and a phosphate.
▪ The functions of the gene are to:
1. Store and transmit genetic information from cell to cell and from parent to offspring
2. Copy or replicate itself with great consistency and precision
3. Undergo mutation or error in copying which would subsequently be copied and replicated.

▪ The manner by which the genetic information is transmitted from cell to cell is made possible
through somatic cell division or mitosis. Mitosis serves the function of cell duplication, with
each cell inheriting a complete diploid set of chromosomes.

▪ The transmission of the genetic material from parent to offspring is made possible through the
reduction division during gamete formation (meiosis) and the subsequent union of gametes
(fertilization).

▪ The random process of chromosome combination during meiosis in the reproductive cell
coupled with random combination of the male and female gametes during fertilization promotes
the generation of genotypes that are different from those of the two parents.

Gametes are reproductive cells or sex cells that unite during sexual reproduction to form a new
cell called a zygote.

▪ Male gametes are called sperm and female gametes are ova (eggs).
▪ Sperm are motile and have a long, tail-like projection called a flagellum.
▪ Ova are non-motile and relatively large in comparison to the male gamete.

Gamete formation

Gametes are formed through a process of cell division called meiosis.

▪ This two-step division process produces four haploid daughter cells.

▪ Haploid cells contain only one set of chromosomes.
▪ Gametogenesis, the production of sperm and eggs, takes place through the process of meiosis.
▪ The production of sperm is called spermatogenesis and the production of eggs is called
oogenesis.

Oogenesis occurs in the outermost layers of the ovaries.

▪ Oogenesis starts with a germ cell, called an oogonium, but this cell undergoes mitosis to
increase in number, eventually resulting in up to one to two million cells in the embryo.
▪ The cell starting meiosis is called a primary oocyte.
▪ This cell will begin the first meiotic division, but be arrested in its progress in the first prophase
stage. At the time of birth, all future eggs are in the prophase stage.
▪ At adolescence, anterior pituitary hormones cause the development of a number of follicles in
an ovary. This results in the primary oocyte finishing the first meiotic division.

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 ▪ The cell divides unequally, with most of the cellular material and organelles going to one cell,
called a secondary oocyte, and only one set of chromosomes and a small amount of cytoplasm
going to the other cell.
▪ This second cell is called a polar body and usually dies.
▪ At ovulation, this secondary oocyte will be released and travel toward the uterus through the
oviduct.

Spermatogenesis occurs in the wall of the seminiferous tubules, with stem cells at the periphery of the
tube and the spermatozoa at the lumen of the tube.

▪ These stem cells, called spermatogonia, go through mitosis with one offspring going on to
differentiate into a sperm cell, while the other gives rise to the next generation of sperm.
▪ Meiosis begins with a cell called a primary spermatocyte.
▪ At the end of the first meiotic division, a haploid cell is produced called a secondary
spermatocyte. This haploid cell must go through another meiotic cell division.
▪ The cell produced at the end of meiosis is called a spermatid. When it reaches the lumen of the
tubule and grows a flagellum (or “tail”), it is called a sperm cell.
▪ Four sperm result from each primary spermatocyte that goes through meiosis.

When the haploid male and female gametes unite in a process called fertilization, they form
what is called a zygote. The zygote is diploid and contains two sets of chromosomes.

Illustration courtesy to: www.biologylibretest.com

Fertilization
Fertilization is a complicated multistep molecular process where two highly methylated and
specified haploid gametes, spermatozoon and oocyte, are coming together forming a male and a female
pronucleus, respectively, and culminating in the fusion of the two pronuclei giving rise to the formation
of the zygote. It involves distinct events with the following order:

1. the migration of spermatozoa through the cumulus matrix,

2. the adhesion and penetration of spermatozoa to the zona pellucida, and
3. the fusion of the two plasma membranes,
4. oocyte activation and a fast block to polyspermy events are taking place,
5. while the male and the female pronuclei are coming together forming the nucleus of the zygote
and finalizing in this way the fertilization process.

▪ The spermatozoa after ejaculation are migrating from the uterus to the oviduct and arrive at the
fertilization site in the ampulla.

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 ▪ In this migration process, molecules, such as fertilin, have been implicated, while the
spermatozoa “locate” the ovulated oocyte by chemoattractants released by the oocytes
themselves.
▪ Sperm are specially equipped with burrowing catalysts and mechanisms for fertilizing an egg.
▪ The head region contains a cap-like covering called an acrosome that contains enzymes that
help the sperm cell penetrate the zona pellucida, the outer covering of an egg cell membrane.
▪ When a sperm reaches the egg cell membrane, its head fuses with the egg.
▪ This triggers the release of substances that modify the zona pellucida to prevent any other
sperm from fertilizing the egg.
▪ This process is crucial as fertilization by multiple sperm cells, or polyspermy, produces a
zygote with extra chromosomes. Polyspermy is lethal to a zygote.
▪ A sperm cell may either have an X or Y sex chromosome, but an egg cell can only have an X
chromosome.
▪ A sperm cell with a Y sex chromosome result in a male (XY) and a sperm cell with an X sex
chromosome result in a female (XX).

B. Chromosomes

Chromosomes are thread-like structures located inside the nucleus of animal and plant cells.

- Each chromosome is made of protein and a single molecule of deoxyribonucleic

acid (DNA).
- Passed from parents to offspring, DNA contains the specific instructions that make
each type of living creature unique.

Parts of the Chromosome

Pellicle
• It is the outer envelope around the substance of chromosome.
• It is very thin and is formed of achromatic substances.

Matrix
• It is the ground substance of chromosome which contains the chromonemata.
• It is also formed of non-genic materials.

Chromonemata
• Embedded in the matrix of each chromosome are two identical, spirally coiled
threads, the chromonemata.
• The two chromonemata are also tightly coiled together that they appear as single
thread of about 800A thickness.
• Each chromonemata consists of about 8 microfibrils, each of which is formed of a
double helix of DNA.

Centromere

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 • A small structure in the chromonema,
marked by a constriction which is
recognised as permanent structure in the
chromosome is termed as the centromere.
• At this point the two chromonemata are
joined together.
• It is known as centromere or kinetochore
or primary constriction.
• It divides the chromosome into two
sections, or “arms.” The short arm of the
chromosome is labeled the “p arm.” The
long arm of the chromosome is labeled the
“q arm.”
• Its position is constant for a given type of
chromosome and forms a feature of
identification.
• The chromosomes are attached to spindle
fibres at this region during cell division.

Secondary constriction or Nuclear Organizer

• The chromosome besides having the primary constriction or the centromere

possesses secondary constriction at any point of the chromosome.
• Constant in their position and extent, these constrictions are useful in identifying
particular chromosomes in a set.
• The chromosome region distal to the secondary constriction i.e., the region between
the secondary constriction and the nearest telomere is known as satellite.
• Therefore, chromosomes having secondary constrictions are called satellite
chromosomes or sat-chromosomes.
• Nucleolus is always associated with the secondary constriction of sat-
chromosomes. Therefore, secondary constrictions are also called nucleolus
organiser region (NOR) and sat-chromosomes are often referred to as nucleolus
organiser chromosomes.
Telomeres

• These are specialized ends of a chromosome which exhibits physiological

differentiation and polarity.
• Each extremity of the chromosome due to its polarity prevents other chromosomal
segments to be fused with it. The chromosomal ends are known as the telomeres.
• If a chromosome breaks, the broken ends can fuse with each other due to lack of
telomere.

Types of chromosomes

Autosomes and sex chromosomes

• Human chromosomes are of two types autosomes and sex chromosomes.

• Genetic traits that are linked to the sex of the person are passed on through the
sex chromosomes. The rest of the genetic information is present in the autosomes.
• Humans have 23 pairs of chromosomes in their cells, of which 22 pairs are
autosomes and one pair of sex chromosomes, making a total of 46 chromosomes in
each cell.
• The table below summarizes the number of chromosomes for selected farm animals:

Common name Chromosome Number (2n)

Water buffalo
River type 50
Swamp type 48
Cattle 60
Horse 64

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 Goat 60
Sheep 54
Pig 38
Rabbit 44
Chicken 78
Pekin duck 80
Mallard duck 80
Muscovy duck 80
Geese 80
Guinea fowl 78
Ostrich 80
Pigeon 80
Quail 78
Turkey 82
Dog 78
Cat 38

Number of centromeres

• Monocentric with one centromere.

• Dicentric with two centromeres.
• Polycentric with more than two centromeres
• Acentric without centromere. Such chromosomes represent freshly broken
segments of chromosomes which do not survive for long.
• Diffused or non-located with indistinct centromere diffused throughout the
length of chromosome.

Location of the centromere

• Telocentric are rod-shaped chromosomes with centromere occupying the

terminal position, so that the chromosome has just one arm.
• Acrocentric are also rod-shaped chromosomes with centromere occupying a
sub-terminal position. One arm is very long and the other is very short.
• Sub-metacentric chromosomes are with centromere slightly away from the
mid-point so that the two arms are unequal.
• Metacentric are V-shaped chromosomes in which centromere lies in the
middle of chromosome so that the two arms are almost equal.

Function and Significance of the chromosomes

The number of the chromosomes is constant for a particular species. Therefore, these are of
great importance in the determination of the phylogeny and taxonomy of the species.

• Genetic Code Storage: Chromosome contains the genetic material that is required by the
organism to develop and grow. DNA molecules are made of chain of units called genes.

