Mekdela Amba University

College Of Natural and Computational Science

Department of Biology
Principles of Genetics (Biol3051)
For 3rd year regular Biology Students

2018/2025
GIMBA, ETHIOPIA
Chapter 3: The cytological basis of heredity
• LEARNING OBJECTIVES
• After studying this chapter, students should be able to:
♣Discuss chromosomes structure, number, shape and type
♣Define cell cycle
♣Identify giant chromosomes
♣Describe the function of chromosomes
♣Demonstrate nature of chromosomes at different stages of cell cycle
♣Compare and contrast mitosis and meiosis and their roles
♣Describe the relationship between Mendelian inheritance with the nature of chromosomes in
meiosis
♣Discuss gametogenesis (spermatogenesis and oogenesis)
♣Analysis double fertilization mechanism in higher plants
• Chromosomes are structures within cells that contain genetic material.

• Cytogenetics is field of genetics that study microscopic examination of chromosomes.

• Cytogeneticist can make observation & examine chromosomal composition.

• This is usually accomplished during actively dividing cells.

• As cell ready to divide, chromosomes become more tightly coiled, shortens, thickening them
thereby increases their diameter so that become visible with light microscope.
• Term genome refers to the entire set of genetic material in a particular organism.

• Nuclear genome refers to complete set of chromosomes that resides in the cell nucleus.

• Eukaryotes have a mitochondrial genome and plants also have a chloroplast genome.

• Unless otherwise noted, eukaryotic genome refers to nuclear genome.

• Bacteria genome is typically a single circular chromosome.

• Each biological species is characterized by certain karyotype (number and morphology of
chromosomes).

• For example, human cells contain 23 pairs or 46 total.

• On rare occasions individuals may inherit an abnormal number of chromosomes above or

below the normal or an abnormal structure.

• Such chromosome abnormalities can often be detected by cytogeneticist with microscopic

examination during actively dividing cells.

• Change of quantity and morphology of chromosome is one of mechanisms of speciation.

3.1. Chromosomes (number, homology, morphology…)
• Chromosome number refers to the total number of chromosomes present in nucleus of cell.

• Organisms with multiples chromosome set are referred to as euploid.

• Eukaryotes such as plants, animals and fungi carry either one chromosome set (haploid) or two sets
(diploid) or three set….

• In these species, both haploid and diploid states are normal euploidy.

• Organisms that have more or fewer than the normal number of sets are called aberrant euploids.

• Polyploids are organisms that have more than two chromosome sets.

• They can be 3n (triploid), 4n (tetraploid), 5n (pentaploid), 6n (hexaploid), and so forth.

• The suffix ‘ploid’ refers to chromosome ‘sets’.

• Haploid or monoploid is an individual normally has only one chromosome set (n) for
example, male bees, wasps and ants.

• Normal life cycles of these insects, males develop by parthenogenesis (development of

unfertilized egg into an embryo without the need for fertilization).

• In most other species, however, monoploid zygotes fail to develop.

• Polyploidy is very common in plants but rare in animals.

• Increase number of chromosome sets indeed has been an important factor in origin of new
plant species.

• Animal species do not show such distribution, owing to the relative rareness of polyploid
animals.
Table: [Link] number of some species including human
Organism Chromosomes no Chromosome arrangement
Netted Adder's-tongue 1260 or 630 pairs highest chr no Diploid

Human 46 or 23 pairs Diploid

Monkey /Chimpanzee/ 48 or 24 pairs Diploid
Donkey 66 or 33 pairs Diploid
Horse 64 or 32 pairs Diploid
Mule 33+32 = 32pairs +1 (Odd no)
Wheat 42 Hexaploid
Barley 20
Maize 20
Livestock 60
Goat 60
Fruit fly 8 or 4 pairs Diploid
Jack jumper ant 1 haploid lowest chromosome no
• Organism with lowest number of chromosome set is Jack jumper ant which have only one
(haploid) chromosome number.

• Before identifying chromosome number of this organism, it was thought that nematode,
Ascaris megalocephalus univalens known as roundworm has only two chromosomes in the
somatic cells (2n=2).
Morphology
• Size: chromosome size is normally measured at mitotic metaphase from shortest 0.25μm in
fungi to longest 30 μm in trillium plants.

• However, most mitotic chromosome falls in range of 3μm in drosophila to 5μm in man and
10μm in maize.

• The monocots contain large sized chromosomes as compared to dicots.

• Organisms with less number of chromosomes contain comparatively large sized

chromosomes.

• Number of chromosomes in each somatic cell is the same for all members of a given species.
Shape
• Chromosome changes shape from phase to phase in continuous process of cell growth and
cell division.
• During interphase /resting phase/, chromosomes occur in of thin, elastic, contractile, thread
like form.

• Whereas in mitotic metaphase & anaphase, chromosome becomes thick and filamentous
which develop clear zone, known as centromere or kinetochore.

• Centromere divides chromosome into two parts and each part is called chromosome arm.

• Position of centromere varies from chromosome to chromosome providing it different shape.

• It can be at the center, near the center, near the end and at the end. Metacentric, sub
metacentric, acrocentric and telocentric respectively.
Chromatin
• It is eukaryotic chromosome composed & consists of DNA, RNA and protein.

• The protein of chromatin could be of two types: histones and non-histones.

• Histones are basic proteins they are enriched with basic proteins arginine and lysine.

• There are five types of histones called H1, H2A H2B, H3 and H4.

• At physiological pH they are cationic and can interact with anionic nucleic acids.

• They form highly condensed structure.

• Non-histones: In addition to histones, chromatin comprise of many different types of non-
histone proteins.

• They are involved in a range of activities, including DNA replication and gene expression.

• They also differ between different tissues of same organism.

• For example, scaffold proteins, Heterochromatin Protein 1, DNA polymerase.

• During cell division nuclear material organize into visible thread like structures named as
chromosomes that stains deep with basic dyes.

• The term chromosome was coined in 1888.

• Chrome is colored and soma is body, hence they mean “colored bodies” which is high order
and arrangement of DNA and proteins.

• It contains nucleotide sequences, many genes or hereditary units, regulatory elements, DNA
bound proteins, which serve in DNA packaging and control its functions.

• Chromosomes vary both in number & structure among organisms (see table 3/1) and the
number of chromosomes is characteristic of every species.

• Sutton & Boveri in 1902 suggested that chromosomes are physical structures of heredity
messengers.
DNA Packaging
• In 1974 Reger Kornberg reported chromosome is made up of DNA and protein.

• eukaryotes DNA is much more complex molecule w/h coiled and folded many times,
associated with various proteins.

• As we discuss above, chromosomal proteins are two types.

• Level of DNA packaging is schematically represented by the f/f three phases and diagram.
First level packing
• Winding or twisting of DNA around protein core to produce "bead-like" structure called
nucleosome.

• This gives packing ratio of about 6.

• This structure is invariant in both euchromatin and heterochromatin of all chromosomes.

• The protein core is composed of 8 histone proteins, two each of H2A, H2B, H3 and H4.

• Histone H1 forms linker between to nucleosomes.

• 146 bp of DNA is wrapped around each nucleosome.

Second level packing
• Coiling of beads in helical structure about 30 nm fiber found in both interphase chromatin
and mitotic chromosomes.

• This structure increases packing ratio to about 40.

• This appears to be solenoid structure with about 6 nucleosomes per turn.

• This gives packing ratio of 40, meaning every 1 μm long axis contains 40 μm of DNA.
Final level
• Fiber is organized in loops, scaffolds and domains that give a final packing ratio.

• About 1000 in interphase chromosomes and about 10,000 in mitotic chromosomes.

