BASIC GENETICS: 1202

Course instructor:
Dr. Ozimati Alfred Adebo
MUK (BSc & Msc), Cornell University
(Ph.D), USA.
 Lecture 1 : BOT1205
Brief course description
■ This course will cover Mendel’s law of inheritance,
■ Deviation from the expected patterns Mendelian
inheritance,
■ The concept of linkage and gene mapping
■ Concept of multiple allelic inheritance,
■ The roles of environmental and genetic factors in sex
determination, causes and consequences of mutation
What is the secret behind the transmission of
hereditary characteristics from generation to
generation?

https://cytogenetics-sites.uchicago.edu/
What creates differences among individuals?
Hereditary variation
 Environmental Variation
 Mendelism/ Mendel`s laws
Mendel's observations led to two laws, regarding the
transmission of hereditary characteristics from generation to
generation.

First law: Principle of Segregation:

Two alleles segregate randomly from each other during the
formation of gametes. i.e. When a pair of allele is brought together
in hybrid or F1, they remain together without contaminating each
other and only segregate during gamete formation

Parental
It means, that each gene has Parents Gametes
a F1 generation
two copies (alleles), and each Aa
parent will give one copy to a A AA Aa
child.
A aa
Aa
a
 Basic Concepts of Genetics/ Mendel`s laws
Second law: Principle of Independent Assortment:
Two genes will assort independently of one another in gamete
production

Important teams to know:

Parental
Gene: The fundamental physical and functional Gametes
unit of heredity Parents
AB Ab
Alleles: are different versions of the same gene. Aa
Homozygous: refers to an individual with two Bb
aB ab
identical alleles.
Heterozygous: refers to an individual with two
different alleles.
Genotype: it refers to the specific allelic
composition of an individual.
Phenotype: refers to the outward appearance of
an individual.
 The genetic material: Genome

• Genome as a term was suggested in 1920 by Hans Winkler, professor

of biology (botany) at the University of Hamburg. Genome word is a
blend of the words gene and chromosome.

• The genome can be defined as the genetic material of an

organism. It consists of DNA (or RNA in RNA viruses). The
genome includes both the genes, (the coding regions), the non-
coding DNA and the genomes of the mitochondria and
chloroplasts.
 What is chromosome?
Chromosome is a thread-like structures, it is consisted of DNA
molecule packed tightly and coiled around a specific proteins called
histones. Chromosomes are located in the nucleus of eukaryotic cells.

DNA
Double helix

DNA
&
Histones

chromosome
 The structure of the chromosome
Chromatid
• Chromatids are two identical parts of each
chromosomes. P-arm(short)

• These chromatids are held together at a point Centromere

named the centromere, which can be located

at any point along the length of the
chromosome. q-arm(long)

Telomere
• Telomere is a region of repetitive nucleotide
sequences. Telomere is located at each end of a
chromosome, it protects the end of the
chromosome from deterioration or from fusion
with neighbouring chromosomes
How does a gene function?
Comparisons of DNA and RNA molecules
 Why study Genetics?

■Take home assignment

 Trait versus Phenotype
Examples
TRAITS PHENOTYPES

1. Height (Humans/Plants) Tall verse short

2. Flower color Presence versus absence
3. Flower purpleness Presence versus absence
4. Weight (Fish/ Heavy versus light
5.??
6.??
8.??
 Inheritance/Heredity
Inheritance is the process by which genetic information is passed on from
parent to offspring
■ Two theories explain inheritance:
– Blending; Evolved from the fact that offspring typically show
characteristics similar to both parents. Therefore are
intermediate between the parents for their trait investigated

– Particulate (Mendelian theory); traits, characters are

determined by discrete units/genes that are inherited intact
across generations.
 Mendel’s experimental design

