Copy PRINCIPLES OF GENETICS

Haramaya University
College of Agriculture and

Environmental Sciences
School of Plant Sciences
Principle of Genetics (Plsc2031)
Credit hrs. 3(2+1)
By:- Tullu Tadessa (MSc)
October 7, 2018
 Role of Genetics
Chapter Contents
 History of Genetics
 Branches of Genetics
 Definition & terms of Genetics
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1. Introduction
 Genetics is the science of heredity (characters transmission from
parents to their offspring) and variation (origin of variation and
gene action).
 Genetics is the study of heritance in all of its manifestations,
 the molecular nature of the genetic material;
 the molecular mechanisms by which genes control metabolism,
growth and development and
 the distribution and behavior of genes in populations.
 The central concept of genetics is that “heredity is controlled by a
factors, called genes-discrete physical particles in living organisms.
Genetical Terminologies
 Heredity: The transmission of characters from parents to off-springs i.e.
the biological similarity between parents and progeny.
 Variation: differences b/n population or b/n parents and their off-springs or
b/n off-springs of same parents
 Inheritance is the process of heredity from parents to progeny.
 Gene is a unit of inheritance, transmitted from parents to offspring
 Genotype: the genetic constitution (genetic makeup) of an organism
 Phenotype: the sum total of observable appearance of an individual
 Homozygous-an individual with identical alleles for a trait (TT/tt).
 Heterozygous-an individual with dissimilar alleles for a trait (Tt).
 Allele: two/more alternative forms of a gene occur at a given locus
Brief History of Genetics
Year Discoverer Discovery
≈ 3000 B.C. Divine Warned Israelites not to breed their cattle and crops (Leviticus 19:19)
2000 B.C. Farmers Improve crops and animals by selective breeding
1830 Schleiden & Schwann Proposed the cell theory (all organisms are composed of cells, which are
derived from preexisting cells)
1985 Darwin and Wallace Proposed the theory of evolution through natural selection (the fittest can
reproduce and continue in life)
1866 Mendel Proposed the heredity law (segregation & independent assortment)
1900 de Vries, Correns and Rediscovered of Mendel law, work independently
Tschermak
1902 Sutton and Boveri Proposed the chromosomal theory of inheritance
1903 Sutton Discovered that genes are located on chromosomes.
1905 Johannsen Coined the terms of ‘genotype’, ‘phenotype’ and ‘gene’
1905 Wilson Coined the term ‘X-chromosome’
1905-08 Bateson and Punnett Discovered of linkage concept
1913 Sturtevant Created the first genetic map
1944 Avery Showed that deoxyribonucleic acid (DNA) was the genetic material.
1953 Watson and Crick Discovered the structure of DNA.
1972 Boyers et al, cloned numerous genes/produced artificial genes and rDNA
1997 Cloned the first mammal, a sheep named Dolly
2000 determined entire human genome
Branches of Genetics
Molecular
i an Population
Genetics
de scan
l be also subdivided Qbased
Genetics uant
i tat on the organism/group
Genetics
e n e tic Gen
etics ive
M en
G of organisms and their affairs it deals with as:-
Cytogenetics
Plant Genetics
“But the principles of all remain the same”

Genetics
Biochemical
Genetics
Animal Genetics
Historically, Genetics have been studied in three broad areas,
Medical
each with its own particular problems, terminologies and ics
Genettools.
Microbial Genetics
There are no fundamental distinctions among these three areas but
v i o ral
a
Beh etics
they are different and complementary
Statistical ways of studying
Gen the same
Human Genetics Genetics
biological entities.
Roles/Applications of Genetics
Generally, the study of genetics make life easy in two basic ways.
 First-progress in fields of Natural Sc. (agriculture, biology and medicine) :-
 Plant and Animal breeding (crops & animals improvement by gene
transfer)
e.g. high protein crops and high milk production, stress resistance etc.
 Biology (understanding of organisms, populations and species evolution)
 Medicine (e.g. Gene therapy, treatment of hereditary diseases)
 Second-become central to human affairs through :-

 Paternity disputes- in deciding the father of a child
 Health counseling e.g. maintaining normal cells
 Immigration- to give or deny a visa e.g. DV
 Forensic Science e.g., crime investigation such as murder or rape
Chapter Summary
 Genetics is the science of heredity and variation.
 The central concept is that “heredity is controlled by a factors (genes)”
 Many yrs ago, farmers knew that it was possible to change/improve
the characteristics of the crops and animals by selective breeding.
 The period from 1944 to the present is the era of molecular genetics
 Historically, three areas genetics studied were; classical, molecular &
evolutionary genetics (with the same principle and no fundamental boundary)
 First, knowledge of Genetics is basic to progress in fields of natural sciences
like agriculture, biology and medicine
 Second, genetics, has become central to daily activities of human affairs
Checkup Questions
 What is genetics?
 Differentiate the following terminologies
Heredity and Inheritance?
Animal Genetics and Plant Genetics
Genotype and Phenotype
 Why is the studies of genetics needed?
 Why do children resemble their parents?
 When did Genetics begin as a set of principles and
analytical procedure?
2. MENDELIAN GENETICS AND ITS
VARIATION
Chapter Contents
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 Mendel’s Experiments and Mode of Inheritance
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 Dominance Principle
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 Segregation Principle
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 Independent Assortment Principle
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 Statistical Analysis of Genetic Data
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 Addition Rule
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 Multiplication Rule
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 Bionomial Rule
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 Modified Mendelian ratio
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 Lethal alleles and Multi-allelism
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 Variation in dominance
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 Gene interactions
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2. MENDELIAN GENETICS AND ITS
VARIATION
2.1. Mendel’s Experiments and Mode of Inheritance
 Sir G. J. Mendel (1822-1884) was Austrian monk who used garden pea
(Pisum sativum) for his experiments and published in 1866.
 His work, however, was rediscovered in 1900, long after Mendel’s death,
by Tschermak, Correns and DeVries.
 Mendel was the first to suggest principles underlying inheritance and so
called as the founder or father of genetics
 he introduced a new formal tool for the analysis of heredity and variation
in organisms, initiated the hybridization experiments that were based on a
new experimental regime: the selection of discrete character pairs.
• Mendel studied the garden pea as his object of study for two main reasons
 First, pea was available from merchants in a wide array of distinct variant
morphological characters that could be easily identified and analyzed.
 The garden pea was easy to cultivate, grown easily in large numbers
and had a relatively short life cycle as inheritance patterns could be
observed in up to two generations per a year
 The plant had discontinuous characteristics such as flower color and
pea texture
 Second, peas can either self-pollinate or cross-pollinate.
 Anatomically, pollination and reproduction of the plant could be

controlled easily i.e. can either self-pollinate themselves or cross-
pollinate with another plant as it has both male and female
reproductive organs.
purple flower white flower Cross fertilization
F1=all purple
Emasculation
Selfing
Generally, Mendel observed that:
• In the F1: only the trait of one parent appeared
• In F2: the trait of two parents appeared with 3:1 ratio
• Traits masked in hybrid progeny (F1) can reappear F2= 3:1
in subsequent generations of all seven traits
Dominant: allele or phenotype expressed in either
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homozygous/heterozygous(AA/Aa)
 Seven different characteristics Mendel investigated in pea plants
Round
tttttt
• Results of Mendel’s F1 crosses for seven traits of pea plant

 His experiments brought forth two (three) generalizations which later
were known as Mendel’s principles of heredity /Mendelian inheritance.
i. law of dominance (Optional) in the two or more intra-allellic interaction
 In a cross of parents that are pure for contrasting traits, only one form of
the trait (DOMINANT) will appear in the next generation by masking
the expression of the second trait (recessive).
ii. Law of segregation or purity of gametes in and
 The two members of a gene pair segregate from each other into the
gametes, so that half the gametes carry one member of the pair and the
other half of the gametes carry the other members of the pair."
iii. Law of independent assortment in two or more characters.
 During gamete formation the segregation of the alleles of one gene is
independent of the segregation of the alleles of another gene.
i. Law of Dominance
ii. Monohybrid Crosses and Mendel’s Law of Segregation
• Monohybrid crosses are a crosses involving the inheritance of one feature only.
• According to the principle of segregation, for any particular trait, the pair of
alleles of each parent separate and only one allele passes from each parent on to
an offspring during the process of sex cell formation (i.e., meiosis). Each gamete
receives one member of a pair of factors and the gametes are pure.
A A a a
Parent 1 Parent 2
F1
A a A a
ii. Monohybrid Crosses and Mendel’s Law of Segregation
• The principle of segregation essentially has four features.
 Alternative versions of genes (alleles) account for variations in
inherited characteristics.
 For each characteristic, an organism inherits two alleles, one from
each parent (may be the same (homozygous; YY and yy), or
(heterozygous; Yy).
 If the two alleles of a gene influencing a specific trait differ, then the
allele that encodes the dominant trait is fully expressed in the
organism's appearance; the other allele encoding the recessive trait
has no noticeable effect on the organism' appearance.
 The two alleles for each characteristic segregate during gamete
production.
iii. Dihybrid Crosses and Mendelian Principle of
Independent Assortment
• A dihybrid cross is a cross between individuals that involves

