CHAPTER 1

Introduction
The term genetic improvement, often considered as synonymous to breeding. The set of measures adopted
with a view to bringing about genetic change within a population is called breeding. Genetic change is
permanent and accumulates over time. Animal breeding is the scientific application of genetic principles to
the improvement of animal populations. Animal breeding addresses the evaluation of the genetic value of
domestic livestock. The science of animal breeding is defined as the application of the principles of genetics
and biometry to improve the efficiency of production in farm animals. Domesticated farm animals are bred
with the aim of-
(i) improving the efficiency of production, and
(ii) improving the quality of the end product produced.
Animal breeders are individuals who have specific arts and skills to “breed good livestock”. We breed animals
for four principal reasons-
i. as sources of usable products or services;
ii. for medical or scientific research
iii. aesthetic, cultural or ethical considerations; and
iv. as pets.
The first leads to animal husbandry and livestock breeds of domesticated species kept for food, fiber and other
services such as transport and power; the second provides laboratory animals of defined genetic lines,
including animals with gene knockouts; the third encompasses breeding for conservation; and the fourth leads
to companion animals used for pleasure or recreation.
Brief History of Animal Breeding
The practice of animal breeding dates back to the Neolithic period (approximately 7000 BC), when people
attempted to domesticate wild species such as caribou, goats, pigs and dogs. History of animal breeding of all
four major domestic species is 1000's of years old. Domestication of cattle began in 6000 to 8000 BC.
Domestication of sheep and swine is about 4800 BC. Animal breeding starts with domestication. Although
there are several theories about the domestication process, it is generally admitted that selective breeding led
to modern domestic animals. After domestication, animals were selected in different environments and for
different traits, leading to the modern breeds. References to breeding can be found in ancient Greeks and
roman authors, however, modern reading practices start with the work of Robert Bakewell.
Robert Bakewell
Robert Bakewell (1725-1795), the only surviving son of Robert and Rebecca Bakewell was born at Dishley,
Leicestershire, England on 23 May 1725, Bakewell's father was a farm manager, with a farm of 440 acres at
Dishley. He travelled throughout Europe considerably, studying agriculture on the continent. In 1760, upon
his father's death, Bakewell inherited the Dishley farm. By visiting a large number of farms all over the
country, he had already acquired wide theoretical knowledge of agriculture and stock-breeding.
He was the eighteenth-century English Agricultural reformer. Bakewell used experimental plots of land to test
methods of irrigation, fertilization and crop rotation which were already part of the ongoing British
Agricultural Revolution, but his most remembered innovations were in the realm of livestock breeding. He is
regarded as the father of animal breeding in laying the foundations of the Shire horse, Dishley Longhorn cattle
and Leicester sheep. The first documented genetic improvement of cattle was accomplished by Robert
Bakewell during the period between 1760 and 1795. Prior to that time, natural selection primarily determined
the evolution of cattle. However, Bakewell was the first, so far as is known, to introduce man's intellect as the
determining force in the evolution of the bovine species.
Previously livestock of both sexes were kept together in the fields with random breeding. Using a system, he
called "in and in", Bakewell was the first to separate males from females, allowing mating only deliberately
and specifically.

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He was the first to:
(i) emphasize the importance of accurate breeding records,
(ii) improve animals for meat production and carcass quality,
(iii) establish the trade in ram-letting on a large scale,
(iv) introduce the concept of progeny testing to evaluate the genetic potentials of young sires,
(v) introduce the systematic and methodical selection of breeding stock,
(vi) develop a population of superior breeding animals through selection for specific traits, and
(vii) apply inbreeding and linebreeding to produce a herd possessing uniform superiority.
He also promoted the concepts-
(i) Like produces like,
(ii) inbreeding produces prepotency and
(iii) breed the best to the best.
Bakewell and his contemporaries in Europe pioneered the development of diverse breeds of beef and dairy
cattle, sheep, pigs and horses.
He started with the old Lincolnshire breed of sheep that he turned into the New Leicester. These sheep were
big and delicately boned, had good quality fleece and fatty fore quarters in keeping with the popular taste for
fatty shoulder mutton. He also began the practice of hiring out his prize rams to farmers to improve their own
stock. The value of his own stock was quickly recognized, and in one year he made 1200 guineas from the
letting of a single ram. He established the Dishley Society to maintain the purity of the New Leicester breed.
These sheep were exported widely, including to Australia and North America, and have contributed to
numerous modern breeds. Bloodlines of these original New Leicesters survive today as the English Leicester
(or Leicester Longwool), which is primarily kept for wool production.
Robert Bakewell was the first to breed cattle to be used primarily for beef. Previously, cattle were first and
foremost kept for pulling ploughs as oxen, but he crossed Longhorn heifers and a Westmoreland bull to
eventually create the Dishley Longhorn. They ate less and put on more weight than any other breed.
He extended his breeding experiments to horses, producing a new and particularly useful type of farm horse.
He bred the Improved Black Cart horse, which later became the Shire horse. This horse would become
valuable throughout the country side as a way to increase water income to the farm.
He also bred the Small White pig. He disregarded the damaging effects of inbreeding and due to this, he had
fertility troubles with his new breeds, but he is still considered as the first farmer practising modern animal
breeding. He died on the first of October 1795, at Dishley.
Modern Science of Animal Breeding
Animal breeding as a modern science belongs to the 20th century. Although numerous geneticists and
biometricians have made significant contributions to the development of this science, J.L. Lush (1896-1982)
of Iowa State University is considered the father of the modern science of animal breeding. Lush defined
concepts like heritability, and proposed methods of selection including the information of relatives. The
several editions of his book "Animal Breeding Plans” contributed to spread the new knowledge among
scientists, technicians and breeders. Lush and his students developed major scientific procedures applicable
to the genetic improvement of farm animals.
How Is Animal Populations Improved?
The purpose of animal breeding is not to genetically improve individual animals - once an individual is
conceived, it is too late to change the genotype of that animal - but to improve animal populations, to improve
future generations of animals. To this task breeders bring two basic tools:
i. selection and
ii. mating.
Both involve decision making. In selection, it is decided which individuals become parents, how many
offspring they may produce, and how long they remain in the breeding population. In mating, it is decided
which of the males we have selected will be bred to which of the females we have selected.

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Basis for Genetic Improvement
Differences among animals result from the hereditary differences transmitted by their parents and the
environmental differences in which they are developed. With minor exceptions, each animal receives half its
inheritance from its sire and half from its dam. Units of inheritance are known as genes which are located on
chromosomes. The chromosomes and genes are paired with each gene being located at a particular place on a
specific chromosome pair. Thousands of pairs of genes exist in each animal but since only one member of
each gene pair comes from each parent the particular combination of genes is determined purely by chance.
Tissue in the ovaries and the testicles produces the reproductive cells, which contain only one member of each
chromosome pair. The gene, from each pair going to each reproductive cell is purely a matter of chance.
The female calf is born with all of her potential eggs already produced and stored in the ovaries. Once she
reaches puberty, one egg, sometimes two, will be released from the ovaries during each oestrous cycle
throughout the remainder of her reproductive life. The male, on the other hand, does not produce sperm cells
until he reaches puberty. Sperm are then produced in the testicles by a process that requires about 60 days.
Because cattle have 30 pairs of chromosomes and only one chromosome from each pair is contained in each
sperm cell, there are 1.1 billion different combinations of chromosomes that may be contained in the sperm
cells.
When a reproductive cell, or sperm cell, from a male fertilizes a reproductive cell, or egg, from the female,
the full complement of genes is restored. Some reproductive cells will contain more desirable genes for
economically important traits than others. The union of reproductive cells that contain a high proportion of
desirable genes for economically important traits results in a superior individual and offers the opportunity for
selection. The chance segregation in the production of reproductive cells and recombination upon fertilization
results in the possibility of genetic differences among offspring of the same parents. Some individuals will be
genetically superior, some average and others inferior. Those that are superior, if selected as parents of the
next generation, contribute to herd improvement. Genetic improvement is a slow process and can take several
generations to see an improvement in a trait. The basis of genetic improvement is recombination and random
fertilization.
Nowadays, animal breeding is much dominated by science and technology. In some livestock species, animal
breeding is in the hands of large companies, and the role of individual breeders seems to have decreased. There
are several reasons for this change. Firstly, the breeding industry has taken up scientific principles. Looking
was replaced by measuring, and an intuition was partly replaced by calculations and scientific prediction.
Other major developments were caused by the introduction of biotechnology. These are roughly the
reproductive technologies, and the molecular genetic technology.

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 CHAPTER 2
Population Genetics in Animal Breeding
Population
The term population refers to a group of individuals belonging to the same breed or species that lives in the
same geographic area and that actually or potentially interbreeds. For example, from a genetic viewpoint, all
the breeding largemouth bass in a small lake in a given year constitute a population. A population shares a
common gene pool. Populations are dynamic. They expand and contract through changes in birth and death
rates, migration, or contact with other populations. The dynamic nature of populations has important
consequences and can, over time, lead to changes in a population's gene pool. Populations can be described
by age structure, geography, birth and death rates, and allele frequencies.
Gene Pool
The collection of all the genes and the various allelic forms of those genes within a population at any one time
is called its gene pool.
Species
A species is a population or group of populations whose members have the potential to interbreed with one
another and produce viable offspring, but who cannot produce viable offspring with other species.
Population Genetics
Population genetics is the science of genetic change in population. Population genetics is the quantitative study
of the frequencies of alleles and genotypes in populations, and the forces which maintain or change the
frequencies of particular alleles and genotypes in populations. Population genetics is the field of genetics that
studies heredity in groups of individuals for traits that are determined by one, or only a few genes. Population
genetics focuses on the extent and pattern of genetic variation in natural populations and the explanations for
these observations. Application of genetic principles to entire populations of organisms constitutes the subject
of population genetics, Mendel's rules describe how genetic transmission happens between parents and
offspring. Population genetics describes how genetic transmission happens between a population of parents
and a population of offspring.
Large Population
A large population is one in which the number of adults is in the hundreds rather than in the tens.
Effective Breeding Population
The term effective breeding population is used because the real breeding population may be much smaller
than actual population. For example, with humans, a large segment of the population is nonbreeding because
of age or even artificial birth control. Not all individuals contribute gametes to the next generation. The
effective population size is the number of individuals in the population that successfully pass genes to the next
generation. The smaller the effective population size, the faster a population will drift, and the faster one of
the alleles in the population will become fixed. The effective population size (Ne) is always either equal to or
less than the absolute population size (N). If sexes are equal number and all individuals have an equal
probability of reproducing, Ne = N Otherwise,
(4 × Nf × Nm)
Ne =
Nf + Nm
Where, Nf and Nm is the numbers of breeding females and males, respectively. Effective population size is the
number of adults contributing gametes to the next generation. It includes the number breeding females plus
number breeding males. Remember that if, for example, one male contributes most of the gametes, his alleles
will be present at a higher frequency in the next generation.

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Genetic Structure of Populations
The genetic structure of a population is determined by the gene pool. In the case of diploid, sexually
reproducing individuals, the structure is also characterized by the distribution of alleles into genotypes. Thus,
the genetic structure can be described in terms of both allelic and genotypic frequencies.
Genotypic Frequencies and Allelic Frequencies
A frequency is a proportion or percentage, and always ranges between 0 and 1. To determine the frequency of
the genotypes or alleles at a given locus in a population, we must first count the number of individuals having
different genotypes. The genotype frequency is percentage of each genotype present in a population.
number of individuals with the genotype
Genotype frequency =
total number of individuals in the population

We do this for each of the genotypes at the locus. The sum of the genotypic frequencies should 1.
For each allele, the allele frequency is the percentage of alleles of a particular gene are present in a population.
Number of copies of given allele in the population
Allele frequency =
Total number of all alleles in the population
If an allele becomes 0, then the allele is said to be lost, that is the allele is permanently eliminated from the
population. The other allele, whose frequency is now 1.0, is "fixed", which means that all individuals in the
population will be homozygous for that allele. This continues for all future generations (in the absence of
mutation).
If we consider an autosomal locus in a diploid, sexually reproducing species, allelic frequencies can be
measured in either of two ways:
i. from the observed of different genotypes at particular a locus, or
ii. from the genotypic frequencies
The first way is simply by counting alleles:
Number of a alleles
Frequency of the a allele, q =
Total number of alleles
The expression "frequency of" can be shortened to f (). For example, the frequency of the a allele will be
written as f(a). Since the homozygotes have two of a given allele and heterozygotes have only one, and since
the total number of alleles is twice the number of individual, we can calculate allelic frequencies in the
following manner. For example, imagine a population of 100 diploid individuals with 35 AA, 48 Aa, and 17
aa individuals. Each AA homozygote has two A alleles, while each Aa heterozygote possesses only one A
allele. Therefore, the number of A alleles in the population is (2 x the number of AA homozygotes) + (the
number of Aa heterozygotes), or (2 x 35) + 48 = 118. Because every diploid individual has two alleles, the
total number of alleles in will be twice the number of individuals, or 2 x 100 = 200. Then,
118 82
f(A) = p = = 0.59 Similarly, f(a) = q = = 0.41
200 200
Alternatively, because the frequencies of the two alleles, A and a, must add up to 1, q = 1- p, if we know
that p = 0.59, then q = 1 - 0.59 = 0.41.
Another way of calculating allele frequencies is based on knowledge of the genotype frequencies, which in
this example are:
35
f(AA) = = 0.35
100
48
f(Aa) = = 0.48
100
17
f(aa) = = 0.17
100

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We derive an expression for calculating p and q based on genotype frequencies as follows:

(2 x number of AA homozygotes) + (number of Aa heterozygotes)

f(A) = p =
2 x total number of individuals
2 x number of AA homozygotes number of Aa heterozygotes
= +
2 x total number of individuals 2 x total number of individuals
1
= f(AA) + 2 𝑓𝑓(𝐴𝐴𝐴𝐴)
and,
(2 x number of aa homozygotes) + (number of Aa heterozygotes)
f(a) = q =
2 x total number of individuals
2 x number of aa homozygotes number of Aa heterozygotes
= +
2 x total number of individuals 2 x total number of individuals
1
= f(aa) + 2 𝑓𝑓(𝐴𝐴𝐴𝐴)
Thus, allele frequencies can be calculated as the frequency of homozygotes plus half the frequency of
heterozygotes as follows:
1 1
p = f(A) = f(AA) = 𝑓𝑓(𝐴𝐴𝐴𝐴) = 0.35 + 𝑥𝑥 0.48 = 0.35 + 0.24 = 0.59, and q = 1 – 0.59 = 0.41
2 2

Note that these two methods (counting alleles and using genotype frequencies) are algebraically identical and
thus give identical results. Although calculating allele frequencies from genotype frequencies may be quicker
than calculating them directly from the number of genotypes, more rounding error will occur, As a result,
calculations from direct counts are usually preferred. The use of allele frequencies offers several advantages
over the genotype frequencies. First, in sexually reproducing organisms, genotypes breakdown to alleles when
gametes are formed, and alleles, not genotypes, are passed from one generation to the next. Consequently,
only alleles have continuity over time, and gene pool evolves through changes in the frequencies of alleles.
Furthermore there are always fewer alleles than genotypes. So the gene pool can be described with fewer
parameters when allele frequencies are used. For example, if there are three alleles segregating at a particular
locus, six genotypes will form and frequencies must be calculated for each to describe the gene pool.
Phenotype Frequency
Number of individuals with certain phenotype
Phenotype frequency =
Total number of individuals in the population
Allele Frequencies with Multiple Alleles
In the case of multiple alleles, the frequency of an allele can be calculated as the sum of the frequency of its homozygote
plus half the frequency of each heterozygote that carries the allele in question.
Suppose, we have three alleles A1, A2, and A3 - at a locus, and we want to determine the allele frequencies. Here, we
employ the same rule that we used with two alleles; we add up the number of alleles of each type and divide by the total
number of alleles in the populations.
P=f(A1) = (2 X A1A1 + A1A2 + A1A3) / (2x total number of individuals)
q=f(A2) = (2 X A2A2 + A1A2 + A2A3) / (2x total number of individuals)
r=f(A3) = (2 X A3A3 + A1A2 + A2A3) / (2x total number of individuals)
Allele frequencies can also be determined from the genotype frequencies by:

P = f(A1) = f(A1A2) + ½ f(A1A2) + ½ f(A1A3)

q = f(A2) = f(A2A2) + ½ f(A1A2) + ½ f(A2A3)

r = f(A3) = f(A3A3) + ½ f(A1A3) + ½ f(A2A3)

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Allele Frequencies at an X linked Locus
Calculating allele frequencies at an X-linked locus is slightly more complicated, because males have only a
single X-linked allele. However, we can use the same rules like autosomal loci. Remember that each
homozygous female carries two X-linked alleles, heterozygous females have only one that particular allele,
and all males may have only a single X-linked allele. To determine the number of alleles at an X-linked locus,
we multiply the number of homozygous females by 2, and then add the number of heterozygous females and
the number of hemizygous males. We next divide by the total number of alleles in the population. When
determining the total number of alleles, we add twice the number of females (because each female has two X-
linked alleles) to the number of males (who have a single X-linked allele). Using this reasoning, the
frequencies of two alleles at an X-linked locus (XA and Xa) are determined with the following equations:
P = f(XA) = {(2 x XA XA females) + (XA Xa females) + (XA Y males)} / { (2 x number of females) + (number
of males)}
q = f(Xa) = {(2 x Xa Xa females) + (XA Xa females) + (Xa Y males)} / { (2 X number of females) + (number
of males)}
Allele frequencies at an X-linked locus can be determined from the genotype frequencies by:
P = f(XA ) = f(XA XA ) + ½ f(XA Xa ) + ½ f(XA Y)
q = f(Xa ) = f(Xa Xa ) + ½ f(XA Xa ) + ½ f(Xa Y)
Students should strive to understand the logic behind these calculations, not just memorize the formulas. If
you fully understand the basis of the calculations, you will not need to remember the exact equations and will
be able to determine allele frequencies for any situation.

The Hardy Weinberg Law

𝑝𝑝2 + 2𝑝𝑝𝑝𝑝 + 𝑞𝑞 2 = 1

𝑝𝑝2 = dominant homozygous frequency (AA)

2pq = heterozygous frequency (Aa)
𝑞𝑞 2 = recessive homozygous frequency (aa)
The unifying concept of population genetics is the Hardy Weinberg Law/Theorem/Principle/Equilibrium. In
1908, Godfrey H. Hardy, a British mathematician, and Wilhelm Weinberg, a German physician, independently
shown that a simple relationship often exists between allele frequencies and genotype frequencies in a
population of diploid, sexually reproducing individuals. This relationship, generally known today as the
Hardy-Weinberg law. This law states that if an infinitely large, random mating population is free from outside
evolutionary forces (i.e. mutation, migration and natural selection), then both allele and genotype frequencies
remain constant from generation to generation and the genotype frequencies will be p2 for the AA genotype,
2pq for the Aa genotype, and q2 for the of aa genotype, where p is the allele frequency of A and q is the allele
frequency of a. This shows that Hardy-Weinberg proportions are really binomial proportions.
A population with constant allele and genotype frequencies is said to be in Hardy-Weinberg equilibrium
(HWE). The equilibrium is neutral i.e., if it a perturbed, it will be re established after one generation of random
mating at the new allele frequencies, and they will also remain stable thereafter.
It is important to understand that outside the lab, one or more of these influences are always in effect. That is,
Hardy-Weinberg equilibrium is impossible in nature. Genetic equilibrium is an ideal state that provides a
baseline against which to measure change. The most important role of Hardy-Weinberg law is that it is the
foundation upon which population genetics is built.

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Assumptions of Hardy Weinberg Equilibrium
The following major assumptions or conditions are necessary for the Hardy-Weinberg law to hold (apply):
1. Random mating or panmixia
The first of these assumptions is random mating.
2. Infinitely large population or large enough that sampling error is negligible
The second assumption of the Hardy-Weinberg equilibrium is that the population is infinitely large. Most
of the populations of domestic animals with which we are concerned are small populations. In small
populations chance factors (sampling error) may produce large changes in allele frequencies.
3. No mutation or migration
Allele and genotype frequencies may be changed by the loss or addition of alleles through mutation or
migration. The third and fourth assumptions of the Hardy Weinberg equilibrium are that there is no such
allelic loss or gain in the population due to mutation or migration.
No natural selection
One assumption of HWE is that individuals of all genotypes have equal rates of survival and equal
reproductive success. The final assumption necessary to the Hardy-Weinberg equilibrium is that there is no
natural selection occurring.
Artificial selection will also perturb (disturbs) Hardy-Weinberg equilibrium of captive populations. In
summary, the Hardy-Weinberg equilibrium is exactly true for an infinitely large, randomly mating population
in which mutation, migration, and natural selection do not occur
Proof of Hardy Weinberg Equilibrium
A population in which the parent generation possesses alleles A₁ and A2 in frequencies p and q, respectively,
and p + q = 1. The probability that any particular sperm possesses the A₁ allele is p, and, likewise the
probability that any particular ovum has the A₁ allele is also p. Therefore, the probability that the uniting sperm
and ovum both contain A1 equals the product of the two probabilities; that is, the probability of the genotype
A₁A2, is p2. The probability that the ovum possesses allele A₂ is q. Consequently, the probability that an A₁
sperm, which has the frequency p, pairs with an A2 ovum is pq and, vice versa, the probability that an A2
sperm, which has the frequency q, pairs with an A2 ovum is q2. Therefore, the composition of the F₁ generation
is p² A₁A₁ + 2pq A₁A₂ +q2 A2A2 (Figure 2.1).
gametes
A1 A2
f(A1) = p f(A2) = q

Gametes A1,f(A1) = p A1A1 A1A2

f(A1A1) = p2 f(A1A2) = pq
+ A2,f(A2) = q A1A2 A2A2
f(A1A2) = pq f(A2A2) = q2

Figure 2.1 The HWE frequencies that result from random mating.
After random mating, the frequency of the A₁A1, homozygote is p2 and the frequency of the A₁A2 heterozygote
is 2pq. Thus, the frequency of the A1 allele, the frequency of its homozygotes plus half the frequency of the
heterozygotes, is
F(A1) = f(A1A1) + ½ f(A1A2) = p²+ ½X2pq =p² + pq=p(p+q) = p (remember, p +q=1)
Thus, in a randomly mating population of sexually reproducing diploid individuals, the allele frequency, p,
does not change from generation to generation. After such equilibrium is attained, gene and genotype
frequencies will, theoretically, remain constant from generation to generation.

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Testing for Fit to Hardy Weinberg Equilibrium
To determine whether a given population is in Hardy-Weinberg equilibrium, we first compute allele
frequencies (p and q) from the observed frequencies of the genotypes. Allele frequencies should be calculated
as the frequency of homozygotes plus half the frequency of heterozygotes. Then we can determine whether
the three genotypes (A1A1, A1A2, and A2A2) occur with the frequencies p2, 2pq, and q2. If they do, then the
population is considered to be in Hardy Weinberg equilibrium; if they do not; then the population is considered
not to be in Hardy-Weinberg equilibrium. In order to determine whether observed and expected allele
frequencies are the same, the chi-square test can be used.
Estimation of Gene Frequency Using the Hardy Weinberg Law
Estimation of allele frequencies using the Hardy-Weinberg law would include the following:
1. The frequency of the recessive allele is equal to the square root of the frequency of recessive individuals.
2. The frequency of the dominant allele is 1 minus the frequency of the recessive allele
3. The proportion of homozygous dominant individuals in that population would be equal to the square of the
frequency of the dominant allele.
4. The frequency of heterozygotes, or carriers of recessive abnormalities in that population would be two times
the frequency of the dominant allele times the frequency of the recessive allele.
To permit estimation of the gene frequency when there is complete dominance the population must be in
genotypic equilibrium. Only two phenotypes are discernible for characters with dominant inheritance. For
example, Aberdeen Angus has two phenotypes for coat colour, black and red. Individual having the latter
phenotype are homozygous recessive and are undesirable by standards of pedigree breeders. Using the Hardy-
Weinberg law, we may estimate the frequencies q of the gene for red coat color from the frequency of the red
phenotype. We may assume that 5 red calves are born in a herd of 500. The frequency of red phenotype is
0.01; consequently, the gene frequency is √0.01 = 0.10.
Having calculated that 10% of the genes at this locus are those specifying red coat color, we may determine
that the genotype frequencies in this population are 0.01 bb, 0.18 Bb and 0.81 BB. Thus 18% of the animals
are heterozygous for a gene that actually determines the phenotypes of only 1% of the animals. Selection
against this rare gene is rather inefficient for it can eliminate only 10% of the undesirable genes.
Estimating the frequency of heterozygotes in a population is an important part of genetic counselling.
Extensions of Hardy Weinberg Equilibrium to Multiple Alleles
When two alleles are present at a locus, the Hardy-Weinberg law tells us that at equilibrium the frequencies
of the genotypes will be p², 2pq, and q2, which is the square of the allele frequencies (p+q) 2. This is a simple
binomial expansion and this principle of probability theory can be extended to any number of alleles. For
example, with alleles A1, A2, and A3, with frequencies p, q, and r, the genotype frequencies at equilibrium
should be:
(p+q+r)2 = p² (A₁A₁) + q² (A₂A₂) + r²(A3A3) + 2pq (A1A2) + 2pr (A1A3) + 2qr(A2A3)
The square of the allele frequencies can be used in the same way to estimate the expected frequencies of
genotypes when four or more alleles are present at a locus.
Extensions of Hardy Weinberg Equilibrium to Sex linked Alleles
The calculation of allele frequencies for a sex-linked recessive trait is rather simple, although the same
conditions necessary for the application of the Hardy Weinberg law to autosomal traits also apply. The genes
which reside in the differential region of X chromosome only, are called sex-linked or X-linked genes. For a
sex-linked recessive trait the frequency of the allele is equal to the frequency of males in the population that
express the trait phenotypically. The frequency of the dominant allele of a sex-linked recessive trait is
calculated as usually by subtracting the frequency of the sex-linked recessive allele from 1. For example, if 8

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percent of the males in a population show a sex-linked recessive trait, the frequency of the recessive allele is
0.08. The frequency of its dominant allele would be 1.00 -0.08 = 0.92.
A number of human diseases, such as hemophilia and muscular dystrophy, are determined by recessive alleles
on the X chromosome. These diseases are much more common in males than in females. If alleles are X-
linked, females may be homozygous or heterozygous, but males are hemizygous. For X-linked alleles in
females, the Hardy-Weinberg frequencies are the same as those for autosomal loci: p² (XAXA), 2pq (XA Xa),
and q2 (XaXa). In males, however, the frequencies of the genotypes will be p (XAY) and q (XaY), the same as
the frequencies of the alleles in the population. The frequency of affected males, XaY, is q, while the frequency
of affected females, XAXA, is q2. If q is 0.004, the frequencies of affected males and females are 0.004 and
0.000016, respectively. In other words, the ratio of affected males to females is q: q2 or 1: q. Thus, if q = 0.005,
the ratio is 200: 1. For this reason, recessive X-linked traits are more common among males than among
females.
Factors Changing Hardy Weinberg Equilibrium
Genetic structure of the population is in equilibrium, when the population is large, randomly mating, and free
from mutation, migration, and selection. For many populations, however, the conditions required by Hardy
Weinberg law do not hold. Populations are frequently small, mating may be non-random, and mutation,
migration, and selection may be occurring. In these circumstances, allele frequencies and consequently of
genotype frequencies do change. Four evolutionary forces account for most of the changes in allele frequencies
and consequently of genotype frequencies in populations. These are: mutation, migration, selection, and
genetic drift. They form the basis of cumulative change in genetic characteristics of populations. There are
two sorts of process through which change in allele frequencies and consequently of genotype frequencies,
are brought about. They are systematic process and dispersive process. In systematic process both the amount
and direction of the changes can be predicted, while the dispersive process the amount may be predicted but
not the direction. The second type of changes occurs only in small populations. The systematic process
includes mutation, migration and selection.
Mutation
Mutation affects Hardy Weinberg equilibrium by changing one allele to another and thus changing allele
frequencies and consequently of genotype frequencies. Mutation is the ultimate source of all genetic variation.
The rate of change in allele frequency from the mutation is very low because spontaneous mutation rates are
low ranging from ~10-4 to 10-6 mutations/gene/generation for most cases (1 new mutation in 10,000 -
1,000,000 genes per individual per generation). Such rare events will tend to be of minimal significance, but
over a long time period could have a slight effect upon frequencies. Consider a simple model in which two
alleles A₁ and A₂ exists. A1, mutates to A2, at the rate of u, and A₂ mutates back to A2, at a rate of v per
generation.
𝑢𝑢
A₁ A₂
𝑣𝑣

If p is the frequency of A1, and q is the frequency of A2, the increase in the frequency of A₂ from forward
mutation is u x p. Using the same logic, the frequency of alleles A₂ can be decreased by backward mutation
by the amount v x q. Overall then, the change per generation in the frequency of A₂ (Δq) due to mutation is:
Δq = up-vq
The maximum positive value for this change is u, when p= 1 and q = 0. The maximum negative value is v,
when p= 0 and q = 1. However, because the mutation rates u and v are generally small, the expected change
due to mutation is also quite small. For example, if u = 10-5, v=10-6, and q = 0.0, then: Δq =(0.00001)(1.0)-
(0.000001) (0.0) = 0.00001
If the mutation is in one direction only then the mutating allele will gradually decline in frequency.
Mutations provide the necessary raw material for evolutionary change, but by themselves new mutations do
not have a measurable effect on allele or genotype frequencies.

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Migration (Gene Flow)
Migration or transfer of animals from one population to another by way of purchase or exchange can play a
major role in changing the genetic structure of the population. The term migration usually implies movement
of organisms. In population genetics, however, we are interested in the movement of genes, which may or
may not occur when organisms move. Movement of genes takes place only when organism’s gametes migrate,
and contribute their genes to the gene pool of the recipient population. This process is also referred to as gene
flow, that is, genetically effective migration. Migration is the movement of fertile individuals or the transfer
of gametes between populations. Migration is similar to mutation in the sense that allele frequencies are
changed by adding or removing alleles. The policy of grading-up is an example of migration.
Let us consider a large population consists of a proportion m of new immigrants in each generation, the
remainder, 1-m, being natives. Let the frequency of a certain allele be qm among the migrants and qn among
the natives (Figure 2.2). Then, the frequency of the allele in the mixed population, q₁, will be

q1=mqm+(1-m)qn=mqm + qn - mqn = m(qm-qn)+qn

The change in allele frequency, Δq, from before to after the migration event is

Δq = q1-qn = m(qm -qn) + qn – qn= m(qm -qn)

This final equation indicates that the change in allele frequency from migration depends upon two factors: (i)
the proportion of the migrants in the final population and
(ii)the difference in allele frequency between the migrants and the natives
If either the size of the migrant drops to zero (m=0) or the allele frequencies in the migrants and natives are
identical (qm =qn), then we can say that the change in allele frequency is zero under the influence of migration.

qn Native
qm Migrants

1–m
Natives
m
m New immigrants

Figure 2.2 Diagrammatic view of migration.