He did his experiments on the

pea plants. This was achieved by
two different methods:
1)Self-fertilization: occurs when
pollen falls from the stamen
onto the carpel of the same
flower.
2)Cross-fertilization: occurs when
pollen of one plant is used to
fertilize a different plant.
 Mendel’s experiment using garden pea…….
■ Reasons Mendel used garden pea (Pisum sativum)
for his genetic studies:
 Convenience of handling: Peas could be easily grown in
pots or in fields and each plant only occupied a small space
 Controlled mating: The flower structure of pea ensures
selfing pollination
 Short life cycle: Pea complete their life cycle within 70 days
thus producing many generations in succession
 Large fertile offspring‘: Hybrids resulting from crossing two
pure line were perfectly fertile and many in number
 Presence of variations: Peas have main sharply defined
inherited differences e.g. plant height (Tall vs dwarf), seed
shape (round vs wrinkled )
 Mendel’s Experiment
■ Common terminologies used in Mendel’s crossing
expt.
– P generation; Parental generation
– F1 generation; First generation offspring or filial
– F2 generation; Second generation offspring
– Dominant; Allele that dominates over others
– Recessive; Allele whose phenotype expression is “hidden” in
presence of a dominant allele
– Hybrid; An offspring from crossing two pure lines of contrasting
characters e. g Tall vs dwarf
 More Mendelian Terminologies………………..
Locus: The physical location of the alleles of a gene on it's chromosome.
Genotypic ratio: The expected numbers of different genotypes produced by
a particular cross.
Phenotypic ratio: The expected numbers of different phenotypes produced
by a particular cross.
Monohybrid Cross: A cross between two individuals in the same species in
which one genetic trait is documented.
Dihybrid Cross: A cross between two individuals in the same species in

which two genetic traits are documented.

 Reasons for success of Mendel’s work
 The experiments well designed and conducted with great care
 The choice of his experimental material, the common garden pea.
 Mendel studied the inheritance of only one pair of contrasting
characters at a time
 The characters he chose were discrete/qualitative (Yellow vs
Green Pod Color)
 The contrasting forms of each of the seven characteristics were
governed by single gene, in any case one form was complete
dominant over the other
 Mendel did not face gene interactions (Epistasis)
 Knowledge on probability theory eased his understanding of his
findings
 He maintained particulars of pedigree records
 1 5

4
6

Note: Phenotypes in the left column are dominant,

and the ones in the right column are recessive.

The seven characteristics that Mendel observed in peas

 Mendelian Monohybrid cross

– Example of shape in Peas i.e. Round seed shape is dominant over wrinkled seed
shape
Diagrammatic illustration of hybridization scheme
Monohybrid cross for stem length:

P = parentals TT  tt
true breeding, (tall) (dwarf)
homozygous plants:

F1 generation Tt
is heterozygous: (all tall plants)
First two offspring generations
(F1, and F2) from the cross
between a tall and dwarf plant
Using punnett square to determine the
phenotypic and genotypic segregation ratios
■ A useful tool to do genetic crosses
■ For a monohybrid cross, you need a square divided by
four….
■ Looks like
a window
pane…
We use the
Punnett square
to predict the
genotypes and phenotypes of
the offspring.
Punnett square to determine segregation ratio
STEPS:
1. determine the genotypes of the parent organisms
2. write down your "cross" (mating)
3. draw a p-square

Parent genotypes:
TT and t t

Cross
TT  tt
 Punnett square
4. "split" the letters of the genotype for each parent & put
them "outside" the p-square
5. determine the possible genotypes of the offspring by
filling in the p-square
6. summarize results (genotypes & phenotypes of
offspring)
T T
TT  tt
t Genotypes:
Tt Tt
100% T t

Phenotypes:
t Tt Tt 100% Tall plants
 Secret of the Punnett Square
■ Key to the Punnett Square:
■ Determine the gametes of each parent…
■ How? By “splitting” the genotypes of each parent:

If this is your cross

T T  t t

The gametes are:

T T t t
Once you have the gametes…

T T  t t

t t

T Tt Tt

T
Tt Tt
Segregations of Monohybrid gene : Complete
Dominance

Punnet Square
 Class exercise:

If you cross a homozygous tall pea plant with

heterozygous tall plant. What genotypic and
phenotypic ratios do we obtain at F1
 Another example: Flower color
For example, flower color:
P = purple (dominant)

p = white (recessive)

If you cross a homozygous Purple (PP) with a

homozygous white (pp):
PP  pp

Pp ALL PURPLE (Pp)

Example of Punnett square for flower color in peace

A Punnet square is one

Pp
way to predict the self-fertilize
outcome of a cross by
1/2 P eggs 1/2 p
showing all the possible
combinations of all the
possible gametes. 1/2 P

1/4 PP 1/4 Pp

sperm
1/2 p

1/4 pP 1/4 pp
 Solving single-gene (monohybrid) crosses with Mendelian
(dominant-recessive) inheritance in tomatoes.

