Animal breeding

Illustration of DNA Double Helix from Wikipedia.

PRINCIPLES OF ANIMAL GENETICS

ASM 391

Natural Resources Development College

Animal Science Department

By

E.Msimuko.


Introduction

• Genetics is the science of heredity and variation

• It is the scientific discipline that deals with the differences and similarities among related individuals

• All animals have a predetermined genotype that they inherit from their parents.

• However, an animal’s genotype can be manipulated by breeding and more advanced scientific techniques (genetic engineering and cloning).


• For many years, managers of agricultural systems have manipulated the genetic makeup of animals to:

• improve productivity,

• increase efficiency

• and adaptability.

• Successful manipulation of the genetic composition of animals requires a depth understanding of fundamental principles of genetics.


Mendelian Genetics

• Gregory Mendel is recognized as the father of genetics

• in the 1850’s and 1860’s, he developed his theories without any knowledge of cell biology or the science of inheritance- he failed his teachers exams

• In later years, genes, chromosomes, and DNA were discovered and people began to understand how and why Mendel’s theories worked.

Photo courtesy of Wikipedia.


• Mendel proposed three principles to describe the transfer of genetic material from one generation to the next.

• The Principle of Dominance

• The Principle of Segregation

• The Principle of Independent Assortment

The Principle of Dominance – in a heterozygous organism, one allele may conceal the presence of another allele. Aa or Pp


The Principle of Segregation – in a heterozygote, two different alleles segregate from each other during the formation of gametes. Aa individual will produce two gametes- A-alleles and a-alleles

The Principle of Independent Assortment – the alleles of different genes segregate, or assort, independently of each other. PpBb x PpBb gives 9:3:3:1

Later studies have shown that there are some important exceptions to Mendel’s Principle of Independent Assortment, but otherwise, these principles are recognized as the basis of inheritance.


Knowledge of which allele has been inherited at one locus gives no information on the allele has been inherited at the other locus

P/p B/b

PB Pb pB pb

25% 25% 25%

25%


• Mendel’s experiments dealt with the relationship between an organism’s genotype and its phenotype.

• Genotype – the genetic composition of an organism.

• Phenotype – the observable or measurable characteristics (called traits) of that organism

• Two organisms may appear to be similar, but they can have different genotypes.

• Similarly, two animals may have the same genotypes, but will appear to be different from each other, if they have been exposed to different environmental conditions throughout their lives.


The relationship between phenotype and genotype is expressed as the following equation:

P = G + E

P = phenotype – observed attributes (Yield, Quality)

G = genotype- A, D, E, and

E = environment- breed, Nut. A.H, Climate, housing and research

If two individuals with identical genotypes are exposed to the same environmental conditions, such as nutrition, climate, and stress levels, their phenotypes (measurable and observable characteristics) should be the same

“What you see is what you get”


• To understand Mendel’s principles and the relationships between phenotype and genotype, it is necessary to understand;

• what makes up the genetic material of animals and

• how this is transferred from one generation to the next.


Genetic Material

The body is made up of millions of cells which have a very complicated structure.

These cells are made up of many parts that have specialized roles.

1. Nucleolus 5. Rough Endoplasmic Reticulum 9. Mitochondria

2. Nucleus 6. Golgi Apparatus 10. Vacuole

3. Ribosome 7. Cytoskeleton 11. Cytoplasm

4. Vesicle 8. Smooth Endoplasmic Reticulum 12. Lysosome

13. Centrioles


The nucleus contains chromosomes that are visible under the microscope as dark-staining, rod-like or rounded bodies.

Chromosomes occur in pairs in the body cells.

The number of chromosomes in each cell is constant for individual species, but it differs among species. Suis-38, caprine-60, carnis 78, galus-78, bovine-60,


Chromosomes are made up of tightly-coiled strands of DNA.

DNA is a complex molecule composed of deoxyribose, phosphoric acid, and four bases.

Individual genes are located in a fixed position (known as the loci) on the strands of DNA.

A chromosome is made up of two chromatids and a centromere. The chromatids are formed from tightly coiled strands of DNA. If these strands of DNA are stretched out, individual genes can be identified.eg DT


A gene is made up of a specific functional sequence of nucleotides, which code for specific proteins.

A specific protein is produced when the appropriate apparatus of the cell (the ribosome) reads the code.

Image courtesy of Wikipedia.



• In somatic cells (body cells), chromosomes occur in pairs, known as homologous chromosomes as a result, genes also occur in pairs except in virus(RNA)

• Somatic cells are referred to as diploid, or 2n.

• Gametes (reproductive cells) are referred to as haploid, or n - do not have paired chromosomes


When discussing different generations in genetics, the first generation is referred to as the parent or P generation.

Their offspring are referred to as the first filial or F1 generation.

P X P = F1

When individuals from the F1generation are mated with each other, their offspring are referred to as the F2 generation.

F1 X F1 =F2


Principle of Dominance

• In animals, chromosomes are paired and, therefore, genes are paired.

• These paired genes code for the same trait, but they are not identical.

• They can have different forms, known as alleles.

• For example, sheep and cattle can be polled or horned.

• One gene codes for this trait and the two possible forms (alleles) of the gene are polled or horned


Hereford Cattle

USDA photo from Wikipedia.

Photo from IMS.

A capital letter is used to denote the dominant form of the gene (P) and a small letter is used to denote the recessive form of the gene (p).