• Final level of packaging is characterized by 700 nm structure seen in the metaphase

chromosome.
Diagrammatically
Euchromatin
• Genetically active DNA, lightly-stained regions of chromosome with basic dyes are called
euchromatin.

• It is loosely packed chromatin, rich actively participate genes in transcription process.

• Of course extent of condensation varies during life cycle of cell, plays an important role in
gene expression & regulation.

• During interphase chromatin are decondensed & known as euchromatin leading to gene
transcription and DNA replication.

• It contains around 90% of entire human genome. For example, housekeeping genes.
Heterochromatin
• It is defined as the area of chromosome which is tightly packed and condensed form of DNA
in the nucleus darkly stained with DNA staining dye.

• They are highly condensed, ordered and organized areas in nucleosomal arrays.

• It resembles chromatin of cells undergoing mitosis.

• They contain repetitive DNA found at centromeres and telomeres form heterochromatin.

• There are two type heterochromatins; facultative and constitutive.

Table: 3/2 difference summary between heterochromatin and euchromatin

No Euchromatin Heterochromatin

1 Form loosely packed DNA Form tightly packed DNA

2 Low DNA density High DNA density

3 Found both in prokaryotic and eukaryotic Only found in eukaryotic

4 Has active state Has inactive state

5 Early replication Late replication

6 Has no sticky region Has highly sticky region

7 Actively participate in transcription Has no role in transcription

Important parts of eukaryotic chromosome
• Centromere: is condensed regions within the chromosome that are responsible for the
accurate segregation of replicated chromosome during mitosis and meiosis.

• Telomere: region of DNA at the end of the linear eukaryotic chromosome that are required
for replication and stability.

• Telomere replication: Telomere replication is an important aspect in DNA replication.

Human chromosome karyotype
• It is photographic descending arrangement of chromosome
Giant chromosomes
• Some cells at certain particular stage of their life cycle nuclei contain giant or large sized
chromosomes.

• Polytene and lampbrush chromosomes are examples of giant chromosomes.

۞ Polytene chromosome
• Giant chromosomes were first observed in 1881 & after in nuclei of secretory cells or salivary
glands of chironomas larvae or diptera & drosophila.

• Since they discovered in salivary glands of insects, they termed as salivary gland
chromosomes.
• The name polytene chr. was coined due to occurrence of many chromonemata (DNA) in them.

• Larva salivary gland cells of drosophila, mosquito and chironema contain high DNA content
chromosomes.

• Giant chromosomes also occur in malpighian tubules, rectum, gut, foot pads, fat bodies,
ovarian nurse cells etc.

• Polytene chrs. replicate several times without nuclear division (endomitosis) and resulting
daughter chromatids do not separate but remain aligned side by side.

• During endomitosis nuclear envelope does not rupture, no spindle formation.

• Polytene chromosomes are visible during interphase & mitosis prophase.

• They are 100 times thicker, contain 1000 to 2000 chrs, than chrs. found in other cells.

• As stained & viewed under cpd microscope at 40X magnification display ~5000 bands.

• This is equivalent to 85% of DNA is bands and the rest 15% is inter bands.

• Individual bands correlated with particular genes, constant within species, helps in
chromosome mapping during cytogenetic studies.
Lampbrush chromosome
• Lampbrush chromosomes were first observed in 1882 in sections of salamander oocytes.
• Look like brushes used for cleaning lamps, hence the name lampbrush chromosome.

• can be observed during prophase I in oocytes of all animal species vertebrates &
invertebrates, mollusca, echinodermata, several insect species, shark, amphibians, reptiles,
birds & mammals (humans) even in plants.

• They are smaller in invertebrates than vertebrates.

• Observed in oocytes because oocytes are high in DNA content.

3.2. Cell cycle
• Cell cycle is life story of cell, through which it passes from one stages to the next.

• It is sequence of events by which cell duplicates its genome, eventually divides into two
daughter cells.

• This process is critical to genetics because, through cell cycle, genetic instructions are passed
from parent to daughter cells.

• New cycle begins after cell has divided and produced two new cells.
• Then undergo additional cell cycles.

• Although cell cycle is continuous process, cell growth, DNA synthesis, assembling molecules
and final division phenomena occur in specific stage of cell cycle.

• Replicated chromosomes distributed to daughter nuclei by complex series of events under

stringent controlling mechanism.

• Cell division is crucial process in all living organisms; for growth, DNA replicate, replace lost
cell, repair damaged tissue, reproduce organism.

• All these processes must be take place in coordinated way to ensure correct cell division.
Phases of cell cycle
• Cell cycle consists of two major phases.

• These are interphase and mitosis phase.

• Interphase is first period cell cycle, in which cell grows, develops, DNA, RNA, proteins are
being produced, hundreds of biochemical reactions are taking place.

• Interphase is extended period of growth and development.

• Interphase comprises gap 1 (G1), synthesis (S), and gap 2 (G2).

• The second phase is mitotic phase (M- phase).

• This is active cell division period that consists four nuclear division parts.

• Mitotic phase takes place as a result of lysosomal action.

• Important role of cell cycle is produced cell contains full complement of chromosomes no net
reduction or increment in chromosome number.

• Cells divide once in approximately every 24 hours.

• Let’s see each phases of cell cycle one by one:

Interphase (resting phase)
• It is the first phase of cell cycle.

• Throughout interphase, chromosomes are relaxed, uncoiled, invisible, individual

chromosomes cannot be seen with microscope only as diffuse chromatin.

• It holds about 90% of duration of cell cycle.

• Sometimes it is called resting phase, but cell is preparing for division by undergoing both cell
growth and DNA synthesis at this time.

• The interphase is divided into three further phases: G1, S, and G2.
G1 (Gap 1 phase)
• Interphase begins with G1 (for gap 1).

• G1 phase is interval between mitosis & initiation of DNA replication.

• During G1 phase cell is metabolically active, continuously grows, necessary proteins for cell
division are synthesized.

• This phase lasts several hours but does not replicate its DNA.

• There is critical point in the cell cycle, termed as G1/S checkpoint.

• After this checkpoint has been passed, the cell is committed to enter in S phase.

• Before reaching G1/S checkpoint, cells may exit from active cell cycle in response to
regulatory signals and pass into non-dividing phase.

• This non-dividing is called G0, which is stable state during which cells usually maintain
constant size.

• They can remain in G0 for an extended period of time even indefinitely or they can re-enter
G1 and active cell cycle.

• Many cells never enter G0 rather, cycle continuously.

S (Synthesis phase)
• After G1, cell enters to S phase (for DNA synthesis), in which each chromosome duplicates.

• During S-phase, DNA is synthesis /replication/ takes place, amount of DNA will be double
per cell.

• DNA synthesis must take place before the cell proceeds to next stages such as G2 and mitosis.

• If DNA synthesis is blocked (with drugs or by a mutation), the cell will not be able to undergo
mitosis.
G2 (Gap 2 phase)
• After S phase, the cell enters G2. At this phase, several additional biochemical events
necessary for cell division take place.

• Assembling cytoplasmic materials necessary for mitosis and cytokinesis.

• An important G2/M checkpoint is reached in G2; after this checkpoint has been passed, cell is
ready to divide and enters M phase.

• Although length of interphase varies from cell to cell type, mammalian cell spends about 10
hours in G1, 9 hours in S & 4 hours in G2.

• Therefore, interphase stays about 23 hours

• This condition changes dramatically when interphase draws to close & cell enters M phase.

• Fig. 3/4 Cell cycle

3.3. Mitosis (phases, significance to maintain genetic constancy)
• Mitosis is 2nd phase of cell cycle or period of active cell division & process of nuclear division
undergoes.

• Mitosis is a continuous process.