inheritance two pairs of contrasting traits at a time to see if the
factors for two different traits segregated independently of each
other during gamete formation.
• After crossing, he found a phenotypic ratio of 9:3:3:1 in F2
• Thus, according to the principle of independent assortment, different
pairs of alleles influencing different characters are passed on to the
offsprings independently of each other. Thus, a pea plant’s
inheritance of the ability to produce yellow or green seed color is
independent of the inheritance of the round or wrinkled seed
character.
iii. Dihybrid Crosses and Mendelian Principle
of Independent Assortment
2.2. Statistical Analysis of Genetic Data
• There are three mathematical operations to determine the probability that a

cross between two individuals will produce a particular outcome.
• Probability is a chance that an event will occur in the future and it

depends on the number of possible outcomes.
The formula for probability (P) is: Probability = Number of times an event occurs (m)
Total number of events (n)
• In genetic problems, when two heterozygous tall pea plants (Tt) are
crossed, the phenotypic ratio of the offspring is 3 tall to 1 dwarf.
Probability = Number of individuals with a given phenotype
Total number of individuals
• Ptall = 3 tall / (3 tall + 1 dwarf) = 3/4 = 75%
• Pdwarf = 1 dwarf / (3 tall + 1 dwarf) = 1/4 = 25%

• The deviation between the observed and expected outcomes is called the
random sampling error
1. Mutually Exclusive Events: The Addition Rule
• states that ‘the probability that one of two or more mutually
exclusive events will occur is equal to the sum of the individual
probabilities of the events’.
•In determining the proportion of round seeds expected from the cross
Ww × Ww, round-seed phenotype results from the expression of either
of two genotypes, WW and Ww, which are mutually exclusive. In any
particular progeny organism, the probability of genotype WW is 1/4
and that of Ww is 1/2. Hence the overall probability of either WW or
Ww is
2. Independent Events: The Multiplication Rule
•
• states that ‘the probability that two or more independent events will
occur is equal to the product of their individual probabilities’.
• In crosses for seed shape and color, two traits are independent, and
the ratio of phenotypes in the F2 generation is expected to be 9/16
round yellow, 3/16 round green, 3/16 wrinkled yellow, and 1/16
wrinkled green by considering traits separately, because they are
independent.
• Then, among the 3/4 of round seeds, ¾ should be yellow, so the
overall proportion of round yellow seeds is expected to be 3/4 × 3/4
= 9/16. Likewise, among the 3/4 of the seeds that are round, there
should be 1/4 green, yielding 3/4 × 1/4 = 3/16 as the expected
proportion of round green seeds.
3. Binomial Expression Equation
• The probability of obtaining any of the three possible genotypes in a
monohybrid cross can be represented mathematically using a binomial
expression. The sum of the probabilities must be equal to 1.
• Therefore: 1 = p2 + 2pq + q2 where, p = the probability of inheriting the
first allele (usually the dominant) and q = the probability of inheriting the
second allele (usually the recessive).
• So in Aa X Aa cross, the probability of inheriting the A allele (p) from
each parent is 1/2, and the probability of obtaining the a allele (q) is 1/2.
• Therefore, the probability of obtaining AA genotype is p2 or 1/4 (1/2* 1/2
= 1/4) and the probability of obtaining an aa individual is q2 (also 1/4).
• The probability of obtaining a heterozygous individual (Aa) is 2pq or 1/2
(2* 1/2* 1/2 = 1/2).
Statistical Analysis to Test Hypothesis
•
Statistical Analysis to Test Hypothesis
• If the two genes assort independently, the cross should result in 1:1:1:1
ratio of the four phenotypic classes.
Phenotype (n) Observed Expected (0-e) (0-e)2 ∑(0-e)2

e
Smooth, yellow 154 142 +12 144 1.01
Smooth, green 124 142 -18 324 2.28
Wrinkled, yellow 144 142 +2 4 0.03
Wrinkled, green 146 142 +4 16 0.11
Total 168 568 0 3.43
• Calculated X2 value is 3.43 and the tabulated value of X2 at n-1 degree of

freedom and 5% probability level is 7.82. The calculated value being less
than the tabulated value (insignificant) implies that the observed
phenotype is statistically similar to the expected phenotype or in other
words our hypothesis of the two genes assorting independently is true.
2.3. Modified Mendelian Ratio
a. Lethal Alleles and Multiple Alleles
• Lethal Allele is an allele that has the potential of causing the death of an
organism. A lethal gene causes death of individual in the appropriate
genotype before they reach adulthood. Some lethal genes kill only in the
homozygous condition and are recessive lethal. Dominant lethals cause
death even when present in the heterozygous condition.
• Multiple alleles are more than two forms of the same gene in the
population. An individual has only 2 alleles for a gene but many different
alleles for a gene can exist within a population. A gene with more than 2
alleles is said to have multiple alleles.
b. Variation in Dominance
• Deviation from complete dominance and complete recessive resulting in

deviation from Mendelian ratios.
a) Incomplete dominance is the occurrence of the intermediate phenotype in
which the phenotype of a heterozygote is between those of the two
homozygotes.
• In this a cross between organisms with two different phenotypes
(heterozygote) produces offspring with a third phenotype that is a blending
of the parental traits (the corresponding homozygotes).
• There is no dominant or recessive allele. Both alleles contribute equal to
the production of phenotypes, so the heterozygous genotype produces a
phenotype that is intermediate between those produced by the two
homozygous genotypes. E.g. Red X White ==> Pink
p1 F1 p2
Incomplete dominance
b) Codominance refers to a situation when phenotypes of both homozygous

parents are expressed at the same time i.e. both alleles of a pair are fully
expressed in a heterozygote individual, thus the F1 heterozygote exhibits
the phenotypes of both homozygote parents
• In this, a cross between organisms with two different phenotypes produces
offspring with a third phenotype in which both of the parental traits
appear together.
• E.g. Red x White ==> Red & White Spotted

c) Over-dominance is a condition in genetics where the

phenotype of the heterozygote lies outside the
phenotypical range of both homozygous parents.
• Over-dominance can also be described as heterozygote

advantage; where in heterozygous individuals have a
higher fitness than homozygous individuals i.e. Aa is
superior to both AA & aa.
c. Gene Interactions
• Two or more genes governing the development of a single character,

in such a way that they affect the expressions of each other in
various ways
• Epistasis: [Greek "epi + stasis = to sit on top/standing upon"] is an
interaction between alleles at two different gene loci that affect a
single trait,
• the action of one locus masks the allelic effects at another locus.
• The locus whose expression is masked is described as hypostatic,
and the locus whose alleles cause the masking is epistatic.
c. Gene Interactions
d. Penetrance and Expressivity
• Penetrance is defined as the fraction of individuals with a particular
genotype that express at least some degree of the expected
phenotype. Penetrance can be:
– Complete (100%)–the proportion of organisms whose phenotype matches
their genotype for a given character.
– Incomplete–less than 100% of the individuals with particular genotype exhibit
the phenotype expected in the population.
• Expressivity is the degree to which a penetrant gene or genotype is
phenotypically expressed & described qualitatively or quantitatively.
• E.g. One diseased plant/animal may be very affected, whereas
another with the same disease may be less severely affected.
• A genotype that is always expressed has a penetrance of 100 percent.
e. Pleiotropy
• Pleiotropy is the situation in which a single gene is responsible for

a variety of traits.
• For example, a plant that inherits a null allele for a gene in the
starch biosynthetic pathway (such as ww in pea) may make less
starch in seeds. Therefore the seeds may be less viable.
• The plant may also be unable to make starch in other parts such as
roots or leaves; this could also change the characteristics of the
plant.
Summary of Dominance Relationships
Variation Dominance
X complete
X incomplete
X codominance
X over dominance
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Checkup Questions
 Describe the work of Mendel briefly and why he was considered as father of
genetics
 Why G. Mendel chose garden pea (Pisum sativum) for crossing?
 What are the phenotype and genotype ratio of F2 generation in monohybrid
and dihybrid?
 List and describe the Mendelian principles of inheritance
 Practice the three statistical analysis of genetic data
 Interpret the value of calculated X2 wrt tabulated
 List and explain the case for Modified Mendelian ratio to predict
experimental observations.
MENSCHEN FOR MENSCHEN
Agro-Technical and Technology