In the example, the polled allele is dominant and is, therefore, denoted by P, while the horned allele is recessive and denoted by p.

Because genes are paired, an animal can have three different combinations of the two alleles: PP, Pp, or pp.


• When both genes in a pair take the same form (PP or pp), the animal is referred to as being homozygous for that trait.

• An animal with a PP genotype is referred to as homozygous dominant.

• An animal with the pp genotype is referred to as homozygous recessive.

If one gene in the pair is the dominant allele (P) and the other gene is the recessive allele (p), the animal is referred to as being heterozygous for that trait and its genotype is denoted as Pp.

• If an animal has the allele combination PP, it will be polled.

• If the combination is pp, the animal will be horned.

• If it is a heterozygote, the animal will have both traits (Pp), but the animal will be polled because the polled allele (P) is the dominant form of the gene. Mendel’s principle of dominance states that in a heterozygote, one allele may conceal the presence of another.


In this example, the polled allele is concealing the horned allele and, therefore, is referred to as the dominant allele.


Principle of Segregation

• When animals reproduce, they only pass on half of their genetic material to their offspring

• The offspring will only receive one allele from each parent.

• The Principle of Segregation explains some of the differences that are observed in successive generations of animals and can be used to predict the probability of different combinations of alleles occurring in offspring.


Considering these three types of individuals, six combinations of the various genotypes are possible:

• PP x PP (both parents are homozygous polled),

• PP x Pp (one homozygous polled parent and one heterozygous polled parent),

• PP x pp (one homozygous polled parent and one homozygous horned parent),

• Pp x Pp (both parents are heterozygous polled),

• Pp x pp (one heterozygous polled parent and one homozygous horned parent), and

• pp x pp (both parents are homozygous horned)


The genotypes of the parents can be used to predict the phenotypes of the offspring

Predicting the Genotypes and Phenotypes of Offspring by:

A punnett square - grid-like method that is used to display and predict the genotypes and phenotypes of offspring from parents with specific alleles.

The male genotype is normally indicated at the top and the female genotype is indicated in the vertical margin.


When crossing homozygous dominant parents (PP x PP), all

offspring will be homozygous dominant polled individuals.

All polled


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


When crossing a heterozygous parent with a homozygous dominant parent (Pp x PP), the expected offspring would occur in a 1:1 ratio of homozygous dominant to heterozygous individuals.

Phenotypically, all offspring would be polled. When crossing a homozygous dominant parent with a homozygous recessive parent (PP x pp), all offspring would be heterozygous and polled.


• If two heterozygous parents are crossed (Pp x Pp), one can expect a genotypic ratio of 1:2:1, with one homozygous dominant polled, two heterozygous polled, and one homozygous recessive horned individuals.

• The expected phenotypic ratio of offspring would be 3:1 (polled to horned).


. Segregation

Alleles separate during meiosis


Considering Multiple Traits-Dihybrid Cross

Commonly, there are multiple traits that need to be considered when mating animals.

For example, consider that cattle can be horned or polled and white-faced or red-faced.

The horns and red-faced coloring are recessive traits.

If two individuals with two pairs of heterozygous genes (each affecting a different trait) are mated, the expected genotypic and phenotypic ratios would be:



Genotypes – 1 PPWW, 2 PPWw, 2 PpWW, 4 PpWw, 1 PPww, 2 Ppww, 1 ppWW, 2 ppWw, and 1 ppww;

Phenotypes – 9 polled, white-faced; 3

polled, red-faced; 3 horned, white-faced; and 1 horned, red-faced offspring.


The Law of Independent Assortment

• When considering multiple traits, Mendel hypothesized that genes for different traits are separated and distributed to gametes independently of one another.

• Therefore, when considering polled and white-faced traits, Mendel assumed that there was no relationship between how they were distributed to the next generation.

In most cases, genes do assort independently.

• However, advances in genetics have shown that an abnormal situation, called crossing-over, can occur between genes for different traits.

• Crossing-over is an exchange of genes by homologous chromosomes during the synapses of meiosis prior to the formation of the sex cells or gametes.


10. Independent Assortment

Bb

diploid (2n)

B

b

meiosis I

B

B

b

b

sperm

haploid (n)

meiosis II

• Chromosomes separate independently of

eachother

Bb

Ff

b

F

B

f

b

f

B

F

Bb

Ff

Bb

Ff

This means all gametes will be different!


Other Concepts in Genetics

• Non-traditional inheritance involves alleles that are not dominant or recessive.

• Incomplete, or partial dominance, & co-dominance are two examples of non-traditional inheritance.

• Recent studies in sheep has indicated another form of inheritance called POLAR DOMINANCE

• Partial, or incomplete, dominance occurs when the heterozygous organism exhibits a trait in-between the dominant trait and the recessive trait.

eg Homozygous mice are black (BB) or white (bb) and the heterozygous mice will be grey (Bb).

When a pure, brown-eyed sheep is crossed with a pure, green-eyed

sheep, blue-eyed offspring are produced.


Codominance

• Codominance occurs when a heterozygote offspring exhibits traits found in both associated homozygous individuals.

• An example of codominance is the feather color of chickens.

• If a homozygous black rooster is mated to a homozygous white hen, the heterozygous offspring would have both black feathers and white feathers

• Roan is a coat color in horses (sometimes dogs and cattle) that is a mixture of base coat colored hairs (ex. black, chestnut) and white hairs. Neither the base coat color or the white hairs are dominant nor do they blend to create an intermediate color.