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 Genes are those sections of the DNA which code for specific proteins required by the cell for
its proper functioning.
• Sex Determination: Humans have 23 pairs of chromosomes out of which one pair is the sex
chromosome. Females have two X chromosomes and males have one X and one Y
chromosome. The sex of the child is determined by the chromosome passed down by the
male. If X chromosome is passed out of XY chromosome, the child will be a female and if a Y
chromosome is passed, a male child develops.
• Control of Cell Division: Chromosomes check successful division of cells during the process
of mitosis. The chromosomes of the parent cells insure that the correct information is passed
on to the daughter cells required by the cell to grow and develop correctly.
• Formation of Proteins and Storage: The chromosomes direct the sequences of proteins
formed in our body and also maintain the order of DNA. The proteins are also stored in the
coiled structure of the chromosomes. These proteins bound to the DNA help in proper
packaging of the DNA.

C. The cell cycle: mitosis and meiosis

Actively dividing eukaryote cells pass through a series of stages known collectively as
the cell cycle. The cell cycle has two gap phases (G1 and G2); a synthesis or S phase in
which the genetic material is duplicated; and an M phase, wherein mitosis partitions the
genetic material and the cell divides.

• G1 phase. Metabolic changes prepare the cell for division. At a certain point - the
restriction point - the cell is committed to division and moves into the S phase.
• S phase. DNA synthesis replicates the genetic material. Each chromosome now
consists of two sister chromatids.
• G2 phase. Metabolic changes assemble the cytoplasmic materials necessary for
mitosis and cytokinesis.
• M phase. A nuclear division (mitosis) followed by a cell division (cytokinesis).
The period between mitotic divisions - that is, G1, S and G2 - is known as interphase.

Downloaded from University of Leicester- online Biology class

https://www2.le.ac.uk/projects/vgec/highereducation/topics/cellcycle-mitosis-meiosis

C.1. Mitosis

▪ Mitosis is a form of eukaryotic cell division that produces two daughter cells with the same
genetic component as the parent cell.

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 ▪ Chromosomes replicated during the S-phase are divided in such a way as to ensure that
each daughter cell receives a copy of every chromosome.
▪ In actively dividing animal cells, the whole process takes about one hour.
▪ The replicated chromosomes are attached to a 'mitotic apparatus' that aligns them and then
separates the sister chromatids to produce an even partitioning of the genetic material. This
separation of the genetic material in a mitotic nuclear division (or karyokinesis) is followed
by a separation of the cell cytoplasm in a cellular division (or cytokinesis) to produce two
daughter cells.

Mitosis, although a continuous process, is conventionally divided into five stages:

o prophase,
o prometaphase,
o metaphase,
o anaphase and
o telophase.

Downloaded from University of Leicester- online Biology class

https://www2.le.ac.uk/projects/vgec/highereducation/topics/cellcycle-mitosis-meiosis

Prophase
Prophase occupies over half of mitosis. The nuclear membrane breaks down to form a number of
small vesicles and the nucleolus disintegrates.

A structure known as the centrosome duplicates itself to form two daughter centrosomes that migrate
to opposite ends of the cell. The centrosomes organise the production of microtubules that form the
spindle fibres that constitute the mitotic spindle. The chromosomes condense into compact
structures. Each replicated chromosome can now be seen to consist of two
identical chromatids (or sister chromatids) held together by a structure known as the centromere.

Prometaphase
The chromosomes, led by their centromeres, migrate to the equatorial plane in the mid-line of the cell
- at right-angles to the axis formed by the centrosomes. This region of the mitotic spindle is known as
the metaphase plate. The spindle fibres bind to a structure associated with the centromere of each

14
chromosome called a kinetochore. Individual spindle fibres bind to a kinetochore structure on each
side of the centromere. The chromosomes continue to condense.
Metaphase
The chromosomes align themselves along the metaphase plate of the spindle apparatus.

Anaphase
The shortest stage of mitosis. The centromeres divide, and the sister chromatids of each
chromosome are pulled apart - or 'disjoin' - and move to the opposite ends of the cell, pulled by
spindle fibres attached to the kinetochore regions. The separated sister chromatids are now referred
to as daughter chromosomes. (It is the alignment and separation in metaphase and anaphase that
is important in ensuring that each daughter cell receives a copy of every chromosome.)

Telophase
The final stage of mitosis, and a reversal of many of the processes observed during prophase. The
nuclear membrane reforms around the chromosomes grouped at either pole of the cell, the
chromosomes uncoil and become diffuse, and the spindle fibres disappear.

Cytokinesis
The final cellular division to form two new cells. In plants a cell plate forms along the line of the
metaphase plate; in animals there is a constriction of the cytoplasm. The cell then enters interphase -
the interval between mitotic divisions.

C.2. Meiosis

Meiosis is the form of eukaryotic cell division that produces haploid sex cells or gametes, which
contain a single copy of each chromosome from diploid cells or cells that contain two copies of each
chromosome. The process takes the form of one DNA replication followed by two successive nuclear
and cellular divisions (Meiosis I and Meiosis II). Just like in mitosis, meiosis is preceded by a process
of DNA replication that converts each chromosome into two sister chromatids.

Prophase I
The homologous chromosomes pair and exchange DNA to form recombinant chromosomes.
Prophase I is divided into five phases:

Leptotene: chromosomes start to condense.

Zygotene: homologous chromosomes become closely associated (synapsis) to form
pairs of chromosomes (bivalents) consisting of four chromatids (tetrads).
Pachytene: crossing over between pairs of homologous chromosomes to form
chiasmata (sing. chiasma).
Diplotene: homologous chromosomes start to separate but remain attached by
chiasmata.

Diakinesis: homologous chromosomes continue to separate, and chiasmata move to

the ends of the chromosomes.

Prometaphase I
Spindle apparatus formed, and chromosomes attached to spindle fibres by kinetochores.

Metaphase I
Homologous pairs of chromosomes (bivalents) arranged as a double row along the metaphase plate.
The arrangement of the paired chromosomes with respect to the poles of the spindle apparatus is
random along the metaphase plate.

This is a source of genetic variation through random assortment, as the paternal and maternal
chromosomes in a homologous pair are similar but not identical. The number of possible
arrangements is 2n, where n is the number of chromosomes in a haploid set. Human beings have 23
different chromosomes, so the number of possible combinations is 2 23, which is over 8 million.

15
Anaphase I
The homologous chromosomes in each bivalent are separated and move to the opposite poles of the
cell

Telophase I
The chromosomes become diffuse and the nuclear membrane reforms.

Cytokinesis
The final cellular division to form two new cells, followed by Meiosis II. Meiosis I is a reduction
division: the original diploid cell had two copies of each chromosome; the newly formed haploid cells
have one copy of each chromosome.

D. Nature and functions of gene

Following the model of Watson and Crick, the gene or DNA is composed of a linear sequence
of nucleotides. Each nucleotide contains an organic base, a pentose sugar and a phosphate.

• There are four (4) nucleotide bases;

Purines: Adenine (A), Guanine (G)
Pyrimidines: Cystine (C) Thymine (T).

• The strands are arranged in coiled, spiral or helical manner. The strands are held together by
hydrogen bonds between pairs of bases with the phosphate and sugar forming the outside of
the helix.
• The two strands are complementary to each other:

A-------T
C--------G

16
 • During cell multiplication, the two strands separate and each strand combines with the new
string of nucleotide in exactly the same
pairing as before. The strand also separates
during replication.
• Each strand serves as the template for the
synthesis of a new complementary strand,
thus maintaining the of the genetic
continuity.

• Transcription is the process by which DNA

is copied (transcribed) to mRNA, which
carries the information needed for protein
synthesis.
• The mRNA formed in transcription is transported out of the nucleus, into the cytoplasm, to the
ribosome (the cell's protein synthesis factory).
• It directs protein synthesis. Messenger RNA is not directly involved in protein synthesis −
transfer RNA (tRNA) is required for this. The process by which mRNA directs protein synthesis
with the assistance of tRNA is called translation.

The genetic code

The genetic code is almost universal. It is the basis of the transmission of hereditary information
by nucleic acids in all organisms. There are four bases in RNA (A,G,C and U), so there are 64 possible
triplet codes (43 = 64).

In theory only 22 codes are required: one for each of the 20 naturally occurring amino acids,
with the addition of a start codon and a stop codon (to indicate the beginning and end of a protein
sequence).

• Many amino acids have several codes (degeneracy), so that all 64 possible triplet codes are
used. For example, Arg and Ser each have 6 codons whereas Trp and Met have only one.
• No two amino acids have the same code but amino acids whose side-chains have similar
physical or chemical properties tend to have similar codon sequences, e.g. the side-chains of
Phe, Leu, Ile, Val are all hydrophobic, and Asp and Glu are both carboxylic acids.
• This means that if the incorrect tRNA is selected during translation (owing to mispairing of a
single base at the codon-anticodon interface) the misincorporated amino acid will probably
have similar properties to the intended tRNA molecule.
• The synthesis of protein as specific combinations of amino acids, and amino acids as specific
combinations of the bases, thus there is magnitude of information that may be genetically
coded.
• Translation starts when codon AUG appears, and it will stop when either codon UAA, UAG
and UGA appears.

17
 • The table below shows the amino acids are that coded in each codon:

To sum up the process, refer to the figures below:

Photo courtesy of: www.google.com

18
 Module 3. Principles of Mendelian Genetics
Law of segregation

Gregor Mendel studied inheritance of traits in pea plants. He proposed a model where pairs of
"heritable elements," or genes, specified traits. Genes come in different versions, or alleles.
A dominant allele hides a recessive allele and determines the organism's appearance. When an
organism makes gametes, each gamete receives just one gene copy, which is selected randomly.
This is known as the law of segregation.