College
Harar Branch
Principle of Genetics (AEC1013)
Credit hrs. 4(2+2)

41
P From Previous Session
0
M 4: 5
0
 Genetics is the science of heredity and variation.

 The central concept is that “heredity is controlled by a factors (genes)”
 Children resemble their parents because they inherit their parents’ genes.
 In past farmers change/improve the characteristics of the crops and animals
by selective breeding though the true starting point of our understanding about
genetics began in the 1866, by G. Mendel-Father of Genetics
 Generally, three areas genetics studied were; classical, molecular &
evolutionary genetics (with the same principle and no fundamental boundary)
 First, knowledge of Genetics is basic to progress in fields of natural
sciences like agriculture, biology and medicine
 Second, genetics, has become central to daily activities of human affairs
42
0
P
M 4: 5
From Previous Session
0
2. MENDELIAN GENETICS AND ITS VARIATION

 Mendel studied the garden pea as his object of study for two main reasons
 First, pea was available from merchants in a wide characters,
 Second, peas can either self-pollinate or cross-pollinate.
 He brought two (three) generalizations -Mendelian inheritance.
i. law of dominance: In a cross of parents that are pure for contrasting traits,
only one form of the trait (DOMINANT) will appear in the next generation
ii. Law of segregation or purity of gametes:- The two members of a gene pair
segregate from each other into the gametes
iii. iii. Law of independent assortment in two or more characters.
 During gamete formation the segregation of the alleles of one gene is
independent of the segregation of the alleles of another gene. 43
0
P
M 4: 5
0
Testing Rules for segregation and Independent Assortment
1. Punnet Square:- is a grid system for predicting all possible

genotypes of progeny resulting from a cross.
2. Test cross:- is crossing of DOMINANT PHENOTYPE and unknown
genotype with a known homozygous recessive individual
3. Progeny Testing- self-fertilizing F2 individuals and
producing an F3, to predict the frequencies of the phenotypic

classes that would result.
44
P 2.2. Statistical Analysis of Genetic Data
0
M 4: 5
0
• Probability is a chance that an event will occur in the future and it

depends on the number of possible outcomes.
Probability = Number of individuals with a given phenotype
Total number of individuals
1. Mutually Exclusive Events: The Addition Rule
Prob (YY and WW)=Prob (YY) * Prob (WW)
3. Binomial Expression Equation 1 = p2 + 2pq + q2
 Goodness of fit
45
P 2.3. Modified Mendelian Ratio
0
M 4: 5
0
1. Lethal Allele is an allele that has the potential of causing the death of an organism.
2. Multiple alleles are more than two forms of the same gene in the population.
3. Variation in Dominance
 Incomplete dominance phenotype of a heterozygote is between the two homozygotes.
 Co-dominance phenotypes of both homozygous parents are expressed at the same
time
 Over-dominance phenotype of heterozygote lies outside the phenotypical range of
both homozygous parents.
4. Gene Interactions: Two or more genes governing the development of a single character
5. Penetrance fraction of individuals express at least some degree of the expected phenotype
6. Expressivity is the degree to which a penetrant gene or genotype is phenotypically
7. Pleiotropy is the situation in which a single gene is responsible for a variety of traits 46
Chapter Contents
At
 th
De e e
sc nd
of of
 c
rib
e
 Sex Determination and Sex Linkage
 Cell cycle and Sexual Reproduction
th
 Chromosomal Theory of Inheritance
De hr t e
 sc om he ch
St rib os fea ap
at
e e om te
Co t he e s
tu
re r,
nc th
ep e c , yo
ch e l m u
tu
liz ro l cy o rp sh
e ou
 Chromosomes, its morphology & nomenclature
mo cle ho ld
th so s lo
e ma a g y ab
se an le
x l t nd
he th d to
de or ei no
te r me
rm y o sig
in f n i
nc
la
at in fi
io h e c a
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3. CHROMOSOMAL BASIS OF INHERITANCE
n rit nc re
& an e
47
se ce
x
lin
ka
g
3. CHROMOSOMAL BASIS OF INHERITANCE
3.1. Chromosomes-features, morphology & nomenclature

 The term chromosome means “colored body” was coined by W. waldeyer in
1888.
 It was first discovered when staining techniques were developed.
 Chromosomes occur in pairs and the paired chromosomes are called homologous
chromosomes and the cell having paired (2n) chromosome is called a diploid
chromosome.
 In gamete cells, chromosome occurs in single and it is called haploid or n
chromosome and when they fuse, they from the diploid cell.
 When viewed under microscope, chromosomes differ in size and morphology

within and between species.
 The chromosome is best seen after it has duplicated but before the identical
48
 DNA of all eukaryotic chromosomes is associated with numerous

protein molecules (nucleoprotein) in a stable, ordered aggregate
called chromatin.
– Some proteins determine chromosome structure and changes in structure
that occur during the cell division/cycle while other proteins play roles in
regulating chromosome functions.
 Thus, chemically chromosome composed of DNA, RNA, histones

and non-histones proteins. The major class of proteins comprises the
histone proteins which are largely responsible for the structure of
chromatin.
 The genetic significance of DNA and protein compaction into
chromatin and finally into chromosome is that it greatly facilitates
49
the movement of genetic material during nuclear division.
Structure of a chromosome consists of a single DNA strand packaged by proteins.

50
 Each chromosome has a distinct attachment point for microtubules

(fibers) that makeup the mitotic and meiotic spindle apparatuses
 The attachment point occurs at a constriction in the chromosome

called centromere-composed of several specific DNA sequences.
 The kinetochore is the proteinaceous structure on the surface of the

centromere to which microtubules of the spindle attach.
 When a cell divides, spindle fibers attach to the centromere of each

chromosome and pull the sister chromatids to opposite poles.
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52
Morphological features of chromosomes
 Based on the chromosome length and centromere position on the

chromosomes, individual chromosomes named as follows:-
 Metacentric-the centromere is in the middle of the chromosome, with
equal arms length (1:1 arm ratio) and form a V shape at anaphase.
 Telocentric-the centromere is at the end of the chromosome (arm ratio
of 0:1)
 Acrocentric-the centromere is very near the end of the chromosome
(1:3 or more arm ratio), or;
 Subtelocentric or submetacentric:-the centromere is somewhere in
between metacentric and acrocentric (1:1 to 1:2.9 arm ratio).
53
chromosome classification and nomenclature based on centromere position 54

• Three terms are referred in the identification of chromosomes.
i. Karyotype is the number, size, and morphology of a chromosome set

of a cell in an individual or species i.e. a complete set of all the
metaphase chromatid pairs in a cell.
ii. Karyogram is the physical measurement of chromosomes from a

photomicrograph, where chromosomes are arranged in descending
order (longest to shortest)
iii. Idiogram represents a diagrammatic sketch (interpretive drawing) of