• However, for descriptive purposes, it breaks into four nuclear division stages:

• Prophase, metaphase, anaphase and telophase (Greek: pro- before; meta- mid; ana- back;
telo- end).

• Finally, telophase is followed by cytokinesis.

• Timing of four stages varies from species to species, from organ to organ within species, even
from cell to cell.

• It involving reorganization of all components of the cell.

• Since number of chromosomes in parent and progeny is the same, it is also called an
equational division.

• Specific cellular events occur during each stage to ensure the cell divides properly.

• Mitosis is universal process that result two identical daughter cells from a single mother cell.
Mitotic spindle
• The mitotic spindle: the process of mitosis involves an apparatus called spindle fibers.

• This structure is composed of microtubules, hollow cylinders made of protein subunits.

• Microtubules provide shape and structure to a eukaryotic cell as well as allow the cell to
move like cilia and flagella.
Prophase
• Prophase is the initial phase of mitosis.

• This stage is characterized by formation of spindle, shortening, thickening, condensed, so

individual chromosomes become into compact structure & visible.

• Due to disintegration or breaks down of nuclear envelope & nucleolus disappears it form
number of small vesicles..

• Nucleolus is darkly stained body in nucleus that is involved in ribosome construction &
formation of nucleolar organizer.

• Centrosomes organize production of microtubules that form spindle fibers to constitute

mitotic spindle.
• Each replicated chromosome can now be seen to consist of two identical chromatids (or sister
chromatids) held together by a structure known as the centromere.

• Spindle fibers are initially nucleated at the centrosome and grow outward into the cytoplasm.

• These proteinaceous complex fibers at the centromere of each sister chromatid are called
kinetochore microtubules.

• They ensures that sister chromatids movement to opposite poles during anaphase.

• The number of microtubules that attach to each kinetochore differs in different species.
• It seems that 1 attaches to each kinetochore in yeast, 4 to 7 attach to each kinetochore in the
fetus of rat cells, 70 to 150 attach in the plant Haemanthus.

Fig. 3/5 Prophase fig. 3/6 kinetochore

Metaphase
• During this phase chromosomes move to equator of the cell k/as metaphase plate .

• This happens as kinetochore microtubules exert opposing tension on the two sister
kinetochores.

• Alignment of the chromosomes on this plate marks the end of metaphase.

Fig. 3/7 metaphase

Anaphase
• During this phase, physical separation of sister chromatids and move toward opposite poles
on the spindle.

• kinetochore & microtubule motor, disassembling moves and pulling chromosomes.

• Anaphase is the shortest stage of mitosis.

• The centromeres divide, and the sister chromatids of each chromosome are pulled apart or
'disjoin' and move to the opposite ends of the cell, pulled by spindle fibers.

• The separated sister chromatids are now referred as daughter chromosomes.

• Each daughter cell receives the same chromosome. Then after spindle fibers begin to
disappear.

• Metacentric chromosomes appear V-shaped, sub-telocentrics appear J-shaped, and telocentrics

appear rod-shaped.

• Fig. 3/8 Anaphase

Telophase
• It is final stage of mitosis.
• Cell now reverses or return to interphase state. Such as chromosomes uncoil, nuclear envelope
re-forms, (reappears), protein begin to synthesis.

• Chromosomes uncoil and become diffuse no longer visible, spindle fibers disappear.

• Cytokinesis start.

• Fig. 3/9Telophase
Cytokinesis
• It is cytoplasmic division follows telophase but it is not part of mitosis or meiosis.

• It is the process of division of cytoplasm into two daughter cells (opposed to karyokinesis,
which is division of nucleus).

• Daughter cells grow to reach their regular size during this period.

• Two new daughter cells will form.

• In plant cells, “cell plate” is formed along metaphase plate; whereas in animals cell by
constriction or by (cell furrow).
• Difference of plants & animals cytokinesis is due to the presence and absence of cell wall in the two
cell types respectively.

• Then the cell enters to interphase.

• Fig. 3/10 Animal and plant cell cytokinesis

Significance of mitosis
• Mitosis results diploid daughter cells with identical genetic complement.

• Growth of multicellular organisms is due to mitosis.

• It also contribute significant role is cell repair.

• For example, upper layer of epidermis cell, cells lining of gut, blood cells are being
constantly replaced by mitosis.

• Apical meristematic tissues & lateral cambium, results continuous growth of plants
throughout their life by mitotic division.
• Mitosis important means of reproduction mechanism for asexually reproduce organisms such
as bacteria, yeast, by budding, binary fusion.

• Cytokinesis & mitosis result two daughter cells, each with genetic material identical to parent
cell.

• Exact distribution of genetic material to daughter cells, ensures stability of inheritance traits
from generation to the next.

• Cells have evolved complex life functions; with mitosis, they will produce offspring cells with
same capabilities.
• Biological aim of mitosis is supplying identical genetic information of two daughter cells.

• Fig. 3/11 Mitosis

3.4. Control of the cell cycle
• Cell cycle is series ordered events that leads a cell to divide itself into two daughter cells.

• It is complex and highly regulated process.

• Gene regulation is phenomenon that genes can be expressed at high or low levels, at early or
adult stage.

• Ability to regulate genes provides many benefits to eukaryotic organisms.

• For many years, biochemical events of controlling cell cycle & its progression were
completely unknown.

• But research has now revealed many details of process.

• Progression of cell cycle is regulated at several checkpoints.

• One of checkpoint is G1/S, comes just before cell enters into S phase & DNA replication.

• When this point has been passed, DNA replicate is allowed.

• The 2nd critical checkpoint, is G2/M, at the end of G2, before cell enters mitosis.

• They ensure all cellular components are present & in good working order before cell
proceeds to next stage.

• Checkpoints are necessary to prevent cells with damaged or missing or extra chromosomes
from being proliferating.
• Both G1/S & G2/M checkpoints are regulated by two protein molecule interaction.

• They are
Cyclin
 Cyclin dependent kinase (CDK).

• [] of the first protein oscillates during cell cycle whereas the 2nd protein cannot function
unless it is bound to cyclin.

• Both are called by different names in different organisms, here we use terms applied to yeast.
Let’s see
• G2/M checkpoint, it is regulated by cyclin B, which combines with CDK to form M-phase
promoting factor (MPF).

• After MPF is formed, it is activated by addition of phosphate group to CDK amino acids.

• Amount of cyclin B changes throughout cell cycle, but CDK amount is remains constant.

• For instance, during G1, cyclin B levels are low; so amount of MPF also is low.

• As more cyclin B is produced, it combines with CDK so ing MPF amounts.

• Near the end of G2, amount of active MPF reaches critical level, which permit cell to divide.
• MPF [] continues to increase, reaching a peak in mitosis.

• Active form of MPF is protein kinase enzyme that adds phosphate groups to certain other
proteins.

• Active MPF brings many events associated with mitosis, such as nuclear-membrane
breakdown, spindle formation, chromosome condensation….

• At the end of metaphase, cyclin is abruptly degraded, which lowers amount of MPF initiating
motion in anaphase.

• Ultimately this brings mitosis to close, MPF brings its own demise by destroying cyclin.
• Generally, high levels of active MPF stimulate mitosis whereas low levels of MPF bring
return to interphase conditions.

• Stimulate factor synthesis cyclin B and activate MPF, whereas other factors inhibit MPF.

• The sum total of factors together determine whether the cell passes through G2/M checkpoint
& ensure mitosis or inhibit until conditions are appropriate for division.

• For example, DNA damage inhibits activation of MPF; so cell is arrested in G2 and does not
undergo division.
• Life cycle of complex eukaryotic organisms involves progression developmental stages to
achieve mature organism.

• Some genes are expressed only during early stages of development, such as embryonic stage,
whereas others are expressed in adult.