Selection
Whether artificial or natural, selection can have a marked effect upon gene frequency. Natural selection can
be defined as differential reproduction of genotypes. It simply means that individuals with certain alleles
produce more offspring than others; therefore those alleles increase in frequency in the next generation. It is
the most powerful factor for producing changes in the genetic structure of the population.
Random Genetic Drift (Chance Effects)
The breeding individuals of any generation produce a potentially infinite pool of gametes. In the absence of
fertility differences, the allele frequencies among gametes will equal the allele frequencies among adults. Only
a few of these gametes will participate in fertilization and be represented among zygotes of the next generation.
In other words, each successive generation is the result of a sample of gametes of the parent generation, that
is, there is a process of random sampling that take place in going from one generation to the next. A sample
may not be an accurate representative of a population, especially if the sample is small. Allele frequencies will
tend to change from one generation to the next purely as a result of sampling error. Because there is variation
among samples due to chance, the allele frequencies among gametes and zygotes may differ. The larger the
sample, the greater the probability that the allele frequencies of the offspring represent accurately allele

11 | P a g e
frequencies in the parental population. When population is small or when alleles are rare, changes in allele
frequencies take place due to chance alone. These random changes in allele frequencies due to sampling error
of gametes or due entirely to chance are known as random genetic drift or simply drift. Genetic drift occurs in
all populations, but it has a major effect on small populations. The smaller the population size, the larger is
the magnitude of genetic drift. It can make alleles fix in the population or disappear from it.
Imagine that a population produces an infinitely large pool of gametes, with alleles in the proportions p and
q. If random mating occurs and all the gametes unite to form zygotes, the proportions of the genotypes will be
equal to p², 2pq and q², and the frequencies of the alleles in these zygotes will remain p and q. If the number
of progeny is limited, however, the gametes that unite to form the zygote constitute a sample from the infinite
pool of potential gametes. Just by chance, or by 'error', this sample may deviate from the larger pool; the
smaller the sample, the larger the potential deviation.
Consider, for instance, two human beings heterozygous for the recessive allele that causes phenylketonuria
(Figure 2.3). If they mate and produce a single child, there is a chance that the child will have the disease.
There is also a ½ chance that the child will heterozygous like its parents, and finally, there is a ¼ chance that
the child will homozygous for the normal allele. In the first case, the frequency of the harmful allele has
increased from 0.5 in parents to 1.0 in the child, in the second case it has stayed the same, and in the third
case, it has decreased from 0.5 to 0. Overall, the probability of a change in the allele frequency is 0.5.
Parents Cc X Cc

Child CC Cc cc

Probability ¼ ½ ¼
Change in frequency of c -0.5 0 +0.5

Figure 2.3 Random changes in allele frequency for phenylketonuria.

Mutation and drift are of little practical importance in animal breeding. The most important single force for
changing gene frequency and making genetic improvement is selection.
Mutation generates all new alleles, but drift, migration, and selection determine the frequency of alleles in a
population.

Characteristics of Genetic Drift (Short Note)

There are four important characteristics of genetic drift:
1. Allele frequencies tend to change from one generation to the next simply as a result of sampling error.
2. There is no systematic bias to changes in allele frequency. The allele frequency is as likely to increase from
one generation to the next as it is to decrease.
3. If the process is allowed to continue long enough without input of new genetic material through migration
or mutation, the population will eventually become fixed for only one of the alleles originally present.
4. The time to fixation on a single allele is directly proportional to population size, and the amount of
uncertainty associated with allele frequencies from one generation to the next is inversely related to population
size.

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Causes of Genetic Drift
All genetic drift arises from sampling error. There are several ways in which sampling error occurs in natural
populations.
1. Genetic drift arises when population size remains continuously small over many generations, especially
when subpopulations are isolated. Unfortunately, this situation is frequent, particularly where populations
occupy marginal habitats, or when competition for resources limits population growth. In such populations,
genetic drift plays an important role in the evolution of allele frequencies.
2. Another way in which genetic drift arises is through founder effect. When a population is initially
established by a small, and therefore genetically unrepresentative, sample of the parent population, the genetic
drift observed in the subpopulation is referred to as a founder effect. Although the population may
subsequently grow in size and later consist of a large number of individuals, the gene pool of the population
is derived from the genes present in the original founders. Chance plays a significant role in determining which
genes are present among the founders, and this has a profound effect upon the gene pool of the subsequent
population.
3. A third form of sampling error is called bottleneck effect. Bottleneck effect is a form of genetic drift that
occurs when a population is drastically reduced in size. During such a population reduction, some genes may
be lost from the gene pool as a result of chance. After the bottleneck, the parents of the next generation have
been reduced to a small number and may not be genetically representative of the original population. Imagine
a small group of humans inhabiting in an island. Suppose that this population consists of only 100 individuals,
50 of whom have green eyes and 50 of whom have brown eyes. For this example, we assume that eye colour
is determined by a single locus and that the allele for green eyes is recessive to brown (BB and Bb codes for
brown eyes and bb codes for green). The frequency of the allele for green eyes is 0.6 in the island population.
A typhoon strikes the island, killing 50% of the population. Those individuals who die all have brown eyes.
After the typhoon, the allele frequency for green eyes is 1.0. The frequency of the green-eye, allele has changed
from 0.6 to 1.0, simply as a result of chance.
Effects of Random Drift
All the effects of random genetic drift have one feature in common; they involve a loss of genetic variability.
As population lose their variability, they become more homozygous, and, consequently, less heterozygous.
The effect of drift therefore be studied by monitoring the reduction in the frequency a heterozygotes.

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 CHAPTER 3
Quantitative Inheritance in animal breeding
Traits in Farm Animals:
A trait is any observable or measurable characteristic of an animal.
Observable traits: Traits we would normally mention in describing the appearance of an animal. Example
include coat color, size muscling, leg set, udder confirmation etc.
Measurable Traits: Traits we would likely refer to in describing how an animal has performed. Examples
include body weight, daily milk production, fleece yield etc.
There are hundreds of traits of interest in domestic animals. While all traits are important, it is imperative to
decide on the merit of each traits since inclusion of many traits in breeding program is difficult and
improvement of each trait is slower. Traits in farm animals can be categorized into five basic categories namely
(i) reproductive
(ii) production
(iii) quality
(iv) aesthetic and
(v) Behavioral traits.
Reproductive traits are also referred as fitness traits that are normally concerned with reproduction and
survival. Examples of such traits are litter size, conception rate, calving rate, gestation length, survivability,
services per conception, service period, calving interval, twinning length, dystokia, etc.
Production traits include milk yield, growth rate, feed efficiency, weaning weight, fleece yield, egg
production, slaughter weight, age at slaughter etc.
Quality traits are referred to meat, milk, wool and eggs quality. Meat quality refers to carcass composition,
back fat thickness in pig, eye muscle area in all carcass etc.
Aesthetic traits are usually features of more aesthetic nature where personal preference is important. Example
include coat color, coat type, udder shape, physical appearance, horn shape, polledness, feather color, fighting
etc.
Behavioral traits are those involved in animal welfare. Examples includes temperament, docility of pet dogs,
bulls for ploughing, horse for riding broodiness etc.
In none of the examples of traits mentioned above is the appearance or performance of a particular animal
described. An animal may be red and weight 343 kg at 1year of age, but red coat color and 343 kg yearling
weight are not the traits the traits are simply coat color and yearling weight. Red and 343 kg are the observed
categories of performance for the traits of coat color and yearling weight. They are the phenotypes for these
traits.
Visible or otherwise measurable properties of traits are called phenotypes, while the genetic factor responsible
for creating the phenotypes are called genotypes. The word genotype is used in several ways. We can speak
of an animal genotype is general, referring to all genes and gene combinations that affect the array of traits of
interest to us. An example used later on in this selection involves a 'Tropically adapted ' genotype. In this case,
the genotype includes all the genes and genes combinations affecting heat resistance, parasite resistance, and
other traits that make up tropical adaptation. We can also speak of an animal’s genotype for a particular trait,
referring to just those genes and gene combination that affect that trait (e.g. heat resistance) or, we can limit
the definition of genotype even further in which case it refers to a particular gene only. In any case, the
genotypes of animal’s descendants are what we can change with breeding methods. Favorable changes in
genotypes result in improved phenotypes.
In animal breeding, we are mainly concerned with changing animal population generically. From a genetic
point of view, therefore we want to know not only the most desirable phenotypes, but the most desirable

14 | P a g e
genotypes as well. That is because an animal’s genotype provides the genetic background for its phenotypes
and it is the genetic materials that is passed on from parents to offspring.
The genotype of domestic animals determines the degree to which the animals are suited for their function in
society. The key to determining the traits of importance and optimal genotypes for those traits is a thorough
analysis of the many interaction among components of the system.

Qualitative or Mendelian Traits

Some traits are simply inherited. They are determine by just one locus or a few loci. Environment usually
plays relatively minor role in influencing the phenotypic category. They exhibit only a few distinct phenotypes
with a sharp distinction between phenotypes. There is usually a simple relationship between the genotype and
the phenotype. A given genotype will generally result in the same phenotype. These are known as qualitative
traits. Example of qualitative traits are sex, coat, color and blood antigens. Others example included green
versus yellow peas, red eyed versus white eyes in Drosophila and the ABO blood group in humans. A good
example is the horned/polled character in cattle of European origin (polled means naturally without horns). A
single gene determines whether a cow is horned or polled. The allele for polled is dominant to the allele for
horned. In general black is dominant to other colors in cattle. Selection for simply inherited trait is different
from selection for typical polygenic traits. With simply inherited traits, we do not deal with breeding values
and their prediction, or even with the concept of heritability. Rather, we are only interested in knowing whether
an individual possess the specific allele or alleles of interest and we select animal based on that knowledge.
Quantitative Traits
Most trait in animal are determine by the effect of multiple genes and by the environment. These are known
as multifactorial traits, quantitative traits, metric character, additive traits or polygenic traits. Polygenic
inheritance describe the inheritance of trait that are determine by the effects of multiple genes and by the
environment. Example of polygenic inheritance in human includes traits such as skin color, eye color, hair
color, body shape, height & weight.
With some qualitative traits, difference in phenotype result largely from difference in genotype & the
environment plays a minor role. With other quantitative traits, difference in phenotype result largely from the
effects of the environment and the genetic factors play a minor role. However, most quantitative traits fall
between these extremes & both genotype & environment must be taken into account in their analysis.

Properties of metric characters:

1. They are controlled by many genes. Individual genes have little effect upon the trait. Collectively this genes
can have large effects.
2. They are significantly influenced by the environment. For example, it is obvious that adult size in most
organisms is affected by the amount of available resources. Thus food availability will determine size in an
inbred line of mice, just as light and soil differences will result in phenotypic variation in height among the
clones of a fruit tree.
3. It appears that additive, dominance and epistatic effects can all contribute to the phenotype of a quantitative
trait, but generally additive gene action is the most important.
4. Many quantitative characters are correlated with others. In mice, for example, body size and litter size are
correlated, larger mice tends to have larger litters.
5. Most metric characters have a continuous distribution in a population. The frequency distribution of such
traits often more or less closely approximates a normal curve.
6. Individuals with the same genotype may have different phenotypic values and individuals with the same
phenotypic value may have different genotypes.

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 QUALITATIVE TRAITS ( DISCRETE QUANTITATIVE TRAITS ( CONTINUOUS
VARIATION) VARIATION)

Usually controlled by only one or a few loci Controlled by many loci. More than 3.
Individuals can be correctly classified according Difficult to classify phenotypes into distinct
to phenotypes. ( e.g. Mendel’s peas) categories because they usually follow
continuous distribution. ( human height)
Show mendelian inheritances. ( monogenic) Complex mode of inheritance ( polygene )
Little environmental effect Moderate to great environmental effect
Genotype can be easily determined Difficult to identify animals with superior
genotypes
The genotype is directly corresponding to The genotype is not directly corresponding to
phenotype. phenotype.

Classification of Quantitative Traits:

There are 3 types of quantitative traits -
• Continuous
• Meristic
• Threshold traits
Continuous traits have a continuous range of phenotypes. They are expressed according to a continuous
gradation from one phenotype too the next from minimum to maximum, with no clear cut breaks in between.
Weight, height, milk production, growth rate, etc are examples of such traits. The distinguishing characteristics
of continuous traits is that the phenotypes of an individual can fall anywhere on a continuous scale of
measurement, and so the number of possible phenotypes is virtually unlimited. Statistics such as mean,
variance and standard deviation can be used to describe continuous traits; correlation, regression and analysis
of variance are statistical procedures that are used for studying continuous traits.
Two other types of quantitative traits are not continuous.
Meristic or countable traits are traits in which the phenotype is expressed/measured in whole numbers. Some
examples are number of eggs laid by hen, litter size in swine, number of scales on reptiles etc.
Threshold traits are traits that have only two or a few phenotypic classes and can be measured by presence or
absence. In a threshold trait, each individual has an underlying and not directly observable risk or liability
(susceptibility) to express the trait. Liability refers to a degree of genetic risk or predisposition to the trait.
Only those individuals with a liability greater than a certain threshold (cutoff) develop the trait. A liability
below the threshold results in normality. For example, twinning in cattle and parthenogenesis in turkeys. In
many threshold disorders, there may be only two phenotypic categories, such as the presence/absence situation
that occurs for certain disease sates (diseased/normal) or for reproductive states (fertile/sterile). The presence
of a genetic disease in a particular individual is determined by a combination of the individual’s underlying
genetic liability and his or her particular environment.

Quantitative Genetics
The branch of genetics concerned with the study of the inheritance of metric characters is called quantitative
genetics or biometrical genetics. Quantitative genetics is used to characterize continuous traits. Almost any
trait that can be defined shows variation, both within and between populations. Quantitative genetics is
concerned with the analysis of the genetic and environmental basis of this variation.

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Significance of Polygenic Inheritance
Most traits that are important in plant and animal breeding are quantitative traits. In domestic animals,
important quantitative traits include meat quality, milk production per cow, egg lying per hen, fleece weight
per sheep, litter size per sow, height, weight and disease resistance etc. The traditional techniques of
transmission genetics and the newer techniques of molecular genetics provide little information about the
inheritance of these complex traits; that are studied with the techniques of quantitative genetics. Quantitative
genetics plays an important role in our understanding of evolution, conservation and other areas of applied
biology because most of the changes concerned in micro evolution are changes in metric characters.
Quantitative Traits Locus (QTL)
The many genes responsible for polygenic inheritance of particular characteristics are scattered around the
genome. Their positions are known as quantitative traits loci (QTLs). A gene that affects a quantitative trait is
a quantitative trait locus (QTL). Locating QTLs in the genome is important to the manipulation of genes in
animal breeding programs and to the cloning and study of genes in order to identify their functions. In
medicine, the identification of alleles causing predisposition to common multifactorial disease, such as heart
disease or diabetes could lead to improved methods of prevention.
Major Gene and Minor Gene
The relative contribution of each gene to the phenotypes of the quantitative trait would be different - some
loci would have strong effects and others only weak effects, these are termed major genes and minor genes,
respectively. There are however, all intermediate grades, genes that cannot properly be classified as major or
as minor. Furthermore, as a result of pleiotropy the same gene may be classed as major with respect to one
character and minor with respect to another character. The distinction, though convenient, is therefore not a
fundamental one, and there is no good evidence that there are two sorts of genes with different properties.
Contributing and Non Contributing Alleles
Alleles that contribute to the phenotype are called contributing alleles. The alleles that don’t have any effect
on the phenotypes of the quantitative traits are called noncontributing alleles. Let us hypothesize there are two
pairs of independently segregating alleles that control the production of red pigment, alleles R (red), C
(crimson) result in red pigment and alleles R and C result in the lack of pigment in the wheat kernel color
phenotype. Here R and C alleles are contributing alleles and r and c alleles are non contributing alleles.
Why Some Traits Have Continuous Phenotypes?
Multiple phenotypes of a trait arise in several ways. Frequently a range of phenotypes occur because numerous
genotypes exist among the individuals of population - this happens when the trait is influenced by a large
number of genes. For example, when a single locus with two alleles determines a trait, three genotypes are
possible; AA, Aa and aa. With two loci each with two alleles, the number of genotypes is 3²=9. In general, the
number of genotypes is 3^n, where n equals the number of loci with two alleles; if more than two alleles are
present at a locus, the number of genotypes is even greater. As the number of loci influencing a trait increases,
the number of genotypes quickly becomes large. If each genotypes encodes a separate phenotype, many
phenotypes will be present. Because many phenotypes are present and the differences between phenotypes are
slight, the trait appears to be continuous. A second reason that a trait may have a range of phenotypes is that
environmental factors may cause each genotype to produce a range of phenotypes (the norm of reaction).
Which phenotype is expressed depend both on the genotype and on the specific environment in which the
genotype is found. Often, penetrance, expressivity, pleiotropy, epistasis and environmental factors are
involved in producing a continuous distribution of phenotypes (continuous traits).

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Useful Parameters for Quantitative Genetics
Mean/Average
Mean is the sum of all measurements divided by the number of measurements. For example, the arithmetic
mean of five values 4, 36,45,50 and 75 is (4 +36+45+50+75) ÷5= 42. The arithmetic mean of a set of numbers
x1, x2,…xn is typically denoted by x, pronounced ‘ x bar’. Let x1, x2,….Xn be the realized values of a random
variable x, from a sample of size n. the sample arithmetic mean is defined as:
𝑛𝑛
1
x = + � 𝑥𝑥𝑖𝑖
𝑛𝑛
𝑖𝑖−1

The mean is frequently used in quantitative genetics to quickly characterize the phenotypes of a group
of individuals.
Variance
The variance, symbolize as s² or V, is defined as the average squared deviations from the mean. To calculate
s²:
1. Subtract the mean from each individual measurement
2. Square the difference for each
3. Add the squared values
4. Divided by the number of original measurements minus 1(n - 1).
−
∑𝑛𝑛𝑖𝑖−1(𝑥𝑥𝑖𝑖 − 𝑥𝑥 )2
𝑠𝑠 2 =
𝑛𝑛 − 1
The standard measure of variation is the variance. Variance is the measure of how much the individual
measurements spread out around the mean. A small variance implies that most values are close to the mean
and hence the mean provides a good predictor of the character value for a randomly chosen individual.
Conversely, a large variance implies that there is considerable uncertainly in the value of a randomly chosen
individual and the mean is a poor predictor. Note that variance being zero only if all individuals have exactly
the same value (homozygous). the variance is one of the most simple measures that we can calculate the
variation about the mean. Variance is a squared value so it is always positive, but its units are also squared.
(cm2, kg2)
Standard Deviation
Another statistic closely related to the variance, is the standard deviation. It is the positive square root of the
variance.
−
∑𝑛𝑛𝑖𝑖−1(𝑥𝑥𝑖𝑖 − 𝑥𝑥 )2
𝑠𝑠 = �
𝑛𝑛 − 1
The standard deviation is used more often than variance because the standard deviation is in the same units as
the original measurements, while the variance is in square units. Variance and standard deviation provide
information about the phenotypes of a group of individuals. Different notation is used for the mean, variance
and standard deviation of the population and of the sample as shown:
Population Sample
Mean µ x
Variance σ2 s²
Standard deviation σ s

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Standard Error of the Mean (SE):
One final measure of variation about the mean is the standard error of the mean (SE):
SE= -
The standard error (of the mean) is the standard deviation about the mean of a distribution of sample means.
In other words, if we repeated the experiment many times, each time we would generate a mean value.
Coefficient of variation
The coefficient of variation (CV) or relative standard deviation (RSD) is the sample standard deviation
expressed as a percentage of the mean.
Covariance Mean Cross Product (MCP)
Covariance indicates how two variables are related. Covariance is a measure of how much two random
variables changes together. A positive covariance means the variables are positively related, while a negative
covariance means the variables are inversely related. The sign of the covariance therefore shows the tendency
in the linear relationship between the variables. A covariance of zero implies there is no (linear) association
between the two variables, and the variables are said to be uncorrelated. The magnitude of the covariance is
not easy to interpret. The normalized version of the covariance, the correlation coefficient, however shows by
its magnitude the strength of the linear relation.
Suppose we have two variables, x and y . the covariance of x and y is computed by taking the first x values
and subtracting it from the mean of x and then multiplying the result by the deviation of the first y value from
the mean of y. This is done for each pair of x and y values and the products are added together. The sum is
then divided by n or (n -1) to give the covariance of x and y , where n equals the number of xy pairs. The
formula for calculating covariance of sample data is shown below
− −
∑𝑛𝑛
𝑖𝑖=1(𝑥𝑥𝑖𝑖 − 𝑥𝑥 )(𝑦𝑦𝑖𝑖 − 𝑦𝑦 )
CoV(x,y) =
𝑛𝑛−1

x= the independent variable

y=the dependent variable
n= number of data points in the sample
x bar = the mean of the independent variable x, and
y bar = the mean of the dependent variable, y
While the variance provides a measure of variation, the covariance cov(x,y) provides a measure of association
( or covariation) between two traits ( x and y) in the same individual.
Correlation
It is often desirable in genetic studies to know whether there is a relationship between two given characteristics
in a series of individuals. For example, is there a relationship between height of a plant and its weight or
between a phenotypic measurements in parents and offspring? If one increases, doesn’t the other also? The
correlation between two traits measures their tendency to vary in the same direction (positive correlation) or
in opposite direction (negative correlation). In other words, the correlation estimate the incidental variation in
two traits when both traits are affected by outside sources of variation. This tendency is measured in term of
correlation coefficient. The usual measure of the precision of a relationship between two variables x and y is
the correlation coefficient, rxy. Correlation coefficient is a statistic that measures the degree (strength) of the
association (relationship) between two variables. The correlation rxy is defined as,
Correlation = rxy = cov(x,y) / sxsy
In the formula for correlation, the products of the deviations are divided by the product of the standard
deviations of x and y (sx and sy). This normalization by the standard deviations has the effect of making rxy a
dimensionless number that is independent of the units in which x and y are measured. The correlation

19 | P a g e
coefficient can range from 1 to + 1. The sign of the correlation coefficient, whether, it is positive or negative,
indicates the direction of the correlation. If the correlation coefficient is positive, then an increase in one
variable tends to be associated with an increase in other variable. If seed size and seed number is positively
correlated in sunflowers, for example, plants with larger seeds also tend to produce more seeds. A negative
correlation coefficient indicates that an increase in one variable is associated with a decrease in the other. If
seed size and seed number is negatively correlated, plants with larger seed tends to produce fewer seed. The
absolute value of correlation coefficient provides information about the strength of the association. When the
correlation coefficient is close to 1 or to +1, the correlation is strong, meaning that a change in one variable is
almost always associated with a corresponding changes in other variable. On the other hand a correlation
coefficient near 0 indicates a weak relationship between the variables. If there is no relation (if the variables
are independent) then the correlation coefficient will be zero. A correlation between variables means only
that the variables are associated, correlation doesn’t imply that a cause – effect relationship exists between the
two variables.
Correlation are broadly classified as follows:
- 1 to - 0.6= high negative
- 0.5 to - 0.4 = medium negative
- 0.3 to - 0.2 = low negative
-0.1 to +0.1 = negligible (zero)
+0.2 to +0.3 = low positive
+0.4 to +0.5 = medium positive
+0.6 to +1.0 = high positive
Different Types of Correlation:
In animal breeding it is important to recognize three different types of correlations. Just as there are two
possible causes (genetic and environmental) of differences between individuals in expressing phenotype of
one trait, there are also two causes of correlation between two traits or characters.
Phenotypic Correlation (rp):
The phenotypes of two or more traits may be correlated or associated, this means that the traits don’t vary
independently. Phenotypic correlation is the degree to which two traits co vary among individuals in a
population. The correlation calculated from the phenotypic value is referred to as phenotypic correlation.
Phenotypic correlation measures observable association between two traits and is calculated as the ratio of the
phenotypic covariance to the product of the phenotypic standard deviations of the two traits, for example,
there is a positive phenotypic correlation between body size and milk yield because on an average , larger
cows give more milk than smaller cows . On the other hand, cows with higher yields tend to have a lower
butterfat percentage. Therefore, there is a negative phenotypic correlation between milk yield and butterfat
percentage. The phenotypic correlation between two traits can be computed by measuring two phenotypes on
a number of individuals in the population and then calculating a correlation coefficient for the two traits. The
phenotypic correlation is usually influenced by both genotype and environment. One reason for a
phenotypic correlation among traits is that the traits are influenced by a common set of genes. When
same genes affect multiple phenotypes, we say they are pleiotropic. If a gene is pleiotropic, it simultaneously
affects two or more traits and thus the phenotypes of those two traits will be correlated. For example, the genes
that affect growth rates in humans influence both body weight and height, so these two phenotypes tend to be
correlated. Pleiotropy is not only the cause of phenotypic correlation among traits. Environmental factors may
also influence several traits simultaneously and may cause nonrandom association between phenotypes. For
example, adding fertilizer to the soil often causes plants both to grow taller and to produce more flower. if we
measured plant height and counted the number of flowers on a group of responsive plants, some of which
receive fertilizer and some of which didn’t , we would find that the two traits are correlated , those plants
receiving fertilizer would be tall and would have many flowers, while those without fertilizer would be short
and have few flowers. This phenotypic correlation doesn’t result from any genetic correlation (pleiotropy),

20 | P a g e
but from the common effect of the environmental factor, the fertilizer on both plants. There are some pair of
characters for which no phenotypic correlation exists. These are characters that can’t both be measured on the
same individuals. The age at sexual maturity in males and in females is an example of two such character. The
phenotypic correlation has two components parts,
(i) Environmental correlation
(ii) Genetic correlation.

(i) Genetic/Genotypic Correlation :

Genetic correlation is a quantitative measure of the association at the genetic level between two traits. The
genetic correlation is that portion of the phenotypic correlation between two traits that is due to inheritance. It
is estimated as the ratio of the genetic covariance between to traits to the products of the genetic standard
deviation of the two traits. To measure genetic correlations use same breeding design as for additive variance
but measures two traits instead of just one. The cause of genetic correlation are still not entirely clear. They
appear to be due mainly either to pleiotropy or to linkage between two loci. Genetic correlation are very
important and useful to a breeder. The main value of genetic correlations is to predict changes in correlated
characters that result from selection in one character. If the two traits are genetically correlated, they evolve
together. Any genetic change in one trait occurring as a result of selection will simultaneously alter the other
trait. Such correlation often presents problems for animals and plant breeders. Genetic correlation may be
positive or negative. A positive genetic correlation means that genes causing an increase in the magnitude of
one trait bring about a simultaneous increase in the magnitude of the other. In chicken, body weight and egg
weight have a positive genetic correlation. If breeders select for a heavier chickens, thereby favoring the genes
for large body size , the size of the chicken will increase and the mean weight of eggs produced by these
chickens will also increase. This increase in egg weight occurs because the genes that produce heavier chicken
have a similar effect on egg weight. Some traits exhibit negative genetic correlation. In this case, genes that
cause an increase in one trait tend to produce a corresponding decrease in other trait. Egg weight and egg
number in chicken have a negative genetic correlation. When breeders select for chickens that produce larger
eggs, the average egg weight increase but number of eggs laid by each chicken decrease. Milk yield and
butterfat percentage have a negative genetic correlation in cattle. When breeders select for increased milk
yield, the amount of milk produced by the cows may go up, but the butterfat percentage will decrease at the
same time. Negative genetic correlations among traits often place practical constraints on the ability of
breeders to select for desirable traits. Knowing about the presence of genetic correlations before undertaking
an expensive breeding program is essential in order to avoid the production of associated undesirable traits in
the selected stock.
(ii) Environmental Correlation :
It measures the association between traits due to environmental factors and is calculated in a similar manner
as the genetic correlation but using environmental covariance and standard deviations. Environmental
correlation which is not strictly speaking the correlation of environmental deviations but the correlation of
environmental deviations together with non-additive genetic deviations. Environmental correlation exists
because specific environmental conditions produce certain features in animals which result in a correlation
between these features and the environmental conditions.
Regression:
The correlation coefficient tells us about the strength of association between variables and indicates
whether the relationship is positive or negative, but it provides little information about the precise
relationship between the variables. Regression analysis is used to determine the precise relationship between
variables. A graph is plotted for the individual data points, one on the x axis and the other on the y. The
regression is the line that best fits the points (the squared vertical distance from the points to the regression
line is minimized). Regression is the predicting value of one variable, if the value of the other is given. If the
two variables are linearly correlated, then the regression line can be represented with the equation:
y=a +bx

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Where, x and y are values of the two variables, b is the slope (regression coefficient) and a is the y intercept.
The slope can be calculated from the covariance of x and y and the variance of x in the following manner: b=
𝑐𝑐𝑐𝑐𝑐𝑐(𝑥𝑥,𝑦𝑦)
𝑠𝑠 2 𝑥𝑥

Regression coefficient represents the slope of the regression line, indicating how many units of change in the
dependent variable (the effect) result from or are caused by each unit of change in the independent variable
(the cause). For example, a slope of 0.5 for the regression of the father (value on the x axis) and son height
(value on the y axis) would mean that for each 1cm increase in height of a father, the expected height of the
son would increase 0.5 cm. The y intercept (the point at which the regression line crosses the y axis) is the
expected value of y when x is zero. If a cause and effect relationship does exist between the two variables, we
can predict a y value given any x value. Note that, the prediction equation cannot predict y exactly for a given
x, because there is a scatter around the line. The equation predicts the average y for a given x, if large samples
are taken.
Regression analysis is a common method for measuring the extent to which variation in a trait is genetically
determined. When stating a regression (cause and effect) relationship the units of the independent and
dependent variables must be used.
Measuring Continuous variation/Distribution:
Phenotypes are not easily grouped into classes when a continuous range occurs. Instead, a frequency
distribution is commonly used. In a frequency distribution, the classes consist of specified ranges of the
phenotype, and the number of individuals in each class is counted. The distribution of a trait in a population
is a description of the population in terms of the proportion of individuals that fall within a certain range of
phenotypes. The frequency distribution of a continuous trait can be summarized by its mean and variance. The
mean represents the center (peak) of the distribution. The variance is a measure of the spread of the
distribution. The variance describes the extent to which the phenotypes are clustered around the mean. A large
value implies that the distribution is spread out, and a small value implies that it is clustered near the mean.
Two distributions may have the same mean, but different variances. A broad curve shows high variability and
a large variance. A narrow curve indicates little variability and a small variance.
The mean and the variance of a distribution do not describe it completely, of course. Nevertheless, for the
purposes of dealing with most quantitative genetic problems, the mean and variance suffice to characterize a
distribution. The distribution of a trait in a population implies nothing about its inheritance.
Normal distribution:
In a large population of animals, continuous traits often show normal distribution which is illustrated in figure
3.1 and is commonly called a bell curve. A normal distribution tells us that the majority of animals in the
population lie reasonably close to average and that there are decreasing numbers of animals at the extremes,
high or low, in expression (or value) of each trait. Individuals above the mean are superior, while individuals
below the mean are inferior. Thus begins the basis for selection. By knowing which animals differ significantly
from average we can get select from this group. While the shape of the bell curve may differ, the principle
of normal distribution of animals performance applies to almost all traits that animal breeders are interested
in.
Normal curves, regardless of the trait for which they are drawn or the units of measurement, show certain
features which always apply if the curve is truly normal. The normal curve is a 'frequency distribution' where
the height of the curve at any point on the base line indicates the frequency or relative proportion of animals
in the population whose phenotype has that particular value.
1. Approximately 67% of the population has values within one standard deviation (±1s) of the mean.
2. Approximately 95% lie within 2 standard deviations (±2𝑠𝑠) of the mean.
3. Over 99% lie within 3 standard deviations (±3𝑠𝑠) of the mean.

22 | P a g e
 99%

95%

67%
Mean (𝑥𝑥)

1s +1

2s +2s

3s +3s

Figure 3.1 Normal distribution curve showing proportions of the data in the distribution those
are included within certain multiples of standard deviation.