A Punnett square can be used to predict genotypes (allele combinations)

and phenotypes (observable traits) of offspring from genetic crosses. A test cross can be used to
determine whether an organism with a dominant phenotype is homozygous or heterozygous.

Example:

Mendel studied the genetics of pea plants, and he traced the inheritance of a variety of
characteristics, including flower color, flower position, seed color, and seed shape. To do so, he
started by crossing pure-breeding parent plants with different forms of a characteristic, such as violet
and white flowers. Pure-breeding just means that the plant will always make more offspring like itself,
when self-fertilized over many generations.

What results did Mendel find in his crosses for flower color? In the parental line, Mendel
crossed a pure-breeding violet-flowered plant to a pure-breeding white-flowered plant. When he
gathered and planted the seeds produced in this cross, Mendel found that 100 percent of the plants in
the next generation had violet flowers.

Conventional wisdom at that time would have predicted that the hybrid flowers should be pale
violet—that is, that the parents' traits should blend in the offspring. Instead, Mendel’s results showed
that the white flower trait had completely disappeared. He called the trait that was visible (violet
flowers) as the dominant trait, and the trait that was hidden or lost (white flowers) the recessive
trait.

19
 Mendel did not stop his experimentation there. Instead, he let the plants self-fertilize. Among
their offspring, called the F2, he found that 705 plants had violet flowers and 224 had white flowers. This
was a ratio of 3.153.153, point, 15 violet flowers to one white flower, or approximately 3:1. The other
characteristics of pea plants that proven to have 3:1 ratio are the following:

20
Law of Independent Assortment

Independent assortment of genes and their corresponding traits was first observed by Gregor
Mendel in 1865 during his studies of genetics in pea plants. Mendel was performing dihybrid crosses,
which are crosses between organisms that differ with regard to two traits. He discovered that the
combinations of traits in the offspring of his crosses did not always match the combinations of traits in
the parental organisms.

States that the alleles of two (or more) different genes get sorted into gametes independently of
one another. In other words, the allele a gamete receives for one gene does not influence the allele
received for another gene.

Example:

Imagine that we cross two pure-breeding pea plants:

1. one with yellow, round seeds (YYRR) and
2. one with green, wrinkled seeds (yyrr).

Because each parent is homozygous, the law of segregation tells us that the gametes made by the
wrinkled, green plant all are ry, and the gametes made by the round, yellow plant are all RY. That gives
offspring that are all RrYy.

The allele specifying yellow seed color is dominant to the allele specifying green seed color, and
the allele specifying round shape is dominant to the allele specifying wrinkled shape, as shown by the
capital and lower-case letters. This means that the \text F_1F1start text, F, end text, start subscript, 1,
end subscript plants are all yellow and round. Because they are heterozygous for two genes, the plants
are called dihybrids (di- = two, -hybrid = heterozygous).

A cross between two dihybrids (or, equivalently, self-fertilization of a dihybrid) is known as

a dihybrid cross. When Mendel did this cross and looked at the offspring, he found that there were
four different categories of pea seeds: yellow and round, yellow and wrinkled, green and round, and

21
green and wrinkled. These phenotypic categories (categories defined by observable traits) appeared
in a ratio of approximately 9:3:3:1

Illustration of the hypothesis that the seed color and seed shape
genes assort independently.

In this diagram, the Y and R alleles of the yellow, round parent and the y and r alleles of the green,
wrinkled parent are not inherited as units. Instead, the alleles of the two genes are inherited as
independent units.

Parent generation: A yellow, round plant (YYRR) is crossed with a green, wrinkled plant (yyrr). Each
parental generation can produce only one type of gamete, YR or yr.

F1 generation: The F1 dihybrid seeds are yellow and round, with a genotype of YyRr. The F1 plants
can produce four different types of gametes: YR, Yr, yR, and yr. We can predict the genotypes of the
F2 plants by placing these gametes along the top and side axes of a 4X4 Punnett square and filling in
the boxes to represent fertilization events.

F2 generation: Completion of the Punnett square predicts four different phenotypic classes of offspring,
yellow/round, yellow/wrinkled, green/round, and green/wrinkled, in a ratio of 9:3:3:1. This is the
prediction of the model in which the seed shape and seed color genes assort independently.

3. Punnett square:

YR Yr yR yr
YR YYRR YYRr YyRR YyRr
Yr YYRr YYrr YyRr Yyrr
yR YyRR YyRr yyRR yyRr
yr YyRr Yyrr yyRr yyrr

22
Plain text = yellow, round phenotype Italic text = yellow, wrinkled phenotype Bold text = green, round
phenotype Bold, italic text = green, wrinkled phenotype

This ratio was the key clue that led Mendel to the law of independent assortment. That's because
a 9:3:3:1 ratio is exactly what we'd expect to see with equal frequency: YR, Yr, yR, and yr. In other
words, this is the result we'd predict if each gamete randomly got a Y or y allele, and, in a separate
process, also randomly got an R or r allele (making four equally probable combinations). We can
confirm the link between the four types of gametes and the 9:3:3:1 ratio using the Punnett square above.

Examples of traits in selected domestic animals:

Some Examples of Dominant and Recessive Traits in

Selected Domestic Animals
From: Genetics of Domestic Animals - Charles E. Stufflebeam
Species Dominant Trait Recessive Trait
Cattle Black Hair Coat Red Hair Coat
Polled Horns
White Face Solid Color
Solid Color Irregular white spotting
Red Yellow
Cloven Hooves Mule feet
Chickens Rose Comb Single Comb
White Skin Yellow Skin
Dominant White Color
Colored Feathers Recessive White
Pea Comb Single Comb
Feathered Shanks Clean Shanks
Black Feathers Red Feathers
Horses Black Hair Coat Chestnut or Sorrel
Bay Nonbay (Black)
Chestnut mane and tail Flaxen mane and tail
Smooth Hair Curly Hair
Sheep Hairy Fleece Wooly Fleece
White Wool Black Wool
Brown Eyes Blue Eyes
Swine Black Hair (Hampshires) Red Hair
White Belt No Belt
Erect Ears Drooping Ears
Mule Foot Cloven Hoof
Dogs Wire Hair Smooth Hair
Black Hair Liver Color
Red Hair Yellow Hair
Solid Color White Spotting
Cats Short Hair Long Hair
Black Hair Brown Hair
Agouti (wild color) Nonagouti
Color White

23
 Chapter 4
Selection in Farm Animals
I. Introduction

In animal production, reproduction is important to increase the population of the herd. However,
in doing so, it is a must that proper selection of parental stock should be done.

Selection is a process of increasing the frequency of the desirable genes and traits, thereby
allowing certain animals to be parents of the future generations. To attain this, animals that do not
possessed the desirable traits are removed or culled. Therefore, animals retained have certain desirable
characteristics which make them produce more.

Selection among and within breeding stocks is the main tool for genetic improvement of farm
livestock. Individual merit is the most efficient method to select for several traits. It can be done for a
single trait and also for more than one character. Progress made in any selection program over a period
of time is known as genetic reach (or loss) in case of some failures and this is affected by heritability of
the traits, generation interval of animals involved and amount of selection pressures applied in the
process.

II. Learning objectives

At the end of the module, the learners should be able to:

1. Understand the principles of selection;

2. Familiarize with the methods of selection; and
3. Understand and familiarize the factors to consider in selecting a breeding stock.

III. Learning content

A. Principles of Selection

Selection is one of the primary forces available to the animal breeder to change the genetic
composition of a population. Within a population, the objective of selection is to accumulate the largest
possible number of genes with favorable effects on the traits of interest. Selection does not create new
genes, but by permitting animals possessing certain genes to leave more offspring, it increases the
frequency of the more desirable alleles.

Natural and Artificial Selection

Natural selection or survival of the fittest, the animals best adapted to their environment survive
and produce the largest number of offspring. A population will show genetic traits over many
generations that help it remain best suited to its environment. These can be physical, structural traits
like a skeleton or musculature that helps it live in that setting, or can even by physiological traits such
as the presence of an enzyme in the digestive tract to help it break down the available food sources.

For example, giraffes, lizards, and many other known species adapted to their environments
through genetic changes to their skeletons. This form of natural selection meant that members of the
population who didn't develop and present these skeletal changes died out. However, giraffes
developed long necks to reach food sources higher up in trees, so members of the giraffe population
who didn't develop a long neck died out. At the same time, certain lizards in one region developed
longer leg bones to help it climb up during periods of flood and to escape predators in the ground;
shorter legged lizards of the same population died out until only the lizards with the long legs survived.

On the other hand, artificial selection is the tool used by man to alter the appearance and
productivity of domesticated animals. It is selection based on a set of rules dictating which individuals
will become parents. Artificial selection differs from natural selection is that in artificial selection, animals
removed from the population may be capable of surviving and reproducing.

A common example of artificial selection in animals is dog breeding. As with racehorses,

particular traits are desirable in different breeds of dogs that compete in dog shows. The judges look at
coat coloring and patterns, behavior, and even teeth.

24
Genetic effects of selection

The basic effect of either natural or artificial selection is the changes in the array of gene
frequencies. Although almost completely hidden, the change in genetic frequency can be observed
through changes in the mean. The change in the mean can be described by comparing successive
generations at the same point in the life cycle of the individuals.

The principle of selection is the same in the case of a single gene and polygenic traits. Hence,
the next generation will be composed of individuals carrying more of the superior genes than those in
the parent generation.