Tomato fruit color can be red

or yellow.
a. A red tomato plant is
crossed with a yellow tomato
plant, and all the offspring
have red tomatoes. Which trait
is dominant?
b. If two of the resulting hybrid
red tomato plants are crossed,
what will be the ratio of
phenotypes in the offspring?
 Monohybrid example in Animals
Question 1:
A rancher wants to cross a homozygous brown horse with a white mare (female).
brown is dominant color. What are the F1 generation genotypes and phenotypes?

P phenotype: A brown A white

P genotype: BB X bb

Gametes: B b

F1: Bb Brown colour

Question 2:
A rancher wants to cross a heterozygous brown horse with a white mare
(female).. What are the genotypic and phenotypic ratios for the F1
generation?

P phenotype: A brown A white

P genotype: Bb X bb

Gametes: B b b

F1: Bb bb
Phenotypic ratio= 1 brown : 1 white (50% brown : 50% white)
Genotypic ratio= 1 Bb : 1 bb (50% Bb : 50% bb)
Question 3:
If an allele for tall plants (T) is dominant to short plants (t). What offspring
would you expect from a Tt x TT cross?

P phenotype: Heterozygous tall Homozygous tall

P genotype: Tt X TT

Gametes: T t T

F1: TT Tt
Phenotypic ratio= 100% tall
Genotypic ratio= 1 TT : 1 Tt
36
Question 5:
A man heterozygous for polydactyly (extra fingers and toes), a dominant trait,
is married to a normal woman. What is the probability of producing an
offspring that has extra fingers or toes?

P phenotype: A heterozygous polydactyly A normal

P genotype: Pp X pp

Gametes: P p p

F1: Pp pp
The probability of producing an offspring that has extra fingers or toes? = 50%
Second law: Principle of Independent
Assortment led to dihybrid inheritance

■ Two genes will assort independently of

one another in gamete production

Parental
Gametes
Parents
AB Ab
Aa
Bb
aB ab
 Mendelian Dihybrid crosses
■ Matings that involve parents that differ in two genes
(two independent traits)
For example
a). Flower color:
P = purple (dominant)
p = white (recessive)

b). Stem length:

T = tall t = short
Dihybrid cross
Example Mendel’s Dihybrid pure crosses
Mendel’s key observations
Dihybrid cross: flower color and stem length

TT PP  tt pp
(tall, purple) (short, white)
Possible Gametes for parents tp tp tp tp
TP TtPp TtPp TtPp TtPp
T P and t p
TP TtPp TtPp TtPp TtPp
TP TtPp TtPp TtPp TtPp
TP TtPp TtPp TtPp TtPp
F1 Generation: All tall, purple flowers (Tt Pp)
 Dihybrid cross F2
If F1 generation is allowed to self pollinate, Mendel observed 4
phenotypes:
Tt Pp  Tt Pp
(tall, purple) (tall, purple)

TP Tp tP tp
Possible gametes:
TP Tp tP tp TP TTPP TTPp TtPP TtPp
Tp TTPp TTpp TtPp Ttpp
tP TtPP TtPp ttPP ttPp
tp TtPp Ttpp ttPp ttpp
Four phenotypes observed
Tall, purple (9); Tall, white (3); Short, purple (3); Short white (1)
 Dihybrid cross

9 Tall purple
TP Tp tP tp
TP TTPP TTPp TtPP TtPp
3 Tall white Tp TTPp TTpp TtPp Ttpp
tP TtPP TtPp ttPP ttPp
tp TtPp Ttpp ttPp ttpp
3 Short purple

Phenotype Ratio = 9:3:3:1

1 Short white
 Dihybrid cross: 9 genotypes
Genotype ratios (9): Four Phenotypes:
1 TTPP
2 TTPp
2 TtPP Tall, purple (9)
4 TtPp
1 TTpp
2 Ttpp
1 ttPP
Tall, white (3)
2 ttPp
1 ttpp
Short, purple (3)

Short, white (1)

How do we determine the genotypic state of
dihybrid and monohybrid dominant traits ?
 Test cross
When you have an individual with an unknown genotype, you do
a test cross.
Test cross: Cross with a homozygous recessive individual.