The roan animal actually has both colored and white hairs.

Photo courtesy of Wikipedia.

• Under these circumstances, neither allele is dominant and neither is recessive.

• Therefore, each allele is denoted by a capital letter.


EPISTASIS

It is possible for more than one gene to control a single trait

This type of interaction between two nonallelic genes is referred to as epistasis.

When two or more genes influence a trait, an allele of one of them may have an epistatic, or overriding, effect on the phenotype.

Comb shape in chickens is an example of an epistatic relationship.


Mutations and Other Chromosomal Abnormalities

Genes have the capability of duplicating themselves, but sometimes a mistake is made in the duplication process resulting in a mutation.

The new gene created by this mutation will cause a change in the code sent by the gene to the protein formation process.

Some mutations cause defects in animals, while others may be beneficial.

Mutations are responsible for variations in coat color, size, shape, behavior, and other traits in several species of animals.

The beneficial mutations are helpful to breeders trying to improve domestic animals.


Changes in chromosomes are reflected in the phenotypes of animals.

Some chromosomal changes will result in abnormalities, while others are lethal and result in the death of an animal shortly after fertilization, during prenatal development, or even after birth.

Changes that can occur in chromosomes during meiosis include:

• Changes in the chromosome number,

• Translocation or deletion – chromosome breakage, and

• Inversion and insertion – the rearrangement of genes on a chromosome.


Sex-Linked Traits

• Sex-linked traits involve genes that are carried only on the X or Y chromosomes, which are involved in determining the sex of animals.

• The female genotype is XX, while the male genotype is XY.

• The X chromosome is larger and longer than the Y chromosome, which means a portion of the X chromosome does not pair with genes on the Y chromosome

• Additionally, a certain portion of the Y chromosome does not link with the X chromosome.

• The traits on this portion of the Y chromosome are transmitted only from fathers to sons.

• Sex-linked traits are often recessive and are covered up in the female mammal by dominant genes.


• The expression of certain genes, which are carried on the regular body chromosomes of animals, is also affected by the sex of the animal.

• The sex of an animal may determine whether a gene is dominant or recessive (Ex. Scurs in polled European cattle).

• In poultry, the male has the genotype XX, while the female has the genotype Xw.

• An example of a sex-linked trait in poultry is the barring of Barred Plymouth Rock chickens. If barred hens are mated to non-barred males, all of the barred chicks from this cross are males, and the non-barred chicks are females.


Sex limited traits


GENETIC OF ANIMAL BREEDING

GENETIC SELECTION

What is the “BEST” Animal?

• Permanent improvements in domestic animals can be made by genetic selection through natural or artificial means.

• Natural selection occurs in wild animals, while artificial selection is planned and controlled by humans.


Animals that exhibit desirable traits are selected and mated.

Animals that exhibit undesirable traits are not allowed to reproduce or are culled

from the herd. Trait- measurable attributes of an individual

presence of horns; Calving easy; Growth; litter size

Phenotype- measurable category/level for a trait in an individua

Horned, polled, assisted, not assisted; WWT, 5,8,1


• The goal of selection is to increase the number of animals with optimal levels of performance, while culling individuals with poorer performance.

• Genetic improvement is a slow process

• Artificial insemination and embryo transfer are breeding methods that are commonly used to decrease the time taken to improve a trait.

• Animals with a best set of genes may have the best Breeding value


• Traits are passed from parents to offspring, but some traits are more heritable than other traits

• Heritability is a measure of the strength of the relationship between BV and phenotype values for a trait in a population

• That is, the genotype of an individual will be expressed more strongly and environment will be less influential for particular traits


Trait Sheep Swine Cattle

Weaning weight 15-25% 15-20% 15-27%

Post-weaning gain

efficiency

20-30% 20-30% 40-50%

Post-weaning rate of gain 50-60% 25-30% 50-55%

Feed efficiency 50% 12% 44%

Fertility 1.0%

Heritability of Various Traits in Livestock

High h2 Phenotypes are good indicators

Low h2 Phenotypes reveals little about BVs


Quantitative and Qualitative Traits

Quantitative traits • Controlled large number of genes, • Economical traits • Exhibit normal distribution and phenotypes

show continuous express- additive gene effect

• Affect genes with large effect Qualitative Traits • Controlled by dominant or recessive genes, • Non additive gene and non- continuous • Single gene


Quantitative genetics


Measuring Heritable Variation

• The value of quantitative traits such a mohair

length or size or in dogs-running speed is

determined by their genes operating within

their environment.

• The size of how a spp grows is affected not

only by the genes inherited from their parents,

but the conditions under which they grow up.



• For a given individual the value of its phenotype (P) (e.g. the weight of a broiler in grams) can be considered to consist of two parts -- the part due to genotype (G) and the part due to environment (E)

• P = G + E.

• G is the expected value of P for individuals with that genotype. Any difference between P and G is attributed to environmental effects.



• The quantitative genetics approach depends on taking a population view and tracking variation in phenotype and whether this variation has a genetic basis.

• We measure variation in a sample using a statistical measure called the variance. The variance measures how different individuals are from the mean and the spread of the data.

• FYI: Variance is the average squared deviation from the mean. Standard deviation is the square root of the variance.