• In addition, complex eukaryotic species are composed of many different tissues contain
variety of cell types.

• Gene regulation is necessary to ensure differences in structure and function among distinct
cell types.

• Cell external signals & internal information together determine whether cells enter division
cycle or terminate cycle.
• Progression of cell cycle is driven by activation and inactivation of CDKs, w/h trigger or
inhibit transition to subsequent phases of cycle.

• CDKs are small serine/threonine protein kinases require association with cyclin subunit for
activation.

• Many levels of regulation drive upon CDKs to force tight control over cell-cycle progression.

• Such regulation involves controlling of gene expression, activating & inhibiting,

phosphorylation & de-phosphorylation of CDKs.

• Multicellular organisms developed from single-cell sperm & egg (n) to zygote (2n) by
fertilization grow to adult & fully matured organism require many rounds of cell division.

• During each division, cells complete an ordered series of events that collectively form the
"cell cycle".
• Cell cycle involve accurate duplication of genome during DNA synthesis phase & segregation
of complete sets of chromosomes to each daughter cells in M phase.

• Summary
• Generally cell cycle checkpoints controls and prevent progression of error cell cycle and cell
division transitions before to completion.

• These are some of the check points at cell division

 DNA-damage induced checkpoint

 DNA-replication induced checkpoint

 Spindle-assembly checkpoint
3.5. Meiosis (phases and significances in chromosome number reduction and
creating genetic variation)
• Meiosis: is specialized type of cell division (nuclear division) that share many features with
mitosis.
• However, it has many distinguishing features from mitosis such as producing four haploid
genetically distinct daughter cells.

• Reduction chr. no in sex cells or gametes is critical for sexual reproduction.

• During fertilization, zygote (2n) is formed proper chr. no for diploid organism.

• Then fertilized egg undergo mitotic/ somatic cell/ divisions to become complex multicellular
organism.
• Unlike mitosis, meiosis occurs only in certain kinds of cells.

• In animals, meiosis begins in primary gametocytes; in higher plants, it takes place only in
sporophyte generation spore-mother cells.

• Other unique feature of meiosis is, it involves two successive nuclear divisions Meiosis I &
Meiosis II.

• Each with its own prophase, metaphase, anaphase and telophase.

• Meiosis produce four haploid cells.

• Each gamete /sex cell/ contains ½ chr. no in humans each gamete contains 23 chromosomes.

• Fertilization of an egg or ovum by sperm, each 23 chromosomes restores diploid 46 chr. no.
• Animals gametes (sperm & egg) formed from diploid tissue (gametocytes) rather than from
haploid gametophyte generation.

• Sperm and egg join to form diploid zygote which develops into mature adult.

• In plants, male gametes from pollen (anther /stamens) unites with female gamete in pistil to
form fertilized diploid zygote.

• Other male gamete combines with diploid endosperm nucleus to form triploid endosperm.
How is meiosis different from mitosis?
• Mitosis consists of single nuclear division & accompanied by single cell division.

• Meiosis, on the other hand, consists of two divisions.

• Mitosis, form the same chr. no as original cell, whereas meiosis causes to reduce chromosome
number by half.

• Mitosis produces genetically identical cells, whereas meiosis produces genetically variable
cells.

• Like mitosis, meiosis is preceded by an interphase stage that includes G1, S & G2 phases.
• The words mitosis and meiosis are sometimes confused.

• They sound a bit alike, both include chromosome division and cytokinesis.

• Don’t let this deceive and mislead you.

• The outcomes of mitosis and meiosis are radically different.

• Several unique events that have important genetic consequences take place only in meiosis.
• Meiosis is general name given to two successive nuclear divisions k/as meiosis I & meiosis II.

• Meiosis takes place in special diploid cells called meiocytes.

• Due to two successive divisions, meiocyte gives rise to four haploid cells .

• In animals & plants, the products of meiosis become haploid gametes.

• Meiosis takes place in gonads to produces gametes sperm & eggs (spermatozoa & ova).

• Before meiosis, S phase duplicates DNA to form sister chromatids, just as in mitosis.
Prophase I:
• During prophase I, the same events that occurred in mitosis also occur.

• Chromatin condenses into visible chromosomes, nuclear membrane disintegrates & spindle
fibres are formed.

• Unique event that occurs during prophase I is synapsis where homologous chromosomes
lineup and fuse together.

• This fusion allows to exchange genetic material b/n two chromosomes in process called
crossing over.
Metaphase I:
• Microtubule from one pole attaches to homologous pair microtubule from the other pole.

• Then pair homologous chromosomes are initiated to line up on the metaphase plate.

• This is distinct from mitosis, since each replicated chromosome lines up by itself on
metaphase plate.

• This is due to the synapsis or cross over event during prophase I.

Anaphase I:
• It is marked by separation of pair of sister chromatids from homologous chromosomes.

• Two chromosomes of homologous pair are pulled toward opposite poles.

• Although homologous chromosomes separate, sister chromatids remain attached and travel
together.

• Again this is different from mitosis in which individual sister chromatids are moved to
opposite ends of the cell.
Telophase I:
• Chromosomes arrive at the poles and the cytoplasm divides.

• The period between meiosis I (Telophase I) and meiosis II (prophase II) is called interkinesis.

• In many organisms, after meiosis I daughter cells begin immediately to prepare for the
second meiotic division.

• However, in others nuclear membrane reappears between telophase I and prophase II, and
there is a period of rest.

• In other word, the period during which membrane is again visible is called interkinesis.
• This means nuclear membrane re-forms around chromosomes clustered at each pole, spindle
breaks down and chromosomes relax.

• On the other hand, some cells during interkinesis chr. remain condensed, spindle does not
break down & no formation of nuclear membrane.

• These cells move directly from cytokinesis into meiosis II.

• Generally, telophase I involves division & separation of maternal cell to produce two
daughter cells.

• These two daughter cells are haploid in chr. no & distinct in genetic make-up due to crossing
over.
• Fig. 3/12 Meiosis I
Prophase II:
• Events are reversed: i.e. chromosomes re-condense, spindle re-forms, & nuclear envelope
again breaks down (disappears).

• Metaphase II: like mitosis metaphase, individual chromosomes line up and joined centrally
by centromeres on metaphase plate with sister chromatids facing opposite poles.

• Anaphase II: kinetochores of sister chromatids separate and chromatids are pulled to
opposite poles of the cell.

• Each chromatid is now distinct chromosome.

Telophase II:
• Chromosomes arrive at the spindle poles, nuclear membrane begins to form around chrs.
(nuclear envelope re-forms), chromosomes relax and are no longer visible.

• After telophase II completed, second cytoplasmic division ( 2nd cytokinesis) follows.

• In cytokinesis cell organelles become evenly distributed among daughter cells.

• Four daughter cells are produced from each meiotic division.

• Of these 4 haploid daughter cells, 3 of them are degenerated cells only one functional cell.
•

• Fig. 3/13 Meiosis II

Significance of meiosis
• Biological value of meiosis consists reduction of chr. no, necessary for reception of gametes
& maintenance of karyotype constancy.

• It increases genetic variability in the population of organisms from one generation to the next
by recombination, crossing-over & synapsis of chromosomes.

• W/h maintain biological variety at level of kind & receptions of new genetic combinations at
descendants enable for the process of evolution.
Genetic variation is very important
• How meiosis generates genetic diversity?
 Through
• Exchange of genetic material between homologous chromosomes.

• Random alignment of maternal and paternal chromosomes.

• Random alignment & random distribution of sister chromatids.