For example, a plant with purple flowers can either be PP or

Pp… therefore, you cross the plant with a pp (white flowers,
homozygous recessive)
P?  pp
 Test cross performance
■ If you get all 100% purple flowers, then the unknown parent
was PP…
P P
p Pp Pp

p Pp Pp
•If you get 50% white,
50% purple flowers, P p
then the unknown p Pp pp
parent was Pp…
p Pp pp
 Dihybrid test cross??
If you had a tall, purple plant, how would you know
what genotype it is?

?? ?? tt pp


1. TTPP =100%
2. TTPp (TP,Tp,TP, Tp x tp, tp,tp,tp) =1:1=50% tall white,50% Tall,purple
3. TtPP =1:1=50% (Tall, purple):50% (Short, purple)
4. TtPp= 1:1;1:1
 Beyond Mendelian Genetics:
Incomplete Dominance
Mendel was lucky!
Traits he chose in the
pea plant showed up
very clearly…
One allele was dominant over another, so phenotypes were
easy to recognize.

But sometimes phenotypes are not very obvious…

 Incomplete Dominance
Snapdragon flowers come in many colors.

If you cross a red snapdragon (RR) with a white

snapdragon (rr)
You get PINK flowers (Rr)! RR  rr

Genes show incomplete dominance

Rr
when the heterozygous phenotype
is intermediate.
 Incomplete dominance
When F1 generation (all pink flowers) is self
pollinated, the F2 generation is 1:2:1
red, pink, white
Incomplete Dominance

R r
R R R Rr

r Rr rr
 Incomplete dominance
What happens if you cross a pink with a white?

A pink with a red?


 Codominance
■ Pure breeding phenotypically contrasting parents produce
progeny in the F1, which are phenotypically a mixture of the
two parental phenotypes
■ Both alleles at a locus equally & fully express themselves in a
heterozygous state

■ Selfing of the F1 progeny produce an F2 progeny that

segregate into three phenotypic classes in ratio of 1:2:1
■ Conventionally, co-dominant alleles at a locus are represented
by different upper case letters
Examples of traits that show codominance

■ Coat color in Animals e.g. goats and cattle

■ A and B blood group in human
■ Normal and sickle cell haemoglobin
Coat color inheritance
Selfing of F1 progeny for a codominant
traits
Example of blood group as codominant trait

■ The alleles for blood group A and blood group B are co-
dominant

■ A person with genotype AA produces antigen A &, the

one with genotype BB produces antigen B on the
surface of their red blood cells.

■ The heterozygotes then produce both A and B antigens

Symbolically illustration of heamoglobin
inheritance in humans
GENE INTERACTIONS
 Mechanism of gene interactions
■ Proteins are the end products of gene expression, so gene interactions are
interactions between proteins that are controlled by these genes (genes do
not interact directly with exception of cases like synapsis and crossing over
during meiosis)
■ Therefore, gene interactions have biochemical basis
Types of gene interactions
Gene interactions can be classified as:
 Allelic gene interaction and
 Non allelic gene interaction
Reminder
■ Allelic genes are genes located at the same loci of homologous chromosomes
■ Non allelic genes are genes located at different loci of homologous chromosomes
or on non homologous chromosomes
 Intra-allelic gene interactions
■ These are interactions between alleles of the same gene located at the
same locus on homologous chromosomes

■ Alleles can interact with each other in complex ways:

 complete dominance,

 incomplete dominance,

 codominance, and

 super dominance (over dominance).