CHARACTERIZING A NORMAL DISTRIBUTION

Mean and variance are two quantities that describe a normal

distribution.

MEAN

VARIANCE


USEFUL PARAMETERS FOR QUANTITATIVE GENETICS

Mean: The sum of all measurements divided by the

number of measurements

in x

NN

xxxx

1...21

Variance: The average squared deviation of the

observations from the mean

222

2

2

1 1

xx

NN

xxxxxxVariance i

n


CORRELATIONS AMONG CHARACTERS OR RELATIVES

0 + —

Covariance:

yyxxN

yxCov ji 1

,


What is heritability?



• heritability is the proportion of the total phenotypic

variation controlled by genetic rather than

environmental factors.



• heritability is the proportion of the total phenotypic

variation controlled by genetic rather than

environmental factors.


The total phenotypic variance may be decomposed:

VP = total phenotypic variance




VG = total genetic variance





VE = environmental variance






VP = VG + VE






heritability = VG/VP (broad-sense)


The total genetic variance (VG) may be

decomposed:



decomposed:

VA = additive genetic variance



decomposed:


VD = dominance genetic variance



decomposed:



VI = epistatic (interactive) genetic variance



decomposed:




VG = VA + VD + VI



decomposed:




heritability = h2 = VA/VP (narrow sense)


Estimating heritability


HERITABILITY

The heritability (h2) of a trait is a measure of the degree

of resemblance between relatives.

h2 =

additive genetic variance (VA)/ phenotypic variance (VP)

Heritability ranges from 0 to 1

(Traits with no genetic variation have a heritability of 0)


HERITABILITY

h2 = VA / VP = VA / (VG + VE)

Since heritability is a function of the environment (VE),

it is a context dependent measure.

It is influenced by both,

The environment that organisms are raised in, and

The environment that they are measured in.


ESTIMATING HERITABILITY FROM REGRESSION

slope = b

= Cov (x,y)/Var (x)

Method of estimation COV(x,y) h2 Slope (b)

Offspring-Single parent ½ VA 2b b = ½ h2

Half-sib ¼ VA 4b b = ¼ h2

Offspring-Grandparent ¼ VA 4b b = ¼ h2

Offspring-Midparent - b b = h2


HERITABILITY OF BEAK DEPTH IN DARWINS’ FINCHES

Illustration of DNA Double Helix from Wikipedia. IN: Falconer & Mackay. Introduction to Quantitative Genetics.1996. Longman.

HERITABILITIES FOR SOME TRAITS IN ANIMAL SPECIES

h2 (%)



• one common approach is to compare phenotypic

scores of parents and their offspring:





Junco tarsus length (cm)

Cross Midparent value Offspring value







F1 x M1 4.34 4.73







F1 x M1 4.34 4.73

F2 x M2 5.56 5.31







F1 x M1 4.34 4.73

F2 x M2 5.56 5.31

F3 x M3 3.88 4.02


Slope = h2

Regress offspring value on midparent value


Heritability estimates from other

regression analyses

Comparison Slope



regression analyses

Comparison Slope

Midparent-offspring h2



regression analyses

Comparison Slope


Parent-offspring 1/2h2



regression analyses

Comparison Slope



Half-sibs 1/4h2



regression analyses

Comparison Slope



Half-sibs 1/4h2

First cousins 1/8h2



regression analyses

Comparison Slope



Half-sibs 1/4h2

First cousins 1/8h2

• as the groups become less related, the

precision of the h2 estimate is reduced.


Role of reproduction in genetic

improvement

DGy = SD *

h2

GI

where

DGy= rate of genetic

progress per year (diff.

bwn.av.peformance of

superior parents selected

to parent the next

generation and the herd

average)

SD = selection

differential

h2 = heritability

estimate, and

GI = generation

interval in years.


improvement


SOW 1ST

LITER 2ND

LITER

1(4) 6 4 0 -2 0 0

2 (2) 4 3 -2 -3 4 6

3 (6) 8 12 2 6 4 12

4 (5) 7 8 1 2 1 2

5 (3) 5 3 -1 -3 1 3

Σ 30 30 0 0 10 23 Mean

(4) 6 6

h2 = 2* 23/10 = 4.6


Heritabilities vary between 0 and 1


Cross-fostering is a common approach

Heritability of beak size in song sparrows


Q: Why is knowing heritability important?



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

response to selection





Let S = selection differential






Let h2 = heritability







Let R = response to selection







Let R = response to selection

R = h2S


THE UNIVARIATE BREEDERS’ EQUATION:

R = h2 S

Response to Selection Selection differential

Heritability

Where:

P

A2

V

Vh

(Additive Genetic Variance)

(Phenotypic Variance)


This is why it’s called “regression”:

offspring “regress” toward the mean!

S is the Selection Differential


S

RESPONSE TO SELECTION WHEN h2 = 1/3

The selection differential

(S) = mean of selected

individuals – mean of the

base population

The response to

selection:

R = h2S

S



VISUALIZING THE SELECTION DIFFERENTIAL


RESPONSE TO SELECTION

For a given intensity of

selection, the response to

selection is determined by

the heritability.