The improvement in the population mean due to selection or response to selection is the mean
phenotypic value of offspring generation minus the mean of the whole parental generation before the
selection. As such, the equation is:

R= M1 - Mo

The genetic change or response due to selection is attributed to:

1. Artificial selection among adults of parent generation

2. Natural differences of fertility among individuals of parent generation,
3. Natural differences in viability among the individuals of offspring generation.

Response to selection may also be predicted as

R= h2S; where h2 is heritability of the trait and S is the selection differential.

Selection differential is the measure of selection applied, which the difference in the mean
phenotypic value of the individuals selected as parents (Ms) and that of the individuals before selection
(Mo). Therefore, S= Ms - Mo.

B. Methods of selection

B. 1. Individual selection

Individual selection is based on an individual’s own performance record or phenotype. All

potential parents have to be recorded for the criteria selection, Also, the required number of animals
most closely meeting the breeder’s objectives is selected.

Individual selection is usually needed for the improvement of growth, feed efficiency and
carcass traits that can usually be measured before puberty, and have moderate to high heritability. This
is particularly the case for meat strains of poultry with no pedigree recording, and for goats and beef
cattle with few sibs.

B.2. Use of information from relatives

Information of ancestors, collateral relatives and the progeny test are also valuable aids to
individual selection for specific traits. The following selection basis or criteria uses relative information
and records:

Selection on the basis of pedigree- the pedigree of an animal is a record of its ancestral line or bloodline.
Pedigree information provides added accuracy in female evaluation, especially in evaluating traits with
low heritability.

For example, in pigs, the pedigree records and information from a number of relatives are often
combined as a family index.

A pedigree index computed as the regression of young sires and dams on the expected progeny
differences of its male ancestors have also been derived for dairy cattle (Schaeffer 1981) and for beef
cattle (Bondoc, et la 1997).

The disadvantage of pedigree selection is usually associated with undue emphasis on remote relatives
resulting in lower intensity selection, and with unwarranted favoritism toward the progeny of favored
individuals.

25
Selection on the basis of progeny tests- progeny testing evaluates the genotype of an animal on the
basis of the average performance of its progenies. Progeny testing is usually indicated for selection of
males when the trait is not measured in males. For example, in selection of sex-limited traits such as
milk production in dairy bulls will be based on progeny records. Progeny testing is not usually advised
for evaluation of females, although for some traits progeny records actually measure the female’s
performance. For example, the weaning weight of her calf is an indication of the beef cow’s milk
production.

An effective progeny-testing program requires that many more animals must be progeny tested than
are required for eventual use. For example, progeny testing programs for males usually will require four
to five individuals be progeny tested for each progeny tested sire that is chosen. The application of
progeny test in the selection of females is definitely limited because of the inability to obtain many
progenies from females. While progeny test can provide an extremely accurate appraisal of an animal’s
breeding value, its major limitation is in the time and expense required to obtain the information. More
importantly, there must be a means of utilizing the superior animals extensively once they have been
located.

Selection on the basis of sib information- Sib testing or selection on records of sibs, such as half sibs
or full sibs is applied to some traits that cannot be measured on the animals that are to be used as
parents and selection can only be based on the values of relatives. Sib selection may also be advised
for such traits as carcass measurements which cannot be obtained on the live animal. However, since
sib records may be environmentally correlated, the accuracy of evaluation may be lower.

In pigs and poultry for example, large families of full sibs are available and selection for most traits is
based on family performance. Family performance can be represented as a part of pedigree selection
wherein information from collateral relatives such as sibs may provide information on the family to
predict the breeding value of an ancestor even if the individual receives no genes from its collateral
relatives.

B.3. Use of measurements of several traits

• Tandem method- This method is time consuming and requires a lot of resources including
money and facilities before each trait in a set of characteristcs can be improved fully based
on desired levels.

• Independent culling method- In this method, there are traits identified and used for the
selection. When one trait does not meet the standard, then the animal is totally rejected even
if the other traits are present.

• Selection index- In this method, is the most applicable when selecting for more than one
quantitative trait. It includes all the traits simultaneously with their corresponding importance
or weights. The selection index is usually in the form of a regression equation applied to all
the members of a given animal population whose traits were previously studied and included
in the selection process.

A. Factors to consider in selecting a breeding stock

Basic consideration in selecting breeder animals

A. Age- in selecting breeders, consider the following:

o Young animals
o Animals that have not parturated for more 3 times
o They have a longer productive life
o Old animals are poor breeders and low breeders- production and breeding efficiency
decline with age

B. Level of performance- animals with highest production level selected and performance is best
indicated by records

o Good performance of animal is indicated by high milk, wool and egg production

26
 o Good mothering ability
o High prepotency which is the ability of a parent to pass good qualities to their offspring

C. Physical fitness- animals selected should be free from any physical defect, to include:
o Mono-eyed
o Limping
o Irregular number of teats
o Scrotal hernia
o Defective and weak backline

D. Health
o Sick animals do not breed well and are expensive to keep
o Animals that are resistant to diseases pass these characteristics to their offspring

E. Body conformation
o Animals for breeding to be selected according to proper body conformation
o Example: A dairy cow should be wedge-shaped with a large udder, this legs, long neck.

F. Temperament or Bahaviour
o Animals with bad behaviors should be culled, to include cannibalism, egg eating,
aggressiveness.

G. Quality of products
o Select animals that give products of high quality as meat, wool, eggs and milk.

H. Mothering ability
o Animals selected should have good mothering ability.
o Animals with good natural instinct towards their young ones.

I. Adaptability
o Animals selected should be well adapted to the prevailing climatic condition in the area.

J. Prolificacy
o Animals selected should be highly prolific, that is animals with the ability to give birth to
many offspring at a time (larger litter)

B. Selection guide in different farm animals

In selecting stocks, consider the following:

A. Cattle
o Level of performance which include milk yield, butter content, length of lactation period
and calving interval.
o Age of the animal
o Reproduction related performance such as fertility, age at first breeding

B. Sheep
o Level of performance which include mothering ability, growth rate, wool quality, carcass
quality, twinning rate
o Absence of inheritable defects

C. Goat
o Fertility
o Mothering ability
o Growth rate
o Twinning rate
o Carcass quality and dressing percentage
o Suitability to the enterprise- milk and meat

27
 o Health of the animal
D. Pig
o Carcass quality and dressing percentage
o Growth rate
o Mothering ability
o Prolificacy
o Number of teats
o Temperament
o Body conformation
o Absence of heredity defects

28
 Chapter 5
Systems of Mating

A. Inbreeding

Inbreeding results from the mating of related animals. It occurs in progeny of related parents.
When related animals are mated, the offspring tend to become more homozygous. The increase in
homozygosity and the accompanying decrease in heterozygosity are the underlying reasons for the
genotypic and phenotypic changes, which are all associated with inbreeding.

Relationship Coefficient

Relationship is based on the probability that two animals are alike in more of their genes than
two other random animals from the breed or population. The coefficient of relationship measures the
probable proportion of genes that are alike for two animals due to their common ancestry.

1. Additive relationship- is the most commonly used measure of relationship. It is a measure of

the fraction of like genes shared by two animals. It is an indication of how reliable one of the
relative’s records will be in predicting the genetic value of the other animal. Additive genetic
relationships among animals are also needed for weighing records of relatives for genetic
evaluation and for computing inbreeding coefficient.
2. Dominance relationship- the dominance relationship between relatives is a measure of the
covariance between the dominance deviations. The dominance relationship between relatives
can be computed from the additive relationship among the parents of the two animals. The
parents must be related if the complete genotype at a locus is identical by descent for the two
animals.

3. Inbreeding coefficient- is defined as the probability that two genes at a locus are identical by
descent. The inbreeding coefficient can be interpreted as:

1. The expected fraction of an animal’s loci which have the pair of genes identical by descent, or
equivalent; and
2. As the fraction of animals with the same pattern of related ancestors having genes identical by
descent at a particular locus.

Moreover, inbreeding coefficient can also be used to measure how closely the parents are related. It
can also measure the amount of inbreeding that has been practiced, which range in value from 0 to 1.

Consequences of inbreeding

Inbreeding does not create the undesirable recessive genes. It merely permits them to be
expressed due to increased homozygosity. Homozygosity reduces vigor since most recessive alleles
in the population are harmful. The decrease in the number of heterozygotes decreases fitness since
some loci in the heterozygote is superior in fitness to either homozygote.

1. Exposure of undesirable recessive gene combination- inbreeding tends to bring to light

undesirable recessive genes. In small populations, some alleles may be lost by chance as
inbreeding progresses. Inbreeding tends to uncover undesirable recessive gene that were
previously concealed by heterozygosity with dominant alleles. Inbreeding in itself is almost
universally harmful.

If an undesirable gene is in the population at a very low frequency, the probability of its
expression is small. Mating of relatives that have an ancestor carrying the gene, however, will
dramatically increase the frequency of expression. In this case, inbreeding can be used as a
method of detecting lethal genes, specifically mating of sire with his daughters to screen all
genes at all loci.

29
 2. Inbreeding depression- Inbreeding depression is the decrease in the average performance of
animals in the population resulting from an increase in the homozygosity of genes with sublethal
and deleterious effects. The decline in the average phenotypic merit is especially true for fertility
traits.

In pigs, for example, the extensive use of a few outstanding boars and/or sows may narrow the
genetic base and result in detrimental effects from long term inbreeding. Reports of average
inbreeding per generation were however low, about 0.5% per generation or about 0.1% or 0.2%
per year in many breeds of livestock.