23 | P a g e
 CHAPTER 4
Phenotypic Variation
Phenotypic variation
In the world of living being no two individuals are alike in respect to all characters .Even individuals that are
absolutely identical in genetic constitution (monozygotic twins), will not be identical phenotypically.
Absolutely similarity with respect to all characters may occur only within a group of individuals with identical
genotypes developing in an identical environment. At present such a situation is non-existent in nature.
Differences among individuals within a population are referred to as variation. Variability of animal
genetic resources may be considered at three different levels-
(i) between species,
(ii) between breed within species, and
(iii) Within breed.
(iv) Animal geneticists have given most attention to this lower level of diversity (Within breed), much
less to between breed variability and hardly any to across species diversity.
Phenotypic variation refers to the observable or measurable differences among individuals within a population
for a particular trait. The amount of variation is usually measured and expressed in terms of the
(i) variance or
(ii) standard deviation.
(iii) Co efficient of variation
Phenotypic variance, represented by Vp, is a measure of the variability of a trait. Observed phenotypic
Variation can be additive or non additive while the environmental attributes. The genetic attributes can be
additive or non additive while the environmental attributes can be permanent or temporary. The raw material
for livestock improvement is genetic variation. Without genetic variability, genetic improvement is not
possible. In the absence of genetic Variation an entire population may go extinct if it is not able to respond
quickly enough to an environmental change. In the 1840s a fungus infected the potato crop in Ireland. There
was very little genetic Variation in the potato plants population and most of the plants died because they were
all vulnerable to the fungus. As a result, 1 million people died and 2 million people left Ireland to live
somewhere else.
Phenotypic Value (P)
Phenotypic value is the value observed when a character is measured on an individual. For example, the body
weight of a particular cow is 300 kg. The value of 300 kg is the phenotypic Value, called P that can be
partitioned into a genotypic value (G) and an environmental deviation (E).
P=G+E
Genotypic Value (G)
Genotypic value is the average of the phenotypic values of all individuals who have the same genotype. For
example, there are 100 individuals in a population who have the same genotype, AA For, a particular trait, the
phenotypic values of the 100 individuals are (1.25, 0.89…2.10). Because all the 100 individuals have the same
genotype, the average of their phenotypic values, 1/100(1.25+0.09+…. +2.10), is the genotypic value of
genotype AA. Genotypic value is the overall effect of all the genes carried by the animal at all loci that affect
the character in question, including nuclear genes, mitochondrial genes and interaction between the genes.
Genotypic value of an animal is the value of its genes on itself and includes additive, dominant and epistatic
effect. Unlike the phenotypic Value G is not directly measurable.
Environmental Deviation (E)
Environment influence the phenotypic Value by increasing or decreasing effect and is measured as
environmental Deviation. Environmental Deviation is the difference between the phenotypic value and the
genotypic value. E=P-G

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The First Genetic Model
One of the fundamental ideas of Quantitative Genetics is that the phenotypic Value P of an individual is the
sum of that individual's genotypic value (G) plus its environmental deviation (E):
P=G+E
Because environmental deviation can be positive or negative, the average of E's for all individuals will be
zero, and thus, the average phenotypic Values is (equal to) the genotypic Value.
Population Mean:
Population mean is the average value of a particular trait in a population as a whole.
Average Effect of Gene:
Genotypes are not transmitted from generation to generation; it is the gene that is transmitted from parent to
offspring. Average effect of a gene is the changes in the population mean caused by the introduction of the
respective gene.
Additive and Non-Additive Gene Effects:
In general, genes express themselves phenotypically in two ways:
(i) additive and
(ii) Non additive.
Additive (independent) gene action means that the phenotypic effect of one allele adds to the phenotypic effect
of other allele at the same locus or other loci in the genotype. Effects of each gene are cumulative and each
allele has a specific value that it contributes to the final phenotype. The effect of a gene independent from
other gene at the same locus or other loci, i.e., a gene has a given plus or minus effect, regardless of which
other member of the pair or allelic series may be present. For example, an allele g may, on the average,
contribute 2 centimeters in height to a plant, and the allele G may contribute 4 centimeters. In this case, the
gg homozygote would contribute 2 + 2 = 4 centimeters in height, the Gg heterozygote would contribute 2 + 4
= 6 centimeters in height, and the GG homozygote would contribute 4 + 4 = 8 centimeters in height. To
determine the genetic contribution to height, we would then add the effects of alleles at this locus to the effects
of alleles at other loci which might influence the phenotype. Genes such as these are said to have additive
effects. In non additive gene action, the phenotypic effect of one gene doesn't necessarily add to the phenotypic
expression of the other, but members of allelic pairs may interact to give a certain phenotype (dominance), or
different loci may interact to produce a particular phenotype (epistasis).
Causes of Phenotypic Variation in Farm Animals:
The genetics of a metric character centers on the study of its variation. The total phenotypic variation for traits
in farm animals is due to genotype or environment, or the joint effects between genotype and environment.
The basic idea in the study of variation is its partitioning into components attributable to different causes. The
partitioning of the variance into its components allows us to estimate the relative importance of the various
determinants of the phenotype. Variation in phenotype of quantitative traits among individuals in a population
derives from three principal sources:
1. Variation in genotype, which is measured by the (genotypic variance VG);
2. Variation in environment, which is measured by the environmental variance (VE); and
3. Variation resulting from the interaction between genotype and environment (VGE).
The importance and influence of each of these sources of variation are discussed in the following sections.

25 | P a g e
Genotypic/Genetic Variance (VG)
The first source/cause of phenotypic variation is the genetic differences among individuals in the population.
The variation in phenotype caused by differences in genotype among individuals is termed genetic variance
and is represented by the symbol VG. The genotype of an individual is fixed at conception and, except
mutation, remains the same for the remainder of its life. Its genetic make up is determined by the genes that it
received from both parents.

Plant height

15 20 25 30
Temperature (°C)

Figure 4.1 Genetic variation

The individual as well as its parents possesses thousands of genes. Probably the only two animals resulting
from sexual reproduction that are alike genetically are identical twins produced from a single zygote. Members
of an inbred line are more likely to be alike genetically than non inbred individuals. Since parents are not
homozygous for all of the genes they possess and since they may differ genetically, no two of their offspring,
with the exception of identical twins, are genetically alike. Parents homozygous for many pairs of genes will
have offspring that are more alike genetically than parents that are heterozygous for several pairs of genes.
Genetic variation exists in all animals because of the random sampling of the alleles during Mendelian
segregation. Figure 4.1 shows a situation where all the variation is due to two genotypes and none is due to
the environment. Here, plant height is influenced by the two genotype with individuals of the G1 type having
greater height than individuals of the G2 type. Plant height is independent of the temperature in which the
plants are raised.
*Identical twins genetically alike but not phenotypically alike

Environmental Variance (VE)

The second cause of phenotypic variation is the environmental variance. The variation in phenotype caused
by differences in the environments to which the individuals in a population have been exposed is termed
environmental variance and is symbolized by VE. Environment includes all non-genetic factors including
climatic factors such as temperature and rainfall patterns, nutritional factors such as soil nutrients or
availability of food resources and various other factors that cannot always be identified by the researcher that
have influenced the character from the time of conception to the time when phenotypic value was measured.
Phenotypic variation in economic traits due to environment is important because
1) They are not transmitted from parents to their offspring,
2) They overshadow variations due to heredity, proper environment is necessary for an individual to reach its
genetic potential,
3) Proper environment is necessary for an individual to reach its genetic potential and
4) Rapid improvements can be made in the efficiency of livestock production by supplying uniform and
superior environmental conditions to breeding animals and those used for commercial production. Figure 4.2
shows a situation where all the variation is environmental and the two genotypes are indistinguishable.

26 | P a g e
 Plate height (cm)
G1, G2

15 20 25 30

Temp

Figure 4.2 Environmental Variation.

When genotype and environment are independent in their effects on phenotype, the total variance equals the
sum of the genetic variance and the environmental variance. Thus,
VP=VG + VE
𝜎𝜎 2t =𝜎𝜎 2g + 𝜎𝜎 2e
Vg=VA + VD +VI
Where, 𝜎𝜎 2t =total variance in phenotype, 𝜎𝜎 2g =genetic variance, and 𝜎𝜎 2e = environmental variance.
Genotype-Environment Interactions (VGE)
In the simplest cases, a specific difference of environment has the same effect on different genotypes i.e., each
environment adds or detracts the same amount from the phenotype. When this is not true, environmental
effects on phenotype differ according to genotype, and a genotype-environment (G-E) interaction is said to be
present. In some cases, G-E interaction can even change the relative ranking of the genotypes in different
environments, so genotype that is superior in one environment may become inferior in another. Genotype-
environment interaction occurs when performances of different genotypes are not equally affected by different
environments. Animals of a certain genotype perform more satisfactorily in one environment than in another.
One environment favors the performance of one genotype over another i.e., favorable genes in some
environments may become unfavorable under other environments. For example, Brahman crosses are superior
to British crosses in southern states and British crosses are superior to Brahman crosses in northern states.
Three different genotypes: A, B and C are used to illustrate this principle (Figure 4.3). No G-E interaction is
illustrated between genotypes A and B because they performed relatively same in both environment 1 and 2,
although genotype A performed better than B in either environment. An interaction is demonstrated between
genotype C and the other two genotypes A and B. Genotype C is superior in performance to either genotypes
A and B in environment 1, but was inferior to either in environment 2.
Interaction of genotype and environment is common and is very important in both plants and animals. Because
of interaction, no one plant/animal variety will outperform all others in all types of environment, and
plant/animal breeders must develop special varieties that are suited to each growing area. If there is no
interaction, then the best genotype in one environment will be the best in all. But if there is much interaction
the particular genotypes must be sought for particular environment.
Genotype-environment interactions are undeniably an important aspect of performance (phenotypic
expression). However, calculating the level of impact is difficult. Therefore comparison of individuals is best
accomplished when the environment of the individuals is similar, and the environment of their offspring will
also be similar. The practical implication indicated is that if G-E interactions are important, prospective parents
should be evaluated and selected under the same conditions in which their offspring will be produced. The G-

27 | P a g e
E interaction determines if a genotype is widely adapted for an entire range of environmental conditions or
separate genotypes must be selected for different sub environments. Breeding plans may focus on the G-E
interaction to select the best genotype for a target environment.

Genotype A

12
Performance in arithmetic unit

Genotype B
11

10

3
Genotype C
2

Environment 1 Environment 2

Figure 4.3 Genotype-Environment interactions.

The phenotypic variance composed of differences arising from genetic variance, environmental variance, and
G-E interaction, can be represented by the following equation:
VP=VG+ VE+ VGE
The relative contributions of these three factors to the phenotypic variance depend upon the genetic
composition of the population, the specific environment, and the manner in which the genes interact with the
environment. These components can be determined accurately controlled breeding experiments between
inbred lines.
Partitioning Genetic Variance (Components of Genetic Variation)
The genetic variance can be subdivided into components arising from different types of gene action. There
are three purely genetic components:
1. Additive genetic variance (VA);
2. Dominant genetic variance (VD); and
3. Interaction (epistatic) genetic variance (VI)
Additive Genetic Variance (VA)
Some of the genetic variance occurs as a result of the additive effects of genes on the phenotypes. The
phenotypic variance due to additive effects of genes is the additive genetic variance and is symbolized by VA.
Additive variance arises from alleles whose contribution to the variance is additive and independent of other
genes. In other words, an allele contributing to additive variance exerts its particular quantitative effect
whatever its allelic partner at that locus and whatever alleles are present at other loci. Its effect is therefore
repeatable from one generation to the next.
If the heterozygote is exactly intermediate between the homozygotes, the contribution of dominant component
is zero; that is, the entire genetic component is additive. The additive genetic variance is responsible for the
resemblance between parents and offspring. The additive genetic variance is the basis for the response to
selection. The effect of selection depends on the amount of additive genetic variance and not the genetic
variance in general.

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Dominant Genetic Variance, or Dominance Variance (VD):
Some genes may exhibit dominance, and this comprises another source of genetic variance, the dominant
genetic variance (VD). Dominant genetic variance is due to dominance relationships among alleles. Dominance
occurs when two alleles at a particular locus on a chromosome interact, and one allele masks the expression
of the other allele at that locus. Dominant variance arises from alleles whose effects depend upon the allele
with which they are partnered at a locus. For example, the dominance of the polled allele in cattle over horned
recessive allele. The contribution of such genes to the genetic variance thus varies from one generation to the
next as allelic pairings change. Heterozygotes express these, but are equally likely to pass the recessive allele
offspring. Expression depends upon the allele received from the other parent, so this variation does not
correlate well between parents and offspring. If the heterozygote is not exactly intermediate between the
homozygotes, there is some dominance. In the presence of dominance, the heterozygote Gg would contribute
8 centimeters in height to the phenotype, the same amount as the GG homozygote. Thus a population
consisting of both genotypes would have genetic variance but there would be no corresponding phenotypic
variance.
Interaction Variance (VI) (Epistasis)
Interaction variance is due to interactions among loci that act on the same characteristic. If there is more than
one locus affecting the character, then epistatic interactions may occur among alleles at different loci. When
epistasis exists, alleles at different loci interact to determine the phenotype. The presence of epistasis adds
another source of genetic variation, called epistatic or interaction variance (VI). For example, AA may be
expressed differently according to whether alleles BB, Bb, or bb are present at another locus. These genes are
likely to be inherited independently, so combinations in the parents are broken up at gametogenesis. New
combinations are made in the offspring, so interactions are not passed intact from parents to offspring.
Importance of Heredity and Environment:
Frequently discussed has been the question of whether genotype or environment is more important in the
expression of economic traits. It is now recognized that both are of very great importance. The best possible
inheritance will not result in a superior herd/flock unless the proper environment is also supplied so that the
animals can reach their maximum genetic potential. Nevertheless, the best possible environment will not
develop a superior herd/flock unless the animals possess superior inheritance. Genetic superiority will be
passed from parent to offspring, superior environment will not. It can readily be seen that the limit to
performance is set by the animals own genotype, and the best possible environment will not cause that
individual to exceed its own genetic potential.
Every quantitative character is genetically determined but is subsequently realized in a particular environment.
Any attempt to determine exactly the degree to which the phenotypic value of a character in a single individual
depends on heredity or environment would amount to biological nonsense, since the two factors cannot operate
independently.
Stability of Genotypes:
Genetic-environment interactions (G-Es) are great interest when evaluating the stability of breeding animals
under different environmental conditions. The reliability of genotype performance across different
environmental conditions can be an important consideration in animal breeding. Animals of certain genotype
perform well in all environments. For example, Friesian breeds of cattle introducing all over the world for
milk production is performing almost good in milk yield. Strains or hybrids of White Leghorn are doing well
in almost all tans of environments in sin egg production. This is the stability of genotypes. When a genotype
perform well in all environment it is called to be in Stability of Genotypes

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Measures of Genetic Variations:
Proportion of polymorphic loci
Using the allelic frequencies calculated for a given gene, a gene can be defined as polymorphic (2 or more
alleles in substantial frequency) or monomorphic (having only one allele in high frequency). The simplest
measure of genetic variation is to categorize loci as polymorphic or monomorphic and then to calculate the
proportion of all polymorphic loci. A gene is considered monomorphic if the frequency of the most common
allele is 0.99 or greater (if all other alleles combined have a frequency of 0.01 or less). A gene is called
"polymorphic" if there is more than 1 allele present in at least 1% of the population. Some genes have 2 alleles:
they are "dimorphic".
For example, given a sample of 400 individuals, 320 with normal genotype (HbA HbA), 72 carriers (HbA
HbS) and 8 (mostly young individuals) had sickle cell disease (HbS HbS).
𝟑𝟑𝟑𝟑𝟑𝟑 𝟕𝟕𝟕𝟕 𝟖𝟖
P= = 𝟎𝟎. 𝟖𝟖; H= = 𝟎𝟎. 𝟏𝟏𝟏𝟏; Q= =0.02
𝟒𝟒𝟒𝟒𝟒𝟒 𝟒𝟒𝟒𝟒𝟒𝟒 𝟒𝟒𝟒𝟒𝟒𝟒

p=0.8+ 𝟏𝟏�𝟐𝟐(0.18) = 0.89

q=0.02 +𝟏𝟏�𝟐𝟐 (0.18) = 0.11

If 30 loci are examined (by electrophoresis) and 15 of the loci in a population are polymorphic, then the degree
15
of polymorphism in that population = =0.5.
30

Estimates from several samples or sub populations can then be averaged to obtain a measure of variation in
the overall population.
Heterozygosity of the population:
A second approach of measuring genetic variation is to calculate average heterozygosity over all loci; that is,
average frequency of heterozygous individuals over all loci in a population. This takes into account all levels
of genetic variation rather than just classify loci into 2 categories. Average heterozygosity for a sample of n
loci is given as:
1
H= (HA+HB + HC +............+ HE) where, HA is heterozygosity for gene A, and so on.
𝑛𝑛

If HA = 0.5, HB = 0.0 HC = 0.1, HD = 0.0 HE = 0.2 and n = 5,

1
Then, H= (0.5 +...+ 0.2) = 0.16 i.e., 16% of the loci in a given individual are heterozygous for the variants.
5
Three of the above loci are polymorphic (A, C and E) i.e., has the most common allele with a frequency of <
0.99
3
Proportion of polymorphic loci = = 0.6
5

Heterozygosity is a good measure because it estimates the probability that 2 alleles taken at random from the
population are different.
Surveys of the genetic variations in various species demonstrate that up to 20% of the genes examined by
electrophoresis are polymorphic and that 10% of these genes are heterozygous in a given individual.
Heterozygosity is of major interest to students of genetic variation in natural populations. High heterozygosity
means lots of genetic variability. Low heterozygosity means little genetic variability.

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 CHAPTER 5
Genetic Parameters
In animal breeding, knowledge of the genetic properties of the traits is the first prerequisite in establishing a
selection program. The estimation of genetic parameters is an important issue in animal breeding. Estimation
of genetic parameters is synonymous with the estimation of variance components. First of all, estimating
additive genetic and non additive genetic variances contributes to a better understanding of the genetic
mechanism. Secondly, estimates of genetic and phenotypic variances and covariance’s are essential for the
prediction of breeding values and for the prediction of the expected genetic response of selection programs.
Parameters that are of interest are
(i) Heritability
(ii) Genetic correlation and
(iii) Repeatability, and those are computed as functions of the variance components.
Genetic parameter is the raw material for animal breeding.

Heritability
The most basic question to be asked about a quantitative trait is whether or not observed variation in the
character is influenced by genes at all. It is important to note that this is not the same as asking whether or not
genes play any role in the character's development. Gene mediated developmental processes lie at the base of
every character, but variation from individual to individual is not necessarily the result of genetic variation.
The possibility of speaking a language at all depends critically on the structures of the central nervous systems
as well as the vocal cords, tongues, mouth and ears which depend in turn on the nature of the human genome.
There is no environment in which cows, for example, will ever speak. Although the particular language
humans speak varies from nation to nation, this variation is totally non genetic. The concept of heritability is
used as a statistical tool to evaluate the relative contributions of genes and environment to variation in a
specific trait determined by many loci. Heritability is the proportion of the total phenotypic variation in a
population that is due to genetic differences among individuals.
The most common summary statistic in quantitative genetics is the heritability of a character. Heritability
can be defined as the ratio of genetic variance to phenotypic variance (total variance). It is an indicator
of the proportion of the observable variation in a trait in the parental generation which will be passed to the
offspring generation. The heritability estimates tell us how much of the variation in the distribution of a trait
can be attributed to genetic cause.

Heritability in the broad sense (H2 or H2B or HB or h2B)

Broad sense heritability is the proportion of the phenotypic variance in a population in a given environment,
that is due to genetic effects including additive, dominance and epistasis. It measures the strength of the
relationship between the phenotypic values for a trait and the genotypic values.

𝑉𝑉𝐺𝐺 𝑉𝑉𝐴𝐴 + 𝑉𝑉𝐷𝐷 + 𝑉𝑉𝐼𝐼

𝐻𝐻 2 = =
𝑉𝑉𝑃𝑃 𝑉𝑉𝑃𝑃
Broad sense heritability measures how much of the total variance in phenotypic results from differences in
genotype. It includes genetic variation from all types of genes. It ignores the fact that the genetic variance may
be of the additive, dominance, or interactive sort. It also assumes that genotype environment interaction is not
important. Thus, its usefulness is questionable.

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Heritability in the narrow sense (h² or h2N)
Narrow sense heritability is the proportion of the phenotypic variance that is due to additive genetic effects
only.
𝑉𝑉𝐴𝐴
h2 =
𝑉𝑉𝑃𝑃
The difference between the broad sense heritability, H², and the narrow sense heritability, H² is that includes
all of the genetic contributions to variation, whereas h² includes only the additive effects of alleles. Since VA
is never greater than VG, it is evident that narrow sense heritability is never greater than broad sense
heritability. In general, the narrow sense heritability of a trait is smaller than the broad sense heritability. The
two types of heritability are equal only when the alleles affecting the trait are additive in their effects. The
term heritability is normally used in the narrow sense unless otherwise specified.
The heritability of a trait is always positive ranging from 0.00 to 1.00. A heritability of 1.00 indicates that all
of the variation in the population is genetic; heritability of 0.00 indicates that none of the phenotypic variation
in the population is genetic i.e. the variation is wholly environmental in cause; and heritability of 0.50 means
that 50 percent of the phenotypic variation arises from genetic differences among individuals. Heritabilities
of 0 are found in highly inbred populations with no genetic variation. Heritabilities of 1 are expected for
characters with no environmental variance in an outbred population if all genetic variance is additive. For
many traits in many populations, values of heritability are somewhere between 0.00 and 1.00.
Quantitative geneticists are more interested in the narrow sense heritability. It is useful in predicting the
phenotypes of offspring. Consequently, it is an important statistic in programs to improve agricultural crops
and livestock through selective breeding. Additive genetic variance (VA) is passed on reliably from parent to
offspring. The situation is quite different when dominance and epistatic interactions affect the phenotype
because they cannot be passed on intact. The effect of selection depends on the amount of additive genetic
variance and not on the genetic variance in general. Therefore, the narrow sense heritability, not the broad
sense heritability, is relevant for the prediction of response to selection. Heritability is a measure of how much
of the variation in a herd/flock is genetic in origin. Selection of parents will only result in a change in progeny
performance if the selected trait is heritable.
Traits with low heritability (h2 < 0.20): reproductive traits like days open, calving interval, litter size,
conception rate, longevity or productive life.
Moderately heritable traits (h2 of 0.2 to 0.4): Growth traits, milk yield, fat yield and protein yield.
Highly heritable traits (h2 > 0.4): Carcass traits and traits related to skeletal dimensions like mature body
weight, fat and protein% in milk.
There are some exception to these generalizations.
Understanding Heritability (Important Points about Heritability)
Despite their utility, heritability estimates have a number of significant limitations. Unfortunately, these
limitations are often ignored. As a result, heritability is one of the most misunderstood and widely abused
concepts in all of genetics. Some of the important qualifications and limitations of heritability are as follows:
1. Heritability does not indicate the degree to which a trait is genetic; it measures the proportion of the
phenotypic variance among individuals in a population that results from genetic differences. Genes often
influence the development of a trait, and thus the trait may be said to be genetic. However, the differences
in phenotype among individuals may not be genetic at all. Suppose that genes are critical in determining
the phenotypes of a trait. If all individuals in a population have identical genes at the loci that control the
trait, then the genetic variance VG = 0, the heritability must be zero. Although the heritability in this case
is zero, it would be incorrect to assume that the trait is not under genetic control. It simply means that there
is no usable genetic variation (VA) left to exploit and further selection will be ineffective. Similarly, a high
heritability does not negate the importance of environmental factors influencing a trait; a high heritability
might simply mean that the environmental factors that influence the trait are relatively uniform among the
individuals studied.

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2. Heritability is a population statistic not a value associated with a single individual. It does not indicate
what proportion of an individual's phenotype is genetic. Since it is based on the variance, which can only
be calculated on a group of individuals, heritability is characteristic of a population. An individual does
not have heritability, a population does. A heritability of 0.40 for cold tolerance means that within that
population, genetic differences among individuals are responsible of 40% of the variation. Therefore, 60%
is due to environmental causes. However, that does not mean that the cold tolerance of a certain individual
is due 40% to genetic causes and 60% to environmental causes.
3. Heritability is not a biological constant i.e., not fixed for a trait. The heritability estimate is specific to the
population and environment you are analysing. High environmental variance causes lower h2 than low
environmental variance, although genetic effects stay constant. The heritability value for a trait depends
upon the genetic make up and the specific environment of the population. In general, the heritability of a
trait is different in each population and in each set of environments.
4. Genetic parameters such as heritability must change as a consequence of selection for two conceptually
different reasons: the reduction in variance among selected individuals, and the change in gene frequency
due to selection. Heritability declines with inbreeding and selection.
A heritability estimate is a figure that relates to a specific trait at a specific time in a specific population of
animals living under specific environmental conditions. Heritability of a trait varies from one population to
another and from one environment to another.
Importance of Heritability Estimates
The heritability of a trait is a central concept in quantitative genetics. It is the single most important
consideration in determining appropriate animal evaluation methods, selection methods and mating systems.
Knowledge of heritability is useful in plant and animal breeding because it can be used to predict the
magnitude and speed of population improvement.
● Heritability is important in selection. The accuracy of selection is higher for a highly heritable trait that a
lowly heritable trait. The larger the accuracy of selection, the larger is the expected response due to
selection.
● Heritability estimates can be used to predict the response to a single generation of selection. If heritability
is close to zero, the population will show very little response to selection, no matter how strong the
selection.
● Heritability value of a trait determines the type of selection strategies (animal evaluation methods) to be
used for the improvement of that trait. If a trait is medium to high in heritability (above 30%), selection
based upon the individual's own merits i.e., mass selection allows a relatively rapid rate of improvement.
Conversely, when the trait has a low h2, you should use other methods to identify genetically superior
individuals such as progeny test.
● Heritability is important in prediction of breeding values and producing ability. When heritability of a trait
is high, phenotypes are generally good indicators of underlying breeding values, and phenotypic selection
will be effective in changing the level of the trait. When heritability is low, phenotypes reveal little about
breeding values, and phenotypic selection will be ineffective.
● More improvement can be made in low heritability traits, such as those associated with fitness by using
mating systems that take advantage of heterosis. As a rule, the lower the heritability of a trait, the greater
the heterotic response from various outbreeding mating systems. One such system is the hybrid inbred
method. A large number of inbred lines are created. These are then crossed in all possible combinations,
and the cross that gives the best hybrid is chosen. Then new inbred lines are developed from these best
hybrids, and again crosses are made to find the best second cycle hybrid. This scheme selects for
dominance effects, because it takes the best heterozygote.
● Heritability is important in management. If it is low, more success would be obtained if the environmental
conditions under which the individual will be grown are optimized such as improving nutrition and
management practices.

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Methods of Estimation of Heritability
Continuous traits are often determined by multiple genes and by environmental factors. To assess heritability,
we must:
1. Measure the variation in the trait.
2. Partition the variance into components attributable to different causes.
Three general methods are used to estimate heritability. (These three are the method)
i. First, we can measure heritability from the response of a population to selection.
ii. Second, we can estimate directly the components of variance by minimizing one component; the
remaining variance can then be attributed to other causes. For example, by minimizing environmental
causes of variance we can estimate the genetic component directly. Or, by eliminating the genetic
causes of variance, we can estimate the environmental component directly.
iii. Third, we can measure the phenotypic resemblance among relatives.
Heritability from Response to Selection measure
In practice, heritability can be calculated as realized heritability: gain (𝛥𝛥G) divided by selection differential
(S).
𝛥𝛥𝛥𝛥
Heritability, h2 =
𝑆𝑆
If there is no gain (𝛥𝛥G = 0), then the heritability will be zero, and breeders will know that no matter how much
selection they practice, they will not improve their flocks and might as well not waste their time. Since this
value is calculated after the breeding has been done, it is referred to as realized heritability. Quantitative
geneticists treat the realized heritability as an estimate of the true heritability. In order to obtain an estimate of
h², selection ought to be carried out for several generations and one must also maintain a central group where
no selection takes place.
Response to selection declines with time as the selected population becomes homozygous for various alleles
controlling the trait. As response declines, the calculated heritability value itself declines. After intense or
prolonged selection heritability may be zero. It does not mean that the trait is not controlled by genes, hence,
heritability is specific for a particular population at particular time. Intense selection exhausts the genetic
variability, rendering the response to selection, and thus heritability itself, zero.
Minimizing Variance Component
Variance components can be minimized by several different ways. If we use genetically identical organisms
(inbred lines, clones and identical twins), then the genetic variance (VG) is zero and all that is left is the
environmental variance (VE). The total phenotypic variance (VP) in a genetically heterogeneous population
should be measured by subtracting the environmental variance (VE) of the genetically homogeneous
population from VP, we obtain the value of VG. From this we can calculate heritability in the broad sense.
Genetic variance can be measured directly by minimizing the influence of the environment. Environmental
variance may approach zero if all important environmental factors, such as food, moisture and temperature,
are known and carefully controlled. This is most easily done with plants grown in a greenhouse. Under that
circumstance, environmental variables, such as soil quality, water, and sunlight, can be controlled to a very
high degree. Hence, the variance among individuals grown under these circumstances is almost all genetic
variance. The total phenotypic variance can be obtained from the plants grown under natural circumstances.
Here we again can calculate heritability in the broad sense.
Heritability from the Phenotypic Resemblance among Relatives
Perhaps the most important approach used to measure components of genetic variance and heritability is based
on the phenotypic resemblance between relatives (genetically related animals). The relative importance of
genetic and environmental factors for a particular trait can be estimated from the phenotypic resemblance
between relatives. The amount of phenotypic resemblance among relatives for the trait provides an indication
of the amount of genetic variation for that trait. If trait variation has a significant genetic basis, the closer the

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relatives, the more similar their appearance. Obviously, close relatives share more genes with one another than
with nonrelatives or distant relatives, and thus should have greater phenotypic resemblance. For example,
monozygotic twins share all of their genes; siblings share one half of their gene on average; and first cousins
share one eighth of their genes. As a result, phenotypic values between close relatives should be more highly
correlated than those between distant relatives.
If the additive genetic variance is important in determining the differences among individuals, then we expect
that offspring should resemble their parents. We must first measure the phenotypes of parents and offspring
in a series of families, and then statistically analyze the relationship between their phenotypes. Correlation
and regression are appropriate for this type of problem. In case of farm animals, is estimated from the
phenotypic likeness among relatives and the following methods are usually used:
Heritability from parent offspring regression
Parent offspring regression is one of the most commonly used methods of estimating heritability. The
estimation of heritability from the regression of offspring on parents is comparatively simple straight forward.
There are three types of parent offspring regression: two single parent offspring regressions, and the midparent
offspring regression. A specific trait is measured for both the parent and the offspring at the same age and
compared using regression. If we plot the observations on offspring against the values of their parents (either
sires, dams, or their average), we can perform offspring parent regression. A graph of offspring values (y)
against the average of their two parents (x) for a particular trait will have a slope (b) equal to the narrow sense
heritability of that trait. The formula for a straight line graph is y = a + bx,
Where, a is a constant; and b is the slope of the regression line.
So, h2= b
● Regression of offspring on mid parents (mean of sire and dam phenotype for the trait)
h2= bo𝑝𝑝 (𝑝𝑝= average of the parents)

● Twice the regression of offspring on dam

h2= 2 bo𝑑𝑑
● Twice the regression of offspring on sire
h2= 2 bo𝑆𝑆
Offspring parent regression is not often used in practice. It requires data on 2 generations, and uses only this
data. It is also not able to utilize genetic relationships among parents.
Sib analysis
Heritability estimates also may be determined from the resemblance between full brothers or full sisters (full
sibs), and half brothers or half sisters (half sibs). A number of males (sires) are each mated to several females
(dams), the males and females being randomly chosen and randomly mated. A number of offspring from each
female are measured to provide the data. The individuals measured thus form a population of half sib and full
sib families. It is assumed that no selection is practiced. The estimation of the heritability from sib (brother
and sister analysis is illustrated below:
I. Intraclass correlation among half sibs.
h2= 4 x correlation among half sibs.
II. Intraclass correlation among full sibs.
h² = 2 x correlation among full sibs.
The relation of observed and expected correlations between relatives is a direct measure of heritability in the
narrow sense. We can thus define h²=robs/ rexp in which robs (observed) is the observed correlation between the
relatives and rexp(expected) is the expected correlation. The expected correlation is simply the proportion of the
genes in common. For example, parents and offspring have half their genes in common.
Heritability is the proportion of the differences between animals that is transmitted to the offspring. Thus, the
higher the heritability for any trait, the greater the possible rate of genetic improvement. When evaluating

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animals, every attempt should be made to subject all animals from which selections are made to as nearly the
same environment as possible. This results in a large proportion of the noted differences among individuals
being genetic and will increase the effectiveness of selection.
Heritable and Non Heritable Traits
The question of whether or not a trait is heritable is a question about the role that differences in genes play in
the phenotypic differences between individuals or groups. Heritable traits are defined by their ability to be
passed from one generation to the next in a predictable manner. In principle, it is easy to determine whether
any genetic variation influences the phenotypic variation among organisms for a particular trait. If genes are
involved, then on the average the biological relatives should resemble each other more than the unrelated
individuals do. This resemblance would be reflected as a positive correlation between parents and offspring,
and between siblings. Parents who are larger than average would produce offspring that are larger than the
average. The more seeds plants produce the more seeds the siblings will produce also. Such correlations
between relatives are however, evidence of genetic variations only if the relatives do not share a common
environment more than the non relatives do. In experimental organisms, there's no problem in separating
environmental from genetic similarities. The offspring of a cow producing milk at a high rate and the offspring
of a cow producing at a low rate can be raised together in the same environment to see whether despite the
environmental similarity, each resembles its own parents. In natural populations, and especially in humans,
this is difficult to do.
Familiarity and Heritability
Traits are familial if members of the same family share them, for whatever reason. Traits are heritable only if
the similarity arises from shared genotypes. When members of the same family share a trait, the trait is said
to be familial. Familial traits may arise because family members share genes or because they are exposed to
the same environmental factors. Thus, familiarity is not the same as heritability.
Repeatability
For some characters, it is possible to measure performance more than once on the same animal. For example,
fleece weight can be measured each year on each sheep, milk production of dairy cows can be measured on
the same cow each lactation. Such characteristics for which the animals have more than one performance
record during its lifetime are said to be repeatable/repeated. For repeatable traits, the environmental effects
are divided into two types:
1. Permanent environmental effects (EP): Permanent environmental effects are those factors which
permanently affect the performance of the animal. They influence all records of the same animal in the
same way. Examples include nutrition at early stages of development affects the ability of beef and dairy
cows to produce milk permanently, a permanent problem in the udder will affect milk production during
all productive life of the cow or ewe.
2. Temporary environmental effects (ET): The environmental effects which do not affect performance
permanently. These factors vary from season to season or year to year, so they do not influence different
records in the same way. Examples include forage quality, weather conditions, and some management
practices.
Repeatability (r) is the proportion of the phenotypic variance (total variance, VP) that is due to permanent
differences between individuals, both genetic and environmental,

𝑉𝑉𝑉𝑉 +𝑉𝑉𝑉𝑉 +𝑉𝑉𝑉𝑉 +𝑉𝑉𝑉𝑉𝑉𝑉

r=
𝑉𝑉𝑉𝑉
Repeatability ranges from 0.00 to 1.00. This is an indication of the ability of an animal to maintain its
superiority in a particular trait from year to year. Repeatability of milk yield in successive lactations in a dairy
herd is 0.40. It means that 40% of the total variation in milk yield in this herd is due to genetic and permanent
environmental differences, and 60% is due to temporary environmental variation.
Repeatability measures the strength of the relationship between repeated records. Therefore, repeatability can
be estimated as the correlation between repeated records on the same animals.