the karyogram
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56
57
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3.2. Cell Cycle- life cycle of a cell
 The process of cell division is composed of the division a nuclear
(Karyokinesis) and a cytoplasmic (cytokinesis) component.
 In somatic cells, the cell cycle consists of two phases: interphase-90%
(preparation phase) and mitotic-10% (dividing) phase.
 During interphase, the cell is not undergoing active division, but the
chromosomes are replicated in preparation for division.
 Interphase has three stages:
i. G1 (gap 1) –cell prepare for DNA/chromosome replication (25%)
ii. S - DNA replication (synthesis) (40%)
iii. G2 – cell prepares for cell division (25%)
 The product of chromosome duplication at S phase is two exact copies
(sister chromatids), held together by the replicated but un-separated
59
 mitotic-10% (dividing) phase.
 Two major processes are involved in the genetic continuity of
nucleated cells: mitosis and meiosis.
 Mitosis is division of the somatic cell and results in two identical
daughter cells having diploid (2n) chromosome number, each with the
same number of chromosomes as the parent cell.
 During Mitosis:-
i. Each chromosome is present as a duplicated at the beginning of nuclear division.
ii. Each chromosome divides longitudinally into identical halves that become
separated from each other.
iii. The separated chromosome halves move in opposite directions, and each
becomes included in one of the two daughter nuclei that are formed.
60
3.2. Cell Cycle- life cycle of a cell Mitosis
 Stages of mitosis
 Mitosis has four stages: Prophase, Metaphase, Anaphase & Telophase
1. Prophase: Chromatin in the nucleus begins to condense and becomes
visible in the light microscope as chromosomes.
 The nucleolus disappears and centrioles begin moving to opposite
ends of cell and fibers extend from the centromeres.
 The nuclear membrane dissolves and proteins attach to the
centromeres creating the kinetochores.
 Microtubules attach at the kinetochores and the chromosomes begin
moving.
61
2. Metaphase: Spindle fibers align the chromosomes along the plane
of the equator called the metaphase plate so that their centromeres
become aligned in one plane halfway between the two spindle poles.
 This organization helps to ensure that, when the chromosomes are
separated, each new nucleus will receive one copy of each
chromosome.
62
3. Anaphase: The paired chromosomes separate at the
kinetochores and move to opposite sides of the cell.
Motion results from a combination of kinetochore
movement along the spindle microtubules and through
the physical interaction of polar microtubules.
 By the end of this stage the two sets of daughter
chromosomes approach the poles
63
4. Telophase: Chromatids arrive at opposite poles of cell and
new membranes begin form around the daughter nuclei.
 The chromosomes disperse and are no longer visible
under the light microscope. The spindle fibers disperse,
and cytokinesis or the partitioning of the cell may also
begin during this stage.
 At the end of this phase, the cell now reverses the step of
prophase to return to the active interphase state (the G 1
64
phase of the cell cycle).
65
66
67
68
 Significance of mitosis
i. Genetic stability-daughter cells are genetically identical to the
parent cell which results in genetic stability within populations.
ii. Growth-the number of cells within an organism increases by
mitosis and this is the basis on growth in multicellular organisms.
iii. Cell replacement-cells are constantly dying and replacement of
cells and tissues involves mitosis.
iv. Regeneration-some animals are able to regenerate whole parts of
the body and production of the new cells involves mitosis.
v. Asexual reproduction-mitosis is the basis of asexual reproduction,
the production of new individuals of a species by one parent. 69
3.2. Cell Cycle- life cycle of a cell Meiosis
 Meiosis is the division of the gamete cell and results in four cells
having haploid (n) chromosome number, which is half of the
genetic material as the parental cell.
During Meiosis:-
 The genetic material must be reduced to half when recombine to form
zygotes;
 Two successive nuclear divisions without intervening chromosome

replication (copying the chromosomes once, but dividing twice) to produce
four cells with haploid gametes;
 The first division, meiosis I, separates homologous chromosomes.
 The second division, meiosis II, separates sister chromatids.
70
 Stages of meiosis
 The two nuclear divisions of a normal meiosis are meiosis I-
reductional division & meiosis II-equational division.
 As a result of meiosis, four daughter cells are formed from one parent
cell with half chromosomes number of the parent cell.
 Usually the parent cell is diploid and the daughter cells are haploid.
 Meiosis I is a reductional division (reduction of chromosomes number

from diploid to haploid) through homologous chromosome separation
 It consists of prophase I, metaphase I, anaphase I and telophase I,

characterized as follows: 71
Stages of meiosis
72
 Stages of meiosis: Meiosis I
 Prophase I
The chromosomes become shorter and thicker
Homologous pairs forms
Crossing- over occurs,
Formation of spindle apparatus
Nuclear membrane and nucleoli disappear
 Prophase of meiosis I can be divided into five stages

namely Leptotene, Zygotene, Pachytene, Diplotene, Diakinesis
73
74
•Metaphase I
- Homologous pairs of chromosomes (bivalents) arranged as a double row
along the metaphase plate. The arrangement of the paired chromosomes
with respect to the poles of the spindle apparatus is random along the
metaphase plate. (This is a source of genetic variation through random
assortment, as the paternal and maternal chromosomes in a homologous
pair are similar but not identical.
- Broken down of nuclear membrane
• Attachment of spindle to pair of homologous chromosome (bivalent) and

75
aligns across the equatorial plane of the spindle
Anaphase I
- Homologous chromosome pairs separate and migrate toward
opposite poles, i.e. sister chromatids pulled to the same pole
- Reduction division is occurs at this stage, because it reduces the
number of chromosomes to half.
- For every tetrads there is now one chromosome in the form of a
chromatid pair known as dyad or monovalent at each pole of the cell.
- Separating homologous into different daughter cell accomplished.
76
•Telophase I
- Chromosomes (each with two sister chromatids)
complete migration to the poles and new nuclear
membrane may form
- Cytokinesis may occurs to produce two cells
77
 Stages of meiosis: Meiosis II
• Meiosis II is an equational division (results in separation of the

sister chromatids), as it does not further reduce the chromosome
number per cell and basically similar to mitotic cell division in
which chromatids of each chromosome are pulled to opposite poles.
• For each original cells entering meiosis I, four cells emerge at

telophase II.
• Like that of meiosis I, Meiosis II consists of prophase I, metaphase

I, anaphase I and telophase I, characterized as follows:
78
 Stages of meiosis: Meiosis II
1. Prophase II
- Chromosomes become condensed
- Spindles formed
2. Metaphase II
- Chromosomes align at the metaphase plate or equatorial plane
3. Anaphase II
- The chromatids are pulled to the opposite poles of the spindle
4. Telophase II
- Nuclear envelop forms and cytogenesis takes place
79
 Significance of Meiosis
 Sexual reproduction- at fertilization the nuclei of the two gamete
cells fuse and form zygote with two sets of chromosomes (2n).
 Genetic variation- Because of crossing over and randomness of the
process of chromosomal segregation, very large number of different
chromosomal combinations is formed in gametes which are sources
of variation with in the population.
 Diploid number of chromosomes is reduced in a such way that each
of four daughter cells has one complete haploid chromosome set
 The behavior of any tetrad at meiosis follows the pattern of Mendel’s
rule of segregation and independent assortment. I.e. alleles of one
gene segregate independently of alleles of other gene. 80
81
82
3.3. Chromosomal Theory of Inheritance
 This theory states that “chromosomes are the carrier of the genes
and genes were physically located in the chromosomes” or
 inherited traits are controlled by genes residing on chromosomes
faithfully transmitted through gametes, maintaining genetic
continuity from generation to generation”.
 The strongest evidence was Mendel's principles of segregation and
independent assortment paralleled the behavior of chromosomes in
meiosis.
 The transmission of chromosomes from one generation to the next

closely paralleled the pattern of transmission of genes from one
generation to the next.
83
3.4. Sex Determination and Sex Linkage
• Sex determination in a biological system is the development of
sexual characteristics in an organism.
• Most sexual organisms have two sexes (males and females).
• In many cases, sex determination is genetic: males and females have

different alleles or even different genes that specify their sexual
morphology.
• In animals, this is often accompanied by chromosomal differences.
• In other cases, sex is determined by environmental variables (such

as temperature) or social variables (the size of an organism relative
to other members of its population). 84
Genetic sex-determination systems
• XX/XY sex-determination system is one of the most familiar,

found in human beings and most other mammals.
• In the XY sex-determination system, females have two of the
same kind of sex chromosome (XX), while males have two
distinct sex chromosomes (XY).
• Some species (including humans) have a gene SRY on the Y
chromosome that determines maleness; others (such as the fruit
fly) use the presence of two X chromosomes to determine
femaleness. 85
• XX/X0 sex determination system is a variant of the XY system,
in which females have two copies of the sex chromosome (XX)
but males have only one (X0).
• The 0 denotes the absence of a second sex chromosome.
• This system is observed in a number of insects, including the

grasshoppers, crickets and cockroaches.
• The nematode C. elegans is male with one sex chromosome

