Animal Breeding

GEB 206

Md. Faruk Hasan

Dept. of Genetic Engineering and Biotechnology,
University of Rajshahi

03.03.2020
Introduction of Animal Breeding
What is an animal?
The definition of an animal is a member
of the biological kingdom Animalia, and
is typically characterized by a
multicellular body, specialized sense
organs, voluntary movement,
responses to factors in the environment
and the ability to acquire and digest
food. A horse, lion and human are each
an example of an animal.

With few exceptions, animals consume

organic material, breathe oxygen, are
able to move, can reproduce sexually,
and grow from a hollow sphere of cells,
the blastula, during embryonic
development.
 What is Breed?
 A breed is a specific group of
domestic animals having
homogeneous appearance
(phenotype), homogeneous
behavior, and/or other
characteristics that distinguish it
from other organisms of the same
species.
 Breeds are formed through
genetic isolation and either
natural adaptation to the
environment or selective
breeding, or a combination of the
two.
 Despite the centrality of the idea
of "breeds" to animal husbandry
and agriculture, no single,
scientifically accepted definition
of the term exists.
 A breed is therefore not an
objective or biologically verifiable
classification but is instead a
term of art amongst groups of
breeders who share a consensus
around what qualities make some Fig.: This example shows four different breeds of the
members of a given species domestic cattle, which all vary widely in appearance .
members of a nameable subset.
 Breed characteristics
Breed specific characteristics, also known as breed traits, are
inherited, and purebred animals pass such traits from
generation to generation.
Thus, all specimens of the same breed carry several genetic
characteristics of the original foundation animal(s).
In order to maintain the breed, a breeder would select those
animals with the most desirable traits to achieve further
maintenance and developing of such traits.
At the same time, the breed would avoid animals carrying
characteristics undesirable or not typical for the breed,
including faults or genetic defects.
The population within the same breed should consist of a
sufficient number of animals to maintain the breed within the
specified parameters without the necessity of forced
inbreeding.
Domestic animal breeds commonly differ from country to
country, and from nation to nation.
Breeds originating in a certain country are known as "native
breeds" of that country.
 List of Breeds
Mammals Bugs Birds
Cat Breeds

Apis
 
Chicken Breeds
Cattle Breeds

Mellifera 
Duck Breeds
Dog Breeds
 Subspecies 
Goose Breeds
Police Dog Breeds


Pigeon Breeds
Water Buffalo Breeds


Domestic Pig Breeds



Turkey Breeds
Donkey Breeds


Goat Breeds


Guinea Pig Breeds



Horse Breeds


Rabbit Breeds


Fancy Rat Varieties



Laboratory Rat Strains



Sheep Breeds

 Animal Breeding
Animal breeding is a branch of animal science that
addresses the evaluation (using best linear unbiased
prediction and other methods) of the genetic value
(estimated breeding value, EBV) of livestock.
Selecting for breeding animals with superior EBV in growth
rate, egg, meat, milk, or wool production, or with other
desirable traits has revolutionized livestock production
throughout the entire world.
The scientific theory of animal breeding incorporates
population genetics, quantitative genetics, statistics, and
recently molecular genetics and is based on the pioneering
work of Sewall Wright, Jay Lush, and Charles Henderson.
Why is animal breeding important?
Animals and livestock contribute 40 percent of the global value of
agricultural output and contribute to the livelihoods and food
security of almost a billion people worldwide. Advances in animal
breeding, genetics, and genomics are facilitating a more efficient
industry.

Who is the father of animal breeding?

It was home to Jay L. Lush (1896 – 1982), who is known as the
modern father of animal breeding. He advocated that instead of
subjective appearance, animal breeding should be based on a
combination of quantitative statistics and genetic information.

What are the objectives of animal breeding?

• The improved growth rate.
• Increased production of milk, meat, egg, wool, etc.
• Superior quality of milk, meat, eggs, wool, etc.
• Improved resistance to various diseases.
• Increased productive life.
• Increased or, at least, acceptable reproduction rate.
Classification of Breeding Systems
Under the selected breeding system selected males and females are
mated. The breeding system can be classified into five different ways
depending on their phenotypic and genotypic relations.
The five breeding systems are:
1. Random mating or Panmixia: It is a system of mating in which each male
individual has an equal opportunity to mate with the female individual and
vice versa. This mating system generally takes place in nature where the
number of males and females are assumed to be equal.
2. Phenotypic assortive mating: In this type of mating animals which are
phenotypically alike are allowed to mate among themselves. This is also
called “like to like” mating.
3. Phenotypic disassortive mating: Here individuals which are
phenotypically unlike are allowed to mate. It is also called “unlike to unlike”
mating. For example, mating of tall with short individuals.
4. Genetic assortive mating: In this system individuals, which are closely
related genetically are allowed to mate. This is also known as inbreeding.
5. Genetic disassortive mating: This system is just opposite to the previous
system where mating takes place between less closely related individuals.
This is also called as out breeding.
Domestication of animals

Dogs and sheep were among the first animals to be domesticated.