3. Practical uses of inbreeding- with inbreeding, the mates are chosen to have a common
ancestral (pedigree) background or relationship. In animal production, inbreeding can be
utilized to increase the prepotency of an individual, to detect lethal genes to evaluate an
individual, to achieve concentrated use of a genetically superior individual through line
breeding, and to develop inbred lines for later crossing to take advantage of the concept of
heterosis.

Increased prepotency- prepotency has reference to the ability of an animal to stamp its
characteristics on its offspring to the exclusion of the effects of genes from the other parent.
Inbreeding is the only known method of increasing prepotency leading to greater uniformity
within lines, strains or breeds.

Detection of lethal genes- inbreeding increases the occurrence of deleterious genes, which
would allow culling of affected and carrier animals and thereby reduce the frequency of the
detrimental genes.

For example, the critical evaluation of an animal involves mating him to a certain number of his
female relatives to test for the presence of undesirable recessive genes. Once the sire is tested
in this manner and he does sire any progeny that express the undesirable recessive genes,
then it may be desirable to utilize the sire in the line breeding program.

Concentrated use of a genetically superior animal- concentrated use of a genetically

superior animal is accomplished through the use of a milder form in inbreeding known as line
breeding. The primary objective of line breeding is to maintain a high degree relationship
between animals in the pedigree but at a rather low level of inbreeding. Thus, line breeding
should be utilized in more herds of relatively high genetic merit, which are devoted primarily to
production of breeding stock or the livestock industry.

Formation of inbred lines- inbreeding may be used to separate a breed into strains, lines or
families. A strain, line or family represents a group of animals having a genetic relationship.
Inbreeding (in combination with selection) can be utilized to develop genetically different inbred
lines for later crossing to take advantage of heterosis. The linecrosses resulting from mating
between inbred lines would have mostly heterozygous loci and thus might be superior to non-
inbred animals if there is some form of dominant action.

B. Outbreeding

Outbreeding refers to mating of animals less closely related than the average of the population
from which they came. It is the opposite or mirror image of inbreeding and the genetic consequences
of outbreeding are also the opposite of those in inbreeding. In general terms, the fitness lost on
inbreeding tends to be restored on outbreeding.

Outbreeding increases the heterozygosity in a population. It increases the frequency of

heterozygotes at the expense of the homozygotes. It also destroys family, line or strain formation, tends
to increase average phenotypic merit of animals, and tends to reduce prepotency of an animal.

Topic 1. Forms of outbreeding

30
Outcrossing- refers to the mating of unrelated animals within a particular breed. The idea is to mate
unrelated animals within a breed that are considered to be genetically superior for certain traits. This
mating procedure followed by most purebred livestock breeders tends to bring about immediate
improvement for certain traits, especially those that express high heritability values.

For example, when a swine breeder wishes to reduce the backfat thickness within the herd, outcrossing
is done. Since backfat thickness in swine is a trait which expresses a relatively high heritability value,
average backfat thickness within a herd would be expected to decline when purebred boars with low
probe backfat thickness measurements are used.

Linecrossing- refers to the mating of animals from different inbred lines. Linecrossing takes advantage
of both the increased homozygosity within an inbred line and the differences between inbred lines.
Progeny resulting from crossing two highly inbred lines are generally uniform in genotype and
consequently more uniform in their performance than those from random mating populations. Inbred
lines most diverse in origin, hence it expresses more heterosis in the crosses.

Crossbreeding- refers to the mating of animals from different breeds. Breeds, however, can also be
considered as lines within the species that differ in gene frequencies. The differences in frequency are
usually a result of emphasis on different trait selection (e.g. selection for milk yield versus beef
production in cattle), or of natural selection if the breeds originate from different geographical locations
(e.g. development of tropical breeds of cattle as compared to temperate zone breeds).

The purpose of the crossing is partly to make use of heterosis to improve the fertility and partly to
combine the different characteristics for which the lines were previously selected.

For example, in meat production, a desirable quality in the final product is rapid growth and what is
desired of the final cross is to produce large numbers of rapidly growing individuals. To attain this, it
requires good fertility in the mother coupled with good growth rate in the progeny. Current crossbreeding
systems in the farm animals are thus based on F 1 hybrid females with good fertility, which is derived
from heterosis. The growth rate on the other hand of the crosses may not be as good as the best of the
lines, but the increased numbers produced by the fertile hybrid mothers in a 3-way cross or backcross
make the crossing more economically advantageous.

The most common crossbreeding systems utilized straightbred sires: two-breed crossing, backcrossing,
three-breed crossing, four-breed terminal cross or topcrossing, crisscrossing or two-breed rotation,
three or four breed rotation.

The use of genetically superior sires for crossbreeding, however, is just as important as for the
straightbred operations. Crossing of two animals inferior with respect to a particular trait will, on the
average, result in a crossbred also inferior in this trait.

Two-breed crossing or single crosses:

Breed (A) (sire) x Breed (B) (dam)

(50% A – 50% B)
All progenies marketed

In a two-breed cross (crossing or two purebred), all crossbred progeny is sold, and as a result
do not provide for replacement females. Straightbred replacement females have to be purchased or
produced in another herd. The two-breed crossing system only takes advantage of heterosis expressed
by the crossbred progeny.

In this terminal cross program, the crossbred progeny never enters the breeding populations.
Otherwise, mating of crossbreds with other crossbreds will eventually result in a considerable variation
in performance because of the segregation and recombination of genes in the crossbred progeny.

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Backcrossing:

Breed A (sire) x Breed B (dam)

Breed A (sire) x (50% A - 50% B)

Replacement females

(75%A - 25%B)
All progenies marketed

Backcrossing is the mating of crossbred females with one of the parent purebreds. The
crossbred (A X B) females have half of their genes in common with breed A sires. Heterosis will only
have an effect on 50% of breed B genes in the A x B females. Heterosis, is only 50% as strong as in a
single cross. Backcrossing may, however, result in a more uniform set of progenies.

Three-breed crossing:

Breed A (sire) x Breed B (dam)

Breed C (sire) x (50% A - 50% B)

Purchased or produced
in another herd

(25%A - 25%B - 50%C)

All progenies marketed

In a three-breed cross, all triple crossbred progeny are also sold, with two-breed cross females
females purchased or produced in another herd. Sire breeds other than the two purebreds could be
used as the terminal sire breed. This crossing system yields the maximum heterosis. It takes advantage
of heterosis expressed by the crossbred progeny and the crossbred dam.

Example:

In pigs, two-breed or three-breed crossbred sows are highly prolific, have better fertility, bigger
and more uniform litter, and heavier piglets at birth. The slaughter hybrid pigs are outstanding in terms
of growth rate, feed conversion efficiency and carcass quality (Penalba, 1992).

Four-breed terminal cross or topcrossing:

In this system, the breeder may develop two specialized crosses, for example, the A x B
crossbred animal may provide growth to its progenies through increased milk yields and perhaps better
livability. The other cross C x D, would be a fast gaining, high market weight, or good carcass type of
breed or breed cross.

32
 Breed A (sire) x Breed B (dam) Breed C (sire) x Breed D (dam)

(50%A - 50%B) x (50%C - 50%D)

Paternal line, Maternal line,
Female progenies marketed Male progenies marketed

(25%A - 25%B - 25%C - 25%D)

All progenies marketed

Crisscrossing:

Crisscrossing is the same as a two-breed rotational crossing system. With natural mating,
females within a herd are initially assumed to be easily divided into those that are predominantly of
breed A and those that are predominantly of breed B.

Under the crisscross system, it produces its own replacement females compared to the three-
bred crossing system, which does not provide for replacement females. Where AI is practiced, it may
be possible to maintain all breeding females in a single unit, thereby eliminating a need for several
herds during the breeding season.

HERD 1 HERD 2
Breed A (sire) x Breed B (dam) Breed B (sire) x Breed A (dam)

Breed B (from x (50%A - 50%B) Breed A (from x (50%B - 50%A)

herd 2 sire) females herd 1 sire) females

Breed A (sire) x (25%A – 75% B) Breed B (sire) x (25%B – 75% A)

females females

Breed B (from x (62.5%A- 37.5B) Breed A (from x (62.5%B- 37.5A)

herd 2 sire) females herd 1 sire) females

Breed A (sire) x (31.25%A – 68.75%B) Breed B (sire) x (31.25%B – 68.75%A)

females females

Breed B (from x (65.62%A - 34.38%B) Breed A (from x (65.62%B - 34.38%A)

herd 2 sire) females herd 2 sire) females

(33.33%A- 67.67%B) (33.33%B- 67.67%A)

Three-bred rotation:

Breed A sires are exposed to breed B females resulting in the production of ½ A – ½ B

replacement females. These two-breed cross females are then mated to sres from breed C resulting in
the production of ¼ A – ¼ B – ½ C females, which are then bred to breed B sires. The sire breeds are
used on a rotation basis with breed A, breed C and breed B sires being used in that order. The breed
composition of the crossbred progeny will stabilize at 58%- 28%-14% depending on the last breed of
sire used of rotation.

Heterosis realized from the three-breed rotation will stabilize at about 85.7% of maximum
possible for crossbred progeny heterosis and at about 85.7% of the dam (maternal) heterosis.