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Importance of Repeatability Estimates
The knowledge of repeatability of a character is useful in many ways.
1. It sets the upper limit of heritability. Heritability indicates the relative contribution of VA to VG whereas
repeatability indicates the relative contribution of VG + VEP to VP. Because of this, we can conclude that for
repeatable characters, heritability is never greater than repeatability.
2. Repeatability estimates for the various traits may be used in selection for future performance of the same
individual. When the repeatability estimate for a trait is high, selection on the basis of the first record should
be effective.
3. Repeatability is important in making culling decisions. When r is high we can cull animals of poor
performance on the basis of the first record. When r is low one should wait for more records before making a
culling decision on the animal.
4. It is useful in prediction of producing ability (most probable producing ability, MPPA) from n previous
records and therefore the animal's next record from the current and previous records. If r is high, we can
predict the animal's next record more accurately. If r is low then the prediction of the next record has low
accuracy.

𝒏𝒏𝒏𝒏
MPPA = PA = (𝑃𝑃i −𝑃𝑃)
1+(𝑛𝑛−1)𝑟𝑟

𝑃𝑃i is the average of the n records of the animal

𝑃𝑃 is the mean for all animals.
Suppose a cow has three milk records: 4000 kg in the first record, 5000 kg in the second, and 6000 kg in the
third. Suppose also that the mean of all cows is 4600 kg and the repeatability of milk yield is 0.60, then the
predicted producing ability of this cow is:

(3)(0.60)
PÂi = (5000 - 4600) = 327kg
1+(3−1)(0.60)
5. Repeatability is important in prediction of breeding values from multiple records on the same animals;

𝑛𝑛ℎ²
BV = (𝑃𝑃i - 𝑃𝑃)
1+(𝑛𝑛−1)𝑟𝑟
For the previous example if heritability of milk yield in this population is 0.25 then
(3)(0.25)
BV₁ = (5000 - 4600) = 204.6kg
1+(3−1)(0.60)

Producing Ability (PA)

Producing ability is the performance potential of an animal for a repeated trait (the ability of the animal to
repeat its performance in future records). Producing ability is a function of all permanent factors (which
permanently affect the performance potential of the animal) which include:
(i) all genetic factors and
(ii) all permanent environmental factors.
The average of PA is 0 across the population because it is expressed as a deviation from the mean.
Importance of Producing Ability
● It is important to commercial producers as a measure of productive capacity.
● Typically dairy farmers feed their cows according to their producing ability.
● Therefore, prediction of PA is quite useful in practice. The predicted value of PA is called Most
Probable Producing Ability (MPPA).
● P = µ + MPPA is a prediction of the animal's next record.

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Differences between Heritability and Repeatability
Points Heritability Repeatability
Definition The relationship between individuals in The relationship of the same individual in the
the successive generation successive records such as milk production, fleece,
weight etc.
Value Always lower than repeatability Always higher than heritability
2
Formula Heritability, h = VG/VP Repeatability, r = (VG+VEP)/VP
Expression It doesn’t need to express several times It is measured for those traits which are expressed
of a record between individuals several times during an animal lifetime such as
milk production of dairy cow
Intraclass Not same as intraclass correlation of the Same as intraclass correlation of the repeated
correlation repeated records of the same individuals records of the same individuals

***Heritability (h2) indicates the relative contribution of VA to VP. But Repeatability (r) indicates
contribution of VG + VEP to VP.
h2 = VG/VP and
r = (VG+VEP)/VP
= (VG/VP) + (VEP/ VP)
= h2 + a positive value
r > h2
So, here we can see that Repeatability is always higher than heritability. (Written)

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 CHAPTER 6
Selection
There are two ways in which the action of the breeder can change the genetic properties of the
population; the first by the choice of individuals to be used as parents, which constitutes selection, and
the second by control of the way in which the parents are mated, which embraces mating systems.
Through selection and mating all improvement of domesticated animals and plants has been made.
Selection
Selection is the process in which certain individuals in a population are preferred to others for the
production of the next generation. It is the process that determines which individuals become parents,
how many offspring they may produce, and how long they remain in the breeding population. Selection
is the Keystone of the arch of animal improvement. It is the most important single force for changing
gene frequency and making genetic improvement. Selection makes genetic variation and is used to
make long term genetic change in use of additive genetic change in animal population. Selection can
occur on different parts of the life cycle of an individual: the embryo might be defective, the foetus
might not survive to birth, the immature offspring might be killed, and the individual might not be able
to find a mate or might be sterile. Selection cannot be based solely on the effects of the genes which
may influence the expression of a single desired trait, rather the entire individuals or zygote must be
chosen.
*Unit of selection= individual not trait
Selection is of two general kinds, natural or that due to natural forces, and artificial or that due to the
efforts of man. Some research workers have divided selection in farm animals into two kinds, one
known as automatic and the other as deliberate selection. Permanent improvements in domestic animals
can be made by genetic selection through natural or artificial means.
Purpose of Animal Selection or Objectives of Selection:
The purpose of animal selection is to identify and select superior breeding animals which possess a
large proportion of superior genes for a desirable trait, or traits.
Natural Selection
Selection is not an invention of modern man. It has been going on the nature since life first exists on
earth. In nature individuals that are best suited to their environment survive and produce the largest
number of offspring. Natural selection is a process whereby one phenotype and, therefore one genotype
leaves relatively more offspring than another genotype, measured both by survival and reproduction.
Selection occurs whenever individuals with a particular genotype have an advantage in survival or
reproduction over other genotypes. Natural selection corresponds to the term survival of the fittest
known from Darwin's theory of evolution or Rule of Jungle. It eliminates the unsuccessful genetic
combinations and allows the most successful to multiply. The alleles that enhance survival and
reproduction increase in frequency from generation to generation, and populations become adapted to
their environment. Natural selection is the dominant force in the evolution and has shaped much of the
phenotypic variation observed in nature. Through natural selection, traits that contribute to survival and
reproduction increase over time.

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We commonly think of natural selection as affecting wild animals and plants, but in fact it affects both
the wild and domestic species. All animals with lethal genetic defects, for example, are naturally
selected against they never live to become parents.
Natural selection results from the difference among individuals in survival or reproduction rate (or
both) in their environment. Natural selection is a very complicated process, and many factors
determine the proportion of individuals that will reproduce. Among these factors are differences in
mortality of the individuals in the population, especially early in life; differences in the duration of the
period of sexual activity; the degree of sexual activity itself; and differences in degrees of fertility of
individuals in the population.
There is no agent involved in natural selection. Survival and differential reproduction are the basis
of natural selection. Organisms not possessing the beneficial traits either die or don't have as many
offspring.
Three kinds of natural selection are directional, stabilizing and disruptive selection.
1. Directional selection: Selection favouring individuals at one extreme of the distribution, and
selects against the average and the other extreme. For example, antibiotic resistant bacteria only
bacteria that can tolerate the antibiotic can survive.
2. Disruptive, or diversifying, selection: Selection favoring the two extremes rather than the
intermediate.
3. Stabilizing selection: Selection favoring intermediate phenotypes rather than those at one or both
extremes. For example, human birth weight.
Evolution by Natural Selection as a Syllogism
If individuals in a population vary with respect to a particular trait that has some genetic basis, and
if the variants differ with respect to their abilities to survive and reproduce in the present environment,
then there will be an increase in the frequency of individuals having those traits that increased fitness
in the next generation.
Artificial Selection
Selection by man represents the addition of new standards -related to an animal's ability to serve human
needs to the natural standards of ability to survive and reproduce. Artificial selection means selection
made by the breeders. It may be defined as the efforts of man to increase the frequency of desirable
genes, or genotypes, by locating and saving for breeding purposes those individuals which have the
ability to produce superior performing offspring. Even when artificial selection is practiced natural
selection also seems to have a part. It is the process in which humans direct the differential reproductive
success of individuals in a breeding population.
The practice among breeders of choosing a select group of organisms from population to become the
parents of the next generation is termed artificial selection. In artificial selection, humans, not nature,
select the individuals that are to survive and reproduce. If the selected traits have a genetic basis, then
the genetic structure of the selected population will change over time and evolve. Artificial selection is
"managed evolution". Artificial selection can be a powerful tool in bringing about rapid evolutionary
change, as evidenced by the extensive variation observed among domesticated plants and animals. For
example, all breeds of domestic dogs are derived from the gray wolf that was domesticated some 10,000
years ago. The large number of breeds that exist today, encompassing a tremendous variety of sizes,
shapes, colors, and even behaviors, has been produced by artificial selection and selective breeding.
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The kind of selection of primary interest in animal breeding is artificial selection. The idea behind
artificial selection is simply this: to let individuals with the best sets of genes reproduce so that the next
generation has, on average, more desirable genes than the current generation of animals. The animals
with the best sets of genes are said to have the best breeding values. They are the individuals with the
highest value as parents. In selection, we try to choose those animals with the best breeding values: the
animals that will contribute the best genes to the next generation.
A common experience in artificial selection programs is that as the population becomes more and more
extreme, its viability and fertility decreases. As a result, eventually no further progress under selection
is possible, despite the presence of genetic variance for the character, because the selected individuals
do not reproduce. The loss of fitness is tied to linked sterility genes that are carried along with the
selected loci. In such cases, a number of generations without selection allow recombinants to be formed,
and selection can then be continued. Artificial selection is natural selection; the only difference is what
environment it happens in. In artificial selection, we humans are the environment that drives the
evolution of something else.
Natural selection occurs in wild animals, while artificial selection is planned and controlled by humans.
*Basis of selection is fitness.
Fitness
Fitness is the ability of an individual to 1. Survive and 2. Reproduce in its specific environment. The
proportionate contribution of offspring to the next generation is called the fitness of the individual. An
individual's fitness is affected by its Genes. The genotype that compared with other genotypes, leaves
relatively more offspring that survive to reproduce has the higher fitness. In natural selection more fit
individuals tend to increase their numbers each generation, at the expense of less fit individuals. Alleles
that confer higher fitness tend to take over in the population, causing a loss of less fit genes. Fitness is
usually computed to vary from 0.0 to 1.0 and is always relative to a given population at a given time,
Fitness is a consequence of the relationship between the phenotype of the organism and the environment
in which the organism lives, so the same genotype will have different fitness in different environments.
For example, in a normal environment, fruit flies with long wings may be more fit than fruit flies with
short wings. But in a very windy environment, a fruit fly with limited flying ability may do better than
the long winged genotype, which will be blown around by the wind. No genotype is unconditionally
superior in fitness to all others in all environments. The fitness of a genotype is a consequence of all
phenotypic effects of the genes involved.
Fitness is a function of the genotype. We will define the "relative fitness" of the best genotype as equal
to 1.0 Fitness is often symbolized as in a given environment the genotype that leaves the most offspring
is usually assigned a fitness of W= 1 and a lethal genotype has a fitness of 0. Any other genotype has a
fitness value between 0.0 and 1.0. For example, suppose that the genotype G₁G₁ on the average
produces 8 offspring, G₁G₂ produces an average of 4 offspring, and G₂G₂ produces an average of 2
offspring. The G₁G₁ genotype has the highest reproductive output, so its fitness (W₁1) is 8/8 = 1.
Genotype G₁G₂ produce on the average 4 offspring for the 8 produced by the most fit genotype, so the
fitness of G₁G₂ (W12) is 4/8 =0.5. Similarly, G₂G₂ produces 2 offspring for 4 the 8 produced by G₁G₁,
so the fitness of G₂G₂ (W22) is 2/8 = 0.25.
Components of Fitness

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Natural selection can act at any stage of the life cycle of an organism. The particular variable of the
life cycle upon which selection acts is termed a component of fitness. The two major components
of the fitness of a genotype are viability and fertility. The viability means the probability that a newly
formed zygote of the specified genotype survives to reproductive age. The reproductive success of a
genotype can be affected by its prenatal, juvenile, or adult survival. The fertility means the average
number of offspring produced by an individual of the specified genotype during the reproductive
period. Some genotypes may be more fertile than other genotypes. Together, viability and fertility
measure the contribution of each genotype to the offspring of the next generation.
Selection Coefficient
A number of factors can decrease the fitness value, W, below one. A selection coefficient measures the
sum of the forces acting to prevent reproductive success. Selection coefficient is a measure of the
relative intensity of selection against a genotype. The selection coefficient is symbolized by S and
equals 1-W. In our example, the selection coefficients for G₁G₁ are S= 0; for G₁G₂, S = 0.5; for G₂G₂,
S=0.75. Thus, as the selection coefficient increases, fitness decreases, and vice versa.
Units of Selection
It is usually considered that the unit of selection is the individual organism, because it is individuals
which either survive or die and which reproduce more or less successfully than others. There is no
continuity in individuals in a sexually reproducing (diploid) species. Individuals grow, old and die, and
their genome is split up at gametogenesis. However, copies of their alleles are passed on into new
combinations. The only continuity is in the continuation of the copies of alleles. Selection act on
particular alleles in relation to their average contribution to their own transmission through all the
individuals that carry copies of them.
Genetic Effect of Selection
Genetic effect of selection to change the allele frequencies in desirable direction. Selection does not
create new alleles, Selection is practiced to increase the frequency of desirable alleles in a population
and to decrease the frequency of undesirable alleles. If the frequency of desirable alleles is increased
the proportion of desirable genotypes will also increase as a result the population mean will increase in
the selected population. This may be illustrated by the following example, where A is the desirable
allele and a is the undesirable allele:
P AA x aa
F₁ All Aa (Frequency of 4 is 0.50)
F₂ 1 AA, 2 Aa, and 1(aa (Frequency of gene A is F2 is still 0.50
Let us assume that we cull all aa individuals in the F₂. If this were done, the remaining genes would be
four A and two a. Thus, the frequency of the A allele would be increased to 0.67 and that of the a allele
would be decreased to 0.33. The increased frequency of the A allele when the aa individuals were culled
would also increased the proportion of AA individuals in the population. If the frequency of the A allele
were 0.50 (if it is assumed that requirements of the Hardy Weinberg Law were met), the proportion of
AA individuals would be 0.50 multiplied by 0.50 or 0.25. However, if the frequency the A allele were
increased to 0.67, the proportion of the AA individuals would be 0.67 multiplied by 0.67 or 0.449. If
the frequency of the desirable allele increased, the proportion of individuals homozygous for the

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desirable allele also is increased. The result of successful selection is then to genetically improve future
generations of a population by increasing over time the proportion of desirable genes.
Long Term Effects of Selection (Selection Limits)
Continuous genetic improvement is possible for a trait in selection for generation after generation as
long as the genetic variation exists in the population. But at the later generation response to selection
will be low and ultimately ceased, this stage is known as selection limit: further selection will not
response and the population will be in selection plateau. The observed records of progress show a
definite plateau as drawn in Figure 6.1. The plateau is usually caused by the population running out of
usable genetic variation. However, if some new genetic variation is introduced into the population
progress from selection continues until the population reaches another plateau and so on. There are a
number of ways in which breeders can introduce new genetic variation into their selected populations.
For instance, mutation to favorable variants or (recombination between favorable and unfavourable
genes may allow selection to proceed further. Another approach is to cross new genes from other breeds
into the selected populations. In future there is even the possibility of synthesizing new variation from
basic chemical components by genetic engineering.
Selection Differential
Selection differential (S) is the difference between the mean of the selected parents and the mean of the
population before selection. It is the superiority of the selected parents over the mean of the population
from which they come,
S = Mean of selected individuals - Mean of the unselected base population
This is a measure of how good the parents chosen to produce the next generation will be. The selection
differential, S, measures the within generation change in the mean.
For example, if the average daily gain in a group of calves is 1.0 kg and those selected for breeding is
1.5 kg than the selection differential would be 0.5 kg. If the h2 of average daily gain is 0.4, the genetic
gain would be,
∆G = h2 × S = 0.4 × 0.5 = 0.2 kg.
Breeder’s Equation: ∆G = h2 × S
The expected population mean in the next generation would be 1. + 0.2 = 1.2 kg.
Selection differential of male animals can be quite large because less number of males can be used for
breeding, whereas in females selection differential usually is less. When force of selection among males
and females is different, the real selection differential is the mean selection differential of the two sexes.
i.e.,
S = (Sm + Sf)/2
Where, Sm is the selection differential for males, and Sf is the selection differential for females.
To calculate selection differential for males:
Mean of selected males 2.00 kg/day gain
Overall herd mean 0.25 kg/day gain

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Selection differential (2.00 - 0.25) = 1.75 kg/day gain

To calculate selection differential for females:

Mean of selected females 0.75 kg/day gain
Overall herd mean 0.25 kg/day gain
Selection differential (0.75 - 0.25) = 0.50 kg/day gain
These two selection differentials are then averaged to give:
{1.75 (for males) + 0.50 (for females)}/2 = 2.25/2 = 1.13 kg/day
Note, what happens when there is no selection of females i.e., where the selection differential equals 0.
The calculation then is:
{1.75 (for males) + 0 (for females)}/2 = 1.75/2 = 0.88 kg/day
Every effort should be made to obtain the maximum selection differential possible for the trait or traits
of greatest economic importance and highest heritability. There is potential for greater selection
differential among those traits that have a greater variation within a population. Breeders cannot change
the heritability of a trait; however we need to understand its role in selection decisions. The generation
interval can be reduced by using mainly young sires and utilizing technologies such as JIVET (juvenile
in vitro embryo transfer), but a short generation interval alone will not necessarily lead to genetic
improvement. The selection differential is our primary tool to drive genetic improvement.
Selection Intensity
The intensity of selection is measured by the magnitude of the selection differential. Selection
differential can be conveniently expressed in terms of standard deviation units, this standardized
selection differential is called the intensity of selection, symbolized by ‘i’ i.e.,
Intensity (i) = Selection differential (S) ÷ Phenotypic standard deviation (op)
Therefore, S = i x op
The phenotypic standard deviation (the standard deviation of the animal's phenotype is simply a way
of describing the variation normally found in the trait for a particular population.
The selection intensity (i) is directly related to the percentage of the individuals selected. Selection
intensity may be very different in males and females. The selection intensity in bulls is high because
only a small number of bulls are needed to produce adequate amounts of semen for cow population. In
cows, however, selection intensity is lower because farmers need about 75% of their females for herd
replacement. Usually, selection is more effective in males than females. This arise because in almost
all species fewer males are required than females and as a result greater intensity of selection can be
practiced in males, especially if AI is used.
Generation Interval

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Generation interval is the time interval between generations and is defined as the average age of the
parents when their offspring are born. Obviously it varies greatly between species and particular
breeding plans but some general average values, in years, are as follows:
Species Generation interval
Man 25
Horse 9 - 13
Beef cattle 4-6
Dairy cattle 5-7
Cat/sheep 3-4
Dog 4-5
Pig 1-2

To ensure rapid progress the aim is to keep the generation interval short. Genetic gain per year depends
upon the generation interval in each species. Artificial insemination and embryo transfer are breeding
methods that are commonly used to decrease the time taken to improve a trait. In general, a breeder is
interested in progress per unit of time rather than per generation. The quicker the generation interval
the more rapid the progress, Rate of genetic change increases when the generation interval decreases.
The Selection Response or Genetic gain (∆G)
The change produced by selection that chiefly interests us is the change of the population mean. This
is the response to selection, which will be symbolized by R. It is the difference of mean phenotypic
values between the offspring of the selected parents and the whole of the parental generation before
selection. The response R is the between generation change in the mean
R= O - P
O= Mean of the offspring of the selected parents
P= Mean of the parental generation before selection
Strictly speaking, the breeders' equation only holds for predicting a single generation of response from
an unselected base population.
Factors Affecting Rate of Improvement from Selection
The genetic progress expected for a single quantitative trait in one generation of selection may be
calculated as: ∆G = h2 × S (The Breeders' Equation), It is the core of all improvement.
Genetic gain per generation = heritability x selection differential
= h x i x 0?p
Genetic gain per year = (heritability X selection differential) / generation interval in years.
These equations are at the core of all improvement. The progress resulting from selection of superior
parents for a given trait depends on heritability, selection differential and generation interval in years.
Maximum gain will result when the selection differential (S) and the heritability (h) are high and the
generation interval (GI) is low. The amount of expected genetic gain over a period of time for a trait
depends upon the heritability of the trait (h2), intensity of selection (i), phenotypic standard deviation

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(?p), and generation interval (t). Five key factors influence the rate of genetic improvement or response
to Selection. They are :
• The accuracy of selection;

• The heritability of the trait (h2);

• The selection differential (S);

• The generation interval (GI); and

• Genetic correlation among traits.

Accuracy of selection refers to the ability to select animals that truly are genetically superior for a given
trait. It is dependent upon the genetic evaluation techniques used, such as animal model. To achieve
rapid genetic change, accuracy of selection must be high.
If selection is based on more than one trait, the genetic association between traits becomes important.
Genetic variation decreases as selection progresses and inbreeding may set in if selection goes on for
long because the selected population becomes very closely related.
Aids to Selection
Selection is the process of making decisions about animals in the light of information. To make
selection decisions, there is a number of well recognized sources from which the required information
can be obtained. These are referred to as aids to selection. Different aids to selection describe the
procedure of estimating genetic merit of an individual from its own phenotypes and that of its relatives.
They are:
• Individual selection or mass selection

• Pedigree information

• Progeny performance

• Family selection

Individual or Mass Selection

Individuals are selected solely on the basis of their own phenotypic value for a trait or traits. In this
type of selection, the performance of the individual is the only information used in making selection
decisions. No attention is paid to the pedigree of the animal or the performance of its sibs or of any
progeny it may have produced.
For example, if we were using phenotypic selection for weaning weight to determine whether a
particular ewe lamb was to be kept for breeding, we would base our decision strictly on her own
weaning weight.
This method is usually the simplest to operate and in many circumstances it yields the most rapid
response. It should therefore be used unless there are good reasons for preferring another method.
It is of two kinds:
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 • Performance test; and

• Lifetime performance records

Performance test:
The comparison of animals based on their own individual performance is usually called a performance
test. Performance testing is the systematic collection of comparative production information.
Performance testing involves recording the performance of the animal(s) under study and making
decisions in the light of those records. The usefulness of performance data increases as the heritability
increases. In fact, the accuracy of a single record on an individual is the square root of the heritability.
It is done in selecting beef cattle, pigs and sheep for body type, growth rate and feed conversion
efficiency. Here the best individuals are selected from a group of animals that have been similarly
treated (they are contemporaries) in the same environmental condition.
Lifetime performance records:
Here the breeder has more than one record of an animal's performance, such as a series of lactation
yields in a cow, annual fleece yield in a sheep, repeated litter size in sheep, goat and sow. Lifetime
records are extremely valuable, as animals that have produced well over a long life have proved that
they may have the genetic ability to survive and then perform in their environment.
In general mass selection is only really suitable for traits of moderate to high heritability. Individual
selection also has shortcomings which can be summarized as follows:
• Several important traits, including milk production in dairy cattle, maternal abilities in brood
cows, ewes, and sows, and egg production in poultry, are expressed only by females. Thus,
selection of breeding males cannot be based on their own performance.

• Performance records for milk and egg production and other maternal qualities are available only
after sexual maturity is reached.

• In cases of low heritability, individual merit is a poor indicator of breeding value.

Pedigree Selection
Pedigree is a record/chart/list of an individual's ancestors related to it through its parents. Complete
pedigree information is a prerequisite for modern breeding and the ranking of parents and offspring for
selection decisions. Pedigree selection is based on ancestor’s performance record. Pedigree information
is valuable because each individual receives half of its genes from each parent (with the exception of
sex linked genes).
In some instances, some selections may need to be made before the individual expresses the trait(s),
such as feed lot gain and feed efficiency. Pedigree selection is applied when the characters can be
measured in one sex. For example, a bull calf is selected on the basis of the milk yield in mother and
grandmother: It is also applied for characters which are measured relatively late in life.

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For example, litter size in ewes and does. A study of pedigree is important in detecting carriers of
recessive genes. Records of ancestors' performance help to increase the accuracy of individual
selection. Pedigree selection is much more accurate when the heritability of the trait is high. The
correlation between pedigree information and the individual's breeding value approaches the theoretical
0.71 as heritability approaches 1.0. Probably the two greatest dangers of pedigree selection are:
1. Undue emphasis on relatives, particularly remote relatives, with the result that intensity of individual
selection is reduced, and
2. Unwarranted favouritism toward the progeny of favored individuals.
Guides to pedigree selection:
1. Ancestors more closely related to the individual should receive most emphasis in pedigree appraisal.
2. When the heritability of the trait is low, the more remote ancestors should receive relatively more
emphasis, but when heritability is high, they provide almost no new information.
Progeny Testing
Selection of parents on the basis of mean performance of its progeny is called progeny testing. Progeny
testing attempts to evaluate the genotype of an animal on the basis of its progeny's performance. The
genetic principle behind progeny testing is simple. As each parent contributes a sample half of its genes
to each offspring, than the more samples (offspring) that are examined the more accurate is the
assessment of the parents. Progeny testing is widely applied in animal breeding. It is a technique
generally used for males because they are responsible for more progeny in their lifetime than any one
female. Artificial insemination has made a wide scope for progeny testing in dairy cattle. Progeny
testing is done for selection of bulls in dairy cattle. It is also applied in sheep, pig and poultry.
It has been said, "Individuality tells us what an animal seems to be, his pedigree tells us what he ought
to be, but the performance of his progeny tells us what he is.
Usually, progeny testing is undertaken for traits of low heritability and for which performance is thus
a poor guide. It is, obviously, used for traits expressed in one sex (e.g., milk production) and those
measurable only after death (e.g., some carcass traits). To be effective, progeny tests require:
• As many sires on test as possible (five to ten minimum).

• The random mating of dams to ensure that specific sires are not mated simply to very good or
very poor dams and that sires get similar numbers young/old mates.

• As many progeny per sire to be produced as possible (ten minimum for some traits but 200 to
300 for others such as dystocia).

• Progeny to be unselected during the test. Progeny to be treated in the same way or comparisons
made within the herd/flock and year/season groupings.
Given these standards, progeny testing can be very effective and the most accurate way of measuring
genetic merit. Obviously the reliability increases with heritability and the number of progeny being
tested.
Although the progeny test can provide an extremely accurate appraisal of an individual's genetic worth,
it is time consuming and increases the generation interval. For example, a dairy bull will be about 6
years of age before he has sufficient progeny lactating to allow estimates of his breeding worth for
milking traits.

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Family or Sib Selection
Whole families are selected or rejected as units, according to the mean phenotypic value of the family.
Individual are thus not acted on. The families may be of full sibs or half sibs. The circumstances under
which family selection is preferred are:
• When the of the character is low, and
• When the character is sex limited.