 INTER-ALLELIC GENE INTERACTIONS
■ The genes of an individual do not operate isolated from one another, but obviously
are functioning in a common cellular environment.
 Thus, it is expected interactions between genes would occur.
■ It means that a trait can be controlled by numerous genes, perhaps up to 100 or
more.
 Mechanism of inter-allelic gene interaction
Most cell processes are the culmination of a set of reactions linked together into a
pathway. Each of the reactions is controlled by a different enzyme, and each enzyme
is the product of a separate gene.
Enzyme 1 Enzyme 2
Molecule A → Molecule B → Molecule C
In the hypothetical pathway above, molecule A is converted into molecule B by
enzyme 1 and molecule B is then processed to become molecule C by enzyme 2. If
either enzyme 1 or enzyme 2 is defective, molecule C cannot be manufactured,
producing a mutant phenotype. Defects in enzyme 1 or 2 may show up as one or two
mutant phenotypes. The result of defects in such pathways leads to modified
Mendelian phenotypic ratios for crosses. The simplest cases of gene interaction to
consider are those in which only two genes are interacting to produce a single
phenotype, normally.
 INTER-ALLELIC GENE INTERACTIONS
■ There are various ways in which genes at different loci can interact with each other.
■ Non-allelic genes can interact with each other in complex ways:
■ Complementation. Complementation is a kind of gene interaction where the
manifestation of a character is determined by presence of two dominant genes of
different allelomorphic pairs simultaneously giving a ratio of 9:7. Example: Flower color
in sweet pea.
■ Epistasis. Sometimes the effect of gene interaction is that one gene masks (hides) the
effect of another gene at a different locus, a phenomenon known as epistasis. It may
be dominant or recessive
■ Polygenic inheritance
Polygenic inheritance is a pattern responsible for many traits which are governed by the
cumulative effects of many genes. Polygenic traits are not expressed as absolute or
discrete characters. Polygenic traits are recognizable by their expression as a gradation of
small differences (a continuous variation). Human polygenic traits include height, weight,
eye color, intelligence, skin color, many forms of behavior. The biological role of polygeny is
to increase trait stability.
Complementary Gene action
Complementation vs non-complementation
 Genotype X environment interactions
■ The expression of a gene can be altered not only by other genes, but also by
the environment.
■ Such environmental variables as light, temperature, and nutrition can sharply
affect the translation of a genotype into a phenotype. For example, Siamese
house cats have light color except on their ears, nose, tail, and paws. The
expression of gene responsible for this hair color pattern is temperature-
sensitive. The enzyme that catalyzes the production of dark pigment in these
cats is unable to work at the normal body temperature. In lowering of
temperature the enzyme is activated and can produce pigment that darkens
the ears, paws and tail.
■ Thus, the phenotype of an organism is a function of the interactions of
genotype and environment.
■ Temperature also affects primrose flower color and fur of Himalayan rabbits.
In buttercup plant (Ranunculus peltatus), leaves below water-level are finely
divided and those above water-level are broad, floating, photosynthetic leaf-
like leaves.
 Gene Linkages

■ Today shall now know that traits are not all inherited
independently of each other.
■ Scientific discoveries have found that traits that are
located on the same chromosome tend to be inherited
together.

■ Traits located on the same chromosome are said to

show linkage.
■ By the end of topic you should be able to:
– Define linkage and crossing over
– Explain the different types of linkage
– Describe general characteristics of linked genes
– Detect occurrence of linkage genes (Hypothesis testing for
presence or absence of linkage)
– Understand the concept of crossing over
– Explain different types of crossing over
– Compute cross over frequencies
– Difference between linkage and crossing over
– Mention the importance of linkage and crossing over in specie
improvement (crop and animal breeding)
 The theory of chromosome inheritance
■ Sutton and Boveri proposed the chromosome theory of
inheritance. According to their theory, many genes are located in
each chromosome in a linear fashion.

■ Therefore all genes located on the same chromosome move to the

same pole during cell division.
■ Consequently, such genes will fail to show independent
segregation and therefore would tend to be inherited together.