(X0); with a pair of chromosomes (XX) it is a hermaphrodite.
86
• ZW sex-determination system is found in birds and some insects.
• It is reversed compared to the XY system: females have two

different kinds of chromosomes (ZW), and males have two of the
same kind of chromosomes (ZZ).
• Haplodiploidy: in this case haploid individuals are males while

diploid are generally female but may be sterile males.
• It is found in insects belonging to Hymenoptera, like ants and bees.
• Thus, if a queen bee mates with one drone her daughters share ¾ of
their genes with each other, not ½ as in the XY and ZW systems.
87
• Non-genetic sex-determination systems also exist in nature.
• In some species of reptiles, including alligators and the tuatara, sex
is determined by the temperature at which the egg is incubated.
• Other species, such as some snails, practice sex change: adults start
out male, and then become female.
• In tropical clown fish, the dominant individual in a group becomes
female while the other ones are male.
• In some arthropods, sex is determined by infection.
• Some species have no sex-determination system. Earthworms and
some snails are hermaphrodites; a few species of lizard, fish and
insect are female and reproduce by parthenogenesis.
88
• Sex Linked Traits are traits whose loci are on the sex chromosomes,
so their transmission to offspring is affected by the sex chromosome
complement of the individual.
• Because the gene controlling the trait is located on the sex
chromosome, sex linkage is linked to the gender of the individual.
• Usually such genes are found on the X chromosome thus the Y
chromosome is missing such genes.
• The result is that females will have two copies of the sex-linked gene
while males will only have one copy of this gene.
• If the gene is recessive, then males only need one such recessive
gene to have a sex-linked trait rather than the customary two
recessive genes for traits that are not sex-linked.
89
• This is why males exhibit some traits more frequently than females.
• X-linked traits have a number of interesting aspects.
• First, because females possess two X chromosomes and males

possess only one, X-linked recessive traits appear far more commonly
in males than in females. This is clear from simple statistics.
• A male will show the X-linked recessive trait due to receiving only a
single copy of the allele, because he has no second X chromosome to
carry a dominant allele which might hide the recessive.
• Females must inherit the recessive trait twice to show it, just as they
do for any other recessive trait.
90
• There are also a very few genes which are Y-linked (or holandric),
carried on the Y chromosome and passed directly from father to son.
• Every son has a copy of his father’s Y chromosome.
• In any pedigree showing unbroken lines of male descent, all of the

connected males have copies of the same Y chromosome, and thus
share any Y-linked characteristics.
91
• Sex limited traits are generally autosomal (not found on the X/Y
chromosomes).
• The genes for these traits behave exactly the same way that any
autosomal gene behaves.
• The difference here comes in the expression of the genes in the

phenotype of the individual.
• Sex-limited traits are expressed in only one gender. The traits are
associated with primary or secondary sexual characteristics, and
thus are expressed only in the gender which utilizes those
characteristics.
• E.g. milk a lactating 92
• Sex influenced traits are also autosomal, the difference is in the
ways the two genders express the genes.
• E.g. baldness pattern in humans. This gene has two alleles, “bald”
and “non-bald.” The behaviors of the products of these genes are
highly influenced by the hormones in the individual, particularly by
the hormone testosterone.
• In the presence of high levels of testosterone, the baldness allele has
a very powerful influence.
• In the presence of low levels of testosterone, this allele is quite
ineffectual.
93
• All humans have testosterone, but males have much higher than
females.
• The result is that in males, the baldness allele behaves like a
dominant allele, while in females it behaves like a recessive allele.
• As in all cases, dominance only matters in the heterozygote, so this
means that heterozygous males will experience hair loss and
heterozygous females will not.
• Even homozygous females may experience no more than a thinning
of their hair, but many develop bald spots or have receding
hairlines.
94
• An interesting note about this gene is that it is often incorrectly
identified as X-linked because of an illusion that males inherit it
from their mothers. Males can inherit baldness from either parent,
but if a son gets it from his father, both father and son will be bald,
and nobody really notices, as we expect sons to look reasonably like
their fathers. But if a son loses his hair and his father does not, that’s
noteworthy, and the conclusion people have drawn (correctly) is that
the son inherited baldness from his mother.
• But recall that with X-linkage sons always inherit traits from their
mothers and never from their fathers. In the case of baldness, a son
can inherit from either parent. It is just that we notice it more in the
case of inheritance from the mother.
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P
M 4: 5
Checkup Questions
0
 Describe the work of Mendel briefly and why he was considered as father of
genetics
 Why G. Mendel chose garden pea (Pisum sativum) for crossing?
 What are the phenotype and genotype ratio of F2 generation in
monohybrid and dihybrid?
 List and describe the Mendelian principles of inheritance
 Practice the three statistical analysis of genetic data
 Interpret the value of calculated X2 wrt tabulated
 List and explain the case for Modified Mendelian ratio to predict
experimental observations.
96
Haramaya University

Credit hrs. 3(2+1)
97
February 20, 2024
P From Previous Session
0
M 4: 5
0
 Genetics is the science of heredity and variation with the central concept of
“heredity is controlled by a factors (genes)”
 Children resemble their parents because they inherit their parents’ genes.
 Generally, the study of genetics applied in two basic ways.
 First-progress in natural sciences like agriculture, biology and medicine
 Second-become central to daily activities of human affairs
 though farmers improve the crops and animals before, the true understanding
about genetics began in the 1866, by Mendel who studied the garden pea for
two main reasons available & applicability.
 He brought three generalizations -Mendelian principle of inheritance.
i. law of dominance,
ii. Law of segregation and
iii. independent assortment 98
0
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 The genetic data can be analyzed statistically through Addition Rule,

Multiplication Rule, Binomial Equation and Goodness of fit (X2)
 Simple Mendelian model is not sufficient to predict experimental
observations in all situations and Lethal Allele, Multiple alleles,
Variation in Dominance, Gene Interactions, Penetrance, Expressivity,
Pleiotropy are Modified mendelian ratio
 Chromosomes occur in pairs-called homologous chromosomes and the cell

having paired chromosome (2n) is called a diploid chromosome.
 In gamete cells, chromosome occurs in single-called haploid or n
chromosome
99
100
 Mitosis is division of somatic cell and results in two identical daughter cells
having diploid (2n) chromosome number, the same as the parent cell.
101
 Meiosis is the division of the gamete cell and results in four cells having haploid (n)
chromosome number, which is half of the genetic material as the parental cell.
During Meiosis:-
 The genetic material must be reduced to half when recombine to form zygotes;
 Two successive nuclear divisions without intervening chromosome replication to

produce haploid gametes, so that; each of the four cells resulting from the two
meiotic divisions receives one chromosome of each chromosome set from original
parental cell.
• Meiosis reduces chromosome number by copying the chromosomes once, but

dividing twice.
• The first division, meiosis I, separates homologous chromosomes.
• The second division, meiosis II, separates sister chromatids. 102
103
3.3. Chromosomal Theory of Inheritance
 The chromosomes transmission is closely paralleled with the pattern of genes
transmission across generation and it is the basis for Chromosomal Theory of
Inheritance-states that “chromosomes are the carrier of the genes and genes were
physically located in the chromosomes” or inherited traits are controlled by genes
residing on chromosomes.
 Most sexual organisms have two (males and females) sexes which is
determined by either
 Genetic factors like XY, X0, ZW and Haplodiploidy and,
 non-genetic factors like temperature, social factors and infection etc .
 Sex Linked Traits-exactly found on sex chromosomes, so their transmission

through generation is affected by the sex chromosome
 Sex limited and Sex influenced traits are generally autosomal-the difference
104
4. LINKAGE, CROSSING-OVER AND CHROMOSOME MAPPING
Chapter Contents
o
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 Gene linkage, its types and uses
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 Crossing over, its types and uses
ou
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 Gene recombination
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 Gene/chromosome mapping
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Des
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At
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 106

4. LINKAGE, CROSSING-OVER AND CHROMOSOME MAPPING
4.1. Gene linkage, Recombination and Chromosomal Exchange

Linkage is
 Tendency of genes to remain together in their original combination during
inheritance
 the association of genes located on the same chromosome such that they
tend to be inherited together.
 a situation of two or more genes located on the same chromosome, close
enough together that the frequency of recombination b/n the two loci is
less than 50%.
 The linkage was firstly reported by Bateson and Punnet in 1906.
 Linkage provides a way to map genes on chromosomes.
 Linked loci undergo recombination during crossing over of meiosis.
107
 Based on crossing over: Linkage may be classified into two as:-

i. Complete linkage: is where there is complete absence of recombinant
types due to absence of crossing over as in case of males of Drosophila
and females of silkworms,
ii. Incomplete/partial linkage: If some frequency of crossing over also
occurs between the linked genes, it is known as incomplete / partial
linkage as in maize, pea, Drosophila female and several other organisms.
The Significances of Linkage in Plant Breeding are:-

iii. limit the variability among the individuals.
ii. linkage between genes controlling two different desirable characters will
help in simultaneous improvement of both the characters.
iii. Linkage is undesirable when desirable and undesirable genes are linked.
108
Characteristics of Linkage
i. involves two or more genes located close to each other in same chromosome in
a linear fashion.
ii. reduces variability.
iii.Its strength depends on the distance between the linked genes. Closer the
genes, higher the strength and vice versa.
iv. may involve either coupling or repulsion configuration on same chromosome.
 cis/coupling configuration-the arrangement of the A and B alleles in the
dihybrid where one chromosome carries both mutants and the other
chromosome carries both wild-type alleles
 trans/repulsion configuration-meaning “across,”-the alternative arrangement
where the two mutants or two wild-type alleles are across from each other.
 Crossing over (chromosomal cross over) is
 the exchange of genetic material between homologous chromosomes that

results in recombinant chromosomes.
 the process where homologous chromosomes pair up with each other and
exchange different material of there genetic material to form recombinant
chromosomes.
 Occurring during meiosis I and may also occur during mitotic division
which may result in loss of heterozygosity.
 important for the normal segregation of chromosomes & genetic variation
 Chiasmata is the point where two homologous non-sister chromatids
exchange genetic material during crossing over during prophase I meiosis.