• Production and fusion of haploid gametes

• Crossing over & synapsis between homologous chromosomes

Table 3/3 Comparison between mitosis & meiosis
No Distinguishing Meiosis Mitosis
features

1 Definition Means of sexuall reproduction, chr. no reduced by Process of asexual reproduction cells divide into
½ through separation of homologous chr. in diploid two exact copy of daughter cells formed, equal no
cell of chromosome
2 Function Produce gametes for sexual reproduction Growth, repair, asexual reproduction

3 Occur In gonad cell of plant, animal In somatic cell of all organisms

4 Produce Four haploid genetically different daughter cells Two diploid genetically the same daughter cells

5 Chr. no Reduced by half (homologous pairs separates) Remain the same with the parental chromosome

6 No of division Two nuclear and cytoplasmic division One division of nucleus and cytoplasm
3.5.1. Correlation of chromosome behavior in meiosis with that of Mendelian factors)
• While explaining laws of inheritance, Mendel suggested that the factors were hereditary units
which were transmitted from cell to cell and generation to generation.

• However, Mendel didn’t know at all about physical explanation of his results.

• After Mendel Wilhelm Roux pointed out the importance of chromosomes in the heredity.

• He suggested that chrs. were strings of bead-like stru w/h present in the nuclei of cells.

• He also tried to explain mechanism of gene transmission from cell to cell.

• The concept of chromosomal inheritance theory was formulate by two scholars.

• They are Walter Sutton (American) & Theodor Boveri (German biologist) in early 1900s.

• The two investigators independently working with meiosis & recognized behavior of
Mendel’s hypothesis. particles

• During production of gametes in peas precisely parallels to behavior of chrs. at meiosis.

• Look: genes are in pairs (so are chrs); alleles of gene segregate equally into gametes (so do
members of pair of homologous chrs.); d/t genes act independently (so do different chr. pairs).
• Both investigators reached the same conclusion, which was parallel behavior of genes and
chromosomes strongly suggests that genes are located on chromosomes.

• After studying cell division, they proposes that chrs. are the location of Mendel’s “factors”

• They verified behavior of chrs. in meiosis & fertilization provided physical evidence of
Mendel’s Law of Segregation.

• Mendel knew nothing of the chromosomes and meiosis.

• By the process of fertilization the original number of chromosomes is restored in the zygote.
3.5.2. Gametogenesis (spermatogenesis, Oogenesis)
• Gametogenesis is general process by w/h gamete cell formation (sex cells) in male & female
in sexually reproducing organisms.

• It occurs via special nuclear division k/n as meiosis.

• It reduce chr. no by ½ & produce haploid cells (n) from diploid cells (2n).

• There are two main types of gametogenesis:

• Spermatogenesis (in males) & Oogenesis (in females).

Spermatogenesis
• Gametes in male animal (spermatogenesis) takes place in the testes. Or

• The process of production of sperm cell by spermatogenesis occurs within glands k/n as
testes.

• Spermatogenesis produces four haploid sperm cells.

• Testes contain spermatogonial cells that divide by mitosis to produce two cells.

• One of these remains spermatogonial cell, the other cell becomes primary spermatocyte.

• Spermatocyte progresses through meiosis I & meiosis II to produce four haploid cells, which
are known as spermatids.
• These cells then mature into sperm cells.
• The structure of sperm cell has long flagellum, neck & head.

• The head of sperm contains haploid nucleus and an organelle at its tip, known as an acrosome.

• An acrosome contains digestive enzymes that are released when sperm meets an egg cell.

• These enzymes enable sperm to penetrate outer protective layers of the egg and gain entry into
the egg cell’s cytosol.

• In animal without mating season, sperm production is continuous process in mature males.

• For example, mature human male produces several hundred million sperm each day.
• Diploid primordial germ cells divide mitotically to produce diploid cells called spermatogonia.

• Each spermatogonium can undergo repeated rounds of mitosis, giving rise to numerous
additional spermatogonia.

• Spermatogonium then initiate meiosis & enter into prophase I now called primary
spermatocyte.

• Spermatocyte cell is diploid because homologous chromosomes have not yet separated.

• Each primary spermatocyte completes meiosis I, giving rise to two haploid secondary
spermatocytes then undergo meiosis II, each produces two haploid spermatids.
• Each primary spermatocyte produces total of 4 haploid spermatids, w/h mature & develop
into sperm.

• Fig. 3/14 Spermatogenesis

Oogenesis
• Production of gametes in female (oogenesis) begins much like spermatogenesis.

• Diploid primordial germ cells within the ovary divide mitotically to produce oogonia.

• Like spermatogonia, oogonia can undergo repeated rounds of mitosis or they can enter into
meiosis prophase I still these cells are diploid called primary oocytes.

• Each primary oocyte completes meiosis I.

• Here the process of oogenesis begins to differ from that of spermatogenesis.

• In oogenesis, cytokinesis is unequal (asymmetric division) most of the cytoplasm is

allocated to one of the two haploid cell called secondary oocyte.
• Smaller cell, which contains ½ chrs. but only small part of cytoplasm, is called the first polar body; it
may or may not divide further.

• Secondary oocyte completes meiosis II & again cytokinesis is unequal most of cytoplasm passes into
one of the cells.

• Larger cell, which acquires most of cytoplasm, is ovum, mature female gamete; the smaller cell is
second polar body.

• Only the ovum is capable of being fertilized, polar bodies usually disintegrate.

• Oogenesis produces single mature haploid egg cell gamete from each primary oocyte.

• The place of meiosis in sexual cycle of two organisms, flowering plant and multicellular animal.
• These cycles are two of the many variations found among eukaryotic organisms.

• Cellular events that produce reproductive cells in plants and animals differ in
• Number of cell divisions
• Number of haploid gametes produced
• Relative size of the final products

• Overall result is the same: meiosis gives rise to haploid, genetically variable cells that then
fuse during fertilization to produce diploid progeny.
• In female animals, oogenesis, production of egg cells, occurs within specialized diploid cells
of ovary known as oogonia.

• Quite early in the development of ovary, oogonia initiate meiosis to produce primary oocytes.

• For example, in humans, approximately 1 million primary oocytes per ovary are produced
before birth.

• These primary oocytes are arrested enter in dormant phase at prophase of meiosis I, remaining
at this stage until the female becomes sexually mature.

• Beginning at this stage, primary oocytes are periodically activated to progress through
remaining stages of oocyte development.
• During oocyte maturation, meiosis produces only one cell that is destined to become an egg,
as opposed to the four gametes produced from each primary spermatocyte during
spermatogenesis.

• How does this occur? As shown in fig.3/15, a and b show the first meiotic division is
asymmetrical and produces secondary oocyte and much smaller cell, known as polar body.

• Most of the cytoplasm is retained by secondary oocyte and very little polar body, allowing
the oocyte to become larger cell with more stored nutrients.

• The secondary oocyte then begins meiosis II.

• In mammals, secondary oocyte is released from ovary an event called ovulation and travels
down the oviduct toward the uterus stimulated to complete meiosis II.

• Finally, secondary oocyte produces haploid egg and second polar body.

• During this journey, if a sperm cell penetrates the secondary oocyte, the haploid egg and
haploid sperm nuclei unite or undergo fertilization to create diploid nucleus of new individual.