33
 Breed A (sire) x Breed B (dam)

Breed C (sire) x (50% A - 50% B)

Replacement females

Breed B x (25%A - 25%B - 50%C)

(sire) replacement females

Breed A x (12.5%A - 62.5%B - 25%C)

(sire) replacement females

Breed C x (56.25%A - 31.25%B - 12.5% C)

(sire) replacement females

Breed B x (28.125%A - 15.625%B - 56.25%C)

(sire) replacement females

(58%A - 285B - 14%C)

stabilized three-breed cross

Four-breed rotation:

Breed A sires are bred initially to breed B females resulting in the production of ½ A - ½ B
replacement females. These two-breed crosses are then mated to breed C sires resulting in the
production of ¼ A – ¼ B – ½ C females, which are then bred to breed D sires. The 1/8 A – 1/8 B – ¼ C
– ½ D replacement females are then mated to breed B sires. Breed composition of the crossbred
progeny will stabilize at approximately 53% - 27% - 13% - 7% depending on the last breed of sire used
in the rotation.

Heterosis realized from the four-breed rotation will stabilize at about 93.3% of maximum
possible for crossbred progeny heterosis and at about 93.3% of maximum possible for dam heterosis.
The system yields less heterosis than the three-breed cross system. The four- breed rotation, however,
produces its own replacement females with only 1% loss in heterosis.

As more sires are included in a specific rotation, the heterosis stabilization value will increase
toward that expressed by the three-breed terminal cross system.

Breed A (sire) x Breed B (dam)

Breed C (sire) x (50% A - 50% B)

Replacement females

Breed D x (25%A - 25%B - 50%C)

(sire) replacement females

Breed B x (12.5%A - 12.5%B – 25%C – 50%D)

(sire) replacement females

(53%A – 27%B – 13%C – 7%D)

stabilized four-breed cross

34
C. Grading up

Grading up is a mating procedure whereby sires of a given breed are mated to a particular kind
or breed of female and their female offspring generation after generation. Through the stock importation-
and dispersal program, purebred sires of a specific breed are mated to so called “native” females in an
effort to develop a population resembling the breed from which purebred sires came.

The first-generation offspring carry 50% of inheritance of the purebred and depending upon
genetic superiority of original females, the first-generation female offspring can usually be expected to
represent a considerable improvement over their dams in terms of overall productivity.

The second-generation results in offspring with 75% of inheritance of the purebred, in

subsequent generations, the proportion of inheritance remaining form the original females is halved
with each generation. With six crosses of purebred sires, grade animals carry 98.4% of the hereditary
material of the purebred. However, heterosis is expected to decline with advancing generations of the
grading up process as presented in the table below:

Generation Sire breed Dam breed Progeny Percent heterosis

Maternal Progeny
1 A B ½A½B 0.0 100/0
2 A ½A½B ¾A¼B 100/0 50.0
3 A ¾A¼B 7/8 A 1/8 B 50.0 25.0
4 A 7/8 A 1/8 B 15/16 A 1/16 25.0 12.5
B
5 A 15/16 A 1/16 31/32 A 1/64 12.5 6.25
B B
6 A 31/32 A 1/64 62/64 A 1/64 6.25 3.125
B B
: : : : : :
N A 0.0 0.0

D. Species hybridization

The cross of two species is the widest kind of outbreeding currently employed. The two species
may have descended from common parent stocks, but as a result of natural selection have diverged
and are now recognized as distinct species. They still have genes in common so that mating between
them can produce offspring. Fertility however, is very low or nil among progeny of most species crosses.

Examples:

1. The cross between Equus asinus (jack of the ass) and Equus caballus (mare of the horse) to
produce mule.
2. The cross between Equus zebra and Equus caballus to produce zebroid.
3. The cross between Bos Taurus (cattle) and Bos grunniens (yak from Tibet) to produce pien niu.
4. The cross between Bos Taurus (cattle) and Bos bison to produce cattalo.

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 Chapter 6.
Development of breeding program in selected livestock and poultry species

Introduction

Animal breeding program is developed with the aim to exploit genetic variation in a sustainable
way. There are genetic improvement programs, within and between breeds. These programs enhance
the competitiveness and sustainability of the animal food production Key in genetic improvement
programs is the estimation of breeding values. Breeding values are the genetic values of an individual
determined by the offspring, this can be based on individual traits or selection index. Breeding programs
have improved as the understanding of the genetic mechanism has increased significantly, just as the
range of characteristics and this is a continues process.

The optimal design of the improvement and dissemination programs is influenced

by genetics and reproduction techniques. The programs have to contribute to the desired genetic
improvement, while restricting the degree of inbreeding.

In this course, the process of developing breeding program for selected livestock and poultry
species will be discussed. Moreover, discussion on economically important traits is also included in
order to provide better understanding on the planned breeding program.

Learning objectives

At the end of the module, the learner should be able to:

• Describe importance of breeding program in livestock and poultry production;

• Describe the process of breeding program development; and
• Describe the economically important traits in selected livestock and poultry species.

Learning content

A. Process of developing breeding program

Introduction to breeding program

In the course of developing a breeding plan, the first activity is to identify and set the breeding
objective. Breeding objective is defined as the 'ideal' animal that a certain producer aims to breed. To
attain this, selection of the animal that fits to the set criteria will be retained in the farm and that will be
used in the succeeding breeding activities. Moreover, a breeding objective will also state the desired
level of improvement in the traits and how long these changes should take. Thus, it should be specific,
measurable and attainable.

As the criteria are already identified, development of breeding program follows. Breeding
program is a planned breeding of a group of animals usually involving at least several individuals and
extending it over several generations. To attain this, it is important to consider source of breeder or its
genetics, either in a nucleus farm or semen processing lab. On the other hand, the method of breeding
should also be considered, either natural mating or use of artificial reproduction techniques such as
artificial insemination or embryo transfer.

Breeding objectives are influenced by a wide range of factors, and have to consider the needs
and priorities of the animal owners or producers, the consumers of animal products, the food industry,
and increasingly also the general public. The relative importance of the different factors varies
depending on the species, and the priorities and development-stage of the country. It also changes
over time. The more important functions and requirements of breeding programs are to:
1. increase production and product quality;
2. increase productivity and cost efficiency;
3. maintain genetic diversity;
4. support the conservation and use of specific breeds; and
5. consider animal welfare and sustainable systems

36
The diagram below illustrates the flow of the breeding program:

Likewise, the environment should also be considered in the course of breeding program development.
It can be noted that the environment will influence the expression of the genes that makes up the animal.
In general, from the onset of fertilization until the retirement or death of the animal, environment will
play important part in the performance of the animal.

The illustration below will provide details on the role of environment in the different physiological stages
of the animal.

Systematic approach to design animal genetic improvement program

Animal breeding strategies for genetic improvement involve a mix of practical alternatives such
as recording and evaluation, selection, crossbreeding, and application of new reproductive
biotechnologies (Bondoc, 1998).

A systematic approach in the design of animal improvement schemes initially considers the
future environment to include production and selection criteria composed of economically important and
quantitative traits should be developed for specific situations before implementing the selection
program. Local testing and selection schemes could then be applied to improve total economic merit.

37
 1. Future environments
2. Breeding objective and selection criteria
3. Testing and selection program
4. Crossbreeding systems
5. Dissemination

B. Quantitative traits of economically importance and heritability pattern

The phenotype or the appearance of the any species depends on two factors: genetics, which
is inherited and environment as affected by climate and management. The genetic make-up of the
animal is inherited from its parents. Thus, heritability determines the degree of resemblance of the
measurement of pass-on traits possessed by the parents to its offspring. These traits are classified
into three:

▪ Reproduction
▪ Production
▪ Product

Another way to look at heritability is how well the offspring will perform similar to their parents.
In highly heritable traits, high performing parents will tend to produce high performing offspring for that
trait. Traits related to reproduction is a lowly heritable trait. The production traits such as growth are
moderately heritable, which means we can make good progress in changing those traits through
selection. Most traits associated with the end product are highly heritable, which means we can
improve carcass characteristics rapidly through our selection practices.
The economically important traits of selected livestock and poultry species are outlined as basis
in the development of breeding programs (Bondoc, 2008).

Carabao (Water Buffalo)

Improvement of carabaos in the Philippines is commonly aimed at enhancing size and genetic
potential for meat and milk production. The following quantitative traits has possible direct and indirect
economic importance in carabao production:

Character group Traits emphasized

Yield Weight- birth, weaning, yearling, two-year weight
Gain in weight
Age at market
Mature weight
Milk production
Strength and endurance for work
Product quality Dressing percentage
Carcass quality (fat depth, rib eye area, marbling)
Cost reduction Reproduction rate (age at first calving, calving interval, days open, number
of services per conception, gestation length)
Calving difficulty
Easy milk
Temperament
Feed efficiency

Dairy cattle

The primary breeding objectives are mainly to increase quantity and quality of milk, increase
viability, adaptability and increase reproductive performance. All of these can be subdivided into
physiology interrelated components such as milk yield, body size, feed intake and nutrient partitioning,
longevity, fertility, fecundity, heat tolerance, and disease resistance.

Character group Traits emphasized

Production type/ Milk yield
conformation Fat yield
Protein yield (per year or lifetime productivity)

38
 Soundness and high degree of detail and uniformity (final class, general
appearance, dairy character, capacity rump, feet and legs, mammary
system, fore udder, rear udder, size and stature)
Cow/ heifer fertility Age at first insemination or first calving
Days calving to first service or calving interval
Days open
Number of services per conception
Cost reduction Somatic cell count (mastitis susceptibility)
Milking speed
Calving ease/difficulty at first parity
Temperament

Heritability of some economically important traits:

Trait Heritability
Yield per lactation (year/lifetime)
Milk Moderate
Fat Moderate
Protein Moderate
Conformation (soundness) Low
Milk constituents
Fat, % High
Protein, % High
Somatic cell count Moderate
Reproduction
Age at first calving Low
Service per conception Very low
Days open Very low
Calving interval Low
Calving difficulty (first parity) Low

Goat

The quantitative traits of the economically important traits in goat are categorized as yield
product, product quality and cost reduction characteristics.