Multiple Trait Selection

Once the breeder has decided on the information he is going to use to aid his selection then he actually
has to do the selection. Methods of selection should be based on clear breeding goals. The main
objective is to improve production per unit of land or animal, using the available resources in a
sustainable manner. Selection can be undertaken as single trait selection or multiple trait selection.
Single trait selection aimed at improving one trait in a breeding program with little or no regard for
improvement in other (associated) traits. Single trait selection produces rapid genetic change, but
unfortunately likely results in undesirable changes in correlated traits. In the real world of animal
breeding, selection for a single trait is rare. The net value of an animal is dependent upon several traits
that may not be of equal economic value. So, it is necessary for animal breeder to improve more than
one trait simultaneously. They practice multiple trait selection. Dairy farmers select for traits related to
yield, butterfat yield and fat% in milk, health, reproduction and type; poultry breeder needs to increase
egg production, egg size, and egg quality. There is a relationship between the number of traits and the
effectiveness of selection. Multiple trait selection is the first step towards more effective selection, but
rate of improvement in any one trait decreases.
For example, if genetic change per year for weaning weights was 4 kg; but if there are 4 traits in the
selection program then only 1 = the amount of original change can be expected i.e., only 2
kg/generation. There are three methods of multiple trait selection:
(i) tandem method
(ii) independent culling levels
(iii) selection index method
Tandem Method
In the tandem method, selection is practised for only one trait at a time until satisfactory improvement
has been made in this trait. Selection efforts for this trait are then relaxed, and efforts are directed toward
the improvement of a second trait, than a third trait, and so on. It is the least efficient selection method
from the standpoint of the amount of genetic progress made for the time and effort expended by the
breeder. It takes several generations for improving one trait before you start improving the other. The
efficiency this method depends a great deal upon the genetic association between the traits selected for.
If there is a desirable genetic association between the traits, so that improvement in one results in
improvement in the other trait not selected for, the method could be quite efficient. If there is little or
no genetic association between the traits, the efficiency would be less than if the traits were genetically
associated in a desirable manner. A negative genetic association between two traits, in which selection
for an increase in desirability in one trait results in a decrease in the desirability of another, would
actually nullify or neutralize the progress made in selection for any one trait. Therefore, the efficiency
of such a method would be low. It is simple to use but not recommended.
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Independent Culling Levels Method
When selection is applied to the improvement of the economic value of animals or plants, it is generally
applied to several characters simultaneously and not just to one, because economic value depends on
more than one character. For example, the profit made from a herd of pigs depends on their fertility,
mothering ability, growth rate, feed efficiency, and carcass qualities. In the independent culling levels
method several traits are considered simultaneously. This procedure involves setting independent
culling level (minimum level of performance) for each trait that is to be improved. Only animals whose
performance is equal or above the culling levels for each trait are selected. The culling level should be
decided with knowledge of heritability, the overall economic importance of the trait and the number of
animals available for selection. For example, suppose culling level for goat milk is 200 kg per lactation
and fat content is 2%. Any animal whose production is 200 kg or higher and fat content is 2% or higher
is selected for breeding.
It does have an important advantage over the tandem method in that selection is practised for more than
one trait at a time. The only disadvantage is that it may cull genetically superior animals for marginal
performance of a single trait. Valuable genetic material may therefore be lost. It is the second most
effective method of selection and most widely used. It is effective when number of traits in selection is
relatively few.
Selection Index Method (Index Selection) (Best, Mostly Used)
This method involves the combining the measurements of two or more character into a single value for
each individual. This single value can be used as the single criterion of selection. The information
needed to construct a selection index is:
• The heritability of each trait to be included in the index.
• The relative economic importance of each trait.
• The genetic correlation among the traits.
• The phenotypic value and standard deviation of each trait.
The index combines the relative merits of each character involving the relative economic importance,
heritability, the phenotypic value and the genetic correlation of the trait. Numbers of methods are
available for computing selection index. When the traits are not correlated each other or slightly
correlated a relatively simple method of constructing selection index can be used.
I = 𝑎𝑎1 ℎ1 2 𝑥𝑥1 + 𝑎𝑎2 ℎ2 2 𝑥𝑥2 + ⋯ … … . … … . . +𝑎𝑎𝑛𝑛 ℎ𝑛𝑛 2 𝑥𝑥𝑛𝑛
Where, a is the relative economic importance; h2 is the heritability; x is the phenotypic value of the
character 1, 2,........ n; and n is the number of trait involved.
For example:
Relative economic importance h2 Phenotypic value
Hen 1 Hen 2 Hen 3
Egg production 5 0.25 150 210 230
Egg size 3 0.5 65 58 52
Hatchability 2 0.1 75 85 90
Then
I₁ = (5x0.25×150) + (3×0.5×65) + (2x0.10x75) = 121.25
I2 = (5x0.25×210) + (3×0.5×58) + (2x0.10×80) = 130.25
I3 = (5x0.25×230) + (3x0.5×52) + (2x0.10×90) = 124.00
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If an index is properly constructed, taking all factors into consideration, it is the most efficient method
of selection in achieving overall genetic improvement in the breeding group. Genetic theory says that
an index is predicted to be √n times as efficient as independent culling levels when n is the number of
traits involved. The greater the number of traits involved, the more reliable the index becomes. This
method has advantages over other methods of artificial selection, such as tandem selection, in that you
can select for traits simultaneously rather than sequentially. Thereby, no useful traits are being excluded
from selection at any one time and so none will stagnate or reverse while you concentrate on improving
another property of the organism. However, its major disadvantage is that the weightings assigned to
each characteristic are inherently quite hard to calculate precisely and so require some elements of trial
and error before they become optimal to the breeder.
When considering which method to employ, index selection will give the greatest overall response to
selection and tandem selection the least, but choice of method will also be influenced by practical
management considerations. In practical viewpoint it is wise to use a combination of selection methods.

Rank Animals on Selection Index

Once the selection index of most relevance has been constructed, the animals available for selection
should then be ranked on that particular selection index. Selection Indexes cannot be used to rank
animals across breeds. Consequently, selection indexes can only be used to compare animals with other
animals of the same breed.
Correlated Response to Selection
Selection for one character almost always produces changes in other characters. For example, selection
for increased growth rate in broilers leads to a correlated improvement in feed conversion efficiency;
selection for increased egg number in chicken results in a correlated decrease in egg size; and selection
for increased fleece weight in sheep leads to a correlated increase in fiber diameter. Genetic change in
an unselected character resulting from selection on another character is called correlated response to
selection. The direction and magnitude of correlated response in an unselected character depends on
the sign and the magnitude, respectively, of the genetic correlation between the unselected character
and the selected character. If, for example, the genetic correlation between two characters is negative,
then an increase in the character being selected will produce decrease in the correlated character.
Genetic correlations between traits and the correlated response to selection brought about by them can
be beneficial. However, if we are unaware of unfavorable genetic correlations, selection for one trait
can lead to undesirable response in others. In cattle, for example, blind selection for growth rate leads
to higher birth weights and more dystocia. If we want faster growth, but cannot tolerate increased
dystocia, we must avoid simply selecting for growth or against dystocia. We need a way to select for
growth rate and against dystocia at the same time. Breeders should limit the number of characteristics
they select for at any time as there is a general rule that as the number of characteristics selected for
increases, there is a corresponding decrease in the progress made in each trait.
Breeding Value
Throughout history, geneticists have studied methods for the identification of superior individuals in
animal populations. Livestock producers would like to select sires of desirable genetics for genetic

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improvement in economically important traits. Selection of desirable genetics to match with a cow herd
is a challenging task. The concept of breeding value provides animal producers an avenue to make
useful selection decisions. The background on breeding value estimation leads to a better understanding
of the merit of expected progeny difference (EPD).
Breeding value (BV) is defined as the value of an individual as a parent. In other words how future
progeny of this animal should perform for this trait within the specific breed. An animal's breeding
value is the total genetic ability of an animal for a given trait. Breeding value is the value of its genes
on the progeny and is related to the additive effects. The value of an individual judged by the mean
value of its progeny is called the breeding value of that individual. It is a property of an individual with
reference to the population to which it belongs. If an individual is mated with a random sample of
individuals from the population, then its breeding value for a given trait is twice the mean deviation of
its progeny from the population mean for that trait. The deviation has to be doubled because the parent
in question transmits only one half of its genes to each offspring, the other half comes at random from
the population. It must be remembered that only half his merit, i.e., % BV, is passed on. So, multiplying
by 2 gives his entire genetic merit for that characteristic. BV can be expressed absolute units or, more
usually, as deviation from the population mean. For example, consider a population of dairy cows made
up of daughters of a large number of sires. The population average of first lactation milk yield is 6000
kg. The progeny of two particular sires, sire A and sire B, within the population, average, 6300 kg and
5950 kg, respectively. The deviation from the population mean for sire A's progeny is therefore +300
kg and for sire B's progeny is 50 kg. Therefore, BV of sire A = +600 kg and BV of sire B= 100 kg, as
deviation from the population mean. Absolute BV of sire A (6000+600) kg = 6600 kg, and sire B =
(6000 - 100) kg = 5900 kg.
In terms of average effects, the BV of an individual is equal to the sum of the average effects of the
genes it carries. An animal's BV is directly proportional to the number of favorable genes that it carries.
BV is determined by the effects of all favorable genes at all loci that affect the trait.
Breeding value is a quantitative genetics term, describing that part of an individual's genotypic value
that is due to the additive effects of alleles. By represents the quantitative effects of the additive gene
action at the loci affecting the trait and is referred as additive genetic value. Before we select animals
to be parents of the next generation, we first estimate their breeding values and choose those with the
best breeding values. An individual only transmits a sample composed of half of its genes to each of its
offspring; this half is a random half of its genes.
The best breeding stock are those animals that are best able to transmit to their progeny the
desired traits at the highest level. In other words, the best breeding stock are those animals with the
highest breeding value. The decision about which animals should be selected as parents for the next
generation is mainly based on assessment of breeding value of individual animals. Genetic evaluation
is central to animal improvement schemes. Estimated breeding value gives an estimate of the
transmitting ability of the parent. Selecting animals based on estimated breeding value maximizes the
response to selection.
Progeny Difference (PD) or Transmitting Ability (TA)
Progeny difference and transmitting ability are practical concepts. These are defined as the difference
between the mean performance of the progeny of a parent and the mean performance of the progeny of
all the parents in the population:
PDi = TAi µ offspring of parent i - µ offspring of all parents
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A parent passes 1/2 of its BV to an offspring. The other half comes from the other parent. These are
used to estimate how future progeny of an animal will compare to progeny of other animals within the
breed. PD or TA is used in practice by some countries to rank animals. The progeny difference itself
represents the transmitting ability of the parent, which is one half of the breeding value. Transmitting
ability is an estimate of the average genetic merit that will be passed from parent to offspring. This
information can be utilized in a breeding program to predict how an animal will produce relative to its
herd mates.
PD = TA= ½ BV
Progeny difference and transmitting ability are not directly measurable but can be predicted using
performance data. The predicted value for PD is called EPD (expected progeny difference) and the
predicted value for TA is called PTA (predicted transmitting ability). Both terms mean the same thing
but EPD is used in beef cattle, swine and sheep breeding while PTA is used in dairy cattle breeding.
Expected Progeny Difference (EPD):
One half of the estimated breeding value is equal to the EPD. An EPD is an estimate of the genetic
value that will be passed onto the progeny of an animal. The word difference implies a comparison. An
EPD is the expected difference between the performance of that animal's progeny and the average
progeny performance of all the animals in the breed, for that trait. Thus, EPDs let us compare or rank
the superiority of individual animals. EPDs provide a prediction of future progeny performance of one
individual compared to another individual within a breed for a specific trait. The EPDS are expressed
in plus or minus values in the same unit of measurement for the trait. For example, weaning weight is
measured in kilograms so the EPD value is in kilograms above or below (+/ ) the breed average. The
EPD values may be used to compare only those animals within a breed. For example, the EPD values
for a Hereford bull may not be compared against the EPDs for an Angus or Limousin bull. Compare
EPDS to the breed average and/or to other animal's EPDs, not to zero. The difference between EPDs
of two bulls is the expected difference in progeny averages when bulls are mated to similar cows in a
herd.
Use of EPD's
EPDS are effective selection and genetic improvement tools for the herd. However, they are only
effective if they are understood and applied correctly. EPD values should be used in conjunction with
pedigree and visual assessment to evaluate seed stock. Successful cattle breeding require a thoughtful
and balanced approach to optimize fertility, growth and carcass merit while improving profitability and
efficiency. EPD's allow valid comparisons of all bulls of the same breed, but they do not allow
comparing
bulls from different breeds. EPD is the most accurate way to rank animals on genetic merit for various
traits. Other uses of EPD's are: measure the value of the animal as a parent for a particular trait;
objectively compare or rank individual animals within a breed, regardless of age or herd location by
removing environmental bias such as climate, feed and special management; help breeders make
informed decisions regarding breeding stock selection by evaluating numerous traits including growth
related traits, carcass and reproductive efficiency; and estimate the average calf performance of one
parent compared to the average calf performance of another parent, assuming similar mates.

Accuracy of the EPD

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Accuracy reflects the reliability of the EPD value. An accuracy value should be provided with the EPD.
EPDS offer producers the most accurate information about animals in a breeding herd. Accuracy is the
amount of reliability of the EPD value. An EPD value without an accuracy value is not very informative.
The accuracy value tells you how much data was used in the calculation so the higher the number, the
more data was used and the more reliable it is. High accuracy values (>0.70) mean the EPD value is
closer to the true breeding value than an EPD value with a lower accuracy (< 0.20). A high accuracy
means the EPD is not expected to change much as further information is obtained. A low accuracy
means the EPD may change quite a bit as new progeny information is gathered. A nonparent bull.
proven sire will have a much higher accuracy than a young sire or Accuracy is useful in managing risk.
You can be relatively confident that animals with high accuracy values will reliably breed as indicated.
Contemporary Group
A contemporary group is generally defined as a group of animals that are of same breed, age, sex and
have been (raised in the same management group) Individuals can be compared only to other
individuals belonging to the same contemporary group. The basis of sound performance testing relies
on correct identification of contemporary groups. Accuracy in estimation of genetic differences within
a group of animals is dependent on accuracy of grouping. Within herd or flock ranking of animals leads
to accurate genetic evaluation i.e., comparing animals that are herd mates or contemporaries. This
process helps to remove sources of environmental variance (non genetic) that impacts on the phenotype
Best Linear Unbiased Prediction (BLUP)
Best Linear Unbiased Prediction (BLUP) is a statistical method of predicting the breeding values of
animals. BLUP needs the variance components (genetic and environmental) for predicting the genetic
values. Physiological effects cause systematic non genetic variations and adjustment for these reduces
the non genetic component of variance. So measurements of performance may be adjusted for a variety
of systematic physiological effects such as age, parity, stage of lactation and sex. This method removes
a very high percentage of environmental variance. BLUP simultaneously ranks males and females, thus
adjusting for non random mating. This method also identifies all animals by pedigree, thus tying the
various herds together and ensuring more accurate across herd rankings. BLUP animal models are now
used in many countries for a number of species, including dairy and beef cattle, wine, sheep and fish.
Tool for evaluating animals include EPDs, pedigree information, DNA test information, and visual
assessment.
Marker Assisted Selection
The potential benefits of using markers linked to genes of interest in breeding programs moves
phenotype based to genotype based selection. Most of the traits considered in animal and plant genetic
improvement programs are quantitative. In classical genetic improvement programs, selection is carried
out based on observable phenotypes without knowing which genes are actually being selected. The
development of molecular markers was seen as a major breakthrough promising to overcome this key
limitation. Molecular markers may be used for a wide range of different tasks, such as to quantify the
genetic diversity and relationships within and between populations, to investigate biological processes
(such as mating systems, pollen movement or seed dispersal in plants) or to identify specific genotypes
(e.g., cloned forest trees).
Molecular/Genetic Marker

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A genetic marker is a known DNA sequence associated with a certain phenotype. Genetic markers have
to be easily identifiable, associated with a specific locus, and highly polymorphic and transmitted by
the standard laws of inheritance from one generation to the next. Genetic markers have the potential to
become an important tool in selecting animals for breeding purposes Different kinds of molecular
markers exist, such as restriction fragment length polymorphisms (RFLPS), random amplified
polymorphic DNA (RAPDs) markers, amplified fragment length polymorphisms (AFLPS),
microsatellites, and single nucleotide polymorphisms (SNPs). The information provided to the breeder
by the markers varies depending on the type of marker system used. Each has its advantages and
disadvantages.
Advantage of Molecular Markers
The advantage of molecular markers for researchers is that they can test for a particular trait as early as
the embryonic stage in animals. There is no longer a need for the organism to develop to a stage at
which the trait can be observed a wait that in some cases can take many years.
Gene versus Marker
Molecular markers should not be considered as normal genes as they usually do not have any biological
effect. Instead, they can be thought of as constant landmarks in the genome. The gene of interest is
directly related with production of protein(s) that produce certain phenotypes whereas markers should
not influence the trait of interest but are genetically linked Marker assisted selection or marker aided
selection (MAS) refers to the use of DNA markers that are tightly linked to target loci as a substitute
for or to assist phenotypic selection. This process is used in plant and animal breeding. It is indirect
selection process where a trait of interest is selected not based on the trait itself but on a marker linked
to it. For example, if MAS is being used to select individuals with a disease, the level of disease is not
quantified but rather a marker allele which is linked with disease is used to determine disease presence.
The assumption is that linked allele associates with the gene and/or quantitative trait locus (QTL) of
interest. MAS can be useful for traits that are difficult to measure, exhibit low heritability, and/or are
expressed late in development. Marker assisted selection (MAS) is a combined product of traditional
genetics and molecular biology. MAS allows for the selection of genes that control traits of interest.
Combined with traditional selection techniques, MAS has become a valuable tool in selecting
organisms for traits of interest, such as color, meat quality, or disease resistance. The success of MAS
is influenced by the relationship between the markers and the genes of interest. The universal nature of
DNA, molecular markers and genes means that MAS can, in theory, be applied to any agriculturally
important species. In addition, MAS can be applied to support existing conventional breeding programs.
Restriction Fragment Length Polymorphisms (RFLPs)
Restriction fragment length polymorphisms (RFLPs) were the first molecular markers used to diagnose
genetic variability in organisms. RFLP uses restriction enzymes to digest (cut) the DNA molecule and
identify regions linked to a trait.
Simple Sequence Repeats or Microsatellites
Simple sequence repeats (SSRs) also called microsatellites) is repeated units of two to six nucleotides)
that occur throughout an organism's genomy. The sequence ATATATAT is one example of a
microsatellite. The sequence GATGATGAT is another example. SSRS are useful as (molecular
markers) because they are highly (polymorphi (have many forms). SSRS have been used successfully
as markers in a wide range of analysis, particularly those involving disease diagnosis and forensics.
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Single Nucleotide Polymorphisms (SNPs)
On average, SNPs will occur in an organism's DNA more than 1% of the time. Because only about 3%
to 5% of an organism's DNA codes for proteins, most SNPs are found outside the regions of genes of
interest. SNPs found in a gene of interest are of particular interest to researchers because they are
directly associated with a desired trait. Because of the recent advances in technology, SNPs are playing
a greater role in selection and diagnosis of genetic traits.

(Lecture)

Aids to selection/Methods of single trait selection:

Selection is a decision making process which depends on information about animal.
Sources of this information about the animal are the aids to selection. Different aids
to selection describe the procedure of estimating genetic merit of an individual from
its own phenotypes that of its relatives.

There are four (4) sources or aids of selection:

i) Individual/Mass selection ( Used when h2 value moderate and high- both)

ii) Pedigree information ( Used when h2 value high)
iii) Progeny performance/testing ( Used when h2 value low and sex
relatedtraits)
iv) Family/sib selection ( Used when h2 value low and sex related traits)

When we select a particular single trait then we can use any of them for this reason
it is methods of selection for single traits.

i) Individual/Mass selection (Used when h2 value moderate and high-

both): Individuals are selected solely on the basis of their own phenotypic
value for a trait or traits. The performance of the individual is the only
information used in making selection decisions.

It is two types:

a) Performance test- based on their own one time individual performance.

Information collected from systematic of comparative production
information.
b) Life time performance test- based on life time performance test. Eg. A
serious of lactation yield in a cow, annual fleece yield in a sheep.
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Use:

 used in case of traits having heritability moderate to high(0.2 to above)

 traits which are expressed in both sex(eg. milk production are expressed in
females. So, Selection of breeding males cannot be based on their own
performance. )
ii) Pedigree information (Used when h2 value high): is based on
ancestor’sperformance record. It is valuable because each individual
receives sample half of its genes from each parent (with the exception
of sex linked genes)

Use:

 used in the traits having high heritability

 traits that expressed in only one sex

More closely related to the individual should receive most emphasis in pedigree
appraisal.

iii) Progeny performance/testing (Used when h2 value low and sex related
traits):Selection of parents on the basis of mean performance of its progeny is
called progeny testing. Best progeny indicate genetically best individual (parent).

Genetic principle behind this→ Sample half of parent gene transmit to progeny.

Use:

o low heritable trait so performance is poor guide

o Sex limited traits eg. Milk production
o Measurable only after death eg. Some carcass traits
o for proven bull
Standards for accurate progeny testing: as many sires on test as possible (5-10
minimum)

• random mating of dams to ensure

• as many progeny per sire to be produced
• Progeny for progeny testing should be contemporary (same treatment
eg.Environment, management and nutrition )
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Limitations:

o time consuming ( minimum 5-6 yrs for bull selection)

o cost high
o low genetic gain due to increase generation interval
iv)Family/sib selection (Used when h2 value low and sex related traits):

Whole families are selected as units, according to the mean phenotypic value of
the family. Individual are thus not acted on. The families may be full sibs or
half sibs.

Use:

• When the h2 of the character is

low
• When the character is sex
limited

Methods of selection for multiple traits: There is a relationship between the

number of traits and effectiveness of the selection.

1. Tandem method
2. Independent culling level
3. Selection Index (SI)

1. Tandem method :

Selection is practiced for only one trait at a time until satisfactory improvement has
been made in this trait. Selection effort for this trait are then relaxed, and effort are
then directed toward the improvement of a second trait and so on.

o Time consuming
o Can’t be used if there is negative correlation between the traits
o Simple to use but less effective so not recommended

2. Independent culling level:

It is generally applied to several characters simultaneously but not just one

because economic value depends on more than one character. Eg. Profit made

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 from a herd of pigs depends on their fertility, mothering ability, growth rate, feed
efficiency and carcass qualities. This procedure involves setting independent
culling level for each of trait that is to be improved. Important
advantage over the tandem method in that selection is practiced for more than
one trait at a time.

4. Selection Index (SI):

Involves the combining the measurements of two or more character into a single
value for each individual. The information needed to construct SI is:

i) The heritability of each trait to be included in the index

ii) The relative economic importance of each trait
iii) The genetic correlation among the traits
iv) The phenotypic value and standard deviation of each trait

I= a1h12x1+ a1h12x1+ ------------------------ + anhn2xn

Where, a1= relative economic importance

h 12= heritability value

x1= phenotypic value

Use:

o Rank and compare animals with other animals of the same breed.
o Most efficient method is index method
Correlated response to selection: Selection for one character almost always
produces changes in other character. Eg. Growth rate and FCR of broiler, Egg size
and egg number.

Breeding value (BV): Value of an individual as a parent for a particular trait.

BV= 2(Progeny mean- population mean)

BV = 2×Transmitting Ability (TA)

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Contemporary group:

Group of animal of – same breed, same age, same sex, same treatment and have
been given opportunity to perform.
Best Linear Unbiased Prediction (BLUP): Statistical method of predicting BV
ofanimals. It needs the variance components (genetic and environmental) for
predicting the genetic values.

Indirect selection: One trait is selected with the response of other trait. eg.
Scrotalsize increase→ fertility and fecundity increase.

Marker assisted selection: it linked to genes in breeding programs phenotype

based and genotype based selection.

Molecular/Genetic marker: it is a known DNA sequence associated with a

certainphenotype. Different form of molecular markers: Restriction fragment
length polymorphism (RFLPs), Random amplified polymorphic DNA (RAPDs),
Microsatellites and Single Nucleotide polymorphisms (SNPs).

Advantages: Can test for a particular trait as early as the embryonic stage in
animal

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 CHAPTER 7
Mating or Breeding System
The transmission of genetic material from one generation to the next is analysed in terms of alleles
rather than genotypes because genotypes are broken up in each generation by the process of segregation
and recombination. When gametes unite in the process of fertilization, the genotypes of the next
generation are formed. The genotype frequencies in the zygote of the progeny generation are
determined by the frequencies with which the various types of parental gametes come together, and
these frequencies are in turn, determined by mating system in which the genotypes pair as mates. Once
superior animals are identified and selected, breeder must decide how these will be mated. A mating
system is all set of rules for mating animals in a production system. The mating system determines the
mode of transmission of alleles from one generation to the next. Mating systems constitute breeding
plans that are designed to combine the genes in a population into the most advantageous genotypic
combinations. Breeding systems aim to improve a single trait or multiple traits. Knowledge of mating
systems is important because producers can use these to preserve genetic superiority and utilize hybrid
vigour.
Selection is the first of the two basic tools used by animal breeders to make genetic changes. The second
tool is mating. Mating is the process of deciding which selected males will be bred to which selected
females. It is distinctly different from selection. In selection, we choose the group of animals we want
to be parents; in mating, we match males and females from the selected group. There are three reasons
for using mating systems: to produce offspring with extreme breeding value, to make use of
complementarity, and to obtain hybrid vigour. Extreme phenotypes can be obtained by mating parents
with extreme breeding values. Mating systems are broadly classified into two types: random mating
and nonrandom mating
Random Mating
Random mating, or panmixia means that any individual of one sex has the equal chance of mating with
another individual of the opposite sex in the population. It is the most commonly used method in
selection experiments as it holds inbreeding to be minimum. The important points are that there should
be no special tendency for mated individuals to be alike in genotype, or to be related to each other by
ancestry. Here, mating pairs are formed independently of genotype. In random mating, the probability
of a particular mating is the product of the genotype frequencies. If the MM genotype makes up 90%
of a population, then the probability of an MM by MM mating is 0.9 x 0.9, or 0.81. If a significant
deviation from this expected value occurred, then random mating did not happen in this population. A
population can undergo random mating with respect to some traits but at the same time, nonrandom
mating with respect to other traits. Any departure from random mating naturally leads to complications
in the relationships between allele frequencies and genotype frequencies. Deviations from random
mating alter genotype frequencies but not allele frequencies.
Nonrandom Mating
Two kinds of deviation from random mating must be distinguished. Deviations from random mating
come about when phenotypic resemblance or genetic relationship influence mate choice. When
phenotypic resemblance influences mate choice, either assortative or disassortative mating occurs.
When relatedness influences mate choice, either inbreeding or outbreeding occurs.
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Assortative and Disassortative Mating
Mating based on phenotypic resemblance is called assortative mating. If the mated pairs (mates) are
phenotypically similar, this is called positive assortative (only assortative) mating. Positive assortative
mating is common in natural populations. For example, humans mate assortative for height; tall men
and tall women marry more frequently and short men and short women marry more frequently than
would be expected on a random basis. Negative assortative (disassortative) mating occurs when
phenotypically dissimilar individuals mate more often than randomly chosen individuals. If humans
exhibited negative assortative mating for height, tall men and short women would marry preferentially
and short men and tall women would marry preferentially.
Genetic Consequences of Assortative Mating
Neither positive nor negative assortative mating affects the allele frequencies of a population, but they
may influence the genotype frequencies if the phenotypes for which assortative mating occurs are
genetically determined. Assortative mating is comparable to inbreeding in the sense that mates with
similar phenotypes will tend to have similar genotypes. Assortative mating increase homozygosity,
whereas disassortative mating increase heterozygosity. Homozygosity will cause gametes to become
less variable. Another effect of assortative mating is to increase the total population variance. However,
assortative mating can lead to change in allele frequency if selection is also acting on the same trait.
Inbreeding and Outbreeding
Various mating schemes of animals are classified under two broad categories: (i) inbreeding and (ii)
outbreeding. Classification depends on the closeness of the genetic/biological relationship between
mates. Within each category, a wide variation in intensity of this relationship exists.
Inbreeding
Inbreeding is the mating of related individuals. That is the simplest definition anyway. Because all
animals within a population are related to some degree, a more technically correct definition of
inbreeding is the mating of individuals that are more closely related than the average relationship
within the breed or population concerned. Inbreeding is a consequence of either pedigree relatedness
or small population size. The most extreme form of inbreeding is self-fertilization (selfing) that is the
mating of an individual to itself. Self-fertilization is characteristic of many flowering plants and some
hermaphroditic animals, including freshwater snails. Other examples include the mating of full sibs
(brother sister), half sibs, parent offspring, first cousins, etc. Inbreeding is a result of the mating of
individuals which are related to one another by having one or more common ancestors. A common
ancestor is one that is present on both sides of the pedigree. An individual who results from inbreeding
is referred to as inbred. If the mated individuals are related, their offspring will to some extent be inbred.
Inbred animals may become homozygous for either desirable or undesirable genes. This fact dictates
that complete and accurate performance records should be maintained and used in order to acquire and
maintain genetic superiority. Inbreeding is of two types: intensive inbreeding and linebreeding.
Intensive Inbreeding
Mating of closely related animals for several generations. Intensive inbreeding is often directly related
to an increase in the expression of many undesirable traits.

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Close Breeding
Intense inbreeding by mating full or half sibs, cousins, or parents to offspring is referred to as close
breeding. Close breeding can produce extremely good, or extremely poor, results. Success and failure
depend on factors such as planning, foundation stock, emphasis on culling, and completeness of
pedigree and performance records, etc. Haphazard close breeding could be very detrimental to the
overall quality of the resulting offspring. To avoid disaster, a careful study of the merits and weaknesses
of the breeding stock should precede a close breeding program.
Close breeding is a valuable tool in genetic research, since it quickly exposes hidden gene types that an
individual carry. Because of its extreme nature and the chance that it may suddenly cause undesirable
effects in the offspring, close breeding is not often used by animal breeders.
Linebreeding
Linebreeding is a special form of inbreeding designed to maintain a high genetic relationship to an
outstanding ancestor while keeping inbreeding as low as possible. It is an attempt to concentrate the
genes of a superior animal in later generations in order to reconstruct the super animal's genotype as
closely as possible in the hopes of producing others just like him. This is done to maintain the superior
traits of an outstanding individual among its descendants thereby increasing the number of animals
which possess these same outstanding traits. The main purpose of linebreeding is to transmit a large
percentage of one outstanding ancestors genes from generation to generation without causing an
increase in the frequency of undesirable traits often associated with inbreeding in practice, line breeding
has been most common with superior sires, mainly because bulls have much greater reproductive rate
than do cows. An example of line breeding would be the use of a single bull as the sire of an animal as
well as its maternal grandsire and also its great grandsire.
Because linebreeding is not based strictly on mating closely related individuals, it does not necessarily
cause a rapid increase in homozygous gene pairs. Consequently, it will not expose undesirable recessive
genes as extensively as close breeding. For this reason, linebreeding is generally a safer inbreeding
program for most breeders.
Genetic Consequences of Inbreeding
Inbreeding has a number of effects, but the chief one and the one from which all the others stem is an
increase in homozygosity. An increase in the number of homozygous loci in inbred animals and an
increase in the frequency of homozygotes genotypes in an inbred population. Accompanying this
increase, there must be a decrease in heterozygosity. At 100% inbreeding no heterozygosity is left.
These simultaneous events are the underlying reasons for the general effects on performance we
observe with inbreeding. Because inbred individuals have fewer heterozygous loci than non-inbred,
they cannot produce as many different kinds of gametes. The result is fewer different kinds of zygotes
and therefore less variation in the offspring. This illustrates that the level of inbreeding in the population
is related to the amount of genetic variation.
To understand how inbreeding changes the genotype frequencies, let us examine the frequency of
heterozygotes when complete self-fertilization occurs over several generations. Assume that we begin
with a population of Aa heterozygotes. If the heterozygote, Aa, is self fertilized, it will produce three
kinds of progeny AA, Aa and aa, in the ratio of 1: 2: 1. At this stage, the frequency of the heterozygotes
is 0.50. If self-fertilization is continues for another generation, the AA homozygotes will produce only
AA progeny, and the aa homozygotes will produce only aa progeny, but the heterozygotes will again
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segregate, reducing their frequency to 0.25. This means that in each generation of self-fertilization, the
percentage of heterozygotes decreases by 50% After a large number of generations, there will be no
heterozygotes and the population will be divided equally between the two homozygous genotypes.
The relationship for heterozygosity in two succeeding generations is a general one; thus, after one
generation the heterozygosity is halved, and after two generations it is again halved, so that the result
is one-fourth the initial value. After t generations of complete selfing, heterozygosity is halved t times,
so that it is (1/2)t of its initial value.
Measurement of Inbreeding
Inbreeding is often measured in terms of the coefficient of inbreeding symbolized by F. This coefficient
can range from 0 to 1. F=0 means there has been no inbreeding meaning that the population is in H-W
equilibrium, and F= 1 means that inbreeding is complete. The inbreeding coefficient measures the
percentage increase in homozygosity relative to the average of the breed. If an individual has an
inbreeding coefficient of 0.25 it means that it is expected to have 25% more homozygous gene pairs
than a non-inbred individual from the same population. This would be the case if full siblings were
mated. Thus, the higher F is, the more inbred the population is. Inbreeding coefficient can be estimated
by two ways –
1. From genotype frequencies: By comparing the number of heterozygotes observed to the number
expected for a population in H-W equilibrium, we can estimate the degree of inbreeding. Inbreeding
coefficient is defined as the percentage decrease in heterozygosity relative to that expected from
random mating. Thus,
F = (Expected heterozygosity - Observed heterozygosity)/Expected heterozygosity
2. From pedigrees: The inbreeding coefficient is the probability that two alleles at any locus in an
individual are identical by descent from the common ancestor(s) of the two parents. This means the
degree to which two alleles are more likely to be homozygous (44 or aa) rather than heterozygous
(Aa) in an individual. There are several methods to compute this percentage, the two main ways are
the path method and the tabular method. The actual level of inbreeding is relative to some base
population, which is assumed unrelated and non-inbred. In practice, the base population is the
population when pedigree recording started. i.e., it is the population in which the parents are
unknown. Effective calculation of inbreeding relies on full and accurate pedigree information.
Where pedigree records are incomplete the calculation may assume no relationship when that may
not be the case. The coefficient of inbreeding is a property of an individual. The formula is as
follows:
Fx = 0.5∑[(1/2)n(1+FA)]
Where, Fx is the inbreeding coefficient of individual X, n is the number of connecting links between
the two parents of X through common ancestors, and FA is the inbreeding coefficient of the common
ancestor A. Thus, if the common ancestor is inbred, a minor calculation must be performed first to
determine FA, before the main calculation can take place. In the main calculation any coefficients of
paths through inbred common ancestors can then be multiplied by (1 + FA).