111
Types of crossing over

 Single crossing over: only one breakage and reunion events of
homologous chromosomes
 Double crossing over :- two simultaneous reciprocal breakage and reunion
events of homologous chromosomes
113
• Recombination is any process in which one or more nucleic acid molecules

are rearranged or combined to produce new combinations of genes or a new
nucleotide sequence, that is new combinations of alleles in the offspring.
• Recombination between unlinked loci occurs during meiosis I, when non-
homologous chromosome pairs align and separate randomly.
115
4.2. Construction of Genetic Maps
Genetic mapping’ or ‘Chromosome mapping’ is the process that uses

genetic experiment to determine:-
 the relative position/locus of genes,
 the order/arrangement genes and
 the spacing/distance between genes along the same chromosome.
The map distance between two genes is based on the frequency of
recombination between them and is measured in map units (mu) so
called a centimorgan (cM).
• A crossover frequency of one percent between two genes is defined
as one map unit. That is, one map unit is the distance between gene
pairs for which one product (1%) out of 100 is recombinant.
117
 The recombination frequency is an approximation of the crossovers

frequency and then the distance between the two genes.
 Genetic mapping has diverse applications in genetics, breeding and

medicine.
 to identify genes responsible for traits
 to develop improved agricultural crops and animal breeds
 to diagnose patients with disease
 to identify genes responsible for diseases
 to locate the risk genes for a host of genetic diseases
 to identify potential suspects through DNA evidence
 to improve upon gene therapy
118
 Steps in genetic mapping

 Genetic mapping requires the production of segregating mapping
populations by crossing two parents with phenotypic difference(s) in
at least one trait of interest.
i. Selection of parents with contrasting phenotypes.
ii. Generation of F1 progeny by crossing above selected parents.
iii. Generation of F2 progeny by self-pollination.
iv. Data collection and calculation of recombination frequency.
v. Construction of genetic map.
119
Mapping Chromosomes by using three-point testcrosses
 This is used as efficient way of mapping genes both for their order in the
chromosome and the distances between them.
 It involves three genes within a relatively short section of chromosome.
 To determine the correct order of the three linked genes, a comparison of
either of double recombinant classes (one with the lowest frequency) with
either of non-recombinant classes shows the gene that is in the middle or
 Simply compare the double crossovers and non-recombinants to find one
of each in which two alleles are identical.
 NB. In calculating map distances from three point test cross data, the
double crossover figure must be added to each of the single crossover
represents single crossover events occurring simultaneously in region-I and
120
II in the same meiosis.
•
121
•
122
 Given: - Female Drosophila heterozygous for ebony body (e+/e), Scarlet

eyes (st+/st) and Spineless bristle (ss+/ss) were test-crossed and the
following testcross progeny were obtained.
Progeny No. of
No. Progeny Phenotype % of progeny
genotype Individuals
1. Wild type
F1: + st + +♀ +X + e ts 134
ss ♂ 134/2000*100= 6.7
2. Ebony
e + ss e + + e ts 16
ss 16/2000*100= 0.8
3. Ebony-Scarlet e st + 136 136/2000*100= 6.8
4. Ebony- Scarlet-Spineless e st ss 156 156/2000*100= 7.8
5 Scarlet + st + 736 736/2000*100= 36.8
6. Scarlet- Spineless + st ss 20 20/2000*100= 1
7. Spineless + + ss 108 108/2000*100= 5.4
8 Ebony- Spineless e + ss 694 694/2000*100= 34.7
Total 2000 100
123
 Are genes e, st and ss linked genes? If yes, verify using Chi-square test.
 What is the gene arrangement/configuration on the Chromosome?
 Write the genes using their correct sequence on the chromosome.
 What is the map distance between the genes?
 Calculate the coefficient of coincidence and interference value based on
which also interpret what it means.
1. Are genes e, st and ss linked genes? If yes, verify X2 test.
1. Null hypothesis: - the observed ratio of progeny s is in equal distribution among each
phenotype (1:1:1:1:1:1:1:1)
2. Alternative hypothesis: - the observed ratio of progeny is not in equal distribution among
each phenotype (1≠1≠1≠1≠1≠1≠1 ≠1)
Table: - Chi-square Calculations.
(O-E)2
No. Progeny Phenotype Expected No. Observed No. O-E (O-E) 2
E
1 Wild type 250 134 -116 13456 53.824
2 Ebony 250 16 -234 54756 219.024
3 Ebony-Scarlet 250 136 -114 12996 51.984
Ebony- Scarlet-
4 250 156 -94 8836 35.344
Spineless
5 Scarlet 250 736 486 236196 944.784
6 Scarlet- Spineless 250 20 -230 52900 211.6
7 Spineless 250 108 -142 20164 80.656
8 Ebony- Spineless 250 694 444 197136 788.544
125
Total 2000 2000 2385.76
Therefore, the computed x2 statistic (2385.76) exceeds the critical value in
the table for a 0.05 probability level (14.07), and then our null hypothesis
of equal distributions should be rejected.
This means the genes on the chromosome of above organisms are linked
genes.
2. What is the gene arrangement/configuration on the Chromosome?
 based on the genetic makeup of parental types :-
Scarlet + st +
Ebony- Spineless e + ss
-the gene arrangement on the Chromosome is trans-arrangement/repulsion

arrangement which means wild type form(s) of the certain gene(s) and mutant type
form of the other gene appear in one member of homologous chromosome and their
corresponding mutant and wild form(s) of other gene(s) on the other member of
homologous chromosome.
127
3. Write the genes using their correct sequence on the chromosome.

•By comparing Double cross over recombinants with Parental type
1. the gene showing the lowest frequency of separation from its parental
combination is the center gene in a three point cross.
Scarlet + st +
Ebony- Spineless e + ss →Parental types
Ebony e + +
 Therefore, the gene order/sequence on the chromosome is
Scarlet- Spineless + st ss →DCO recombinants
st--ss--e or e--ss--st.
2. By Using three cases of trial and error to find the DCO recombinant from
Parental type
st + + st ss +
+ + e. These are DCO recombinants types
+ ss e
. 128
4. what is the map distance between the genes?
F1= + st + ♀ X e ts ss ♂
e + ss e ts ss
No F2 genotype Observed % of observed progeny
. Due toF2 1%
Phenotype
recombination = 1map
progeny No.
unit/cM, the map736+694
distance*between genes
1 Scarlet + st + 736 100= 71.5
ofEbony- Spineless
e-ss, ss-st and e-st is 16.3ecM,+ 14cM
ss and 30.3
694cM respectively.
2000
Non-recombinants
2 Wild type + + + 134 134+156 * 100= 14.5
Ebony- Scarlet- e st ss 156 2000
Spineless Recombinants: e…ss
3 Ebony-Scarlet e st + 136 136+108 *100= 12.2
Spineless + + ss 108 2000
Recombinants: ss…st
4 Ebony e + + 16 16+20 * 100= 1.8
Scarlet- Spineless + st ss 20 2000
DCO: e…ss…st
2000 .
 Recombination frequency e…ss = 14.5 + 1.8 =16.3
 Recombination frequency ss…st = 12.2 + 1.8 =14
 Recombination frequency e …st = 14.5 + 12.2 + 2(1.8) = 30.3
129
5. Calculate the coefficient of coincidence and interference value based

on which you also interpret what it means.
 Coefficient of coincidence is the ratio of observed frequency of double crossover
to the expected frequency of double crossovers.
 Therefore, interference is 1-0.79 = 0.21 or 21%.