Character group Traits emphasized

Yield Weight (birth, weaning, age at market)
Milk production
Product quality Dressing percentage
Carcass quality (fat depth, rib eye, marbling)
Cost reduction Growth rate
Reproduction rate (age at first breeding or kidding, kidding interval, days
open, multiple birth)
Feed efficiency
Viability

Heritability in some economically important traits in goats:

Trait Heritability
Weight
Birth Moderate
Weaning Moderate
Age at market Moderate
Mature Moderate
Maternal ability Low
Reproduction
Multiple births Low
Age at first breeding Low
Carcass

39
 Muscling- quality grade Moderate
Dressing percentage Moderate

Swine
Swine has the advantages for rapid genetic improvement because of its high reproductive rate,
short generation interval, and most of the economically important traits are can be measured. The main
goal in swine breeding is to produce high quality carcasses with low fat and high lean content and free
from odors, and decreasing number of days to market hogs to 9 days.
The quantitative traits in swine improvement with possible direct or indirect economic importance are
summarized below:

Character group Traits emphasized

Yield Weight (Weaning, market, age at market)
Product quality Back fat
Loin eye area
Dressing percentage
Cost reduction Feed efficiency
Embryonic and post-natal mortality
Disease resistance
Reproduction (litter size, litters per year, viability)

In swine, heritability values are low for reproductive traits, low to moderate for weight traits and
moderate to high for carcass traits.

Trait Heritability
Weight
Weaning Low
Market Moderate
Age at market Moderate
Carcass
Backfat thickness Moderate
Loin eye area High
Dressing percentage Moderate
Reproduction
Litter size Low
Litters per year Low
Viability Low

Poultry (Chicken)
Chickens are the main source of poultry meat and eggs worldwide. They are also used as game
fowl. Chicken production is characterized either broiler or layer.

a. Layer chicken
Quantitative traits with possible direct or indirect economic importance for each character group. While
egg production is the trait of primary importance, traits for cost reduction, especially feed conversion is
increasing importance. The selected quantitative traits of layer chicken are as follows:

Character group Traits emphasized

Yield Rate of lay
Age of first egg
Weight
Product quality Firmness of albumen
Shell thickness
Yolk color
Cost reduction Sexual maturity
Feed conversion
Viability
Hatchability
Fertility

40
 Egg production traits have moderate heritability and variability while fertility and hatchability are
lowly heritable. Some of the estimates of heritability is shown below:
Trait Heritability
Mortality
Hatchability Low
Fertility Very low
Egg production
Rate of lay Moderate
Age at first egg Moderate
Weight Moderate
Egg quality
Firmness of albumen Low
Yolk color Low
Shell thickness Low

b. Broiler chicken

Meat producers want a broiler at market weight as soon as possible. A young market weight
broiler is a much more efficient converted of feed than an older broiler. The breeding objective is thus
generally aimed at increased rate and reduced carcass fat production.

The quantitative traits for broiler chicken are summarized below:

Character group Traits emphasized

Yield Weight at market
Growth rate
Product quality Dressing percentage
Breast angle
Cost reduction Feed efficiency
Mortality
Disease resistance

Heritability of some economically important traits are the following:

Trait Heritability
Weight
At market Moderate
Growth rate Moderate
Carcass
Dressing percentage High
Breast angle Moderate

Poultry (Duck)
Improvement of ducks is aimed at higher efficiency of meat and egg production. The breeding
objectives for meat0type ducks include fast growth rate, efficient feed conversion, and lean meat. In
duck egg production, more yolk percentage, thick egg white as measured by albumen height and Haugh
unit are preferred. The quantitative traits with possible direct or indirect economic importance in duck
production are outlined below:

Character group Traits emphasized

Yield Meat: weight at market, growth rate
Egg: total egg production, egg weight, total egg mass, fertility
Product quality Meat: dressing percentage
Egg: percentage of egg composition, albumen height, Haugh unit, egg
shape index, shell thickness, yolk color
Cost reduction Meat: Feed efficiency, mortality, disease resistance
Egg: Body weight, age at sexual maturity, days, feed conversion ratio

41
Heritability estimate

Heritability Estimates tell us what proportion of variation in a given behavior or a disorder is due to
genes versus the environment. These estimates range from 0.0 to 1.0, with 0.0 indicating that genetics
are not a contributing factor at all and 1.0 indicating that genetics are the only factor.

Estimation of heritability in populations depends on the partitioning of observed variation into

components that reflect unobserved genetic and environmental factors. In other words, researchers
recognize that genetic and/or environmental variation exists, but they may not be in a position to assess
either directly. However, this does not prevent them from being able to estimate the relative effects of
both genes and environment on phenotype. Here, heritability can be estimated from empirical data on
the observed and expected resemblance between relatives. The expected resemblance between
relatives depends on assumptions regarding a trait's underlying environmental and genetic causes.
Traditionally, heritability was estimated from simple, often balanced, designs, such as the correlation of
offspring and parental phenotypes, the correlation of full or half siblings, and the difference in the
correlation of monozygotic (MZ) and dizygotic (DZ) twin pairs.
Heritability can also be estimated from the ratio of the observed selection response (R) to the
observed selection differential (S) in artificial selection experiments. This relationship is summarized in
the "breeder's equation," R = h2S.

Estimating Heritability

When estimating heritability from the observed and expected resemblance between relatives,
a model is necessary to specify the expected resemblance in terms of genetic and environmental
factors. Sometimes this model is straightforward; for example, it may posit that the observed
resemblance between half-sibling dairy cows on different farms is due solely to additive genetic factors
inherited from the common parent. In other cases, a model's assumptions may be open to questioning.
For example, in human twin analysis, it is usually assumed that the resemblance between monozygotic
and dizygotic twin pairs due to shared environment is the same.

Recently, new methods that exploit the use of genetic marker data have been proposed and applied to
estimate heritability essentially free of such assumptions regarding the nature of between-family
variation. These methods are based upon the correlation between phenotypic and genetic similarity
within families. They exploit the fact that there is variation in identity (defined here as the proportion of
the genome that is shared identical-by-descent) between pairs of individuals that have the same
expected value and that this variation can be measured with genetic markers. Variation in identity arises
because of the random segregation of chromosomes during meiosis. For full siblings in humans, the
mean identity is 50%, with a standard deviation of approximately 4%. Hence, some full siblings share
only 40% of their genome by descent, while others share 60%. If those siblings who share more of their
genome than average are phenotypically more similar to each other than those siblings who share less
than average, then this similarity is most likely due to genetic factors.

Heritability Is Not Necessarily Constant

Interestingly, heritabilities are not constant. For example, estimates of heritability for first lactation milk
yield in dairy cattle nearly doubled from approximately 25% in the 1970s to roughly 40% in recent times.
Heritability can change over time because the variance in genetic values can change, the variation due
to environmental factors can change, or the correlation between genes and environment can change.

Genetic variance can change if allele frequencies change (e.g., due to selection or inbreeding), if new
variants come into the population (e.g., by migration or mutation), or if existing variants only contribute
to genetic variance following a change in genetic background or the environment. The same trait
measured over an individual's lifetime may have different genetic and environmental effects influencing
it, such that the variances become a function of age. For example, variance in weight at birth is
influenced by maternal uterine environment, and variance in weight at weaning depends on maternal
milk production, but variance of mature adult weight is unlikely to be influenced by maternal factors,
which themselves have both a genetic and environmental component.

42
Heritabilities may be manipulated by changing the variance contributed by the environment. Empirical
evidence for morphometric traits suggests lower heritabilities in poorer environments, but not for traits
more closely related to fitness. Understanding how heritability changes with environmental stressors is
important for understanding evolutionary forces in natural populations.

Misconceptions of the Heritability Concept

There are a number of common misconceptions on the exact meaning and interpretation of heritability,
Heritability is not the proportion of a phenotype that is genetic, but rather the proportion of phenotypic
variance that is due to genetic factors. Heritability is a population parameter and, therefore, it depends
on population-specific factors, such as allele frequencies, the effects of gene variants, and variation due
to environmental factors. It does not necessarily predict the value of heritability in other populations (or
other species). Nevertheless, it is surprising how constant heritabilities are across populations and
species.

Applications of heritability estimation are broad and cross a range of disciplines, from evolutionary
biology to agriculture to human medicine. In humans, estimation of heritability has been applied to
diseases and behavioral phenotypes (e.g., IQ), and it has helped establish that a substantial proportion
of variation in risk for many disorders, like schizophrenia, autism, and attention deficit/hyperactivity
disorder, is genetic in origin.

Heritability estimates in farm animals

Another way to look at heritability is how well the offspring will perform similar to their parents.
- In highly heritable traits, high performing parents will tend to produce high performing
offspring for that trait.
- Traits related to reproduction is a lowly heritable trait.
- The production traits such as growth are moderately heritable, which means we can
make good progress in changing those traits through selection.
- Most traits associated with the end product are highly heritable, which means we can
improve carcass characteristics rapidly through our selection practices.

The economically important traits of selected livestock and poultry species are outlined as basis in the
development of breeding programs (Bondoc, 2008).