The domestication of animals is the mutual relationship between

animals and the humans who have influence on their care and
reproduction. Charles Darwin recognized a small number of traits that
made domesticated species different from their wild ancestors.
Domestication traits are generally fixed within all domesticates, and
were selected during the initial episode of domestication of that animal
or plant, whereas improvement traits are present only in a proportion of
domesticates, though they may be fixed in individual breeds or regional
populations
Development and applications of animal breeds

Use of genomic information in animal improvement

The use of genomic information (sequences or DNA marker polymorphisms)
for the genetic improvement and selection of animals requires the knowledge
of the effect of physically mapped genes with effects on economically
important traits or quantitative trait loci (QTL).
Problems related to false positive detection of candidate genes are also
common. Using crosses between two pig breeds, a polymorphism on the
estrogen receptor locus (ESR) was associated to litter size in pigs with 1.5
piglet advantage for homozygous sows for the beneficial allele, and where
followed by immediate recommendations for commercial use and patenting.
Further research however did not confirm the effect. Different phases of
linkage between the markers and the QTL could explain the fact that the
effect of the ESR locus varied widely between populations. Thus, very
probably, despite the ESR gene is probably a plausible 'candidate' from their
inferred physiological functions, the gene involved seems to be another one,
still unknown, or the effect initially observed was the product of several,
interacting genes.
Problems in animal improvement
Main problems related to the use of molecular genetics in the improvement of
agricultural populations are:
1. Direct use of a discovered QTL effect for selection across families is not possible.
2. By the time the information about the inferred genotypes is known, frequently the
animals involved in the study are not available as candidates for selection, because
they will be too old.
3. Advantage from within-family selection for a QTL bracketed by markers over
BLUP or phenotypic selection alone is frequently low and the methodology to exploit
this information for selection is complex and relatively inefficient.
4. There are statistical estimation errors, causing both false positive and false
negative effects, particularly when the effect of the QTL is small.
5. There is a lack of consistency of the effect of the same QTL between studies,
caused by QTL by genetic background of QTL by environment interactions.
6. The net economic effect of the QTL may be lower than the effect on single traits,
because unfavourable effects on other traits.
7. Selection using QTL is more complex than phenotypic selection alone. QTL
information (whether the information on the QTL is direct or indirect), adds to the list
of traits used as selection criteria. Issues such as reduction of selection intensities
and relative emphasis given to each trait, make optimal selection more difficult, with
a need for adequate relative weights for the QTL, and the polygenic portions of the
genetic variation for each trait at each generation (year).
8. Short-term gains due to MAS may be at the expense of medium to long-term
polygenic responses for important traits.
Animal improvement
Improvement of health in animals by reducing disease prevalence or increasing
resilience, for infectious or parasitic diseases has been difficult. In most cases,
excepting some rare examples such as Scrapie in sheep, complete resistance could
not be obtained with the manipulation of a small number of genes. For most diseases,
single-gene approaches are expected to have only a partial contribution.
For many diseases, heritabilities are often low. That indicates the existence of many
environmental factors affecting both the probability of infection and the response of
the host. In spite of responses attained using conventional selection for some traits
that are used as indicators of disease, the result is not well known. The existence of
contradictory results regarding associations between production and disease
resistance, the complexities of immune and resistance mechanisms and the
interaction with other methods of control such as vaccination, sanitation,