■ This tendency of the genes to remain together in their original

combination during inheritance is called Linkage
 Types of linkages
■ Later T H Morgan, put forth the theory of linkage and
concluded that coupling and repulsive were the two phases of
single phenomenon of linkage
■ Types of linkages: Linkage is generally classified on basis of
three criteria
– i) Cross over ii). Genes involved, iii). Chromosomes
involved.
■ Based on cross over: This type of linkage may be classified
into two; a). Complete and b). Incomplete/partial depending on
absence or presence of recombinants of phenotypes in the
test cross progeny
 Type of Linkage based on crossing over
■ a). Complete linkage: The best example is in male and
female drosophila of silkworms, where there is a
complete absence of recombinant types due to absence
of crossing over.
■ b). Incomplete/ partial linkage: If some frequency of
crossing over also occurs between the linked genes i.e.
Recombinant types are observed besides parental
combinations in the test cross progeny.
 Type of linkage based on involved genes
■ Based on Gene involved: Depending on whether all dominant or
some dominant and recessive allele are linked together, linkage can be
categorized into a). Coupling phase and b). Repulsion phase
■ a). Coupling phase: All the dominant alleles are present on the same
chromosome or all recessive alleles are present on the same
chromosomes;
TR tr
………… ………
TR tr
 b) . Repulsion phase: Dominant alleles of the some genes are linked
with recessive alleles of other genes on the same chromosome.
Tr tR
………… ………
Tr tR
Type of linkage based on chromosomes involved
■ Based on chromosomes involved: This involves the
location of the gene on the chromosome and can be
categorized as; a). Autosomal linkage and b). Sex linkage
(X-chromosomal/allosomal linkages)

■ a). Autosomal linkage: These are genes located on

autosomes (other than sex chromosomes)

■ b). X-chromosomal linkage/ allosomal linkage/ sex

linkage: It refers to linkage of genes located in sex
chromosomes i.e; “X” and “”Y (generally “X”)
 Generally characteristics of linked genes
1. Linkage involves two or more genes which are located in same
chromosome in a linear fashion
2. Linkage reduces variability
3. Linkage may involve either dominant or recessive alleles (coupling
phase) or some dominant and some recessive alleles (repulsion)
4. It may involve either all desirable traits or undesirable traits or
even some undesirable traits linked to undesirable traits.
5. Its observed for oligo-genic traits as well as for polygenic traits
6. Linkage usually involves those genes which are located close to
each other
 Generally characteristics of linked genes

7. The strength of linkage depends on the distance between the linked

genes. The lesser the distance, the higher the strength and vice versa.
8. Linkage leads to higher frequency of parental types than
recombinants in the test cross i.e. when two genes are linked the
segregation ratio of the dihybrid test cross progeny deviates significantly
from 1:1:1:1 ratio
9. Linkage can be determined from test cross progeny data
10. If crossing over does not occur, all genes located on one
chromosome are expected to be inherited together
11. Linkage can be broken by repeated intermating of randomly selected
plants in segregating population for several generations
12. Besides pleiotropy, linkage is an important cause of genetic
correlation between various plant characteristics.
 Detection of linkage
■ From a dihybrid crosses: Presence or absence of linkage is
can be detected by self pollinating individual heterozygous
at two loci.
■ If there is complete dominance at the each locus and no
epistasis, the segregation ratio of the progeny will be
9:3:3:1

■ Presence of linkage either in coupling phase or repulsion

phase will lead to significant deviation from 9:3:3:1 ratio
■ The value of the observed values from the expected ratio is
tested using chi-square test
 Detection of linkage
■ Idealized Mendelian ratios (independent assortment):
– (Dihybrid cross) RrYy x RrYy  9:3:3:1
– (Test cross) RrYy x rryy  1:1:1:1
– These idealized ratios occur when alleles of the two genes don’t “care”
about one another (don’t segregate together)

■ “Linkage” is one of the exceptions to the idealized ratio

Linkage detection in Drosophila using test cross
Linkage detection
Detection of linkage
Detection of linkage
Chi-square test (X2-Test) for detection of linkage
Chi-square test (X2-Test) for detection of linkage
 2-pt cross Example 1
In snapdragons, smooth is dominant to rough, and yellow is dominant
to green. A smooth, yellow individual is crossed to a rough green
individual, and the following cross-progeny are obtained:

195 smooth yellow

21 smooth green
19 rough yellow
165 rough green

Are the loci linked? If linked, what are the genotypes and chromosomal
configurations in the parents?
What is the map distance between the two loci?
 EXAMPLE 2
In guinea pigs, white coat (w) is recessive to black coat (W), and wavy hair (v) is
recessive to straight hair (V). A breeder crosses a guinea pig that is homozygous for
white coat and wavy hair with a guinea pig that is homozygous for black straight
hair. The F1 are then crossed with guinea pigs having white coats and wavy hair in
a series of testcrosses. The following progeny are produced from these testcrosses:
black, straight 30
black, wavy 11
white, straight 12
white, wavy 31
total 84
a.) Are the genes that determine coat color and hair type assorting independently?
Carry out chi-square tests to test this hypothesis.
b.) If the genes are not assorting independently, what is the recombination
frequency between them?
 Linkage and Pleiotropy
■ Similarity: Both linkage and pleiotropy result into a close association
between two or more characters (phenotypic expression).
■ Difference: Pleiotropy refers to the control of two or more characters
by a single gene, while linkage refers to control of two or more
characters by two or more genes that don’t segregate
independently

■ Intermating in segregating populations may break a tight linkage,

although a huge population is required to find out the crossover
products.
■ Lack of a cross over products in spite of repeated intermating
suggest pleiotropy rather linkage
 Crossing over of genes
■ This term crossing over was first used by Morgan and Cattell in
1912. They referred to crossing over as exchange of
homologous segments between non-sister chromatids of
homologous chromosomes.

■ Mechanism of crossing over: Is responsible for recombination

between linked genes and takes place during pachytene stage
of meiosis i.e after the homologous chromosomes have
undergone pairing and before they begin separate.

■ This occurs through the process of breakage and reunion of

chromatids.
 Breaking Linkage by Crossing-over&
Recombination
■ Although linked genes are
generally inherited together, they
can become separated by
crossing-over, which may occur
during a stage of meiosis.
■ During this stage, the four
chromatids sometimes twist
around each other.
■ As they separate, the chromatids
may break, exchange segments,
and rejoin.
Mechanism of crossing-over

Peter J. Russell, iGenetics: Copyright © Pearson Education, Inc., publishing as Benjamin Cummings.
 Types of crossing over
1. Single crossing over: This refers to the formation of single
chiasma between non-sister chromatids of homologous
chromosomes. It involves two linked genes (Two point test
cross)
2. Double crossing over: It refers to the formation of two
chiasma between non-sister chromatids of homologous
chromosomes. It involves three linked genes (Test point test
cross)
3. Multiple crossing over: Occurrence of more than two crossing
overs between non-sister chromatids of homologous
chromosomes. Generally the frequency of such type of
crossing over is extremely low.
 Recombination events are a rare event between linked genes

Parental
C’some
(many)
Dominant

recessive Recombinant
C’some
(few)

Recombinant
C’some
(few)

Parental
C’some
(many)
 P0 RRYY ssyy
rryy The difference
between linkage
SY ry and no linkage

Test cross
F1 RrYy
SsYy x rryy

R R R r
R r
y Y y R r
Y y Y

Y y

F2 progeny Complete Incomplete No linkage

linkage linkage (Indep.
Assortment)
(0% recomb) (X% recomb)

round yellow 1 many 1

round green 0 few 1
wrinkled yellow 0 few 1
wrinkled green 1 many 1
 P0 RRYY ssyy
rryy The difference
between linkage
SY sy and no linkage

Test cross
F1 RrYy
SsYy x rryy

R R R r
R r
y Y y R r
Y y Y

Y y

F2 progeny Complete Incomplete No linkage

linkage linkage (indep.
Assortment)
(0% recomb) (X% recomb)

round yellow 1 many 1

round green 0 few 1
wrinkled yellow 0 few 1
wrinkled green 1 many 1
Incomplete linkage gives us useful map distance information