High heritability

Low heritability


R = h2 S

ESTIMATING h2 USING THE BREEDER’S EQUATION

PP

OO

S

RhSlope

*

*2


Predicting the response to selection

Example: the large ground

finch, Geospiza magnirostris





Mean beak depth of survivors = 10.11 mm






Mean beak depth of initial pop = 8.82 mm







S = 10.11 – 8.82 = 1.29







S = 10.11 – 8.82 = 1.29

h2 = 0.72







S = 10.11 – 8.82 = 1.29

h2 = 0.72

R = h2S = (1.29)(0.72) = 0.93







S = 10.11 – 8.82 = 1.29

h2 = 0.72

R = h2S = (1.29)(0.72) = 0.93

Beak depth next generation = 10.11 + 0.93 = 11.04 mm


RESEMBLANCE BETWEEN RELATIVES

When there is genetic variation

for a character there will be a

resemblance between relatives.

Relatives will have more similar

trait values to each other than

to unrelated individuals.


offspring offspring

parents

offspring

h2 ≈ 0 h2 ≈ ½ h2 ≈ 1

h2 is the regression (slope) of offspring on parents

parents parents

Definition of the regression coefficient (slope):

byx = cov(x,y)/var(x)


• Here x is the midparent value (parental mean), y is the offspring

• The higher the slope, the better offspring resemble their parents. • In other words, the higher the

heritability, the better offspring trait values are predicted by parental trait values.


Evolutionary response to selection

• We want to be able to measure the effect of selection on a population.

• This is called the Response to Selection and is defined as the difference between the mean trait value for the offspring generation and the mean trait value for the parental generation i.e. the change in trait value from one generation to the next.


ARTIFICIAL SELECTION IN DOMESTIC ANIMALS

Grey Jungle fowl




RESEMBLANCE BETWEEN RELATIVES DEPENDS

ON THE DEGREE OF RELATIONSHIP

Monozygotic twins

Full sibs

Parent-offspring

Half sibs

Slope of a plot of two variables (x,y) = Cov (x,y) / Var (x)

x

y


DEGREE OF RELATEDNESS AND THE COMPONENTS

OF PHENOTYPIC COVARIANCE



VEs = variance due to shared environment

Relationship Phenotypic covariance

Monozygotic twins: VA + VD + VEs

Parent-offspring ½ VA

Full sibs (½ VA) +(¼ VD) +VEs

Half sibs, or

Grandparent – grandchild ¼ VA


Modes of selection on quantitative traits






Response to Directional Selection:


Response to Directional Selection:


FACTORS AFFECTING GENETIC

CHANGE AND PROGRESS

• Selection intensity- measures how choosy

breeders are deciding which animal to

selected

• Selection differential- variability of BVs

within a population for a trait under selection

• Generation interval- total time required to

replace one generation with the nesxt

• Accuracy of selection- measure of strength of

relationship between BV and their

predictions for a trait under question.


• Breeding systems aim to improve a single trait or multiple traits.

• Single trait selection – aimed at improving one trait in a breeding program with little or no regard for improvement in other (associated) traits. Determine some economic value of a trait.

• Multiple trait selection – aims to simultaneously improve a number of traits.

• Theoretically, multiple trait selection should result in a faster rate of gain toward a

specific objective.


• Most domestic species now have a recognized system in place that allows breeders to estimate the genetic merit of individuals.

• In the most cattle, sheep, goat, and swine breeders use expected progeny differences (EPDs).

• EPDs are used to compare animals from the same species and breed.

• For EPD values to be used effectively, one needs to know the breed averages, the accuracy of the EPDs, and who estimated the EPDs.

• A high EPD is not necessarily good; it depends on

the trait being considered and breeding objectives.


Dolly the Sheep (the first mammal cloned from adult cells) and many other species have been cloned this way.

Worldwide, the institute that has cloned the most species is Texas A&M University, College of Veterinary Medicine, which to date has cloned cattle, swine, a goat, a horse, deer, and a cat.



The possibility for selecting desired traits at the cellular level holds exciting implications for the genetic improvement of domestic animals.


Summary

• Post-genomic genetics has enormous promise

for tracking down the genes involved in

common complex diseases

• Currently our ability to exploit this potential is

limited by

– study size

– difficulty of correcting for confounding factors


Methods of Selection

• Individual and family

• Half sibs- usually sire families which are the

offspring of same bull but with different

mothers

• Full-sibs- animals sharing both parents eg

piglets

• Individual selection- on the basis of their own

performance (mass selection)


• Simplest method

Also called performance testing

Takes into account of all individual additive

genetic variation that exist in the population

• Family selection- based on the average value

for the family and makes no separate of

individuals

• Advantages:

i. Traits with low heritability

ii. Accounts for environmental variation

iii. Good when the family size is large

However, it tend to increase the rate of inbreeding


• Within family selection-choosing the best

individuals from each family

• Progeny testing:

• Parents/ pedigree

• Computer/ breedplan


Several genes influence some traits.

For example, rate of growth is a trait that is influenced by appetite, energy expenditure, feed efficiency, and body composition.

Photo by Brian Prechtel courtesy of USDA Agricultural Research Service.