 This means 79% of the expected number of double crossover have
occurred or 21% of the expected double crossovers were prevented
from occurring due to interference.
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5. MOLECULAR GENETICS
 Molecular genetics is the field of biology that studies:-
 the structure and function of genes at a molecular level.
 the processes whereby biological information is stored, copied,
repaired and decoded to create protein and other molecules within
cells and tissues.
 the molecular structure of DNA, its cellular activities (including its
replication), and its influence in determining the overall makeup of
an organism.
134
 The material responsible for heritable traits must:-
 contain the information for an organism’s cell structure, function,
development and reproduction.
 replicate accurately so that progeny cells have the same genetic
information as the parental cells.
 be capable of variation. Without variation (such as mutation and
recombination), organism would be incapable of change and
adaptation, and evolution could not occur.
 Long before experiments in the middle of 19 th showed that DNA and RNA
were proved to carry genetic information.
 The Three evidences to prove DNA and RNA as genetic materials are:-
 Transformation
 Phage Labeling
135
 Lysis and reconstitution
5.1. DNA and RNA as the Genetic Material
A. Evidence for DNA as genetic materials
i. Transformation:- DNA transformed R-type bacteria into S-type bacteria.
 Fredrick Griffith (1928)
 the bacteria had to be alive and had to possess the polysaccharide coat in order for
them to be infectious.
 the unknown agent responsible for the change in genetic material was a protein-the
transforming principle.
 Avery et al. (1944)

 the transforming principle (agent) was not protein but was instead DNA.
 DNA transformed R-type bacteria into S-type bacteria.
ii. Phage labeling
 Hershey and Chase (1953) reported that
 that DNA must be the material responsible for the function and reproduction of the
new phages during the infection process and
 the DNA, not the protein, must be the genetic material
136
DNA and RNA as the Genetic Material
B. Evidence for RNA as genetic materials
 Fraenkel-Conrat and Williams (1956) showed that a virus can be separated into its
component parts and reconstitute as a viable virus.
 Fraenkel-Conrat and Singer (1957) isolated the RNA and protein components and
reconstituted the RNA of one type with the protein of the other type
 RNA is the genetic material of TMV.
 Generally, it can be conclude that

 DNA is the genetic material.
 RNA serves as the genetic material in few viruses (retroviruses) that do not have DNA
 To comprise the genes, DNA must:-

 carry the information to control the synthesis of enzymes and proteins with in a cell,
 self-replicate with high fidelity yet show a low level of mutation, and
 be located on the chromosome. 140

DNA and RNA as the Genetic Material
 The progeny viruses isolated from the resulting lesions were

of the type specified by the RNA and not by the protein.
 These results conclusively showed that RNA is the genetic
material of TMV.
5.2. Chemical Composition of DNA and RNA
• Nucleic acids (both DNA and RNA) are made by joining four different
monomeric units of nucleotides in a repetitive way.
• Nucleotides are made of three components: Phosphate group, a pentose (5
carbons) sugar, and a nitrogenous (nitrogen containing) base.
• A nucleoside is a sugar-base compound while nucleotides are therefore
nucleoside phosphates.
142
• The sugars differ only in the presence (ribose in RNA) or absence

(deoxyribose in DNA) of oxygen in the 2’ position. i.e., the two sugars
differ by a chemical group attached to the 2’ carbon hydroxyl group (-OH)
in ribose, a hydrogen atom (-H) in deoxyribose.
143
The nitrogenous bases fall in to two classes, purines and pyrimidines.
In DNA the purines are adenine (A) and guanine (G), and the pyrimidines are
thymine (T) and cytosine (C).
The RNA molecule also contains adenine, guanine and cytosine but thymine
is replaced by uracil (U).
144
145
5.3. DNA Structure and the Central Dogma of Biology
! !
K S
A N
T H
187
6. MICROBIAL GENETICS
 Microbial genetics study the mechanisms of heritable information in
microorganisms, including bacteria, archaea, viruses and some protozoa and
fungi.
 Model organisms have been chosen partly for their different basic biological
properties, and partly for small size of individuals, short generation time, and the
ease with which they can be grown and mated under simple controlled conditions.
 For the study of vertebrate genetics, mice are to be preferred to elephants. The
need to study a wide range of biological and genetic traits has led to an array of
model organisms from each of the basic biological groups. Microorganisms' rapid
growth rates and short generation times are used by scientists to study evolution.
 Microbial genetics also has applications in being able to study processes and
pathways that are similar to those found in humans such as drug metabolism.
 Recombination is the exchange of corresponding DNA segments between
adjacent chromosomes during the special type of cell division that results in the
production of new genetic makeup.
 Recombinant DNA (rDNA) is combining of two or more pieces of DNA
molecules that have been combined together to form a single molecule i.e. hybrid
DNA molecules which have been engineered from at least two different sources.
 Cloning is a procedure which generates a large number of copies of a single
sequence of DNA.
 Gene cloning is the process in which a gene of interest is located and copied
(cloned) out of DNA extracted from an organism. When DNA is extracted from
an organism, all of its genes are extracted at one time. These procedures depend
upon the ability of vectors to continue their life cycles in bacterial or yeast cells in
spite of having foreign DNA inserted into them.
 Because the foreign DNA is carried into the bacterial or yeast cell by these
molecules, they are called cloning vectors.
 The genetics of gene cloning is concerned with selection and use of suitable
carrier molecule or vector, and a living system or host in which the vector can be
propagated.
 To act as a cloning vector a DNA molecule must be capable of entering a host cell
and, once inside, replicating to produce multiple copies of itself.
Two naturally occurring types of DNA molecule satisfy these requirements:

 Plasmids: - are small circles of DNA found in bacteria and some other
organisms. Plasmids can replicate independently of the host cell
chromosome.
 Virus chromosomes, in particular the chromosomes of bacteriophages
which are viruses that specifically infect bacteria. During infection the
bacteriophage DNA molecule is injected into the host cell where it undergoes
replication.
 An ideal host cell should be easy to handle and propagate, should be available as
a wide variety of genetically defined strains, and should accept a range of vectors.
 The basic steps in gene cloning:-
1. A fragment of DNA, containing the gene to be cloned, is inserted into a circular
DNA molecule called a vector, to produce a recombinant DNA molecule.
2. The vector transports the gene into a host cell. Within the host cell the vector
multiplies, producing numerous identical copies, not only of itself but also of the
gene that it carries.
3. When the host cell divides, copies of the recombinant DNA molecule are passed
to the progeny and further vector replication takes place.
4. After a large number of cell divisions, a colony, or clone, of identical host cells is
produced. Each cell in the clone contains one or more copies of the recombinant
DNA molecule; the gene carried by the recombinant molecule is now said to be
cloned.
Genetic Transfer in Bacteria
 Gene transfer is a one-way process in prokaryotes: a piece of genetic material (the
exogenote) is donated to the chromosome of a recipient cell (the endogenote) and
integrated into it.
 The transfer of genetic material between prokaryotes is called horizontal gene

transfer. It takes place in one of three ways: conjugation, transformation, or
transduction.
 Transposable elements and plasmids can move genetic material between

chromosomes and within chromosomes to cause rapid changes in genomes and
drastically alter phenotypes.
 Transformation- is the transfer of genetic material between organisms by small extracellular
pieces of DNA. Once donor DNA is inside the recipient, crossing over can occur. The result
is a recombinant cell that has a genome different from either the donor or the recipient.
 Conjugation: is a process in which there is a unidirectional transfer of genetic information