• Most species of animals are diploid and their haploid gametes are considered to be specialized
type of cell.
• Fig. 3/15 Oogenesis
Summary on spermatogenesis and Oogenesis
• Location: Testes (specifically, seminiferous tubules)

• End product: 4 functional sperm cells from one diploid germ cell
• Process:
• Spermatogonium (2n) → mitosis → primary spermatocyte (2n)

• Primary spermatocyte → meiosis I → 2 secondary spermatocytes (n)

• Each secondary spermatocyte → meiosis II → 2 spermatids (n)

• Spermatids mature into spermatozoa (sperm)

Oogenesis (in females)
• Location: Ovaries
• End product: 1 functional ovum (egg) and 2–3 polar bodies (non-functional)
• Process:
• Oogonium (2n) → mitosis → primary oocyte (2n)
• Primary oocyte → meiosis I → secondary oocyte (n) + polar body (n)
• Secondary oocyte → meiosis II (only if fertilized) → ovum (n) + polar body

Feature Spermatogenesis Oogenesis

1 No of gametes 4 sperm cells 1 ovum + 3 polar bodies

2 Timing Continuous after puberty Begins before birth, resumes at puberty

3 Duration Rapid Long (may take years to complete)

3.5.3. Sporogenesis (microsporogenesis, megasporogenesis male and female
gametophytes formation)
• Life cycles of higher flowering plant alternate b/n diploid sporophyte & haploid
gametophyte generations.

• Meiosis produces haploid cells called spores, which divide by mitosis to produce
gametophyte.

• In these higher sporophyte flowering plants, spores develop into gametophytes that contain
only a few cells.

• Gametophytes are small structures produced within much larger sporophyte.

• Certain cells within haploid gametophytes then be specialized as haploid gametes.

• Fig. 3/ 16 Alternative generative
• However, lower plants, such as mosses, haploid spore can produce large multicellular
gametophyte by repeated mitoses division.

• Meiosis occurs within two d/t structures of sporophyte: anthers & ovaries, which produce
male & female gametophytes respectively.

• Diploid microsporocytes anther /stamens/ or androecium undergo meiosis & produce four
haploid microspores.

• These separate into individual microspores.

• Each microspore undergoes mitosis to produce two-celled structure; one tube cell & one
generative cell both of them are haploid.
• Fig. 3/17 Microspore formation
• Tube cell differentiates into pollen grain, male gametophyte with thick cell wall.

• Generative cell undergoes mitosis to produce two haploid sperm cells.

• This mitosis differentiation occurs only if pollen grain germinates if it lands on stigma &
forms pollen tube.

• Similarly in female flower, (in pistil or gynoecium)

• Gametophytes k/n as megasporocyte produced within ovules in ovaries undergoes meiosis &
produce four haploid megaspores.

• Three of four megaspores degenerate.

• Remaining haploid megaspore further undergoes three successive mitotic divisions.

• Asymmetrical cytokinesis mitotic division produce seven cells 1egg, 2synergids, 3antipodals
& 1central cell.

• These seven-celled known as embryo sac, is mature female gametophyte.

• Each embryo sac is contained within an ovule.

• Fig. 3/18 Mega gametophytes production

Fertilization
• For fertilization occur, specialized cells within male & female gametophytes must meet i.e
pollen grain lands on the stigma .

• This stimulates tube cell to sprout tube grows through style eventually makes contact with an
ovule.

• During fertilization generative cell undergoes mitosis to produce two haploid sperm cells.

• The sperm cells migrate through pollen tube finally reach the ovule.

• One of the sperm enters central cell, which contains two polar nuclei.
• This results triploid (3n).

• This cell divides mitotically to produce endosperm, which acts as food-storing tissue.

• The other sperm enters the egg cell; egg & sperm nuclei fuse to create diploid cell, zygote,
which becomes plant embryo.

• Therefore, fertilization in flowering plants is double fertilization.

• Endosperm uses large plant resources, develop only when an egg cell has been fertilized.

• After fertilization is complete, ovule develops into seed, & surrounding ovary develops into
fruit, which encloses one or more seeds.
• Fig. 3/20 Plant fertilization
Difference b/n animal and plant
• When comparing animals and plants, it’s interesting to consider how gametes are made.

• Animals produce gametes by meiosis.

• In contrast, plants produce reproductive cells by mitosis.

• Gametophyte of plants is haploid multicellular produced by mitotic divisions of haploid spore.

• Within multicellular gametophyte, certain cells become specialized as gametes.

• Fig. 3/21 Alternative generation of human
Chapter 4: Probability and statistical testing in genetics
• Learning Objective: At the end of this chapter students should be able to:

• Differentiate and apply sum rule, product rule and binomial expansion for genetic
probability data

• Explain null and alternative hypothesis

• Discuss chi-square testing in genetic data

• Describe application of probability in genetics

• Use forked-line probability method

Aim to study statistics in Genetics
• Powerful application of Mendel’s work is laws of inheritance can be used to predict outcome
of genetic crosses.

• For example, in agriculture plant & animal breeders are concerned with types of offspring
their crosses will produce.

• This information is used to produce commercially important crops and livestock.

• In addition, people are often interested in predicting characteristics of children they may
have.

• Particularly important to individuals who carry alleles that cause inherited diseases.
• Of course, we can’t see future (we can’t do prophecy) & we definitively predict what will
happen.

• Nevertheless, genetic counselors can help couples to predict likelihood of having an affected
child.

• This probability is one factor that may influence a couple’s decision whether to have children.

• In this section, we will see how probability calculations are used in genetic problems to
predict outcome of crosses.
• To compute probability, we will use three mathematical operations sum rule, product rule &
binomial expansion equation.

• These methods allow us to determine probability of cross between two individuals will
produce particular outcome.

• To apply these operations, we must have knowledge regarding the genotypes of parents &
pattern of inheritance of given trait.

• Probability calculations can also be used in hypothesis testing.

• In many situations, researcher like to discern genotypes & patterns of inheritance for traits
that are not yet understood.

• Traditional approach to this problem is to conduct crosses and then analyze their outcomes.

• The proportions of offspring may provide important clues that allow experimenter to propose
hypothesis.

• Based on quantitative laws of inheritance, transmission of trait from parent to offspring. Can
be explained.

• Statistical methods such as chi square test, can be used to evaluate how observed data from
crosses fit the expected data.
4.1. Application of probability in genetics
• Experimental science, such as genetics, make decisions on hypotheses based on data gathered
during experiments.

• Geneticists have to understanding on probability theory and statistical tests of hypotheses.

• Probability theory allows to construct accurate predictions of what to expect from an

experiment.

• Statistical testing of hypotheses, like chi-square test, allows to have confidence in their
interpretations of experimental data.

• The chance that an event will occur in the future is called event’s probability.
• For example, if you flip a coin, probability of landing head side will be ½, 0.5 or 50%.

• In this case, two possible outcomes (heads or tails) are equally likely.

• This allows us to predict 50% chance that a coin flip will produce heads.

• Probability depends on number of possible outcomes.

• General formula for probability is (P) = Number_of times an evnent occurs

Total number of events

P head = 1 head / (1 heads + 1 tails) = 1/2 = 0.5= 50%

• Recall that when two heterozygous tall pea plants (Tt) are crossed, phenotypic ratio of
offspring is 3 tall to 1 dwarf.

• This information can be used to calculate probability for either type of offspring.

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

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

• When we add probability of all possible outcomes (tall &dwarf), we get sum of 100% (75% +
25% = 100%).

• NB: Always our probability result exist between 0 and 1 [null and sure] event.
• Probability calculation allows us to predict the likelihood that an event will occur in the
future.

• Accuracy of this prediction, however, depends to great extent on sample size.

• For example, if we toss a coin six times, our probability prediction would be 50% heads (three
heads and three tails).

• In this small sample size, however, we would not be too surprised if we came up with four
heads and two tails.

• Each time we toss a coin, there is random chance that it will be heads or tails.
• Deviation b/n observed & expected outcomes is called random sampling error.

• In small sample, error between predicted percentage of heads and the actual percentage
observed may be quite large.

• By comparison, if we flipped a coin 1000 times, percentage of heads would be fairly close to
the predicted 50% value.