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Biological Relationships between Animals
Individuals are considered to be biologically/genetically related when they have one or more common
ancestors. For practical purposes, if two individuals have no common ancestor within the last five or
six generations, they are considered unrelated.
The closest relationship is that of an individual with itself, or self-fertilisation. However, the closest
relationship that is usually possible with mammals is full brother sister (known as full-sib) mating. A
single generation of parent × offspring mating is genetically equivalent to full-sib mating. Other regular
mating systems which lead to a high level of inbreeding include half-sib and cousin matings. An animal
is related to itself by 100 percent. The relationship between a parent and its offspring is said to be 50
percent. The relationship to each grandparent 25 percent, to each great-grandparent 12.5 percent, and
so on. This halving of relationships and genes occurs with each generation. Thus, after only a few
generations, any ancestor is likely to be the source of only a small fraction of the genes of its
descendants. Biological relationship is important in animal breeding because the closer the relationship,
the higher the percentage of like genes the two individuals carry. Closeness of relationship is
determined by three factors:
1. How far back in the two animals' pedigrees the common ancestor appears?
2. How many common ancestors they have?
3. How frequently the common ancestors appear?
It is also influenced by any inbreeding of the common ancestor or ancestors. The rate of inbreeding
depends on the degree of relationship. The inbreeding coefficient, F, for progeny of two individuals, is
half the genetic relationship between the individuals. For example, the inbreeding coefficients for
progeny of full-sibs and progeny of half-sibs are 0.25 and 0.125, respectively.
Biological relationship Coefficient of relationship between Coefficient of inbreeding between mates,
between mates mates assuming previous no inbreeding between
any parents
Parent - offspring; full 50% 25%
sibs
Grandparent grand 25% 12.5%
progeny; half sibs;
double first cousins;
aunt-nephew; uncle -
niece
Great-grandparent 12.5% 6.25%
great- grandprogeny;
first or full cousins;
half-uncle niece; half-
aunt - nephew
Second cousins; half 6.25% 3.125%
first cousins

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Inbreeding depression
Inbreeding causes an increase in homozygosity; affects all loci in a population equally. The danger in
this is that deleterious recessive alleles which are present in a low frequency in the whole population
will become homozygous in inbred offspring. This causes the reduction of the mean phenotypic value
of quantitative traits, such as (size, vigour, fertility and the yield. This decline in performance is called
inbreeding depression. The extent of this decrease in performance, in general, is in proportion to the
degree of inbreeding. The greater the degree of inbreeding, the greater the reduction in performance.
The actual performance reduction is not the same in all species or in all traits. Some characteristics (like
meat quality) are hardly influenced by inbreeding; others (like reproductive efficiency) are greatly
influenced by inbreeding. Usually, the traits most affected will be those concerned with fitness which
tends to be traits that are of low heritability. As inbreeding progresses there will be a decline in fertility
both in litter size and sperm viability, an increase in embryonic mortality, a decline in progeny survival,
a higher frequency of hereditary abnormalities, loss of immune system function and eventually a
lowering of growth rate and milk yield. Detailed studies have indicated that these traits decline more or
less linearly with inbreeding coefficient F. For production traits it is at a magnitude of 0.4 units for an
increase in the inbreeding of one unit or fitness traits the decrease is much higher, at about one unit.
This cause the fact that it is extremely difficult to produce 100% inbred domestic animals.
Inbreeding depression seems to be a nearly universal phenomenon, but the extent of inbreeding
depression various among different organisms. For example, three generations of mating full sibs in
Japanese quail result in complete loss of reproductive fitness. In general, fertility, hatchability and egg
production were affected to a greater extent by inbreeding than were body weights and egg weights.
However, in species adapted to inbreeding, including many crop plants (wheat and peas) and animals
(worms and snails), inbreeding does not expose deleterious alleles because those alleles have generally
been eliminated already.
A linear negative relationship between production traits and the degree of inbreeding predicted.
Therefore it is important to ensure that the inbreeding is kept at the lowest level possible among the
production animals. This can be done using pedigree information before mating, or by use of more
robust systems, such as subdividing the animals into herds, keeping the females in the herd while adding
new males from other herds.
Purposes of Inbreeding
With increasing competition in the global livestock market, owners are continuously trying to increase
the genetic quality of their herds. Inbreeding can be a very effective tool in livestock breeding
programmes when understood and properly used. By incorporating inbreeding into breeding schemes,
several advantages are available:
1. Production of inbred lines: The primary objective of inbreeding is the production of inbred lines
which can be commercially used. In plant breeding, medical research, and animal breeding, inbred lines
are useful because they are genetically uniform for known traits. Inbred lines of mice and rats (lines
that have been brother-sister mated for over a hundred generations) are widely used to test new medical
treatments, and in many other areas of biological research. For some purposes, when for example the
absence of antigenic differences is necessary, it is genetic uniformity that is required. Since inbred
animals have an increased level of similar genes, the animal is more likely to produce progeny with
similar traits. Inbreeding is essential to the development of prepotent animals that uniformly "stamp"

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their characteristics onto their progeny. In particular, animals with an abundance of dominant alleles
will "stamp" their characteristics onto their offspring.
2. Utilization of hybrid vigour: Crossing two highly inbred lines introduces hybrid vigour and
combines the desirable traits of both lines. It is the second main purpose for which inbreeding may be
carried out.
3. Elimination of deleterious alleles: Inbreeding can result in the expression of deleterious recessive
alleles in a homozygous form. Once deleterious traits appear due to inbreeding, natural selection can
cause their removal from the population; therefore, the deleterious alleles will not be passed to future
generations. It enables the breeder to eliminate harmful recessive genes from the population. In a
naturally occurring population, on the other hand, these traits may continue to be passed by carriers in
a recessive form.

Inbred Line
An inbred individual is one whose parents are related, that is, there is common ancestry in the family
tree. A line to be called inbred should have at least 50% of inbreeding coefficient. Inbred lines can be
produced by parent offspring mating, full sib mating, half sib mating and first cousin mating. Three
generations of full sib mating or 6 generations of half sib mating produces inbred lines with 50%
coefficient of inbreeding. The development of an inbred line begins by setting up a large number of
individual full-sibling mating from desired stock. Each generation some lines need to be culled for not
meeting the required phenotypic standards and others die out because recessive lethal genes become
homozygous and are therefore manifest. After 20 generations of full-sibling mating, when essentially
all genetic loci are homozygous or fixed and F approaches 100%, no further genetic change can take
place except through mutation or introduction of different genetic material. Each surviving line thus
becomes a separate inbred line, its genotype representing a selection of genetic material present in the
original sibling pair. As many as 90% of inbred lines may die out during their development thus
underlining the need for initially setting up very many lines. A strain is regarded as an "inbred
strain" when the coefficient of inbreeding, F is greater than 0.986, i.e, after 20 generations of sib-
mating. The coefficient of inbreeding never quite reaches 100 per cent. Therefore, no strain is ever fully
inbred. Once an inbred strain has been established, no further inbreeding depression should occur. The
20 generations of sib-mating standard has been accepted for most other laboratory species, although in
the case of larger species such as the chicken, rabbit and pig, lower levels of inbreeding may be
sufficient for some research purposes.
Incross and In crossbred
When a cross is made between two inbred lines belonging to (same breed it is called an incross, and
between those belonging to different breed in-crossbred.

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Outbreeding
Outbreeding is the mating of individuals that are less closely related than the average of the breed or
population. In outbreeding, the frequency of homozygotes decreased relative to random mating
proportions. These genotypic changes affect all loci in the genome. By increasing heterozygosity there
is a tendency to cover up detrimental recessive genes and improve traits related to physical fitness.
Outbreeding with accurate selection can result in improvement. There are four types of outbreeding
called (i) species cross (ii) crossbreeding (iii) outcrossing (iv) grading up.
Species crossing
Crossing animals of different species is called species crossing. For example, crossing horse to donkey.
One of the criteria in the differentiation of species in accordance with zoological systematic is the
infecundity of individuals belonging to different species when they are mated to each other. In a few
instances they produce offspring. Species crosses usually create sterile hybrids and has rarely been
exploited in livestock breeding. There are difficulties using species with different chromosome numbers
since embryo survival is usually low and even if there is survival there is often sterility. Some crosses
of zoological interest have been undertaken such as lion x tiger (liger or tigon) and wolf x domestic
dog. There are few farm livestock species crosses undertaken. The most famous is the donkey dx horse
giving rise to the mule. There have been crosses of cattle and buffalo, largely undertaken in the USA
and Canada, called beefalo or cattalo; crossing of zebu and yak has been undertaken in the Himalayas.
However, all of these have been of minimal interest beyond that of the mule which has been exploited
at various stages in history. The mules are almost invariably sterile having in the case of the mule an
unbalanced chromosome complement of 2N = 63 derived from the donkey (2N = 62) and the horse (2N
= 64) parents.
Cross Breeding
Cross breeding is the mating of animals of different breeds; the mating of sires of one breed to dams of
another. Contrary to inbreeding, where a linear negative relationship with fitness and production traits
and the degree of inbreeding, it is impossible to predict anything about the effect of crossbreeding.
There are unlimited crossbreeding schemes. The most commonly utilized crossbreeding schemes
include:
Two-Breed Cross: Two-breed cross involves maintaining purebred/straight bred females of a single
breed and mating all females to a bull of another breed.
Single Cross: This is the crossing of any two breeds selected on the basis of performance to produce
crossbred offspring with considerable hybrid vigour. Heterosis is fully expressed.
Backcrossing
A female from a single cross (F₁) is mated back to one of the original parental breeds. Heterosis
expression is half that of the single cross between breeds.
Crisscrossing
Crisscrossing is an extension of backcrossing. Initially, two breeds are crossed (A x B). The crossbred
is then mated back to A to give 75% A and 25% B. This crossbred is then mated to give 62.5% B and
37.5% A. Thereafter breeds A and B are used alternatively.

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Rotational Crossing
In rotational crossing, a series of breeds (two or more) are used in succession. Purebred males used on
crossbred females. The system requires greater management input than grading up. However, a greater
proportion of hybrid vigour is retained. Bull control to ensure the right bulls are mated to the right cows
is a big issue, especially in smaller herds. In extensive areas, producers attempting rotational crossing
should expect and accept some progeny will result from unintended matings.
Two-Breed Rotational Cross
In this system, bulls of two breeds are used. Females sired by a bull of a particular breed mated to a
bull of the other breed.
Three-Breed Rotational Cross
This system is similar to the two-breed rotational cross except that three breeds are used.
Three-breed Terminal cross
The F₁ crossbred females are mated to males of a selected third breed and all offspring (F₂) slaughtered
for meat production. More heterosis can be achieved with this method than with a three-breed rotational
cross.
Under conditions in Asia, crossbreeding of native cattle with several exotic dairy breeds like Holstein
Friesian and Jersey has been practiced on a large scale. The F₁ progeny thus produced have given very
promising results, particularly in terms of increased milk production, in almost all involved countries.
However, in the absence of clear-cut breeding plans and programmes, further breeding of F₁ progeny
has resulted in subsequent generations of F₂ and beyond. In these latter generations the advantages
observed in the F₁ generation have markedly deteriorated, causing great frustration and disillusionment
among cattle raisers regarding the value of cross breeding. There is a need for each country to examine
the issue critically, to clearly define the breeding goals and to implement strict selection programmes.
Strain Crossing
Crossing between strains is called strain crossing.
Top Crossing
Top crossing is a method of outbreeding in which inbred males of one breed are crossed with non-
inbred females of another.
Advantage of Crossbreeding
Intelligent crossbreeding generates hybrid vigour and breed complementarity, which are very important
to production efficiency.
Heterosis, or Hybrid Vigour, or Over Dominance, or Heterozygote Superiority, or
Outbreeding Enhancement
The main reason for cross breeding two breeds is to produce hybrid vigour or heterosis. Mating Polypay
ewes to Suffolk rams is an example of heterosis. This cross takes advantage of the reproductive

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efficiency and moderate maintenance costs of Polypay ewes while producing Suffolk-sired lambs to
meet market requirements for fast-growing, heavy muscled lambs.
Heterosis is defined as the increased performance of offspring compared to the average of the parents
that make up the cross.
Mean of offspring − Mean of parents
Heterosis% = × 100
Mean of parents

Heterosis is the opposite or complementary of inbreeding depression. It usually causes higher viability,
faster growth rate, better fertility and efficient production in the outbred progeny. For example, if the
average value for weaning weight of Breed 1 is 500 kg and the average value for Breed 3 is 600 kg,
and the resulting calf crop after mating these two breeds averages 580 kg, then heterosis for weaning
weight is 30 kg or 5.5%. This extra weaning weight is free because you did nothing more than use a
different breed.
Heterosis is not consistent from one breed to another. Breeds that are more genetically different
(Brahman and Hereford) will exhibit more heterosis than breeds that are more genetically alike
(Simmental and Limousin). The greater the difference in breeds, the greater the effect.
Heterosis results from crosses between inbred lines or between different races or varieties and forms
an important means of animal and plant improvement. The characters that show the highest inbreeding
depression are those that also show the highest heterosis when different populations are crossed. When
two different breeds, strains or inbred lines are crossed, the progeny show an increase of those
characters that previously suffered a reduction from inbreeding, because a harmful recessive allele
inherited from one parent would be likely to be covered up by a normal dominant allele from the other
parent. It is now generally accepted that inbreeding or selection leads to divergence between lines or
breeds and to chance fixation of different, somewhat deleterious, alleles. Because of the general
dominance of the favourable or wild type allele assumed to be present in the other line, this effect is
covered up in the progeny when two lines are crossed, resulting in an increased yield.
Heterosis declines in F2 generation to half that in the F₁. Highest heterosis is likely when breeds crossed
differ markedly in their gene frequencies and the traits under consideration is under dominance control.
Heterosis, just like inbreeding depression, depends for its occurrence on dominance. Loci without
dominance cause neither heterosis nor inbreeding depression.
Heterosis does not occur for all crosses or for all measures of performance. Heterosis is highest for
traits with low heritability that do not respond well to selection, e.g., fitness traits, and lowest for traits
with high heritability that respond well to selection, e.g., carcass and fleece characteristics. Moderate
improvements due to heterosis are seen in moderately heritable traits. Studies have shown heterosis
figures ranging from 2% to 10% on production traits (milk, fat and protein).
Disadvantage of Heterosis
Heterosis is a transient effect. Superior performance observed in crossbred individuals is not transmitted
upon mating. Gene combinations are not transmitted to progeny. Only individual gènes are transmitted
to progeny. Gene combinations are rearranged or lost when crossbred animals are mated together.
Therefore, if the heterosis effect is to be obtained, both parental types must be maintained in pure
breeding on a continuous basis. It should be remembered that heterosis is not the result of
heterozygosity as such but only of heterozygosity involving desirable alleles. If a combination, showing

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heterosis, is found, this combination can be repeated infinitely. An organized crossbreeding system is
needed to take best advantage of hybrid vigour and breed complementarity.
Types of Heterosis
Individual: Advantage of a crossbred offspring over purebred parents.
Maternal: Advantage of a crossbred mother over a purebred mother primarily due to mothering ability.
Paternal: Advantage of a crossbred, father over a purebred father. Not as important as matérnal heterosis
Genetic Expression of Heterosis
Heterosis caused by heterozygosity of genes with nonadditive effects such as dominance, over
dominance and epistasis. For example, where several pairs of genes control one trait, one breed could
be homozygous dominant for several pairs and homozygous recessive for others. While in the other
breed alternative alleles are fixed. Crossing of two different breeds, strains, or lines cause
heterozygosity of gene pairs in the progeny and show increased vigour due to dominance, over
dominance and epistatic gene action.
Breed A × Breed B
AA bb CC dd aa BB cc DD
Aa Bb Cc Dd
Uses of Heterosis
Animal breeder make extensive uses of crossbreeding, strain crossing, and inbred line crossing to take
advantage of heterosis. The crossing of inbred lines to produce hybrids plays a major role in the
improvement of some plants, most notably maize. Crossing is widely used in animal breeding, though
highly inbred lines of farm animals are not available because of the severe loss of fertility from
inbreeding depression. Animal crosses are therefore made between mildly inbred lines or between
different breeds. Crossing highly inbred lines is used also as a method of genetic analysis both with
plants and laboratory animals.
The concept of heterosis is also applied in the production of commercial livestock. In cattle, hybrids
between Black Angus and Hereford produce a hybrid known as a Black Bald. In swine, "blue butts"
are produced by the cross of Hampshire and Yorkshire. Other, more exotic hybrids such as "beefalc"
are also used for specialty markets.
Commercial broilers are produced by crossing different strains of White Rocks and White Cornish The
Cornish provides a large frame and the Rocks provide the fast rate of gain.The hybrid vigour produced
allows the production of uniform birds with a marketable carcass at 6-9 weeks of age. Likewise, hybrids
between different strains of White Leghorn are used to produce laying flocks that provide the majority
white eggs for sale in the United States.
Breed Complementarity
Breed complementarity is the other major advantage of crossbreeding. Breed complementarity implies
using breeds in a crossbreeding programme where their strengths and weaknesses complement one
another. It relates to the fact that there are no perfect breeds, and that each breed possesses certain

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strengths and weaknesses. In a systematic crossbreeding programme, breed resources are combined to
balance the positive and negative aspects of each breed in the cross.
It is important to identify the strengths and weaknesses of different breeds and to determine. the
appropriate role of a breed in a crossbreeding programme. For example, we can produce Suffolk
Polypay lambs by either crossing a Suffolk ram onto Polypay ewes or by crossing a Polypay ram onto
Suffolk ewes. Mating a Charolais to an Angus is an example of crossbreeding, and in fact, the Charolais
x Angus mating is a complementary one. Charolais are large French cattle known for their fast growth
and heavy muscling, Angus are smaller British cattle known for their maternal ability, and the crossbred
offspring benefit for having both kinds of parents. Crossbreeding has principally been applied in the
tropics to exploit breed complementarity. Specifically, specialized exotic (mainly temperate) breeds
have been crossed with indigenous breeds to combine the high productivity of the former with adaptive
attributes of the latter.

Development of Composite or Synthetic Breeds

Crossbreeding can also be used to create new breeds. Almost all goat and sheep breeds started out as
crossbreds. For example, the Suffolk was originally a "cross" between the Southdown and Norfolk
Horn (developed in England). The Kiko is a "cross" between feral (wild) goats and dairy bucks in New
Zealand.
If none of the existing breeds is suitable for the conditions of a particular geographical-economic region
and the local primitive breeds exhibit an unsatisfactory level of performance, the only course left open
is to develop a new breed which, on the one hand, should meet the economic requirements and, on the
other, should be well adapted to the natural environmental conditions of the area. In starting the crossing
operation for the production of a new breed, several breeds may be used according to the actual
standards set for the prospective breed with regard to the type of production wanted and, possibly,
general biological properties) No detail prescription can be given as to how a new breed is to be
developed. For obvious reasons, breed-forming crossing should be accompanied by intensive selection.
Often, after the crossing has been completed, inbreeding also becomes necessary in order to speed up
the consolidation of the advantageous properties in the animal is to become the basis of the new breed.
Forming a stabilised composite breed involves crossbreeding initially, then closing the crossbred herd
at some point and selecting breeding stock from within the herd to form a stabilised new breed over
several generations. A composite breed may be developed from two or more previously established
breeds. The herd may be closed immediately after the Fi generation or after later generations, depending
on the number of breeds included and desired proportions of each parent breed in the new composite
breed. Stabilised composite breeds have the advantage of retaining a proportion of hybrid vigour in a
purebred animal. The amount of hybrid vigour is dependent on the number of parent breeds used to
develop the composite. Once stabilised, the breeding programme returns to purebreeding and requires
less management input. The Braford and Droughtmaster breeds are Australian examples of two breed
composites. Making a new stabilised composite is a major operation that requires many thousands of
breeders and extensive selection over subsequent generations, making it a task that cannot be carried
out by a small business alone. Examples would include, Brangus (Brahmanx Angus), Beefmaster,
Braford (Brahmanx Hereford) and Santa Gertrudis (Longhorn x Shorthorn).
Outcrossing

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Outcrossing is the mating of unrelated animals of the same breed. It is carried out in order not to inbreed
but have animals maintain characteristics of the breed. It is the most widely used breeding system for
most species. Usefulness depends upon accuracy of mating.
One of the best advantages of outcrossing is that it hides detrimental traits by keeping them recessive.
Outcrossing improves fitness traits such as reproductive ability, milk production, kid survivability and
longevity.
Up grading, or Grading up
Up-grading is the mating of purebred sires to unregistered or crossbred dams. It is the gradual changing
of a breed by continuous use of purebred sires. The system has been used all over the world to upgrade
one breed by converting it into another. With this method, own sires are replaced by sires from the up
grading breed. The introduced sires are mated again with females of the hybrid generation and the
operation is repeated for a number of generations. After six generations, the herd has 98.3% of the 'fresh
blood' and generally conforms to the superior breed. Success depends largely on the proper choice of
the breed to be used for up grading, which must be well adapted to the local natural environment. The
better the sires used in such a programme the better the end product.
Outbreeding Depression
The inverse of heterosis, when a hybrid inherits traits from its parents that are not fully compatible,
with deleterious results, is outbreeding depression.
Pure or Straight Breeding
Pure breeding is the mating of animals of the same breed. It is carried out so that the characteristics of
a breed may be maintained. Pure breeding can be classified as inbreeding or outbreeding.
Combining Ability
Combining ability is the capacity of an individual to transmit superior performance to its offspring. It
is the phenomenon with which inbred lines when crossed give rise to hybrid vigour. The only way to
select for combining ability is to grow and examine the progeny. This subject mainly applies to poultry
breeding and has not been widely used in large farm animals. It is of two types:
i. General Combining Ability (GCA)
ii. Specific Combining Ability(SCA)
General Combining Ability
When a breed, strain, family, line or even an individual give good results all other breeds, strains,
families, lines or individuals; this is general combining ability of that particular type. The term 'general
combining ability is used to designate the average performance of a line in hybrid combination. It helps
in identification and selection of best genotype to use in hybridization, as a parent.
Specific Combining Ability
When a breed, strain, family, line/or individual may only produce good results in a specific cross, this
is specific combining ability. It helps in identification and selection of best cross combinations i.e.,
those with the desired output.

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Suffolk is good meat producer. It produces good meat producing lamb when crossed with other breeds.
It is general combining ability.
Poultry Strain A B C Average
A 120 150 180 150
B 150 110 133 133
C 180 140 137 137
Strain A combines well with B and C, it is the general combining ability of strain A. Strain A and C
gives best result in progeny performance. It is the specific combining ability of strain A and C.
Selection for specific combining ability means that selection is practiced to take advantage of hybrid
vigour when non additive gene action is important.
Reciprocal Recurrent Selection (RRS)
RRS is a system of selection for increasing the combining ability of two or more lines or breeds that
have already demonstrated from past crosses that they "nick" or combine well. It is practiced in poultry
for the production of layer and broilers. It is used to improve the combining ability of two or more lines
or strains on the basis of crossbred progeny performance. The objective is to change both populations
gradually, so that they give better results in crosses with each other. The principles involved assume
that individuals in the two lines are not completely homozygous in opposite ways for all pairs of genes
but that one allele may be present at a high frequency in one line and at a low frequency in the other
line. Crossing the lines and selecting the individuals to reproduce each pure line on the basis of the
performance of their crossbred progeny theoretically should make the two lines more homozygous in
opposite directions.
The start is made from two populations, preferably two already known to give some heterosis. when
crossed. These two populations, whose combining ability is to be improved, will be referred to as lines
A and B. Crosses are made reciprocally, a number of A ♂ ♂ being mated to B ♀ ♀ and a number of B
♂ ♂ to A ♀ ♀. The crossbred progeny are then measured for the character to be improved and the
parents are judged from the performance of their progeny. The best parents are selected and the rest
discarded, together with all the crossbred progeny, which are used only to test the combining ability of
the parents. The selected individuals must then be remated to members of their own line, to produce
the next generation of parents to be tested.
These are crossed again as before and the cycle repeated. Deliberate inbreeding is avoided because
random changes of gene frequencies are not desired.

Breed/Line A Breed/Line B

Crossbred Progeny (Decide from the performance

of crossbreds which parents produce superior
crossbreds)

Reproduce purebred from Reproduce purebred from parents

parents producing superior producing superior crossbred
crossbred progeny progeny 74 | P a g e
 Breed/Line B
Breed/Line A

Crossbred Progeny (Decide from the performance of

crossbreds which parents produce superior crossbreds)

Reproduce purebred from

Reproduce purebred from parents producing superior
parents producing superior crossbred progeny
crossbred progeny

Crossbred Progeny (Decide from the performance of Breed/Line B

Breed/Line A crossbreds which parents produce superior crossbreds)

Reproduce purebred from Reproduce purebred from

parents producing superior parents producing superior
crossbred progeny crossbred progeny

Repeat the procedure generation after generation.

Diagram illustrating the procedure to follow in RRS

Combination of Inbreeding and Crossbreeding
Inbred lines are produced by inbreeding and then different lines are crossed. Lines are selected on the
basis of their combining ability. It is usually practiced in poultry for production of layers and currently

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applied in pig production. Commercial hybrid would give maximum heterozygosity and offspring may
exceed either parent in their performance.
Selection and Regular Crossing
The characters that show the greatest inbreeding depression are those that also show the greatest
heterosis when different populations are crossed. Inbreeding and outbreeding alone cannot produce any
improvement; there must be selection at some stage if any improvement is to be made. The greater the
selection applied in any population; the greater will be the increase in average level of inbreeding in
that population. Thus, successful selection programme in closed population incurs inbreeding
depression which has greatest effect on characters associated with viability and reproductive ability.
The most complete utilization of genetic resources can be achieved by:
1. Continual selection within each of two or more populations, and
2. Regular crossing between these populations in order to produce the final commercial product.
This enables exploitation of additive gene effects within populations (through selection), additive gene
effects between populations (through complementarity), and non-additive gene effects (through
heterosis).
Breed Structure
Not all animals in a breed contribute to genetic improvement within that breed. In most cases,breeds
are structured so that only a minority of animals is given that opportunity. The structure of most breeds
consists of a series of subgroups called tiers. In many situations there are three tiers, namely nucleus,
multiplier and commercial (Figure 7.1). Occasionally there are only two (nucleus and commercial), and
sometimes there are more than three (more than one level of multiplier)
In a traditional pyramid, the nucleus tier consists of herds or flocks that breed their own male. and
female replacements. In some cases, they may occasionally import a sire or dam from another nucleus
herd or flock, Multipliers take males and sometimes females from nucleus. with the aim of producing
sufficient breeding stock to satisfy the demands from herds or flocks in the commercial tier.
Nucleus Breeding System (NBS)
Livestock production in developing regions is generally characterized by small herd-size, uncontrolled
mating, and the absence of pedigree and performance recording. These characteristics limit the
implementation of effective genetic improvement programmes. To overcome these problems, nucleus
breeding schemes have been suggested, in which genetic improvement is centrally organized in a
population maintained in research institutes or government farms. NBS is a method of selecting and
using breeding animals, consisting of a small number of elite breeding animals in a nucleus, or upper
tier, and a large number of animals in a lower tier. The fundamental feature of nucleus breeding is that
breeding effort and investment are concentrated on the best (nucleus) material in the breeding
population.
The nucleus may be closed' in the sense that transfer of genetic material from main population to
nucleus occurs only at the initial screening to establish the nucleus (Figure 7.2 In subsequent
generations there would be no further flow of genes from main to nucleus. The closed nucleus is
regenerated after each generation by mating superior individuals selected only from within the nucleus
itself.

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In contrast to closed nucleus schemes, more flexible programs permit animals from the lower tiers to
contribute progeny to the upper tiers. Outstanding selections from both the nucleus and main would,
therefore, be mated to regenerate the nucleus in successive generations (Figure 7.3Open nucleus
systems are hierarchical breeding systems in which animals may be transferred between levels in both
directions. The simplest open nucleus system has two mating groups; a nucleus of elite animals; and a
base in which the general flock is mated. In general, there may be more than two levels, and there may
be several flocks in the one level.

This transfer of genetic material from main to nucleus allows genetic improvement made in the main
population to be incorporated into the nucleus, thus improving the potential nucleus gains beyond what
could be expected in a closed population. Transfer from main to nucleus may also allow inbreeding in
the nucleus to be maintained at acceptable levels over successive generations. The open nucleus
breeding scheme offers a simpler procedure for producing and disseminating breeding stock of known
value. The open nucleus breeding systems showed greater rates of genetic gain and less variation in
selection response than the closed nucleus systems. Efficiently-designed open nucleus breeding
schemes can lead to a 10% to 15% increase in annual response to selection and to a substantial reduction
in rate of inbreeding in the nucleus, when compared with closed nucleus schemes. Several studies
indicated the significance of using open nucleus breeding scheme to improve milk production of buffalo
and increase the rate of genetic gain.
A popular variation on this system is the group breeding scheme.
Group Breeding Schemes (GBSs)
The concept of group breeding originated independently in New Zealand and Australia at about the
same time in (1967. (GBSs are a method of pooling the best genetic material (breeding stock) from a
number of sources (cooperative flocks), and, after selective breeding. redistributing the improved stock
to the members of the group In group breeding scheme, several breeders form a cooperative which
assembles and runs a nucleus herd/flock. Group 17 breeding schemes thus overcome the genetic
isolation experienced by individual flocks by linking them through common breeding stock.
Cooperating farmers initially contribute an agreed number of their best breeding females to the nucleus
flock. This flock is subjected to detailed recording and selection for the required characteristics. Each
year the best males and females produced in the nucleus are used as nucleus breeding stock and high
merit males from the nucleus are distributed to the members. Occasionally, females from the nucleus
herd may be displaced by superior recorded females drawn from the members' farms. This two way
flow of genetic material is an open nucleus scheme maximizes genetic gains and minimizes inbreeding
but does increase the risk of disease in the nucleus flock. A particular feature of GBSs is the initial
genetic lift that can be achieved if the elite nucleus foundation stock is correctly identified. A typical
group breeding scheme consists of a nucleus and 10 to 15 contributing base flocks. Often the base is
managed for commercial production and the nucleus to breed superior sires. The Australian Merino
Society scheme has three levels; a central nucleus, 122 ram breeding cooperatives, and more than 1000
contributors.

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Some Terminology
Species: A group of animals those are so similar they can breed with each other and produce viable
offspring capable of reproduction.
Breed: A population of animals of the same species that share certain defined characteristics that
distinguish it from other breed and which are breed true for those characteristics.
Bloodlines: Bloodlines are groups within breeds; tend to have one common ancestor.
Purebred: Animals registered in a breed or eligible for registry.
Breed Associations: An organization that promotes a certain breed of animal. They control the
registration process of purebred animals of that breed.

Lecture
Mating/ Breeding system:
Mating system is the process of deciding which selected male will be breed/mated
with selected female. The transmission of genetic material from one generation to
the next is analyzed in terms of alleles rather than genotypes because genotypes are
broken up in each generation by the process of segregation and recombination. A
mating system is a set rules for mating animals in a production system. The mating
system determine the mode of transmission of alleles from one generation to the
next. Breeding systems aim to improve a single trait or a multiple traits. Knowledge
of breeding systems is important because producers can use these to preserve
genetic superiority and utilize hybrid vigor. There are three reasons for using
mating systems: i) to produce offspring with extreme breeding value ii) to make use
of complementarity iii) to obtain hybrid vigor

Broadly mating systems of 2 types: i) Random mating/panmixia : Any individual of

one sex has the equal chance of mating with another individual of the opposite sex
in the population. Condition – i) Random manner mating ii) equal chance of mating
(no special tendency or biasness)

In random mating, the probability of particular mating is the product of genotype

frequency.