through direct cellular contact between a donor and a recipient bacterial cell. Genes
transferred between two live cells via sex pilus (gram -) or surface adhesion molecules (gram
+). Transfer mediated by a plasmid: small circle of DNA separate from genome that is self-
replicating but contains no essential genes. Plasmid has genes for its own transfer; Gram
negative plasmids have genes for pilus and Gram positive plasmids have genes for surface
adhesion molecules.
 Conjugation requires cell to cell contact between two cells of opposite mating type, usually
the same species, must be same genus. The ability to conjugate is conferred by the F
plasmid.. Bacterial cells that contain an F plasmid are called “F+”. Bacteria that don’t have
an F plasmid are called “F-”.
 F+ cells grow special tubes called “sex pilli” from their bodies. When an F+ cell
bumps into an F- cell, the sex pilli hold them together, and a copy of the F
plasmid is transferred from the F+ to the F-. Now both cells are F+. The Fertility
factor (F)- allows genes to be transferred from one bacterium carrying the factor
to another bacterium lacking the factor by conjugation. During conjugation
plasmid is replicated and single stranded copy is transferred to recipient.
Recipient synthesizes complementary strand to complete plasmid. Plasmid can
remain as separate circle or Plasmid can be integrated into host cell genome
resulting in permanent chromosomal changes
 Transduction is the transfer of genetic material from one cell to another cell by a
bacteriophage or just “phage”-bacterial viruses.
• Bacteriophage can be defined as obligate intracellular parasites that
multiply inside bacteria by making use of some or all of the host
biosynthetic machinery. Transduction has been found to occur in variety of
prokaryotes, including certain species of Bacteria.
 Bacteriophage can be classified as:
 Virulent: Capable of causing infection and eventually destruction and
death of the bacterial cell. These follow Lytic Cycle.
 Temperate: Does not because destruptic infection instead phage DNA
incorporated into bacterial DNA and replicate (Lysogenic Cycle) and after
some cycle become virulent cause lysis.
1. Genetics of bacteriophage and recombination
• Bacteriophages or phages are viruses that specifically infect bacteria as their
hosts. Like all viruses, phages are very simple in structure, consisting merely of a
DNA or occasionally RNA molecule carrying a number of genes, including
several for replication of the phage, surrounded by a protective coat or capsid
made up of protein molecules.
• Viral DNA is injected into the host cell, where it replicates and directs the
reproduction of the bacteriophage and the lysis of the bacterium.
Basic concepts of quorum sensing in bacteria
•Metagenomics is the cultivation independent analysis of the collective genomes of
microbes within a given environment, using sequence- and function-based
approaches. Though metagenomics is a novel tool in the field of plant-microbe
interaction, the technique has already led to remarkable advances. Among these, the
identification of yet-uncultivable phytopathogens or the description of the plant and
rhizosphere microflora, are two features that may lead to a better description of the
quality of agricultural lands, for instance in the case of disease suppressive soils. At a
more molecular level, the identification of novel density-dependent regulatory
functions (quorum sensing) and antagonizing elements (quorum quenching) that may
be used to develop sustainable, biological control strategies directed at plant
pathogen, are examples of valuable outcomes of metagenomics in the plant-microbe
interaction field.
7. MECHANISM OF GENETIC CHANGE
 Genetic variation can be caused by mutation, random mating, random
fertilization, and recombination between homologous chromosomes during
meiosis (which reshuffles alleles within an organism's offspring).
 Allele frequencies in a population may change due to four fundamental forces of
evolution:
 Natural Selection leads to an evolutionary change when some individuals with
certain traits in a population have a higher survival and reproductive rate than
others and pass on these inheritable genetic features to their offspring. Evolution
acts through natural selection whereby reproductive and genetic qualities that
prove advantageous to survival prevail into future generations.
 Genetic Drift is the change in the frequency of an existing gene variant (allele) in a
population due to random sampling of organisms i.e. is random fluctuations in the
frequency of gene appearance in a population.
 The process may cause gene variants to disappear completely, thereby reducing
genetic variability. In contrast to natural selection, environmental or adaptive
pressures do not drive changes due to genetic drift. The effect of genetic drift is
larger in small populations and smaller in large populations.
 Gene Flow (also known as gene migration) refers to the transfer of genes from the
gene pool of one population to another and may change the frequency and/or the
range of alleles in the populations due to the migration of individuals or gametes that
can reproduce in a different population.
 The introduction of new alleles increases variability within a population and allows
for new combinations of traits.
 Mutation can be defined as a change in the DNA sequence or chromosome of a
living organism. It is the ultimate source of new alleles in a gene pool
 According to their magnitude (mutations can occur at different levels), they can be
divided into three different groups: Gene, chromosome and genome mutations.
 A gene mutation can be defined as any change in the sequence of
nucleotides in the genetic material of an organism.
 A chromosome mutation is a change in the structure or arrangement of the
chromosomes such as duplications or deletions of chromosome segments,
inversions of sections of DNA (reversed positions) and translocation.
 Genome mutations are alterations in the number of chromosomes in the
genome.
 They can be classified into two groups: Aneuploidy and Euploidy.
 Aneuploidy is the losses and/or gains of individual chromosomes from the normal
chromosome set arising from errors in chromosome segregation, and
 Euploidy refers to variations in complete sets of chromosomes.
 Mutation is the process by which DNA base pair/chromosome change is produced.
 It can be the result of any detectable change that affects DNA’s chemical or
physical constitution, its replication, its expression and phenotypic function (base
pairs may be added, deleted substituted, reversed in order or inverted, or
transposed to new positions).
 If a mutant cell gives rise only to somatic cells a mutant spot or area is produced,
but the mutant characteristic is not passed on to the succeeding generation. This
type of mutation is called a somatic mutation.
 However, mutation in the germ line of sexually reproducing organisms can be
transmitted by the gametes to the next generation and producing individual with
the mutation in both somatic and germ line cells. Such mutations are called germ
line mutation which is a source of variation and sometimes important in mutation
breeding.
 Therefore a somatic mutation affects the individual in which it happens, while a
germ line mutation affects individuals of the subsequent generations.
 Mutation can be lethal, sub-lethal, sub-vital or vital to the organism.
 The organism whose genetic material is changed as result of mutation is called
mutant, while normal organism is called wild type.
 Mutations can occur spontaneously or they can be induced.
 Spontaneous mutations occur naturally, without the use of chemical or physical
mutagenic agents which can result from any one of a number of events, including
errors in DNA replication and spontaneous chemical changes in DNA.
 Errors in DNA replication result in base pair substitution, addition
/deletions.
 If addition or deletion mutation occurs in the coding region (exon) of a
structural gene, it will generate frame shift mutations.
 In spontaneous chemical changes, two of the most common chemical events that
occur to produce spontaneous mutations are depurination and deamination of
particular bases.
 In depurination a purine, either adenine or guanine, is removed from the
DNA when the bond breaks between the base and the deoxyribose sugar, and
 In deamination either cytosine or Thymine is removed.
 If such lesions are not repaired, there is no base to specify a complementary base
during DNA replication and this will result in the conversion of a C-G base pair
to a T-A base pair, resulted a transition mutation.
 Mutation can also be induced experimentally by the application/treatment with
mutagens are called induced mutations..
 Mutagen is any physical or chemical agent that significantly increases the
frequency of mutational events.
 Since the rate of spontaneous mutation is so low, geneticists use mutagens to
increase mutation frequency so that a significant number of organisms have
mutations in the gene being studied.
 There are two classes of mutagens:

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Haramaya University

College of Agriculture and

By:- Tullu Tadessa (MSc)

“But the principles of all remain the same”

 Second-become central to human affairs through :-

 Anatomically, pollination and reproduction of the plant could be

purple flower white flower Cross fertilization

• Results of Mendel’s F1 crosses for seven traits of pea plant

• A dihybrid cross is a cross between individuals that involves

• There are three mathematical operations to determine the probability that a

• Probability is a chance that an event will occur in the future and it

• Ptall = 3 tall / (3 tall + 1 dwarf) = 3/4 = 75%

• Pdwarf = 1 dwarf / (3 tall + 1 dwarf) = 1/4 = 25%

Phenotype (n) Observed Expected (0-e) (0-e)2 ∑(0-e)2

• Calculated X2 value is 3.43 and the tabulated value of X2 at n-1 degree of

• Deviation from complete dominance and complete recessive resulting in

b) Codominance refers to a situation when phenotypes of both homozygous

• E.g. Red x White ==> Red & White Spotted

c) Over-dominance is a condition in genetics where the

• Over-dominance can also be described as heterozygote

• Two or more genes governing the development of a single character,

• Pleiotropy is the situation in which a single gene is responsible for

Agro-Technical and Technology

Principle of Genetics (AEC1013)

Credit hrs. 4(2+2)

 Genetics is the science of heredity and variation.

2. MENDELIAN GENETICS AND ITS VARIATION

Testing Rules for segregation and Independent Assortment

1. Punnet Square:- is a grid system for predicting all possible

3. Progeny Testing- self-fertilizing F2 individuals and

producing an F3, to predict the frequencies of the phenotypic

• Probability is a chance that an event will occur in the future and it

1. Mutually Exclusive Events: The Addition Rule

2. Independent Events: The Multiplication Rule

Prob (YY and WW)=Prob (YY) * Prob (WW)

3. Binomial Expression Equation 1 = p2 + 2pq + q2

3.1. Chromosomes-features, morphology & nomenclature

 When viewed under microscope, chromosomes differ in size and morphology

 DNA of all eukaryotic chromosomes is associated with numerous

 Thus, chemically chromosome composed of DNA, RNA, histones

Structure of a chromosome consists of a single DNA strand packaged by proteins.

 Each chromosome has a distinct attachment point for microtubules

 The attachment point occurs at a constriction in the chromosome

 The kinetochore is the proteinaceous structure on the surface of the

 When a cell divides, spindle fibers attach to the centromere of each

 Based on the chromosome length and centromere position on the

chromosome classification and nomenclature based on centromere position 54

• Three terms are referred in the identification of chromosomes.

i. Karyotype is the number, size, and morphology of a chromosome set

ii. Karyogram is the physical measurement of chromosomes from a

iii. Idiogram represents a diagrammatic sketch (interpretive drawing) of

 Two successive nuclear divisions without intervening chromosome

 Meiosis I is a reductional division (reduction of chromosomes number

 It consists of prophase I, metaphase I, anaphase I and telophase I,

 Prophase of meiosis I can be divided into five stages

• Attachment of spindle to pair of homologous chromosome (bivalent) and

• Meiosis II is an equational division (results in separation of the