• In larger sample, we expect the random sampling error to be much smaller percentage.
Important terminology
• Experiment: Practical activity, measurement or observation

• Sample space: totality of all conceivable sample point (e.g. tossing a coin 3 time)

• Outcomes (sample point) set of all possible results of random experiment

• Event: any subset of the sample space

• Mutually exclusive: occurrence of one event dose not affect the other (can’t occur
simultaneously.

• Random experiment: trial with repeated any number of times under similar conditions.
Rule one: Sum rule
• The sum rule used to predict the occurrence of one of two or more mutually exclusive events.
• It is also known as the either-or rule.

• For example, cross between two mice that are both heterozygous for genes affecting the ears
and tail.

• Gene designated de, is recessive allele that causes droopy ears; the other gene represent by De
stands to normal ear.

• An allele of second gene causes crinkly tail represented by allele (ct) which is recessive to
normal allele (Ct).
• Gametes: DeCt, Dect, deCt & dect

• If cross is made b/n heterozygous mice (DedeCtct), predicted ratio of sibling is 9 normal ears
and normal tails, 3 normal ears and crinkly tails, 3 droopy ears and normal tails, 1 droopy ears
and crinkly tail.
• These 4 phenotypes are mutually exclusive. i.e mouse with droopy ears and normal tail cannot
have normal ears and crinkly tail.

a. What is the probability of an offspring which have normal ears and normal tail?

• Or if we closed our eyes and picked an offspring out of litter from this cross

b. What is the probability of mouse with droopy ears and crinkly tail?

• In this case, the investigator wants to predict events will occur mutually exclusive.

• Strategy for solving such genetic problems using sum rule.

Solution
• Cross is b/n DedeCtct × DedeCtct, accomplished by using Punnett square.
• Probability of normal ears and normal tail is
• 9/(9 + 3 + 3 + 1) = 9/16
• Probability of droopy ears and crinkly tail is
• 1/(9 + 3 + 3 + 1) = 1/16
• Add together the individual probabilities.
• 9/16 + 1/16 = 10/16

• This means 10/16 is probability of offspring either normal ears and normal tail or droopy ears
and crinkly tail.

• 10/16 to 0.625, which means that 62.5% offspring are predicted to have normal ears and
normal tail or droopy ears and crinkly tail.
Rule two: Product rule
• Product rule used to predict probability of independent events it is also k/n as the and rule.

• Probability likelihood of two or more independent outcomes from genetic cross.

• Independent events mean occurrence of one event does not affect probability of another
event.

• Suppose genotype AaBbCC was crossed to an individual with genotype AabbCc.

• Question: What is the probability of offspring having genotype AA bb Cc?

• So/n three genes can independently assort, probability of inheriting alleles for each gene is
independent.
• Therefore, we can separately calculate the probability of the desired outcome for each gene.
• Cross: AaBbCC × AabbCc

• Probability that an offspring will be AA = 1/4, or 0.25

• Probability that an offspring will be bb = 1/2, or 0.5

• Probability that an offspring will be Cc = 1/2, or 0.5

• We can use the product rule to determine the probability that an offspring will be AA bb Cc:

• P = ¼ x ½ x ½ = 1/16 or (0.25) (0.5)(0.5) = 0.0625 or 6.25%

Rule three: Binomial expansion equation
• Binomial expansion equation can be used to predict genetic probability of an unordered
combination of events.

• Here events can be produced in an unspecified order.

• For example, we can consider group of children produced by two heterozygous brown-eyed
(Bb) individuals.

• Question: What is probability of two out of five children will have blue eyes?

• In this case, we are not concerned order of offspring birth.

• Instead, concerned with final numbers of blue-eyed and brown-eyed offspring.

• Scenario 1: the firstborn and second child with blue eyes, then the next three with brown eyes.
• Scenario 2: The firstborn child with brown eyes, the second blue & the third with blue eyes, fourth
and fifth with brown eyes.
• Scenario 3: The first born & the second child with brown eyes & the third & the fourth with blue eyes
and the last with brown eyes.
• Scenario 4:
Birth orders

1 2 3 4 5
b B B b b
b b B B B
B b b B B
B B b B b

B B B b B
• All these scenarios would result in two offspring with blue eyes and three with brown eyes.

• In fact, several other ways to have such a family could occur.

• To solve this type of question, the binomial expansion equation can be used.

• This equation represents all possibilities for given set of unordered events.
• P = x = (n ) (q)n-x (p)x
x
• Where

• P = the probability that the unordered outcome will occur

• n = total number of events

• x = number of events in one category (for our case blue eyes)

• p = individual probability of x

• q = individual probability of the other category (e.g., brown eyes)

• Note: In this case, p + q = 1.

• ! denotes factorial. n! is the product of all integers from n down to 1.

Cross: Bb × Bb
• Question: What is the probability two out of five offspring have blue eyes?
• NB: Brown is dominant over blue

• Step 1. Calculate the individual probabilities of blue-eye & brown-eye phenotypes.

• Constructed Punnett square & p of blue eyes is ¼ & p of brown eyes is 3/4
• p = 1/4
• q=¾

• Step 2. Determine no of events in category x (in this case, blue eyes) versus total no of events.

• In this example, no of events in category x is two blue eyed children among total no of five.
x=2
n=5
Step 3. Substitute the values for p, q, x, and n in binomial expansion equation
P = (x=2) = 5
2
• 5! = 5×4×3! = 10 10× (3/4)3x(1/4)2
(5-2) ! 2! 3!2!

• P = 10 (3/4)3(1/4)2 = (10) (27/64)(1/16) = 270/1024 = 0.26 = 26%

• Thus, the probability is 0.26 that two out of five offspring will have blue eyes.

• In other words, 26% of the time we expect Bb × Bb cross yielding five offspring to contain
two blue-eyed children and three brown-eyed children.

• We use multinomial expansion equation to solve unordered genetic problems that involve
three or more phenotypic categories
Forked-line (branched-line) probability method
• Punnet square provides method of visualizing production of gametes and their combination to
produce diploid offesprings.

• In monohybrid cross punnet square contains 4 squares, in dihybrid cross it contains 16

combinations are produced from four gametes.

• For trihybrid cross punnet square has 64 boxes or offesprins.

• Thus ability to analyze cross with punnet square becomes very cumbersome beyond dihybrid
cross.

• Therefore, to calculate probability of events we can use branched- line method.

Example:
• AaBbCc x AaBbCc what is the probability (P) of recessive alleles?

• Solution: first breakdown these genotypes into their independent assorting gene.

• AaxAa = AA, Aa, aA and aa therefore, “aa” = ¼

• BbxBb =Bb, Bb, bB and bb >> “bb” = ¼

• CcxCc = CC, Cc, cC and cc >> “cc” ¼

• So the probability of the recessive alleles is ¼ x ¼ x ¼ = 1/64 = 0.015625 or 1.5625%

• Fig. 4/1 forked-line
4.2. Application of Chi-square to test goodness of fit of the genetic data
• One commonly used statistical method to determine goodness of fit is the chi square test
often written χ2.

• Chi - square test is used to test validity of genetic hypothesis testing and to determine if the
data from genetic crosses are consistent with particular pattern of inheritance.

• To distinguish between inheritance pattern that obey Mendel’s laws versus those do not, the
strategy is make crosses and quantitatively analyze the offspring.

• Based on observed outcome, an experimenter can accept null hypothesis and reject an
alternative hypothesis or reject the null hypothesis and accept an alternative hypothesis.
• The rationale behind statistical approach is to evaluate the goodness of fit between observed
data and data that are predicted from hypothesis.

• Predicted hypothesis is called null hypothesis (H0) that assumes no real difference between
observed and expected values.

• Any actual difference occur presumed is due to random sampling error.

• If the observed and predicted data are very similar, we can conclude that hypothesis is
consistent with the observed outcome.