• Reproduction plays a major role in the

genetic improvement of farm animals

through the application of artificial

insemination (AI) and multiple ovulation

& embryo transfer (MOET). These help to

increase selection differentials on the male

and female sides respectively, leading to

significant increase in the rate of genetic

progress per year, as apparent from the

equation below:


improvement


DGy = SD * h2

GI

where

DGy= rate of genetic progress per

year (diff. bwn.av.peformance of superior

parents selected to parent the next

generation and the herd average)

SD = selection differential

h2 = heritability estimate, and

GI = generation interval in years.


improvement



improvement


SOW 1ST

LITER 2ND

LITER

1(4) 6 4 0 -2 0 0

2 (2) 4 3 -2 -3 4 6

3 (6) 8 12 2 6 4 12

4 (5) 7 8 1 2 1 2

5 (3) 5 3 -1 -3 1 3

Σ 30 30 0 0 10 23 Mean

(4) 6 6

h2 = 2* 23/10 = 4.6


FACTORS AFFECTING GENETIC

CHANGE AND PROGRESS

• Selection intensity- measures how choosy

breeders are deciding which animal to

selected

• Selection differential- variability of BVs

within a population for a trait under selection

• Generation interval- total time required to

replace one generation with the nesxt

• Accuracy of selection- measure of strength of

relationship between BV and their

predictions for a trait under question.


• Breeding systems aim to improve a single trait or multiple traits.

• Single trait selection – aimed at improving one trait in a breeding program with little or no regard for improvement in other (associated) traits. Determine some economic value of a trait.

• Multiple trait selection – aims to simultaneously improve a number of traits.

• Theoretically, multiple trait selection should result in a faster rate of gain toward a

specific objective.


• Most domestic species now have a recognized system in place that allows breeders to estimate the genetic merit of individuals.

• In the most cattle, sheep, goat, and swine breeders use expected progeny differences (EPDs).

• EPDs are used to compare animals from the same species and breed.

• For EPD values to be used effectively, one needs to know the breed averages, the accuracy of the EPDs, and who estimated the EPDs.

• A high EPD is not necessarily good; it depends on

the trait being considered and breeding objectives.


FACTORS THAT AFFECT GENETIC

PROPERTIES OF A POPULATION

• Hardy-Weinberg Law:

• Population size

• Fertility and viability

• Mutation

• Immigration/migration

• Mating system

• selection


Modern Genetics

• In recent years, traditional methods of improvement through selection and breeding have been superseded by genetic manipulation.

• A substantial amount of research has focused

on direct manipulation of genes and DNA.

• transferring a gene from one individual to another

• This area of genetic manipulation makes important contributions to domesticated animals in relation to immunology, vaccines, aging, and cancer.eg bioengineered to have a gene for mastitis resistance


The implications for introducing superior production, conformation, and disease-resistant traits into domestic animals through gene transfer hold considerable promise in the genetic improvement of animals.

Cloning Embryonic cloning of animals involves the chemical or surgical splitting of developing embryos shortly after fertilization and, consequently, developing two identical individuals.

It has been performed successfully in several species of animals


Dolly the Sheep (the first mammal cloned from adult cells) and many other species have been cloned this way.

Worldwide, the institute that has cloned the most species is Texas A&M University, College of Veterinary Medicine, which to date has cloned cattle, swine, a goat, a horse, deer, and a cat.



The possibility for selecting desired traits at the cellular level holds exciting implications for the genetic improvement of domestic animals.


Summary

• Post-genomic genetics has enormous promise

for tracking down the genes involved in

common complex diseases

• Currently our ability to exploit this potential is

limited by

– study size

– difficulty of correcting for confounding factors


Methods of Selection

• Individual and family

• Half sibs- usually sire families which are the

offspring of same bull but with different

mothers

• Full-sibs- animals sharing both parents eg

piglets

• Individual selection- on the basis of their own

performance (mass selection)


• Simplest method

Also called performance testing

Takes into account of all individual additive

genetic variation that exist in the population

• Family selection- based on the average value

for the family and makes no separate of

individuals

• Advantages:

i. Traits with low heritability

ii. Accounts for environmental variation

iii. Good when the family size is large

However, it tend to increase the rate of inbreeding


• Within family selection-choosing the best

individuals from each family

• Progeny testing:

• Parents/ pedigree

• Computer/ breedplan


Animal Breeding Systems

UNIT 4


• Name and explain common breeding systems used in livestock production

• Explain the effects, advantages and disadvantages of using various breeding systems

• Indentify the factors involved in selecting a breeding system

• Calculate the percentage of parental stock in offspring using various breeding systems

Objectives


• Breed for environment- to increase performance

• Increase animal yield

• Improve animal products

• Develop methods of disease control

• Extend range of animal products

• Conservation of genetic resources

• Develop new animals

• Scientific

• Ornaments, sports, and show purpose

Roles of animal breeding


• 2 basic Breeding systems

– Straight breeding

• Mating animals of the same breed

purebred, inbreeding, outcrossing, grading up

– Cross breeding

• Mating animals of different breeds

two-breed cross, three-breed cross, rotation

Systems of Breeding


• An animal of a particular breed

• Both parents are purebred

Purebred Breeding


Characteristics of the breed

1. Eligible for registry in breed

association

2. Tend to be genetically homozygous

3. Specialized business


• Mating related animals

• Linebreeding and Closebreeding refer to how closely related the animals are

• Requires a careful program of selection and culling

• Expensive

• Used most often by Universities for experimental work and Seedstock producers that provide animals for crossbreeding herds

Inbreeding


• Animals are very closely related and can

be traced back to more than 1 common

ancestor

• Examples:

– Sire to daughter

– Son to dam

– Brother to sister


1st Mating • A (Male) X B (Female)