management and chemotherapy, makes the whole issue of selecting for disease
resistance more difficult, in principle, that selecting for production traits. Moreover, we
know that heritable resistance or resilience to more virulent form of pathogens would
be increased by natural selection. As heritabilities for survival are generally low, we
know that the genetic control of disease may be very complex, making difficult to
change the outcome by manipulating single genes.
Other very important applications of genetic markers in animal improvement include
the optimization of mating strategies for non-additive genetic effects, parentage
determination, genetic characterization of diverse animal breeds and populations
using studies of between and within population (breeds) diversity and marker-assisted
introgression of particular alleles.
Use of cloning in animal breeding and improvement
Use of cloning in animal genetic improvement may increase the rates of
selection progress in certain cases, particularly in situations where artificial
insemination is not possible, such as in pastoral systems with ruminants.
Currently, high costs of cloning are one of the main factors limiting their use as
a technique in practical animal breeding. Clonal groups, however more uniform
than full sibs, will have all differences caused by the environmental fraction of
variation for measured traits, which is usually more than 50% of total variation.
Selection among many cloned germlines allows the use of the non-additive
genetic effects. These effects are not exploited when traditional selection
methods involving sexual reproduction are used in animal improvement, but
most of the observed genetic variation between animals is additive. Advantages
in terms of additional genetic progress however, seems to be only marginal
from clone evaluation in selection nucleus herds. Production based on clones of
the best animals of the population, may allow for a one time large 'jump' in
breeding value, so the commercial animals might be very close to those in the
nucleus. However, further genetic improvement must be based in the continued
use of the genetic variation by selection programs.
Use of transgenesis in the improvement of production traits
The technology of transgenesis is potentially useful to modify characters of
economic importance in a rapid and precise way. Contrary to the 'classical' selection
programs, it is necessary a knowledge of the genes that control these characters
and their regulation.
Following is a brief discussion of experiences with transgenesis to alter
economically important traits in livestock.
Growth and meat traits
In most of the earlier work in domestic species (pig, sheep, rabbit) growth hormone
was enhanced by the metallotionein promoter to control its expression. Subsequent
efforts to genetically alter growth rates and patterns have included production of
transgenic swine and cattle expressing a foreign c-ski oncogene, which targets
skeletal muscle, and studies of growth in lines of mice and sheep that separately
express transgenes encoding growth hormone-releasing factor (GRF) or insulin-like
growth factor I (IGF-I). Transgenic pigs and sheep with high levels of serum growth
hormone were obtained, but an increment of its rate of growth was not observed,
and only in some lines average daily gain increased with the supplement of the diet
with high levels of protein. The highest effects were observed in the reduction of
body fat. A large number of different serious pathologies and a severe reduction in
reproductive capacity were described in these animals. There is evidence for the
use of transgenesis allowing to important reductions in body fat and increased
diameter of muscle fiber by increased IGF-I levels and growth hormone without
serious pathological side effects. Australian regulations avoided the commercial
release of these animals.
Use of transgenesis in the improvement of production traits
Wool production
The objectives are to improve production of sheep wool and to modify the properties
of the fiber. Because cystein seems to be the limiting amino acid for wool synthesis,
the first approach was to increase its production through transfer of cystein
biosynthesis from bacterial genes to sheep genome. This approach did not achieve
the efficient expression of these enzymes in the rumen of transgenic sheep.