• In this case, it is reasonable to accept the hypothesis.

• On the other hand in some cases, statistical data reveal poor fit between hypothesis and high
deviation found between observed and expected values.

• If this occurs, the hypothesis is rejected.

• Then the experimenter can propose an alternative hypothesis (H1) that has better fit with the
data.
• For example, Assume you are asked this question about F2 generation:

• Do the observed numbers of offspring agree with the predicted numbers based on Mendel’s
laws of segregation and independent assortment?

• Not all traits follow simple Mendelian pattern of inheritance.

• Chi-square is calculated from number of progeny observed in each of various classes,
compared with number expected in each classes on the basis of genetic hypothesis.

 χ2 = Σ (O − E)2 …………………………….. (equation 1)

E
• Where,
• O = observed data in each category
• E = expected data in each category based on the experimenter’s hypothesis
• Σ = sum /summation/ calculation for each category.
• X = is the Greek letter chi

• The strategy described next provides step-by-step outline for applying the chi square method.
Steps
• Steps1: State genetic hypothesis in detail, specifying the genotypes and phenotypes

• Steps2: Use rules of probability and make clear (explicit) predictions of proportions of
progeny that should be observed if the genetic hypothesis is true.

• Convert the proportions to numbers because (percentages are not allowed in chi- square).

• Steps3: For each class, subtract expected number from observed number. Square this
difference and divide the result by expected number.

• Steps4: Sum up the result of numbers calculated in step 3 for all classes. The summation is
X2 value.

• Steps5: Interprate calculated X2 value.

Example 1:
• What is the chi-square value if an experimenter count 787 tall and 277 short plants with a
total of 1064 F2 progeny from monohybrid cross?

• Solution: The expected phenotypic ratio is 3:1. So equivalent number is 798 tall plants and
266 short plants.
• Difference between observed number and expected number of tall plants is -11

• (O-E) 2 = (787-798)2 = (-11)2 /798=121/798 = 0.15

E 798
• Similarly Difference between observed number and expected number of short plants is 11

• (O-E)2 = (277-266)2 = (11)2 = 121/266 = 0.45

E 266 266

• The x2 value is the sum of 0.15 + 0.45 = 0.60

Note that:
• X2 is calculated using observed and expected numbers, then the result is put in integer or
decimal but NOT in proportions, ratios, or percentages.

• X2 value is reasonable as measure of goodness of fit, because closer the observed numbers to
expected numbers, the smaller the X2 value.

• If the value of X2 = 0, this means that observed numbers fit expected numbers perfectly.

• If the value of X2 is too large, it show large of deviation between observed & expected value.
Example 2: Calculate X2 value from the following table 4.1
2
Phenotype Observed no Expected no Deviation b/n observed & (Deviation)
Expected no
(class) expected
Wild type 99 0.75

Mutant 45 2.25

Total 144 x2 = 3.00

• Expected numbers in the two classes calculated based on genetic hypothesis ratio 3:[Link] trait (3/4) x144
= 108 and recessive trait (1/4) x144 = 36.

• X2 = (99-108)2/108 + (45-36)2/36
= 0.75+2.25
= 3.00
Example 3
• This experiment performed on Drosophila melanogaster (fruit fly), on wing shape and body
color.

• Straight wing and curved wing are designated by w+ and w, respectively; gray body and
ebony body color are designated by g+ and g, respectively.

• Cross: True-breeding fly with straight wings gray body (w+w+g+g+) is crossed to true-
breeding fly with curved wings and an ebony body (wwgg).

• Then all F1 flies are straight wing gray body color. Then they are allowed to mate with each
other to produce an F2 generation.
Outcome: F2 generation:

• 197 straight wings, gray bodies

• 67 straight wings, ebony bodies

• 64 curved wings, gray bodies

• 24 curved wings, ebony bodies

• Total = 352
• Step1. Based on Mendel’s laws of inheritance in F2 generation offspring have 9:3:3:1 ratio
because an independent assortment of two characters. Straight (w+) is dominant to curved (w),
and gray (g+) is dominant to ebony (g).

• The two characters segregate and assort independently from generation to generation.

• Step2. Calculate each individual expected values from 9:3:3:1 ratio probabilities of four
phenotypes in F2 generation.

• Therefore, expected probability of each class is:

9/16 × 352 = 198 (expected number with straight wings, gray bodies)
3/16 × 352 = 66 (expected number with straight wings, ebony bodies)
3/16 × 352 = 66 (expected number with curved wings, gray bodies)
1/16 × 352 = 22 (expected number with curved wings, ebony bodies)
• Step 3. Apply chi square formula, by using observed and expected data values above.

• χ2 = (O1 − E1)2 + (O2 − E2)2 + (O3 − E3)2 + (O4 − E4)2

E1 E2 E3 E4

• χ2 = (197 − 198)2 + (67− 66)2 + (64 − 66)2 + (24 − 22)2

198 66 66 22

• χ2 = 0.005 + 0.015 + 0.060 + 0.182 = 0.262

• Step 4. Interpret the calculated chi square value. This is done using chi square table.
Interpretation
• Before interpreting chi square value, it is better to understand how to use Chi-square table
(see Table 4/3).

• Probabilities, called P values, listed on the head of chi square table like 0.99, 0.95, 0.80,
0.50… that allow us to determine the likelihood of amount of variation.

• Once X2 value has been calculated, next step is interpret whether this value represents good fit
or bad fit to expected numbers this is done with the help of chi square table or graphs.

• If calculated X2 value is too Low, indicates high probability in which observed deviations
could be due to random chance alone.

• So accept null hypothesis because no significant difference between expected and observed
values.
• On the other hand, if the calculated X2 value is too large the probability fit bad.

• Then the observed results do not fit the theoretical expectations.

• This means genetic hypothesis used to calculate expected numbers must be rejected, because
observed numbers deviate too much from expected numbers.

• If High chi square value is obtained, an experimenter becomes suspicious that high
deviation occurred between observed and expected because the hypothesis is incorrect.
• In practice, critical value of P is conventionally chosen as 0.05 (5 percent level). If the P value
is less than 0.05 (5 percent) it is said to be significant at 5 percent level.

• Before determine the probability first determine degrees of freedom (df) in this experiment.

• Degree of freedom is measure of number of independent categories.

• Here phenotype categories are independent of each other so degree of freedom is equal to
number of independent categories minus one.

• In short = n − 1, where n equals total number of categories.

• In the preceding problem, n = 4 (categories are straight wings gray body, straight wings ebony
body, curved wings gray body and curved wings ebony body) thus, degrees of freedom equals
3.
Table 4/3 Chi- squire probability table

Look: From the above 3 examples, the first 2 Ho is rejected whereas the third example Ho is
accepted. This is supported by this chi-square table.
Generally: If the p-value is high, the chi-square value will be low.

• The small χ² → observation close to expected → high p-value. So accept H0 hypothesis.

• The large χ² → observation differ from expected → low p-value . So reject H0 hypothesis.

• Table 4/4 comparison χ² and p-value

χ² value p-value Interpretation

Low High Observed data fit to expected pattern so, fail to reject H₀ or
deviation b/n observed & expected value is insignificant.

High Low Observed data highly differ from expected; so reject H₀ or

Chapter 5: Gene interactions and the influence of environment on gene expression

Learning objectives:

At the end of this chapter students will be able to:

 Describe different types of gene interactions

 Discuss types of dominance relationships, epistasis, polygenic inheritance and pleiotropy.

 Describe gene to gene and gene to environment interaction

 Discuss modifications of Mendelian phenotypic ratios

 Explain the influence of environment on genes expression

 Describe penetrance and expressivity (influence of internal and external environment) of

genes