F1

• ½ A ½ B

2nd Mating

• A

• 1/2A 1/2B

F2

• 3/4A 1/4B

Example


• Mating animals that are more distantly related

• Can be traced back to 1 common ancestor

• Examples

– Cousins

– Grandparents to grand offspring

– Half-brother to half-sister

• Increases genetic purity

• Several generations results in desirable and undesirable genes to become grouped together with greater frequency—making culling easier

Linebreeding


1st Mating

• A x B

• A x C

F1

• ½ A ½ B

• ½ A ½ C

2nd Mating

• 1/2A1/2 B x 1/2A/2C

F2 • ½ A ¼ B ¼ C

Example


• Mating animals from two different lines of

breeding within a breed

• Purpose is to bring together desirable traits

from different lines

• Experience is the best guide to use when

line crossing

Linecrossing


• Mating of animals of different families within the same breed

• Animals are not closely related

• Purpose is to bring into the breeding program traits that are desirable but not present in the original animals

• Used most by purebred breeders

• Popular because it reduces the chances of undeniable traits are still present

• Sometimes used in inbreeding programs to bring in needed traits

Outcrossing


• Mating purebred males to grade females

• Good way to improve quality

• Less expensive

• Use of purebred sires long enough will

eventually lead to the amount of grade

breeding left in the offspring being less

than 1%

Grading Up


1st Mating • A1 x G

F1

• 1/2A:1/2G

• 50% Pure 50% Grade

2nd Mating • A2 x ½ A1 ½ G

F2

• ½ A2 ¼ A1 ¼ G

• 75% Purebred 25% Grade

3rd Mating • A3 x ½ A2 ¼ A1 ¼ G

F3

• ½A3 ¼A2 1/8A1 1/8G

• 87.5% Purebred, 12.5% Grade

Example


• Mating two animals of different breeds

• Offspring is a Hybrid

• Usually results in improved traits because

dominant genes mask undesirable

recessive genes

• Superior traits that MAY result from

crossbreeding are called heterosis

Crossbreeding (X)


• Good record keeping is essential

• Calving difficulties may increase when crossing large breed sires with small breed dams

• Fewer calving problems if large breed dams are used

• Large breed dams have higher maintenance costs

• Artificial insemination allows access to better bulls

• To avoid inbreeding more than 1 breeding pasture may be required

General Considerations Regarding

Beef Crossbreeding Systems


• Terminal Sire Crossed with F1 Females

• Rotate Herd Bull every 3-4 years

• Two Breed Rotation

• Three Breed Rotation

• Four and Five Breed Rotation

• Static Terminal Sire

• Rotational Terminal Sire

• Composite Systems

Beef Crossbreeding Systems


• Replacement crossbred (F1) females in the herd

are purchased and crossed with a terminal bull.

• All offspring are sold.

Rotate Herd Bull Every 3-4 Years

• Same breed of bull is used for years and then

replaced with a bull of a different breed.

• Replacement females are selected from the

herd.

Terminal Sire Crossed with F1

Females


• Bulls from Breed A are crossed with cows from Breed B.

• Resulting heifers are bred to bulls from breed B for the duration of their productive life.

• Replacement heifers from that cross are bred to bulls from breed A.

• Each succeeding generation of replacement heifers is bred to a bull from the opposite breed used to sire the replacement heifer.

Two-Breed Rotation


F Parents Offspring Genes Heterosis

(approx. %) L E

female male

1 L E LE 50 50 100

2 LE L L/LE 75 25 50

3 L/LE E E/(L/LE) 37 63 75

4 E/(L/LE) L L/[E/(L/LE) 69 31 62

5 EL E EEL 34 66 63

Rotational crossing using two breeds


• Same pattern of breeding as the 2 breed

rotation except that a bull from a 3rd

breed is used in the sire rotation.

3 Breed Rotation


• Larger herds

• Bulls from a 4th or 5th breed may be used in

the rotation of sires

• This system requires a higher level of

management and record keeping than 2 and

3 breed systems.

4 and 5 Breed Rotations


Genera

tions

Parents

Off-spring

Genes

Heterosis

Female Male L A B

1 L A LA 50 50 100

2 LA B B/LA 25 25 50 50

3 B/LA L L/(B/LA) 63 12 25 75

4 L/B/LA A A/{L/(B/LA)} 32 56 12 62

5 ETC B ETC 16 28 56 32

6 ETC L ETC 58 14 28 84

Heterosis-in three crossbreeding

After many generations, the breed will settle down to ratio of 4:2:1


• 4 breeding groups

• Group 1 (25% of the herd) mates breed A bulls to

breed A cows to produce replacement heifers for

group 1 and group 2.

• Group 2 (25% of the herd) breeds the AA heifers

to a bull (breed B) to a different breed, producing

crossbred heifers (breed AB)

• Group 3 (50% of the herd) breeds the AB heifers

to a terminal (T) bull selected for its ability to

transmit a high rate of gain.

Static Terminal Sire System


• A subgroup (Group 4, 10% of the herd) of

the 3rd group is composed of AB heifers

being bred for the first time. These AB

heifers are bred to a smaller breed (breed C)

bull to reduce 1st time calving problems.

• All the male offspring of groups 1 and 2 and

all offspring of groups 3 and 4 are sold.

• Any heifers from groups 1 and 2 that are not

kept for breeding are also sold.