TT Tt tt
Genotype freq. 0.4 0.2 0.4
TT × TT = 0.4× 0.4 =0.16 (possibility of TT × TT

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 mating) TT × tt= 0.4× 0.4 =0.16 (possibility of TT × tt

mating) TT × Tt= 0.4× 0.2 =0.08 (possibility of TT ×

Tt mating)

ii) Non-random mating : Any deviation from random is called Non-random mating.
Any departure from random mating naturally leads to complications in the
relationship between allele frequencies and genotype frequencies. In NRM deviation
occurred due to 2 rasons:

1. Phenotypic resemblance/likeness
2. Genetic relationship/Biological relationship

On the basis of phenotypic resemblance NRM mating are 2 types:

1. Positive assortative/ assortative mating / like to like eg. TT × Tt

2. Dissassortative/ Negative assortative mating eg. TT × tt

Genetic consequences of assortative/ Dissassortative mating: Assortative mating

–same phenotype and increase homozygous genotype and decrease heterozygosity.

Classification of mating systems:

On the basis of genetic relationship – Non random mating two types:

i) Inbreeding (Breeding between related individual)

ii) Outbreeding(Breeding between non-related individual)

Genetically related (Biological relationship): have common ancestor up to 5-6

generation and above this they will be genetically unrelated.

Inbreeding: is the mating of individuals that are more closely related than the average
relationship within the breed and population concern.

The offspring from inbreeding are inbred. The offspring from outbreeding are
outbred.

Genetic consequences of inbreeding: inbreeding increases homozygocity and

ultimate fate decrease genetic variation and genetic diversity. In extreme inbreeding
self fertilization or selfing occured eg. Pea plant. It doesn’t occurred in livestock.

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Heterozygocity reduces 50% for per generation of inbreeding.

eg. Tt × Tt (Heterozygocity 100)

Gamete 1 TT 2Tt 1tt

Heterozygous 50% and homozygous 50%

At t generation due to inbreeding heterozygocity decrease (1/2)t eg. at 10 generation

(1/2)10

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It is of two types:

i) Intensive inbreeding- is the mating of closely related animals for several

generations.

Close breeding: Intense inbreeding by mating full or half sibs, cousins or

parents to offspring is referred to as close breeding.

Effect:

o it can produce extremely good or poor results.

o haphazard close breeding could very detrimental to the overall quality of
the resulting offspring.
o success and failure depend on factors such as planning, foundation stock,
emphasis on culling and completeness of pedigree and performance
records.
o Usefulness:
• valuable tool for genetic research
• since it quickly exposes hidden gene types that an individual
carries.
ii) Line breeding : Is a special form of inbreeding designed to maintain a high
genetic relationship to an outstanding ancestor while keeping inbreeding
as low as possible.
Effect:
 to maintain a large percentage of one outstanding ancestor’s genes
from generation to generation without causing an increase of
frequency of undesirable often associated with inbreeding
 it is not based strictly of mating closely related individuals so it does
not cause the increase in homozygous gene pairs

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Outbreeding:
is the mating of individuals that are less closely related than the average of the breed
or population concerned. The frequency of heterozygotes increased and the
frequency of homozygotes decreased.

There are 4 types of outbreeding called

1. Species cross
2. Crossbreeding
3. Out crossing
4. Grading up
1. Species cross: Mating animals of different species. Donkey 2N=62
(Male)× 2N=64 Horse (Female)→ Mule 2N= 63, Lion× Tiger (liger or
tigon), wolf × Domestic dog, Zebu × Yak →Himalayas
2. Crossbreeding: Mating between different breeds of same species.
Brahma × Friesian (Pure breed) →Recognized breed. Fitness trait
linearly decease in inbreeding but according to rules fitness trait linearly
increase with outbreeding but any one can predict about these. There
are unlimited crossbreeding schemes. the most commonly utilized
crossbreeding schemes include:
1. Two breed single cross: Simply male of one breed × Female of
another breed
2. Two breed terminal cross: (Heterosis 50%)
F1 x F1 →F2 →F3-- -
3. Back cross F1 (Female)x Parental breed (male)(Except the male of the
cross) Male will be under same breed but will not same male then it
will be inbreeding.
A x B → F1AB sell male female use for next generation.

Rotational crossing: a series of breeds (two or more breeds) are used in succession.
Purebred males are used on crossbred females.

Two breed rotational cross: Bull of two breeds are used.

Crisscrossing: it is an extension of backcrossing.

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 A x B xC
50% 50% 50%
↓
A B A B C
25% 25% 25% 25%
50%
ABx A ABC x
A 25% 25% 50% ABC x B

↓ ABC x C

A 75%

B 25%

A → 37.5

B → 62.5

Two breed rotational cross

Three - - - - - - - - - -

Four - - - - - - - - -

Ax B Cx D (2 way cross)

↓ ↓

AB x CD (4 way cross)

Strain crossing: Cross between different strain.

Top crossing:
Inbred males of one breed x non-inbred female of another breed Advantages
of cross breeding:

For the production of hybrid vigor

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Breed complementation

Heterosis: Main objective of crossbreeding is heterosis. It defined as the increased

performance of offspring compared to the average of the parents.

Heterosis % = Mean of offspring- mean of parents/ mean of parents x 100

Heterosis is opposite to inbreed depression. Fitness trait will be increased linearly.
When breed will be genetically unrelated then heterosis will be more.

main genetic causes of heterosis is Dominance and epistasis. Heterosis highest in F1

then F2, F3 it will be decreased. For low heritable trait if you do inbreeding then
will be inbreeding depression and for outbreeding effect will be heterosis. The event
of heterosis and inbreeding depression will be for low heritable trait.

Disadvantages of heterosis:

1. It is a transient effect
2. Superior performance observed in crossbred individual is not transmitted
upon breeding.
3. Maxim gene in heterozygous condition then if we do further cross then it
will be decreased.

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Measurement of Inbreeding:
Inbreeding is often measured in terms of the coefficient of inbreeding, symbolized
by F. This coefficient range from 0 to 1. F=0 means there has been no inbreeding
meaning that the population is in H- W equilibrium, and F = 1 means that inbreeding
is complete. The inbreeding coefficient measures the percentage increase in
homozygocity relative to the average of the breed. If an individual has an inbreeding
coefficient of 0.25 it means that it is expected to have 25% of more homozygous gene
pairs than a non-inbred individual from the same population. This would the case if
full siblings were mated. Thus, the higher F is, the more inbred the population is.
Inbreeding coefficient can be estimated by two ways-

o from genotype frequencies

o or pedigrees.

From genotype frequencies: By comparing the number of heterozygotes observed

to the number expected for a population in H- W equilibrium, we can estimate the
degree of inbreeding. Inbreeding coefficient is defined as percentage decrease in
heterozygocity relative to that expected from random mating. Thus,

F= Expected Heterozygocity- Observed Heterozygocity/ Expected Heterozygocity

From pedigrees: The inbreeding coefficient is the probability that two alleles at any
locus in an individual are identical by descent from the common ancestor(s) of the
two parents. This means the degree to which two alleles are more likely to be
homozygous (AA or aa) rather than heterozygous (Aa) in an individual. There are
several methods to compute this percentage; the main two ways are the pathmethod
and tabular method. The actual level of inbreeding is relative to the base
population, which is assumed to be unrelated and non-inbred. In practice, the base
population is the population when pedigree recording started i, e., it is the population
in which the parents are unknown. Effective calculation of inbreeding relies on full
and accurate pedigree information. Where pedigree records are incomplete the
calculation may assume no relationship.

Biological relationships between animals:

Individuals are considered to be biologically/ genetically related when they have one
or more common ancestors. For practical purposes, if two individuals have no

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 common ancestor within the last five or six generations, they are considered
unrelated. The closer relationship is that of an individual with itself, or self-
fertilization.

Inbreeding coefficient= ½ × Relationship coefficient

Parent offspring RC = 50% so, IC =

25%
Full sib RC = 50% so, IC = 25%

Grandparent- grand parent progeny, RC = 25% so, IC

=12.5%
half sibs

Great-grandparent- great-grand parent progeny, RC = 12.5% so, IC

=6.25%first or full cousins

Second cousins; half RC = 6.25% so, IC

=3.125%first cousins

This having of relationships and genes occurs with each generation. Thus, after only
a few generations, any ancestor is likely to be source of only a small fraction of its
descendants. Biological relationship is important in animal breeding because the
closer the relationship, the higher the percentage of like genes the two individuals
carry. Closeness of the relationship is determined by three factors:

1. How far back in the two animals pedigrees the common ancestor appears?
2. How many common ancestors they have?
3. How frequently the common ancestors appear?

Inbreeding depression:
Inbreeding causes an increase in homozygocity; affect all loci in a population
quality. The danger in this is that deleterious recessive alleles which are present in
a low frequency in the whole population will become homozygous in inbred

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 offspring. This causes the reduction of the mean phenotypic value of quantitative
traits such as size, vigor fertility and yield. The decline in performance is called
inbreeding depression. The actual performance reduction is not the same in all
species or in all traits. Some characteristics such as meat quality is hardly influenced
by inbreeding: others like reproductive efficiency are greatly influenced by
inbreeding Usually, the traits most affected by fitness traits that are low
heritability. As inbreeding progress there will be decline in fertility both in litter size
and sperm viability, an increase in embryonic mortality a decline in progeny survival,
higher frequency of hereditary abnormalities, loss of immune system function and
eventually a lowering of growth rate and milk yield. A linear negative relationship
between production traits and the degree of inbreeding can be predicted.

Purposes of inbreeding:
1. Production of inbred lines: The primary objective of inbreeding Production
of inbred lines which can be commercially used. In plant breeding, medical
research, and animal breeding inbred lines are useful because they are
genetically uniform for known traits.
2. Utilization of hybrid vigor: Crossing two highly inbred lines introduces
hybrid vigor and combines the desirable traits in both lines. eg. Broiler and
layer strains.
AA BB CC DD (100% Homozygote CC DD ) × aa bb cc dd
(100% Homozygote)

Aa Bb Cc Dd (100% Heterozygotozygote )
3. Utilizaton of hybrid vigor: Crossing two highly inbred lines introduces hybrid
vigor and combines the desirable traits of both lines.
4. Elimination of deleterious allele: Inbreeding can result in the expression of
deleterious recessive alleles in a homozygous form. Once deleterious traits
appear due to inbreeding, natural selection can cause their removal from
population; therefore the deleterious alleles will not be passed to future
generations.

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Inbred line:
An inbred is one whose parents are related that is there is common ancestry in the
family tree. A line to be called inbred should have at least 50% of inbreeding
coefficient. It can be produced by parent offspring mating, full sib mating and first
cousin mating. Three generations of full sib mating or 6 generations of half sib mating
produces inbred lines with 50% coefficient of inbreeding. After 20 generations of
full sib mating, when essentially all genetic loci are homozygous or fixed and F
approaches 100%, no further genetic change take place except through mutation or
introduction of different genetic material. An inbred strain is defined is the product
of over 20 generations of full sib mating which results in individuals that are 98%
identical to each other. After 40 generations of inbreeding they are 99.5 % similar.
In other words they are almost clones. The coefficient of inbreeding never quite
reaches 100 percent. Once an inbred strain has been established, no further
inbreeding depression should occur.

Incross and In-crossbred:

When a cross is made between two inbred lines belonging to same breed it is called
an incross, and between those belonging to different breed incrossbred.

Types of heterosis:
1. Individual heterosis: Advantage of a crossbred offspring over purebred
parents
2. Maternal heterosis: Advantage of a crossbred mother over purebred
mother due to mothering ability
3. Paternal heterosis: Advantage of a crossbred father over purebred father Not
as important as maternal heterosis.

Genetic expression of heterosis/cause:Heterosis caused by heterozygosity of

genes with nonaddetive effects such as dominance, overdominance and epistasis.

For example, where several pairs of gene control one trait, one breed could be
homozygous dominant for several pairs and homozygous for others.

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 Breed A Breed B
AAbbCCdd ×
aaBBccDD

↓
AaBbCcD
d

Aa Bb Cc Dd

2 3 4 5 6 7 8 9 = 44 Incase of additive gene effect but incase of heterosis effect this

value will be higher due to nonadditive gene effect.

Uses of heterosis: Animal breeder make extensive uses of crossbreeding, strain

crossing and inbred line crossing to take advantage of heterosis. Crossing is widely
used in animal breeding through highly inbred lines of farm animals are not available
because of serve loss of fertility from inbreeding depression. Animal crosses are
therefore made between mildly inbred lines or between different breeds. The concept
of heterosis is also applied in the production of commercial livestock. In cattle,
Black Angus × Hereford → Black Baldy, In swine, Hampshire × Yorkshire →Blue
butts, beefalo, for commercial broiler Male line White Rocks × Female line White
Cornish. The Cornish provides a large frame and the Rocks provide the first rate of
gain. White leghorn are used to produce laying flocks.

Breed complementarity: it implies using breeds in a crossbreeding program where

their strength and weakness complement one another. Charolais × Angus mating is a
complimentary one. Charolais are large French cattle known their fast growth and
heavy muscling, Angus are smaller British cattle known for their maternal ability and
the crossbred offspring benefit for having both kinds of parents.

Development of composite or synthetic breeds: Crossbreeding can also be used to

create new breeds. Southdown × Norfolk horn →Suffolk sheep. Brahman × Angus→
Brangus Brahman × Hereford→ Beefmaster, Bradford (Longhorn × Short horned )
→ Santa Gertrudis

Outcrossing: Is the mating of unrelated animals of the same breed. It is carried

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out in order not to inbreed but have animals maintain characteristics of the breed. It
is the most widely used breeding system for most species.

uses: It hides detrimental traits by keeping them recessive. Improves fitness traits,
milk production, kid survivability and longevity.

Up-grading or Grading up: Is the mating of purebred sires to unregistered or

crossbred dams. It is the gradual changing of a breed by continuous use of purebred
sires. The system has been used all over the world to up-grade one breed by
converting it into another. With this method, own sires are replaced by sires from the
up-grading breed. The introduced sires are mated again with females of the hybrid
generation and the operation is repeated for a number of generations. After six
generations, the herd has 98.3% of the fresh blood and generally conforms to the
superior breed. Success depends largely on the proper choice of the breed to be used
for upgrading, which must be well adapted to the local natural environment. The
better the sires used in such a program the better the end product.

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Male F × Female indigenous

F1 → 1st generation upgrade

50% 50%

Male F × F1Female upgraded

F2 → 2nd generation upgrade 75% Friesian

Male F × F2Female upgraded

F3 → 3rd generation upgrade 87.5% Friesian

After 5-7 generation it will be about 100% , but will not be 100% because there
presence of some indigenous genes. Same bull should not be use after first
generation. If we use same bull then it will be inbreeding in case of out breeding.
Bull will be same breed but different bull.

Combining ability: Is the capacity of the individual to transmit superior

performance to its offspring.

Two types:

1. General combining ability: When a breed, strain, family, line or even an

individual give good results when crossed with all other breeds, strains, families,
lines or individuals; this is general combining ability of that particular type. The term
general combining ability is used to designate the average performance of a line in
hybrid combination. It helps in identification and selection of best genotype to use
in hybridization, as a parent.

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 2. Specific combining ability: When a breed, strain, family, line or even an
individual may only produce good results in a specific cross, this is specific
combining ability. it helps in identification and selection of best cross combinations
i.e., those with the desired output.

Breed structure:

Not all animals in a breed contribute genetic improvement within that breed. In most
cases, breeds are structured so that only a minority of animals is given that
opportunity. The structure of most breeds consists a series of subgroups called tiers.
In many situations there are three tiers, namely nucleus, multiplier and commercial.
Occasionally there are only two (nucleus and commercial), and sometimes there are
more than three (more than one level of multiplier).

In a traditional pyramid, the nucleus tier consists of herds or flocks that breed their
own male and female replacements. In some cases, they may occasionally import a
sire or dam from another nucleus herd or flock. Multipliers take males and sometimes
females from nucleus, with the aim of producing sufficient breeding stock to satisfy
the demands from the herds or flocks in the commercial tier.

Nucleus Breeding System (NBS):

Livestock production in developing regions is generally characterized by small herd
size, uncontrolled mating, and the absence of pedigree and performance recording.
These characteristics limit the implementation of effective genetic improvement
programs. To overcome these problems, nucleus breeding schemes have been
suggested, in which genetic improvement is centrally organized in a population
maintained in research institutes or government farms.

NBS is a method of selecting and using breeding animals, consisting of a small

number of elite breeding animals in a nucleus or upper tier, and large number of
animals in a lower tier. The fundamental feature of nucleus breeding is that breeding
effort and investment are concentrated on the best (nucleus) material in the breeding
population.

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The nucleus may be closed in the sense that transfer of genetic material from main
population to nucleus occurs only at the initial screening to establish the nucleus. In
subsequent generations there would be no further flow of genes from main to
nucleus. The closed nucleus is regenerated after each generations by mating superior
individuals selected only from within the nucleus itself.

In contrast to closed nucleus schemes, more flexible programs permit animals from
the lower tiers to contribute progeny to the upper tiers. Outstanding selections from
both the nucleus and main would therefore be mated to regenerate the nucleus in
successive generations. Open nucleus systems are hierarchical breeding systems in
which animals may be transferred between levels in both directions. This transfer of
genetic material from main to nucleus allows genetic improvement made in the main
populations to be incorporated into the nucleus, thus improving the potential nucleus
gains beyond what could be expected in a closed population. Transfer from main to
nucleus may also allow inbreeding in the nucleus to be maintained at acceptable
levels over successive generations. The simplest ONBS has two mating groups; a
nucleus of elite animals and a base in which the general flock is mated. In general,
there may be more than two levels, and there may be several flocks in the one level.

The open nucleus breeding scheme offers a simpler procedure for producing and
disseminating breeding stock of known value. The ONBS showed greater rates of
genetic gain and less variation in selection response than the closed nucleus systems.
Efficiently designated ONBS can lead to a 10% to 15% increase in annual response
to selection and to a substantial reduction in rate of inbreeding in the nucleus, when
compared with closed nucleus systems. Several studies indicated the significance of
using ONBS to improve milk production.

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 CHAPTER 8
Record Keeping
The old saying, "You can't manage what you don't measure," holds true. Keeping records is an essential part
of good livestock management. To make progress and profit in the livestock business, records must be kept.
Record
Record is information that has been systematically and carefully collected and appropriately (stored for
intended use. To be able to run any economic enterprise successfully carefully thought out, properly collected
and kept records are a must.
Animal Recording
Animal recording is the process of collecting, managing and keeping data about animals on the farm.
Record Keeping
Record keeping is the activity of organizing and storing all the documents, files, invoices, etc. relating to a
company's or organization's activities. A system for record keeping should be established. Use a system that
you can easily and accurately maintain.
• Individually identify animals, as a prerequisite to meaningful records. Be sure to identify purchased or
retained replacement heifers..
• Individually identify calves soon after calving. At a minimum, keep records of calving date, sex, dam,
sire, calving easy code and birth weight.
• An ear tag is likely the most practical form of identification. Whether you choose the basic numbered
panel or electronic ID, use the system that best fits your plans.
• Record all management practices, such as medical treatments and vaccinations. Make sure to record
date, products and dosages.
• Pocket-sized herd record books are easy to carry, but also easy to lose. Maintain a backup record
system in an office ledger or computer.
• Maintain easy access to records for five years and archive older records
Criteria for Record Keeping
1. Must be useful
2. Must be kept in such a form so that it can easily converted into information e.g. date of birth of
animal, age of first estrous, date of first calving
3. it must be simple
4. Duplication must be avoided as much as possible
5. Record must lead to action being taken eg. Body condition score, nutrition status.
The records I be simple, easy and quick to interpret and use. The records should be related to the purpose,
such as selecting heifers, culling cows or forming a nucleus herd for breeding bulls. Records should I satisfy
the following criteria:
1. They must be useful: Unless data which is being recorded will at some future time be used in making
management decisions it should not be recorded at all. Taking records without using them (decisions about
breeding, feeding and management) is a waste of time and money. Records however, are worth the most when
they are used the most.
2. Records must be kept in such a form that they can be easily converted into information: Before
keeping a record, the eventual end use must be decided upon so that the form in which the data are recorded
will facilitate later analysis and interpretation. Too often the end use is not considered, and the usefulness of
the data is severely impaired.

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3. Record keeping systems must be simple: Dairy farmers have enough to do without burdening themselves
with complex record keeping systems that are difficult to understand and time consuming to complete, and
therefore nearly impossible to delegate to employees.
4. Duplication must be avoided as much as possible: Some data may have to be recorded more than once
in different forms, but this must be reduced to a minimum. In other words, if a record is to be made in the
field, the recording system should be such that data can be conveniently entered in the field and does not have
to be re-entered back at the office.
5. Records must lead to actions being taken: Unless a record is specifically intended to be used for some
future action or in management planning it should not be kept." In all records, there should be a 'Remarks'
column explaining the reasons behind any unusual observation. This i very essential in interpreting the
implications of the records, particularly for a third party who may have not been directly involved in taking
the records, but needs to make informed.
Use of Records
The records will:
• Be used in determining profitability
• Be used to compare the efficiency of use of inputs, such as land, labor and capital with that of alternative
production activities.
• Help the investor in improving the efficiency of farm's operations.
• Be used to preserve institutional memory of the enterprise for future reference.
• Should be used for decision making on a farm and should be interpreted in the right way, otherwise there
will be a waste of time, money and energy.
Objectives of Record Keeping or purposes of Record keeping or Importance:
Record keeping is an essential part of good livestock and farm business management. Recording can be done
most easily if animals have some form of identification. Thus, animal recording and identification are
inseparable. Excellent records are the cornerstone of building a financially successful livestock enterprise and
they will be of great help in the development of the livestock husbandry and livestock industry of any country.
Good records maintain and transmit accurate information about the animal. In summary, the importance of
animal identification and record keeping includes:

 Performance evaluation for selection of animal

 Economic evaluation
 Genetic evaluation
 Improve bargaining power of product
 Control of inbreeding
 Aid to culling of low performance
 To asses profit or loss
 Aids better management decision
 Aids in research and husbandry

• Performance evaluation: Adequate and correct record keeping is a valuable tool for assessing the
performance of herd or flock and making good management decisions.
• Economic evaluation, which refers to the assessment of optimal use of resources.
• Genetic evaluation, which refers to the determination of the best candidates for breeding, leading to
successful breeding programmers. Absence of records is a barrier to implementing and evaluating
improvement schemes.
• Improves bargaining power on product.
• Control of inbreeding and aid in breeding planning.
• Aid in culling low performers.
• To assess profitability/losses.
• Aid in grass margin analysis.
• Credit/loan access.

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 • To rationalize labor.
• Aids-in-disease management.
• Aids in better management decisions, such as determining whether there is need for changing feeds,
whether the animals need treatment, weaning, mating, culling, and selling. Etc.
• Aids in research and husbandry: Research depends the records-keeper's files can provide information
increasingly referenced in developing and improving husbandry practices.
Those farmers that keep records and utilize them have animals with higher productivity than those of non-
record keepers. Their animals have increased genetic merit, increased the farmers have overall increased
income.
Types of Records
On-farm records are essential in evaluating and improving the performance of herd/flock within a farming
system. Farmers should have a record book in which all records are kept. This should be stored in a place
where it will not become soiled or wet, making the records useless. The format should be simple and readily
understood by the farmer. The value and relevance of the different types of records will vary with differing
production systems. The major types of records are:
1. Physical (identification) records: Records should be a true indication of the identity, sex, breed, ancestry
and date of birth of the animal.
2. Breeding records
3 Production (Performance) records.
4. Feeding records
5. Financial records
6. Lambing records, which include identity, dam ID, weight, date of birth, type of birth and sex.
7. Growth or weight records kept periodically by recording the body weight of animals.
8. Health records including morbidity, mortality, signs and symptoms, diagnosis, treatments, vaccinations,
etc.
9. Milk production records: Recording once weekly may suffice as this is highly correlated with total milk
production.
10. Testes size: Recording testes size at one year of age can assist in sire selection. Testes size in males is
related to ovarian activity (multiple ovulations) in females.
11. Carcass yield or dressing percentage is a factor that has tremendous economic value, particularly in a
community-based breeding programmer involving meat breeds.
12. Hides and skins: For a crossbreeding programmer there may be a need to record skin quality aspects such
as area of hide, skin thickness, elasticity, pigmentation and density of hair.
Type of Data to Record
Practically, following are what we must record:
1. Animal D, herd, sample/or farmer ID
2. Pedigree (passport data): Dam ID, grand dam ID, sire ID, grand sire ID
3. Relevant parameter values
4. Dates
5. Weights
6. Yields e.g.. Weekly milk yield
7. Body condition scores
8. Growth: Date of birth, birth weight, date of weaning, weaning weight, sale weight, sale date, etc.
9. Fertility: Age at first service, age at first calving, date of calving, number of services per conception, etc.

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Breeding Records
The importance of breeding records is to measure the productive efficiency of the herd and to enable culling
and selection exercise to be carried out for breeding and genetic improvement. A good farmer would like a
cow which gives a calf yearly. Therefore, accurate breeding record of each individual cow is needed and also
a breeding record for the total herd. In addition to this, the data for the breeding record provides information
about when certain cows have to be dried off and when certain cows are due to calve while others need to be
insemination for proper herd management. The important data in breeding records should include:
• the identification of an animal including its birth date
• Sire and dam ID.
• heat dates and comments
• calving dates and comments
• earliest breeding date
• service information
• pregnancy examination
• expected calving date
• drying off date
• any additional remarks
Production (Performance) Records
These records are useful in measuring the performance of the herd/flock and for the economic appraisal of the
enterprise. For successful design and implementation of breeding programmers performance records are
necessary. Crossbreeding programmers need records on performance of indigenous and exotic breeds, and the
crossbreds. Selection schemes need performance records of individuals in a population. Production and
breeding records will give the farmer direct profit but also indirect profit by using progeny tested bulls from
artificial insemination (AI) stations. Progeny testing is only possible if production and breeding figures of
daughters are available. Breeding recording system would be a great help in selecting the bulls for the National
Al services. For dairy industry, the important records are:
• Dairy milk yield
• Milk Content
• Lactation in the fat content, protein, Solids Not Fat) 3
• Lactation length Milk fed to calves
• Milk consumed at home
• Milk sold Milk pails
• Milk spoilt
Feeding Record
These should indicate the amount of feeds given as well as the type of feed. Feeding records should be used
the most for day-to-day management, evaluating pasture management practices and for planning of activities
in the future. The day/to/day management decisions which are to be made are for instance, which cows need
concentrates and how much, cows to be culled and why, etc. Thus the important records are:
• Available fodder on farm
• Quantity fed Concentrate supplemented
• Minerals
• Left-over (per head and per feed, if possible) Spoilage (per batch)
Feed consumption is difficult to estimate on farms where animals graze, but for capital intensive farm
businesses, such as finishing or fattening operations, the amount of concentrate fed should be recorded to
calculate profitability.

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Health Records
Health records are needed to do the required vaccinations at the right time and to prevent disasters like foot
and mouth epidemic. They also provide information about the health status of each individual animal and the
whole herd. Only with the breeding and health records # good and wise decision can be made. The important
records are:
• Vaccination
• Dipping/spraying
• Treatment
• De-worming
• Postmortem
Financial Records
Financial records can be used for cash flow planning, enterprise analysis and other purposes. The records of
the expenditure and revenue should be kept for cash analysis and enterprise appraisal. Economic records are
of paramount tersest in providing the farmer with information concerning the profitability of his farm.
Moreover they are of great help in decision making at the right time. For example, is it profitable to feed
concentrates, is it advisable to apply for a loan or credit to invest in a machinery or technology, is it more
economic to raise the calves with whole or skimmed milk? Answering these questions is only possible if
adequate records are available. Moreover, for tax purposes and for the purpose of getting loans or credit,
economic records are required.
Animal identification
Animal identification is a top priority for any genetic improvement programmer. Animals must be uniquely
identified. Errors in identification can lower estimates of genetic variability and can result in biased genetic
evaluations. Besides being useful for genetic evaluation. Animal identification is important for health and
traceability concerning food safety for humans, which has become very important in recent years.
Proper identification is key to good management. If each animal is clearly identified, keeping records on
treatments becomes a lot easier. If you are going to record information about individual animals, you need to
be able to identify each animal in the herd over a number of years. The identification method should be cheap,
not damaging to the animal and reliable at s distance of at least 2-3 meters and by preference permanent. It is
important to choose a form of identification that is fit for purpose and provides unique identification within
the population being considered. The animal's identification number (ID) may be attached to the animal by a
tag tattoo, sketch, photo, brand or electronic device. Methods of identification can be subdivided into two
categories: permanent and non-permanent.
General Rules on Animal Identification
1. The recorded animal identity must be unique to that animal and never be re-used.
2. The identification number used for a flock or herd must be unique for that flock or herd.
3. The animal's identity must be visible.
4. The animal's identification device/method must comply with legislative requirements.
5. Animals, which lose their identity device must be re-identified and, wherever possible, with their original
number, provided that there is evidence that the animal is. Being correctly identified. Where this is not
possible, a cross reference to the original number must be maintained.

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Permanent Identification Method
1. Tattooing (ear or under).
2. Description diagrams, sketches and photographs).
3. Ear notching/punching (holes at various positions): Easy to read and produces little trauma to animal. Holes
or notches close over a period of time.
4. Brands (hot iron, freeze and chemicals): This may be an animal welfare issue in some countries, especially
if hot branding is employed.
5. Implantable microchip transponders transmit ID.
Temporary Identification Method
1. Tags (Ear-tags, Wing-tags, Flank-tags, Tail-tags and Brisket-tags): The easiest way of identification at
present is to use plastic ear tags. Correct tag placement will minimize tag losses and provide good legibility.
Small metal clips are stamped with individual numbers. Using special pliers, they are applied near the base of
the ear or to the wing. Procedure is quick and causes minimal pain. As with ear notching, the ID can be lost.
2. Neck band, leg band.
3. Collars or neck straps (chains).
4. Color markings (Paint and dyes, Nontoxic, waterproof dyes or markers).
5. Hair Braiding.
6. Naming.
7. Clipping or shaving various locations or patterns.
Animal identification:
i. Temporary identification (ear tags, tags, flank tags, Brisket tags neck bands, leg band, colr
marking, naming, clipping /shaving)
ii. Permanent identification eg. Tattoing most used, decription, ear notching, brunch, implantable
microchip

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 CHAPTER 9
Animal Breeding Programmes
The aim of animal breeding is to genetically improve livestock populations so that they produce more
efficiently under the expected future production circumstances. Genetic improvement is achieved by selecting
the best individuals of the current generation and by using them as parents of the next generation. A breeding
programme is a systematic and structured programme that is set up in order to genetically improve
livestock population. The two key questions in animal breeding are: where to go, and how to get there? An
animal breeding programme involves the answer to these questions. The more important functions and
requirements of breeding programmes are to
i) Increase production and product quality.
ii) Increase productivity and cost efficiency.
iii) maintain genetic diversity,
iv) support the conservation and use of specific breeds, and
v) consider animal welfare and sustainable systems.

General aim: (Lecture)

• More production
• More efficient production eg. Broiler

Components of animal breeding programme (Lecture)

• Formulate the breeding goal and objective
Objectives: such as improvement of related traits with milk production eg. Daily milk yield, lactation
length (Standard lactation period 305 days and dry period 60 days), FCR, early maturity, Age at 1st
estrous and conception and calving interval. Breeding objectives also defined as selection criteria.
• Develop data recording and processing system
How much improvement can determine to see data, Need actual record keeping system. For processing
computer package programme available.
• Genetic evaluation system: (To select best animal): For next generation improvement. Selection best
superior parent.
• Selection and mating system: Different selection and mating system are used for Animal breeding
programme.
• Dissemination of genetic improvement and superiority: Step by step development of entire population.
Through Nucleus → Multiplier → Commercial
Breeding male × Breeding female
↖↓↗
Male or Female
• Monitoring and evaluating system: Within system how much genetic and incase of error
correction

Components of Breeding Programmes

A breeding programme has at least the following components:
1. Defining breeding goal/objective.
2. A data recording system.
3. Genetic evaluation system.
4. Selection and mating system.
5. Dissemination of genetic superiority.
6. Evaluation of breeding programmes.