Milk Composition
Milk proteins are coded by unique copy genes that can be altered to modify milk
composition and properties. Among the different applications of milk modification in
transgenic animals, the following can be highlighted:
1. To modify bovine milk to make it more appropriate to the consumption of infants.
Human milk lacks β-lactoglobulin, has a higher relationship of serum proteins to
caseins, and has a higher content in lactoferrin and lysozyme when compared to
bovine milk. Lactoferrin is responsible for the iron transport and inhibits the bacterial
growth. To introduce the human lactoferrin into the bovine milk, transgenic cows
have been obtained. The elimination of the β-lactoglobulin in the cow milk would be
another interesting objective because is one of the major allergens of cow's milk.
Use of transgenesis in the improvement of production traits
2. To reduce the content of lactose in the milk to allow their consumption to people
with intolerance to lactose. It is considered that 70% of the world population is
lacking theintestinal lactase, the enzyme required to digest the lactose. The
reduction in lactose may be obtained by expressing β-galactosidase in the milk or
diminishing the content of α-lactalbumin. Transgenic mouse with inactivated α-
lactalbumin gene produce milk without lactose. However, a serious practical
drawback of this method is that this milk is very viscous and it is not secreted to the
exterior of the mammary gland, due to the importance of the lactose in the
osmoregulation of the.
3. To alter the content of caseins of the milk to increase their nutritive value, cheese
yield and processing properties. Research has intended to increase the number of
copies of the gene of the κ-casein, to reduce the size of the micelles and
modificating the κ-casein to make it more susceptible to the digestion with
chymosin. This has only been done using the mouse as a model engineered female
bovine foetal fibroblasts to express additional copies of transgenes encoding two
types of casein: bovine β-casein and κ-casein. The modified cell lines of fibroblasts
were used to create eleven cloned calves. Milk from the cloned animals was
enriched for β- and κ-casein, resulting in a 30% increase in the total milk casein or a
13% increase in total milk protein, demonstrating the potential of this technology to
make modified milk.
4. To express antibacterial substances in the milk, such as proteases to increase
mastitis resistance. The objective is to alter the concentrations of antibacterial
proteins such as lyzozyme or transferrin in the milk.
Use of Population Genetics to Animal Breeding and Livestock
Improvement
“Heritability” is an old word and evolution of its use is discussed by, who includes a
long letter from Lush. He was first to adopt heritability in the narrow quantitative
genetics sense as the ratio of additive genetic to phenotypic variation, and therefore
also the square of Wright’s correlation of (additive) genotypic and phenotypic value,
and to use “accuracy” of a predictor of breeding value to compare alternative
selection schemes. Crucially Lush developed what has become known as the
“breeder’s equation” for predicting response in terms of selection differential, R =
h2S. He writes, “for each unit which the selected parents average above t their
offspring will most probably average about σH2/(σH2+σE2) as far above. This
would be literally true if all genes act additively”. Here σH2 is the total genetic
(genotypic) variance. Variation in production traits in livestock was genetic, the
resource for genetic progress. He showed quantitative genetic applications in animal
breeding on “Factors affecting birth weights of swine”. He saw the need to obtain
estimates of parameters such as the heritability free of confounding by
environmental covariances and proposed using daughter dam within sire regression
to avoid bias by herd effects. He considered practical questions such as the relative
accuracy of selection on a cow’s own performance vs. that of her progeny mean.
Lush developed selection index principles to make best use of the data. In the plant
breeding context, had derived a discriminant function, i.e., a selection index. Rates
of progress should be maximized per year rather than per generation and
considered the tradeoff between the high accuracy of a progeny test and the shorter
generation time by selecting on own performance.
Breed club
Breed clubs are associations or clubs with activities centered on a
single, specific breed of a particular species of domesticated
animal.
The purpose of the association will vary with the species of animal
and the goals and needs of the members of the association.
Breed associations or clubs may vary in their goals, activities and
nomenclature from country to country, even for the same breed.
Most domesticated animals, whether they are agricultural animals
such as cattle, llamas, poultry, sheep and pigs, or companion
animals such as pigeons, horses, cats and dogs, have breed clubs
associated with the breed.
Purpose
In general, breed clubs and associations create a written definition of the breed
(called a breed standard) for the breed with which the organization is
associated. Breed clubs also maintain important records, and provide
members with information. Many breed associations also have a social
component, organising various activities such as shows. In addition, they may
regulate breeding or raise funds for research related to the breed.
Examples
• In horses, the Appaloosa Horse Club, established in 1938, maintains a registry for
Appaloosa horses, and has the goal of "preserving the horses’ heritage and history" and
defining the horse breed through bloodline requirements.
• The Canadian Lowline Cattle Association defines its objectives as including "maintain
the purity and improve the breed" of cattle as well as collecting maintaining breed
information and publishing a Herd Book.
• The Essex Pig Society is building up the numbers of the Essex Pig, formerly thought to
be an extinct breed of the domestic pig.
• The American Buttercup Club defines its goal as connecting fanciers of the chicken
breed so that they are "able to share stock and valuable information about the breed."
• The Fantail Club UK, established in 1889, promotes the knowledge and enjoyment of the
exhibition Fantail Pigeon in the United Kingdom.
• In cats, the Selkirk Rex Breed Club maintains a history of the breed and provides care
and grooming tips to owners of the breed.
• Members of the dog breed club for the English Toy Terrier (Black and Tan) are expected
to "conduct themselves in a responsible and sportsman-like manner at all times."
• The OEGB Int'l Society proudly connects hobbyists of Old English Game Bantams from
all around the world to discuss poultry related topics. In addition, it hosts the only US
based OEGB futurity as an annual event called the MegaSpur.
Forming a breed club
With the advent of the internet, anyone can create a "breed club" by putting up
a web page to advertise their animals. Buyers must research any claims of
unaffiliated breed clubs.

Organizations covering groups of breeds

Breeds of animals of a particular species may have an organization that covers
a large number of breeds of the species, even though each individual breed
may have its own breed club. Often the multiple-breed over-association will
maintain the breed records in a central location. An example of this would be
the Canadian Sheep Breeder's Association, incorporated under the Canadian
Livestock Pedigree Act in 1915, which includes fifty different breeds of sheep.

Other types of animal associations

Associations that include all breeds (as well as crossbred and mixed breed
animals) of a particular species also exist. Usually such associations are
organized for particular sports, such as hunting with raptors.