Heritability estimates in dairy cattle

Trait %Heritability

Milk Yield 36%

Body condition score 22%

Somatic cell score 15%

Heritability estimates in goats

Traits % Heritability

Birth interval 10

Multiple birth 15
Maternal ability 15

Birth weight 40

Weaning weight 30

Weight at 1 year old 40

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 Feed conversion ratio 40

Mature weight 60

Carcass weight 60
Scrotal circumference 50

Heritability estimates in swine

Trait % Heritability

Growth and production traits

Weaning weight 20%

Post weaning gain 30%

Feed efficiency 30%

Age to 90kg 30%

Carcass traits

Backfat 50%

Length 60%

Loin eye area 60%

Dressing percentage 50%

Reproductive traits

Age at puberty 35%

Litter size at birth 10%

Conception rate 5%

Heritability estimates in layer chicken

Trait % Heritability

Number of egg produced per bird per 20%

year
Egg weight 57%

Age at first egg 45%

Mortality rate 5%

Excitability 20%

Hatchability 13%

Heritability estimates in broiler chicken

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 Trait %Heritability

Growth traits

Daily feed intake 22%

Average daily gain 26%

Feed efficiency 26%

Body weight 26%

Carcass traits

Starved body weight 27%

Hot dressed weight 28%

Chilled weight 24%

Carcass weight 36%

dressing percentage 28%

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 Chapter 7
Biotechnology applications for animal improvement

Introduction

Biotechnology provides animal breeders with powerful tools for animal improvement.
Biotechnology applications in the areas of biochemical and physiological genetics, molecular genetics
and reproduction in terms of artificial breeding may be utilized in local selection programs to enhance
the rate of genetic improvement.

Biotechnology applications to supplement rather than replace conventional breeding should,

however, be the norm in animal improvement. Traditional selection methods in animal breeding are
well-proven and useful in improving economic merit of farm livestock. The animals will become even
more useful in the future as new technologies are used to increase rates of improvement and to develop
new products and new directions in livestock production.

This course will discuss the emerging biotechnologies that are useful in breeding programs to
improve animal production.

Learning outcomes

At the end of the module, the learners should be able to;

1. Understand the application of different techniques in biochemical and physiological genetics in
animal improvement;
2. Familiarize with the application of modern genetic engineering techniques;
3. Understand the techniques involve in reproductive artificial breeding.

Learning content

A. Techniques in biochemical and physiological genetics

Biochemical and physiological genetics contribute to the elucidation of many genetic and
epigenetic processes, through the search for traits or markers either directly or indirectly useful in the
genetic improvement of livestock and poultry.

Applications of biotechnology in biochemical and physiological genetics to animal improvement

(adapted from Bondoc 2003)

Techniques in biochemical and Applications to animal improvement

physiological genetics
Biochemical and physiological polymorphisms - Document breed characteristics
(such as karyotype characteristics, blood group - Clarify relationships and about
systems, proteins and enzymes) purity/homozygosity among pure-
breeding individuals, lines or sub
populations
- Search for major genes
- Identify markers to screen early
individuals for sex-limited traits and for
traits of low heritability
- Implement marker-assisted selection
- Breed for resistance to disease or
selection against susceptibility to
infectious diseases

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 The discovery of inherited variations in blood groups in cattle and chickens, the development
of routine laboratory techniques such as gel-electrophoresis, biochemical and physiological genetic
information are used in livestock and poultry selection programs.

Polymorphic marker is a defined marker that may contain in a gene or some other specific
features. At present, polymorphic markers may be routinely required in breed certification and registry
work to help resolve disputes about relationship and about purity, homozygosity among pure-breeding
individuals, lines or sub-populations.

In marker assisted selection, a large number of biochemical and physiological markers are
being identified and their location on the genome map are being determined. These markers or group
of markers, is used to locate a genetic loci affecting economic trait performance known as quantitative
trait loci (QTL). The information can complement conventional performance information can be used in
selection or simply document breed characteristics.

Genetic markers used as indirect predictor traits may be used to characterize and document
linked loci of interest. Marker information will be especially useful for early screening of individuals for
sex-limited traits and for traits of low heritability. Another important application of physiological or indirect
traits is in the selection against susceptibility to infectious diseases.

Modern Genetic Engineering

With molecular genetics as a component of modern genetic engineering, the breeder may be
able to control and create new genetic variations. Genetic engineering includes technologies that either
permit direct change in the frequency of gene or genotype or change the characteristics of the life
history of individuals or their gametes, such that some individuals can make a disproportionate
contribution to the gametic or zygotic pool of the population.

The techniques of molecular genetics and modern genetic engineering can be applied to animal
improvement in several ways, such as during identification of superior individuals or genetic groups and
verification of parentage; removal or blocking of undesirable genes; alteration of structural genes to
change the product quality; evaluation of candidates for selection and transfer of genes. The summary
of biotechnology application to animal improvement is summarized below:

Techniques in molecular genetics Applications to animal improvement

Molecular markers (DNA fingerprinting)- RLFP Identify individuals, breeds, lines or strains and
hypervariable mini-satellite DNA sites, verify parentage
oligonucleotide probes, microsatellite analysis
Removal or blocking of undesirable genes Eliminate the effect of undesirable genes
Alteration of structural genes to change product Change product composition and improve its
quality quality or efficiency of its production
Evaluation of candidates for selection Identify animals bearing undesirable or desirable
genetic characteristics

Use genetic marker information in conventional

selection or in direct genetic manipulation of
important QTL

Increase accuracy of selection

Increase genetic variation available for selection

Gene transfer Transfer gene that are potentially more desirable
than those existing within the individual from
within or outside the species.

B. Technique in reproduction or artificial breeding

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 Reproduction is important for the maintenance of superior stocks over successive generations.
In general, reproductive technologies are known to improve the narrow and poor breeder base and to
hasten the inherently slow reproductive rates and long generation intervals of local breeding animals.
The potential value of reproductive biotechnologies in breeding programs, however, depends on both
on their efficiency and cost and the extent to which genetic selection or introduction of new breeding
stock is effective without them.

Techniques in reproduction can be used to improve the male and female reproductive rates or
to alter the reproductive process. Advanced techniques in reproduction or artificial breeding contribute
to higher rates of genetic improvement by controlling the factors affecting the accuracy with which the
breeding values of sires and dams are estimated, the selection intensity, the genetic variation among
individuals, and the length of generation interval.

Techniques for increasing reproductive rates and manipulating the reproductive process (adapted from
Smith 1998)

Technique Uses/benefits
To increase the reproductive rate:
Artificial insemination Semen dilution, freezing
Multiple ovulation Yield of eggs
Estrus synchronization Recipients
Embryo transfer Surgical, non surgical
Embryo freezing Storage
Embryo splitting Twinning
Embryo sexing Chromosomal, antigenic
Sperm sexing Sex determination
Prepubertal gametes Earlier reproduction
To manipulate the reproduction process:
Oocyte culture
Cloning Embryonic/ somatic tissue
Oocyte fusion Female x female
Sperm fusion Male x male
Homozygous diploids Selfing

Artificial insemination and related technologies

Artificial insemination (AI) is the collection of semen from the male and artificially introducing it
into females to obtain pregnancy. The following activities are involved in AI:

1. Collection of semen
2. Dilution of semen to be used to inseminate many females
3. Storage or cryopreservation of semen to allow distribution
4. Detection of estrus
5. Artificial insemination to females
AI can improve the reproductive rate of males. It has the potential to effect rapid genetic
improvement of economic traits in farm animals through the extensive use of semen from proven sires.
AI may also overcome physical or behavioral incompatibilities between breeds or closely
related species, and avoid the transmission of venereal and other diseases. The following are the
related technologies on AI:
AI and related activities Applications to animal improvement
Semen dilution Inseminate many females from a single ejaculate
Cryopreservation (freezing) Allow more widespread use of proven sires even
after their death
Estrus detection and synchronization Improve the reproductive management of
breeding females scattered
Pregnancy diagnosis Determine the need for further insemination

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Multiple ovulation and embryo transfer
Multiple ovulation and embryo transfer involve the use of gonadotrophic hormones to stimulate
ovulation of large numbers of ova and then transplanting fertilized ova to recipients’ females for
pregnancy and parturition.

The principal value of MOET in the local selection program is that it increases the reproductive
rate of females, such as shorter generation interval in the female pathway. MOET allows higher rates
of genetic improvement and therefore mostly benefits carabao, cattle, and goats because of their lower
natural reproductive rate. Unlike AI, MOET is too expensive to the used in commercial breeding.

The costs of transfer can be too high relative to the genetic improvement of economic merit
they provide, even if embryos are obtained from genetically superior females. With higher yields of
embryos and more efficient techniques, however, costs may be reduced so that all the replacements in
an elite or foundation herd can eventually be bred from the best females to improve the genetic merit
of the herd.

The following MOET and ET-based technologies are applied to animal improvement:
MOET and ET-based technologies Applications to Animal improvement

Pre-pubertal and juvenile MOET Reduce average age at breeding of females

Superovulation, in vitro fertilization and embryo May increase selection intensity and lower
transfer generation interval.
Use of innumerable, otherwise unused, follicles
in the ovary for producing young.

Aids research on cloned embryos to improve

animals
Recovery of oocytes from live donor Recovery of oocytes from known genetic merit
Embryo splitting and cloning Multiply genetically superior individuals

Accelerate genetic progress especially if

breeding values of animals supplying the
embryos are estimated more accurately

Monitor traits to be measured

Predetermining the sex of offspring Increase accuracy of selection and selection
intensity
Induced twinning Reduce cost of producing calves
Cryopreservation Establish embryo and gene banks

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