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Defining breeding goal (the purpose of change)
Goal is the purpose to which an endeavor is directed. Breeding goals indicate the direction of a breeding
programme. Before a breeding goal for a breeding programme is determined. Scientists document to what
extent the variation of each characteristic can be attributed to genes and to the environment. Genetic variation
in a characteristic is a prerequisite for improving performance breeding. The through brooding goal also
accounts for how important each characteristic is to the industry (this is normally expressed in economic
terms)
The ultimate goal of animal breeding is to change populations in such a way that their overall economic merit
is increased at the faster rate. In exceptional cases the breeding goal may be simply to maintain current
performance level. Breeding goals can vary between species. Examples of breeding goals include increased
milk, fat, or protein yield; increased longevity, optimal number of kids born; improved conformation scores
(overall and linear); increased profitability, etc. A Long term breeding goal provides the basis against which
improvement can be measured.
Defining breeding objective (what to change and the value of change)
A breeding objective describes traits to be improved and how important are different traits in relation to each
other. Breeding objective is sometimes called, selection objective. The Breeding objective is a function of the
traits that the owner(s) of the animals wish to change. The breeding objective includes all of the traits that
need improvement, even if there are no records on some of the traits) Defining breeding objective is the first
and probably the most important step in a breeding programme. Improving the wrong traits could be equivalent
or even worse than no improvement at all!
Knowledge of the function of the animal and the interactions between the genotype and environment is
necessary if we want to develop appropriate breeding objectives. Parasite resistance is critically important in
tropical climates. Breeding objectives in the Tropics emphasize traits such as tick count (a measure of tick
resistance). In temperate regions, less emphasis is placed on parasite resistance and more emphasis is placed
on other traits.
Breeding objectives must be set at the national, regional or local level. This could be short and long term.
Special care must be taken in dealing with fitness and adaptive traits especially if antagonistic genetic
relationships exist between these and primary production traits. In a dynamic breeding programme the
breeding objectives should be reviewed regularly based on what has been achieved so far and on likely long
lasting changes of the market or agricultural policies.
Breeding objectives generally include the characteristics of importance, the level they should achieve and the
time frame in which this will be achieved. A common fault when setting breeding objectives is to have no
timelines or levels to achieve. By adding levels you can more easily monitor your progress towards the
objective and know where changes need to occur to achieve your goal. Also note that the more traits that you
include, the progress for cach will be slower, however the progress against the objective can still be high.
Traits in a breeding objective should be economically important, heritable, measurable and attainable. When
developing breeding objectives consider the following:
● A breeding objective is generally specific to the requirements of the target market. Depending on the
target market, some traits have greater economic importance than others.
● Monitoring the current herd or flock performance against customer or market requirements and
considering how this performance and the requirements might change over time.
● Some traits are highly heritable. Greater progress towards breeding objectives can be achieved by
targeting traits that are highly heritable Focus on traits of economic importance rather than traits that
have more to do with tradition' or 'personal preference.
● Can continue to be improved within the limitations of the environment and production system.
● Contributes the most to your profit.

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Designing comprehensive animal breeding programme with a specific objective involves economic
considerations. Failure to consider economic aspects in breeding decisions may be, in part, due to a lack of
economic training on the part of animal breeders, and to the
difficulties and uncertainties of predicting the future production and economic conditions which will exist for
progeny generations.
A breeding objective can be simple e.g. breed, or more sophisticated e.g., fat depth. Regardless of the level of
sophistication, it is important to record or list the desired animal traits that impact on enterprise profitability
and estimate the relevant importance of each trait. From here the economic impact of changing cach important
trait can be calculated from financial and production data.
To realize the benefits of a breeding programme, the breeding objectives must be appropriately defined for
the species or breeds, communities and environments concerned, and the strategies laid out can be followed
in practice.
Breeding objectives are influenced by a wide range of factors, and have to consider the needs and priorities of
the animal owners, the consumers of animal products, the food industry, and 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.
Once the breeding objective has been defined, a breeder has to choose suitable selection
criteria and design the breeding programme. Selection criteria used for males may differ from those for
females.
Data recording and collection system
Estimation of genetic parameters and breeding values requires phenotypic data on selection candidates. Thus
a system has to be set up to routinely record data on selection candidates. Without data on selection candidates
it is impossible to identify the best individuals. The way data is collected depends on the species and the traits
in the breeding goal. For example, milk yield cannot be recorded on bulls. Thus to identify bulls of high
genetic merit for milk yield. one has to collect data on daughters of bulls. Dairy cattle breeding schemes
therefore have a system to record data on daughters of test bulls. Milk yield of those daughters is recorded on
common dairy herds, meaning that farmers are involved in the data recording. In beef cattle breeding, growth
performance of bulls can be recorded on the selection candidates themselves, meaning that progeny testing is
not necessary. In beef cattle breeding, data collection therefore takes place at testing stations where the
performance of selection candidates is recorded. The quality of the data is fundamental to the success of
breeding programmes. Without high quality data, it is impossible to accurately estimate genetic parameters
and breeding values.
Genetic evaluation system
Genetic evaluation is central to animal improvement schemes. Genetic evaluation is a valuable tool for genetic
selection that allows for comparison of animals in different environments. After data are recorded, breeding
values have to be estimated. Estimated breeding value gives an estimate of the transmitting ability of the
parent. Selecting animals an based on estimated breeding value maximizes the response to selection. The
common procedure to estimate breeding values in applied livestock breeding is called "BLUP". BLUP and
selection index theory have the same theoretical basis; both are based on regression of breeding values on
phenotypes. Compared to selection index theory however BLUP has the following advantages:
i) it accounts for systematic environmental effects,
ii) it is more flexible than selection index theory and therefore more suitable as an operational tool,
and
iii) it takes account of selection.
The basic principles for genetic evaluations based on individual performance, pedigree, sib and progeny
information are, however, always valid. Generally, the more information included from the individual and its
close relatives, the more accurate the estimated breeding values will be. The use of mass selection, including
pedigree information, seems to provide the best base in many situations for correct ranking of potential
breeding stock in developing countries, especially for animals held in nucleus herds with good record keeping.
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Mass selection is also a valuable method for screening animals to form the initial nucleus population. Within
traditional livestock production systems livestock keepers can identify and rank their stock accurately.
Ranking methods used within these systems can be documented and practically applied if the livestock keepers
are involved in the design of evaluation programmes from the outset.
Selection and mating system
Selection and mating takes place after breeding values are estimated. Selection refers to the process of
choosing the best to be parents, whereas mating refers to the combining of selected parents to maximize
efficiency. Thus selection precedes mating. The selection process determines the genetic improvement of the
population over time, whereas the mating process determines how maternal and paternally derived alleles are
combined within individuals. Selection describes the process of choosing animals that meet the requirements
of the breeding objective and will, in a breeding enterprise, pass particular traits onto their progeny. Once
producers understand the requirements of the target market and have developed breeding objectives that are
aligned to these requirements of the target market and have developed breeding objectives that are aligned to
these requirements, they can begin selecting livestock that meet the breeding objectives. Selection should
consider both subjectively measured traits (visual assessment) and objectively measured traits (genetic
assessment).
Subjective, visual assessment
Visual assessment is an assessment of an animal based on what can be physically seen. While the requirements
will vary depending on the enterprise's breeding objectives, traits to look for when visually assessing livestock
include:
● The conformation or shape of the animal eg, muscling
● Structure of the animal eg, whether the mouth is overshot or undershot.
Objective, genetic assessment
Objective assessment uses actual measurements to assess the relative worth of an animal to an enterprise. One
form of objective assessment is genetic evaluation which provides an insight into the genetic makeup of
animals. This is particularly useful when sires are being acquired to improve a herd or flock according to the
enterprise's breeding objectives. The difficult task of selecting breeding stock based on genetic assessment has
been made easier and more precise through estimated breeding values (EBVs). The choice of breeding method
is perhaps the most important decision to be made when designing a breeding programme, Key issues include:
● What are the level of performance and the potential of genetic improvement selection within the
indigenous breed?
● What alternative breeds are available for crossbreeding and what levels of performance and
adaptability to the environment could be expected from 1st and 2nd generation crosses? How important
are effects of heterosis for the traits of major interest?
● What are the opportunities for keeping purebred stock of two or more breeds being available for
maintaining a long term cross breeding programme?
● In the long run, what are the costs and benefits of crossbreeding compared to within breed selection
aimed at improving the same set of traits?
● Is the formation of a synthetic breed a viable alternative to both pure breeding and crossbreeding with
other breeds?
It is important in the selection process that the selection criterion is clear, and whether the selection is efficient
in relation to the breeding objective.
Dissemination of genetic superiority
In most species, the breeding population and the production population are (partly) separated. Genetic progress
is created in the breeding population, but the final aim is to improve livestock production in the entire
population. Thus genetic improvement created in the breeding population has to be disseminated into the
production population.
In dairy cattle, the breeding and production populations are not strictly separated. Superior cows from the
production population can enter the breeding population, meaning that they are selected as bull dams. Genetic

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progress created in the breeding programme is transferred to the dairy farms by the sale of semen of progeny
tested bulls to the farmers. The sale of semen is the primary source of income for dairy cattle breeding
companies. In addition, a limited number of embryos from the breeding population are sold to the dairy
farmers.
The situation is different in pig and poultry breeding. Pig and poultry production are based on crossbreeding
systems. The breeding populations consist of purebred lines, which are mated together to produce crossbred
offspring. Crossbred offspring are sold to fattening farms or egg producers. The breeding and production
populations are therefore completely separated: crossbred production animals cannot enter the purebred
breeding populations. Dissemination of genetic superiority of the purebred breeding populations takes place
by the sale of crossbred offspring.
Design/structure of breeding programmes
Genetic superiority should be transferred as soon as possible to most of the commercial farms. We often talk
about the design of a breeding programme', suggesting that breeding programmes can be characterized by
some kind of structure. The structure of a breeding
programme is relevant for two aspects of an improvement scheme:
1. The genetic improvement aspect: how do we determine the genetically superior animals?
2. The dissemination aspect: how do we manage that those superior animals disseminate their genes
quickly?
A breeding programme may be one tier (Figure 9.1), two tier (Figure 9.2) or three tier (Figure 9.3). The
traditional model is the pyramid with a small group of breeding animals that are actually improved (the 'elite
breeders' in the nucleus) and underlying levels of (possibly) a multiplier and a commercial. The latter groups
may not be involved in selection, but merely, they receive genes from the nucleus and are therefore improved
over time. The genetic gain of lower tiers is somewhat lower than that of the nucleus, but the rate of
improvement is in principle equal.

Breeding males Breeding females

Select and replace Select and replace

Male progeny Female progeny

Figure 9.1 Diagrammatic representation of one tier breeding programme.

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 genetic improvement

nucleus
measurement
Genetic
gap
dissemination
Commercial producers

Figure 9.2 Diagrammatic representation of two tier breeding programme.

genetic improvement
Nucleus
measurement
Genetic
gap
Multipliers dissemination

Genetic
gap Commercial producers
dissemination

Figure 9.3 Diagrammatic representation of three tier breeding programme.

The structure of breeding programmes depends on both the species and the breeding goal. The optimum design
of a breeding programme will differ between species with large reproductive capacity and species with small
reproductive capacity, between breeding programmes that aim to improve production or reproduction traits,
and low heritable traits versus high heritable traits
Evaluation of breeding programmes
Once a breeding programme is operational it is essential to routinely evaluate the results. Evaluation may
consist of comparing realized genetic improvement and rates of inbreeding with values expected when
designing the breeding programme. When there are clear differences between expected and realized selection
response and inbreeding, then one needs to find the causes of those discrepancies and if possible improve the
breeding programme.
Reasons that breeding programmes do not yield the expected genetic improvement are:
i. the use of inappropriate models for breeding value estimation, for example when the models do not
include systematic environmental effects that are present in the data,
ii. overestimation of the genetic parameters,
iii. preferential treatment among selection candidates resulting in selection of individuals that received
"good treatment" instead of genetically superior individuals, and
iv. Unexpected correlated response in other traits.

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A breeding programme needs to be integrated and its success is largely determined by the scope of farmer
participation. The scope of any breeding programme must be set in relation to the resources available and the
stage of development in the region concerned. It must be kept simple and reliable, at least initially, rather than
sophisticated and vulnerable to several prerequisites that cannot be guaranteed. The design may, therefore,
vary considerably depending on the actual breed, production system and other circumstances. Whatever the
case, the principle of 'KISS (keep it simple to be sustainable) should be emphasized in the startup phase of the
breeding programme.
Limiting Factors in a Breeding Programme
Reproductive rate of breeding animals and uncertainty about true genetic merit of breeding animals make up
the most important limiting factors in a breeding programme. How many and which animals should be selected
is determined by these factors. Most of the main factors that determine genetic gain are directly influenced by
the reproductive rate of the breeding animals,
Limiting factors breeding programme (Lecture)
i) Reproductive rate of breeding animals
ii) Uncertainty about true genetic merit of breeding animals

Reproductive rate and improvement is highly correlated. Definitely you cannot sayit is improved because
you can’t see genotype.
Some Considerations When Designing a Breeding Programme
The effects of selection accumulate over time. The economic benefits of selection also accumulate. Many
important circumstances determine the opportunities for and constraints to the breeding programme.
Agricultural and land use policies, market information and access environmental conditions, characteristics of
animal populations, and infrastructure available are examples of such factors. Basic questions concerning the
choice of an overall breeding strategy include the emphasis on improving indigenous breeds versus the use of
tropical breeds from other areas or 'exotic' breeds. This section highlights some of these key elements which
need to be considered before the final design of a breeding programme at breed level.

Some consideration for breeding programme: (Lecture)

• Agricultural development policy: According to policy we have to breedingdesign. Everything will
be preplanned balancing with policy no more or no less.
• Environment, production system culture and market: Production system varyaccording to locality
or country culture. Without adjustment people will not accept the product. Production will be
according to market demand.
• Infrastructure and role of the farmer
• Matching genotype with the environment
• Balancing rate of genetic gain diversity and environmental effect: Balancewith genetic gain and
diversity.

The agricultural development policy

Animal breeding programmes should be seen in the context of national agricultural policies, aiming at
improving the food and income of a country, region or locality, and of livestock keepers. The long term vision
of the national interests and the breeding objectives must coincide.

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Environment, production system, culture and the market
Any breeding programme is totally dependent on environmental conditions, the production system, the culture
of the people for whom the animals are bred, and the market to which the animals and animal products are
sold Village breeding programmes for smallholder farmers will be different from those of large scale farming
systems. Intensive crop livestock systems, with good feed and health care facilities available, enable more
opportunities for rapid improvement programmes than harsh rangeland systems do. The breeding programme
must be market oriented, i,e., demand driven, yet considering the multipurpose use of the animals and the long
term benefits to the farmer. To develop a programme that considers both the present circumstances and
possible future situations, including market conditions, is a challenging task. This is because there is a
considerable time lag between implementation of the programme and when the benefits of genetic gains are
realized. Therefore, breeding programmes should be somewhat flexible and responsive to variable scenarios
for the future needs of the programmes.
Infrastructure and role of farmers
Infrastructure includes a broad range of essential inputs, which must be available for the breeding programme
to succeed. These include trained staff, facilities for breeding animals and logistics for dissemination of
germplasm, methods and means for recording, handling of data and evaluation of animals, decision making
bodies, finances, etc. Lack of required infrastructure is one of the most serious constraints to developing
indigenous breeds in tropical countries.
Breeding programmes usually assume some kind of cooperation between the participants. The initial
developments of breeding programmes are generally made by the government in collaboration with bilateral
organizations in most developing countries because of the national benefits of improving livestock for food
production and other purposes. In that way, basic investments and structures can be put in place. However,
experience shows that it is extremely important that farmers get involved early in the process to ensure that
their needs are taken into account and that they provide the support needed for the programme to work.
Matching genotypes with the environment
To improve any breed or population, one must clearly understand both the inherent genetic constitution of the
population and how this interacts with the environment. It is only then that meaningful genetic improvement
programmes can be developed. Given that not all components of the environment can be changed, particularly
in low input tropical production systems, one needs to know which genotypes can be used under such
environmental conditions, i.e., different types of production environments need different types of animals.
Balancing rate of genetic gain, diversity and environmental impact
A number of conflicts, e,g; between the desires to achieve both accurate breeding values and high selection
intensity, will occur when designing a breeding programme. Consequently, various issues must be considered
to optimize the programme. The scheme giving the theoretically highest genetic gain may also not always be
the best. For example, applying the highest selection intensity might be biologically possible and will in the
short run lead to large genetic improvements.
In the longer run, however, problems with inbreeding may be encountered due to the faster narrowing genetic
base. It is also well accepted that progeny testing provides excellent opportunities to achieve high accuracy in
estimation of breeding values, but the test resources required leave little room in smaller populations for use
of the reliably tested selected animals. Selection based on progeny testing also prolongs the generation
intervals, contributing to reduced genetic progress.
In intensive production systems large inputs, e.g., of feed resources and health care, may for a time provide
the largest genetic improvements and favour certain genotypes. Later, shortages of resources may not allow
the expected gains to be realized. Therefore, the design of a breeding programme must accommodate a whole
range of complex considerations to provide an optimum solution for the genetic resource utilization. Designing
a sustainable breeding programme means finding the best compromise among all factors that determine the
success of the programme.

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Genetic Lag
The swine breeding herd is often thought of as a pyramid. The top tier of the pyramid represents nucleus
animals. The multiplier tier cross the nucleus lines for production of parent gilts and boars to be used on
commercial farms. The commercial tier then crosses the parent boar and get lines from the multiplier tier to
produce the market hogs that are slaughtered. The time it takes for any genetic improvement made in the top
tier of the pyramid to trickle down to commercial market hogs is called genetic lag.
Genetic lag will be different in each production system and can easily range from 4 to 10 years. This means
that the genetic level of performance of market hogs today was selected in the nucleus lines 4 to 10 years ago
and the improvements being made in the nucleus herds today will not be observed in market hogs until 4 to
10 years from now. If the genetic lag is reduced it means that the pork producer will see the genetic
improvements in the market hogs performance sooner.
Genetic lag is determined by several of the following variables:
1. The rate of genetic progress taking place in the nucleus herd.
2. The genetic superiority of the nucleus boars and gilts transferred to multiplier herds.
3. The length of the generation interval at each level of the pyramid.
4. The number of steps in the breeding system including the multiplier and commercial herds.

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 CHAPTER 10
Conservation of Genetic Resources
The Convention on Biological Diversity defines genetic resources as "genetic material of actual or potential
value." Whereas, genetic material is defined as "any material of plant, animal, microbial or other origin
containing functional units of heredity. Animal Genetic Resources (AnGR) include the genetic resources of
those animal species that are used, or may be used, for the production of food and agriculture, and the
populations within each of them. Farm Animal Genetic Resources (FAnGR) include all animal species,
breeds andstrains (and their wild relatives) that are of economic, scientific and cultural interest to humankind
in terms of food and agricultural production for the present or in the future. There are more than 40 species of
animals that have been domesticated or semi domesticated during the past 10 to 12 thousand years that
contribute directly or indirectly to agricultural production. Livestock have been undergoing constant genetic
change since first domesticated. In contrast to many plant species, there is only a very limited genetic resource-
base in wild populations of animal species that is of interest for farm animal breeding. With the introduction
of industrial farm production bio-diversity is vanishing at rapid rate; every year about 34,000 plant and 5,200
animal species disappear, a rate 50-100 times higher than the losses expected through natural processes. About
1,000 of the 7,616 recognized livestock and poultry breeds extinct in the last 100 years, and 300 of these alone
during the last 15 years. Another 2,000 breeds are at stake if no countermeasures for their conservation are
taken.
Conservation of genetic resources involves any activity that helps to store/maintain the genetic variations of
as many of the world's species as possible. The idea of conserving animal genetic resources focuses on two
separate but interlinked concepts.
(i) The first is the conservation of genes
(ii) the second, the conservation of breeds or populations.
The conservation of 'genes' refers to action to ensure the survival of individual genetically controlled
characteristics inherent within a population or group of populations. It could, for example, be
trypanotolerance, polledness, wool shedding, or a specific milk protein. Such programs require that the
characteristic to be conserved is clearly recognized and identified. Such a characteristic may in fact be a
complicated biochemical function controlled by several sections of DNA on more than one chromosome, but
provided the characteristic can be identified in the appearance or function of the animals that exhibit it, a
program can be developed to conserve it as a gene within the population. Genes can be conserved in crossbred
populations, in gene pools or new composite breeds, as well as in existing breeds.
The conservation of populations or breeds refers to action to ensure the survival of a population of animals as
defined by the range of genetically controlled characteristics that it exhibits. This form of conservation is
applied to endangered species as well as to breeds, and is developed to ensure the conservation of all the
characteristics inherent with a given population, including many which may not have been recognized,
defined, identified or monitored. The differences between breeds may often be due to differences in the
frequency of quantitative genes rather than the presence or absence of unique genes. Such a difference in gene
frequency may result in dramatically different populations with respect to appearance and production in a
given environment. Breeds, one lost, can never be truly reconstituted.
The pressure of selection has resulted in thousands of different mammalian species, each with its own genetic
make-up and each adapted to its own environment. Extinction of species is part of the natural process of
evolution and is irreversible, but is now occurring at a much higher rate than speciation because of human
activities, such as habitat destruction, over-hunting, or competition with introduced herbivores. For some
domestic species, extinction has been rather due to intensive selection of a few breeds imposed by management
techniques and market demands. The aim of animal conservation is to maintain biodiversity because the
removal of a single species can affect the functioning of entire ecosystems.
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Genetic material: Without minimum number of virus, bacteria and all other organisms and some

RNA.

Genetic resource: Genetic material of actual or potential value is genetic resource.

Conservation: is the protection and management of species and habitat.

*Genetic improvement will hamper conservation because genetic frequency is changed.

“The term biodiversity is commonly used to describe the number of variety and variability of living
organisms that can be found in the world/ecosystem/habitat. If variety reduce then biodiversity will be
hampered.”(Lecture)

Components of biodiversity: (Lecture)

• Species diversity: How many types of species there are
• Genetic diversity : How many types of alleles for particular species
• Ecosystem diversity: Different types of ecosystem in a particular area

The Reasons Justification/cause for conservation:

The reasons for conservation of AnGR fall in the following categories:
1. Economic and biological reasons;
2. Historical, social and cultural reasons;
3. Environmental reasons;
4. Risk reduction; and
5. Scientific reasons.

Economic and biological reasons:

Domestic animal diversity should be conserved for their potential economic use in allowing response to
changes in the ecosystem, in market demands and associated regulations, by changes in the availability of
external inputs, by emerging disease challenges, or by a combination of these factors. Genetic variation both
within and between breeds is the raw material with which the animal breeder works. Therefore, any loss of
genetic variation will limit our capacity to respond to changes in economic forces for the exploitation of animal
production in future. Breeds with specific qualities like disease resistance, heat tolerance, ability to survive
and produce under stress and low input conditions need to be preserved for future use. Future requirements of
type and quality of animal produce (milk, draught power) may change and this requires conservation of
animals with better performance in specific production traits. Magnitude of heterosis depends upon the breeds
crossed. For exploiting the heterosis in animal production, it is necessary to maintain breeds which are
complementary to each other and on crossing resulting maximum heterosis. If only a few breeds are kept the
opportunity to develop good crosses is lost. Selection plateau occurs when genetic variation is lost. If genetic
variation exists in other breeds, crosses can be made to overcome this.

Historical, social and cultural reasons:

Domestic animal diversity has an important historical, social and cultural role. Loss of typical breeds, therefore
means a loss of cultural identity for the communities concerned, and the loss of part of the heritage of
humanity. Conservation of historically important, culturally interesting and visually unusual and attractive
populations is very important for education, tourism, etc. Further, conservation of breeds can be a valuable
material of nature and culture. There are also many breeds which may be conserved for their aesthetic value.

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These might include the strain of performing Lippizan horses in Austria, the multihorned and spotted Jacob
sheep of Britain, the cork-screw horned Racka sheep of Hungary or many of the ornamental poultry breeds.

Environmental reason:
Domestic animal diversity is an integral part of the environment in a variety of production systems. The loss
of this diversity would contribute to greater instability and risk, decreased ability to respond to changes of the
environment. Maintenance and development of adapted breeds are of critical importance to ensure that food
security can be achieved sustainably without adverse environmental impact.

Risk reduction:
Genetic diversity is and always will be the fundamental resource for future needs. The only thing certain about
the future is that it will not be exactly as expected. The development of global breeding systems gave
uniformities and loss of genes -genes that may be needed in a future of extreme climate change. Climate
change actually requires increasing diversity for adaptation to changing production conditions and consumer
demands. Ensuring a diversity of farm animal genetic resources is thus an important basis for safeguarding
future food security. We do not know what type of animals will be required in the future, and that we should
therefore conserve a broad biodiversity as an insurance against the unknown future. Genetic diversity is
required in order to secure future food production when new diseases or climate changes appear. A variety of
plants, farm animals and forest trees are the base for all food and agricultural production on earth. Biological
diversity is a key factor for both mitigation and adaptation in a changing climate.

Scientific reasons:
Domestic animal diversity should be conserved for their possible scientific use. This may include the use of
conservation stocks as control populations, in order to monitor and identify advances and changes in the
genetic make-up and production characteristics of selected stocks. They may include basic biological research
in genetics, nutrition, immunology, physiology, biochemistry, diet, reproduction or climatic tolerance, etc., at
the physiological and genetic level. Genetically distinct breeds are needed for research into disease resistance
and susceptibility which could help in the development of better medication or management of disease. It
could also help with the identification of specific genes involved in natural disease or parasite control. Some
populations may also be used as research models in other species, including man. Breeds with unique
physiological or other traits are of great value as they provide missing links in the genetic history of a livestock
species by the study of blood groups or polymorphic traits. Conservation of breeds with unique traits will be
essential for long term research in genetic engineering. Varieties of populations are an asset for research work
in biological evolution, behavioral studies, etc. Diverse populations form an excellent research and teaching
material for students of animal science, ecology, ethology, history, ethnography, etc.

Conservation Methods:
There are two major ways for the conservation of genetic resources: in situ and ex situ.

In situ or on-farm conservation:

In situ conservation is the maintenance of live populations of animals in their original habitats i.e., within the
environment or production systems in which they were developed. For domestic species the conservation of
live animals is normally taken to be synonymous with in situ conservation. This is primarily the active
breeding of animal populations for food and agricultural production such that diversity is best utilized in the
short term and maintained for the longer term. Operations pertaining to in situ conservation include
performance recording schemes, development of breeding programs, ecosystem management, and
management of genetic diversity within populations. In situ conservation requires continued use of a breed by
livestock keepers in the agro-ecosystem in which the breed evolved or is now normally found. This includes
both actual farms and pastoral production systems. Continued management of breeding animals maximizes
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opportunities for utilization and the study of breeds, as well as supporting the maintenance of community
identity and stability.
In situ conservation is considered the most appropriate way of conserving biodiversity. Conserving the
areas where populations of species exist naturally i.e., habitat preservation is virtually, the best way to conserve
biodiversity. That's why protected areas form a central element of any national strategy to conserve
biodiversity. The best strategy is in situ preservation but this may not be a viable option for many rare species
that have extremely small populations or occur outside protected areas.

Ex situ Conservation
Ex situ conservation involves the conservation of plants or animal genetic resources outside their natural
habitats. No large wild terrestrial animal will persist long into the future unless cared for in some way by
man. There will be insufficient habitat for most large species and protected habitats will be in pieces too small
or too unstable to sustain viable populations of the plants and animals they seek to protect. For these and other
reasons conservation biologists will be forced to depend more and more on ex situ care and biotechnology to
help protect diversity at both species and genetic levels. It can be divided into ex situ - in vivo and ex situ- in
vitro conservation.

Ex situ - in vivo conservation (Live, Zoo)

This is simply ex situ conservation, with storage of germplasm as live animals. It may refer to captive breeding
of wild plants or animals in zoos, research institutions, farm parks, etc. or other situations far removed from
their indigenous environment. As for in situ conservation, it is accepted that improvement and natural selection
outside the original environment may alter gene frequencies in the gene pool.

Ex situ - in vitro conservation (Lab, Genetic info)

The first involves the conservation of animal genetic material in the form of living ova, embryos, semen or
somatic cells stored cryogenically in liquid nitrogen that have the potential to reconstitute live animals. The
second is the preservation of genetic information as DNA, stored in frozen samples of blood or other animal
tissue or as DNA segments.
Ex situ conservation provides excellent research opportunities on the components of biological diversity.
Some of these institutions also play a central role in public education and awareness raising by bringing
members of the public into contact with plants and animals they may not normally come in contact with. It is
estimated that worldwide, over 600 million people visit zoos every year.
The specific objective or objectives for conserving a given AnGR will influence the strategy employed in its
conservation. The exact strategy will clearly depend on the conservation objectives. In situ and ex situ
strategies differ in their capacity to achieve the different conservation objectives. In situ conservation is often
regarded as the preferred method because it ensures that a breed is maintained in a dynamic state. This may
be true when the 'dynamics' of a breed are characterized by slow and balanced adaptation to conditions.
However, commercially important breeds are often subject to high selection pressure and larger than desired
levels of inbreeding (a few top sires fathering many offspring), whereas commercially less-important breeds
often have a small population number and are threatened by genetic drift and extinction. Conserving genetic
diversity by keeping live animals outside their production or natural environment (ex situ in vivo) will not
always be able to guarantee the maintenance of the genetic diversity of a breed. Therefore, in vivo conservation
should be complemented by cryopreservation of germplasm. In other words, long term in situ conservation
programs may benefit from a germplasm repository.

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Methods of conservation: (Lecture)
In sito/ on farm conservation: animal maintain in original habitat Eg. Red Chittagong cattle maintain at
Chittagong.
Ex sito/offside conservation: Outside of their natural habitat Eg. Red Chittagong cattle maintain other region
except Chittagong.
Two types:
In vivo conservation: Conserve live animal outside of their natural habitat.
In vitro conservation: gamete, embryo (not live), genetic material
→Cryogenetically conserved in liquid nitrogen for unlimited period.

Complementary Roles of In situ and Ex situ Conservation

Ex situ conservation measures can be complementary to in situ methods as they provide an “insurance policy"
against extinction. These measures also have a valuable role to play in recovery programs for endangered
species. In situ and ex situ conservations are complementary, not mutually exclusive. Ex situ populations can
be released periodically in the wild to augment in situ conservation efforts. Frozen animal genetic resources
or captive live zoo populations can play an important role in the support of in situ programs.

Basic Limitations of Ex situ Conservation

Ex situ conservation efforts have certain basic limitations when compared with in situ conservation. Ex situ
conservation requires, appropriate infrastructure, organization, technical capacity, agreed priorities, sustained
funding and legal arrangements. Legal arrangements could include clarification of ownership, access rules
and if and how benefits should be shared, especially where regional or international cooperation is pursued.
Population size and genetic variability usually be much smaller in ex situ conservation than is needed to
prevent genetic drift. Ex situ populations adapt to captive environment and may not function well in situ. If
ex situ site is destroyed by catastrophe (fire, hurricane, or epidemic), there is a possibility that an entire
population of an endangered species could be destroyed.
Point In situ Conservation Ex situ Conservation
Definition Maintenance of living populations of Conservation of plants or animal genetic
animals in their original habitats. resources outside their natural habits.
Appropriation Best way to conserving bio diversity. Not
Infrastructure Not Requires appropriate infrastructure organization,
technical capacity, legal arrangement etc.
Level Only species level. Protect diversity at both species and genetic level
Rare species Not suitable for conserving rare species Suitable
or outside protected area.
Division Haven’t such division. It is divided into ex situ in vivo & ex situ in vitro.

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