• Two breeding groups needed

• Bulls from breeds A and B are used on a

rotating basis on 50% of the herd providing

crossbred females for the entire herd

• Mature cows in the herd are mated with a

terminal bull to produce offspring, all of

which are sold.

• Replacement females come from mating of

bulls A and B with younger cows in the herd.

Rotational –Terminal Sire System


• Developing a new breed based on

crossbreeding 4 or more existing breeds of

cattle to avoid inbreeding problems

• After development the composite breed is

not crossbreed with other breeds

Composite Breeds


Livestock Breed Composition

Dairy cattle Australian Milking Zebu

Jamaica Hope

Karen

0.33 Sahiwal + red Sindi/0.67 Jersey

o.8 Jersey/0.05 Friesian/0.15 Sahiwal

Brown Swiss/Sahiwal

Beef cattle Bonsmara

Chabray

Santa Gertrudis

Renitole (of madagascar)

0.62 afrikander/0.19 hereford + 0.19

Shorthorn

0.6Charolais/0.38 brahman

0.62 Shortorn/0.38 Brahman

3-breed cross malagasy zebu+

Limousin + Afrikander

Sheep Dorper

Katahdin

Perendale

Dorset Horn/Blackhead Persain

Virgin Island/ Wiltshire Horn +

Suffolk

Goats Boer Local with European, Angora and

Indian blood


Breed

Wt, 2.5

years kg

Weaning

%

Weaning weight (Kg)

Calf Per Cow*

Afrikander(AF) 339 51.4 174 89.4

Angoni (AN) 285 65.1 149 97.0

Barotse (BA) 311 53.8 163 87.0

Boran (BO) 329 64.5 169 109.0

AVERAGE OF CROSSES

AN X BA 302 61.8 158 97.6

AN X BO 312 69.1 160 110.6

BA X BO 340 65.9 173 114.0

Breed and crossbred means (reciprocal

crosses) for Various traits of cattle in Zambia


• 2 basic breeding systems—straight and crossbreeding

• The type of system used depends on: the size of the operation, the amount of money available and the goal of the producer

• Purebred animal are eligible for registry and tend to be genetically homozygous

• Inbreeding increases the genetic purity of livestock but generally reduces performance. It is not generally used by the average producer but rather by those that do experimental work to improve the breed.

Summary


• Outcrossing brings genetic traits into the

breeding program that tend to hide

undesirable traits

• Crossbreeding is the mating of animals

from two different breeds, it is used by

many commercial producers and usually

results in hybrid vigor. This improves

some traits but all little effect on feed

efficiency and carcass traits.


• Occurs when two individuals share the

common ancestor or ancestors;

• Mating of close related animal can either

deliberate or accidental

• More likely to occur

i. in small, self-contained herds flock than

in large population

ii. Small numbers of males

Inbreeding


Systems of Mating:

the rules by which pairs of

gametes are chosen from the

local gene pool to be united in a

zygote with respect to a particular

locus or genetic system.


Systems of Mating:

A deme is not defined by geography but

rather by a shared system of mating.

Depending upon the geographical scale

involved and the individuals’ dispersal and

mating abilities, a deme may correspond to

the entire species or to a subpopulation

restricted to a small local region. The Hardy-

Weinberg model assumes one particular

system of mating – random mating – but

many other systems of mating exist.


Some Common Systems of

Mating: • Random Mating

• Inbreeding (mating between biological relatives)

• Assortative Mating (preferential mating between phenotypically similar individuals)

• Disassortative Mating (preferential mating between phenotypically dissimilar individuals)


Inbreeding: One Word, Several

Meanings

Inbreeding is mating between biological

relatives. Two individuals are related if

among the ancestors of the first individual

are one or more ancestors of the second

individual.


• Inbreeding Can Be Measured by Identity by Descent, Either for Individuals or for a Population (Because of shared common ancestors, two individuals could share genes at a locus that are identical copies of a single ancestral gene)

• Inbreeding Can Be Measured by Deviations from Random Mating in a Deme (either the tendency to preferentially mate with relatives or to preferentially avoid mating with relatives relative to random mating)


Identity by Descent

Some alleles are identical because they are replicated

descendants of a single ancestral allele


Properties of Assortative Mating

• Increases the Frequency of Homozygotes Relative to Hardy-Weinberg For Loci Contributing to the Phenotype Or For Loci Correlated For Any Reason to the Phenotype

• Does Not Change Allele Frequencies –

• Assortative Mating Creates Disequilibrium Among Loci that Contribute to the Phenotype and Is A Powerful Evolutionary Force at the Multi-Locus Level

• Multiple Equilibria Exist at the Multi-Locus Level And The Course of Evolution Is Constrained By the Initial Gene Pool: historical factors are a Determinant of the course of evolution


Disassortative Mating

occurs when individuals with

dissimilar phenotypes are more likely

to mate than expected under random

pairing in the population


Disassortative Mating as an

Evolutionary Force • Is a powerful evolutionary force at the single locus

level, generally resulting in stable equilibrium populations with intermediate allele frequencies and f<0

• It is less powerful as an evolutionary force at the multi-locus level because it produces a heterozygote excess, which allows linkage disequilibrium to break down more rapidly

• Mimics the heterozygote excess of avoidance of inbreeding, but unlike avoidance of inbreeding, it affects only those loci correlated with the relevant phenotype, and it causes allele frequency change.


And now it’s time for….

• Spongebob

Genetics!!!!!

Education

Animal breeding