Test cross
RrYy
SsYy x rryy

R R R r
R r y R r
Y y Y y Y

Y y

F2 progeny Complete Incomplete No linkage

linkage linkage (indep.
Assortment)

round yellow 502 421 247

round green 0 78 252
wrinkled yellow 0 73 248
wrinkled green 408 428 253
(0 map units) 15.1 % (“50” map units)
recombinants
(15 map units)
 Factors that affecting crossing over:
The frequency of crossing over between the two genes the linked
genes is affected by several factors;
1. Distance between the genes: The distance between the two genes is
positively associated with their location in the chromosomes. Crossing over
between the two genes will increase with an increase in distance between
them.
2. Sex: The frequency of recombination is markedly influenced by the sex of
heterozygotes for linked genes; In general heterogametic sex show relatively
lower recombination frequencies than homogametic sex of the same species
3. Age of female: The frequency of crossing over shows a progressive decline
with the advancing age of Drosophilla females
4. Temperature: In Drosophilla, the lowest frequency of crossing over is
observed when females are cultured at 220C. The frequency of
recombination tends to increase at both higher and lower temperatures
 Factors affecting crossing over
5. Nutrition: The frequency of crossing over in Drosophila is affected by
the presence of metallic ions eg. Ca+2 and Mg+2 in food. The higher the
amount, lower will be the crossing over frequency.
6. Chemical use: Treatment of drosophila females with antibiotics such
as mitomycin D and actinomycin D promote crossing over
7.Radiations: An increase in frequency of crossing over is observed
when a drosophila female is are irradiated with x-rays
8. Genotype: Many genes are known to affect the occurence as well as
the rate of crossing over eg. C2G gene of Drosophilla on chromosome 3
prevents crossing over in homozygous state and promotes crossing over
in heterozygous state.
9. Distance from centromere: Centromere tends to suppress
recombination. Therefore gene in the vicinity of centromere shows a
relatively lower frequency crossing over than the chromosome arms
 Recombination # recombinant progeny__
frequency
# total progeny

(can be expressed as a % or a decimal)

 Map distances
• 1% recombination = map unit (mu) or 1 cM
(centimorgan)
e.g. 12% recombination = 12 mu or 12 cM

•Recombination frequency < 50% “linked”.

•50% > Recombination frequencies  “unlinked”

(‘co-segregate’ as if they were on different chromosomes)

•Recombination frequency = 0% recombination “completely linked”

•Typical chromosome: 200 mu

•Typical gene = .01 mu or 60,000 nucleotides
In corn, purple kernels are dominant over yellow kernels,
and full kernels are dominant over shrunken kernels. A corn
plant having purple and full kernels is crossed with a plant
having yellow and shrunken kernels, and the following
progeny are obtained:
purple, full 112
purple, shrunken103
yellow, full 91
yellow, shrunken 94
•What are the most likely genotypes of the parents and
progeny? Test your genetic hypothesis with a chi-square
test (H0 = independent assortment; H1 = linkage, 0.05)
•If the genes are not assorting independently, what is the
recombination frequency between them?
For chi-square tests of linkage, we can only directly test “no linkage” (indep
assortment. We cannot directly test for “linkage” with chi-square analysis
(too many different possible map distances to test).
(Don’t assume that dominant A is always linked with dominant
B,
and recessive a is linked with recessive b.)

What are the most frequent phenotypes you expect from each cross?
In corn, the allele for colored (C) seeds is completely
dominant to the allele for colorless (c) seeds. And in
another gene controlling for seed tissue, the allele for
full seeds (F) is dominant to shrunken (f). A true-
breeding colored shrunken-seeded plant was crossed
with a true-breeding colorless, full-seeded plant. The
F1 colored-full plants were test crossed to the doubly
recessive type (colorless, shrunken). The F2 progeny
are as follows:

Colored, full 1841 Are the genes linked?

Colored, shrunken 2286 What is the map
Colorless full 2436 distance?
Colorless shrunken 1805 ?
Total 8,368
In corn, the allele for colored (C) seeds is completely
dominant to the allele for colorless (c) seeds. And in
another gene controlling for seed tissue, the allele for
full seeds (F) is dominant to shrunken (f). A true-
breeding colored full-seeded plant was crossed with a
colorless, shrunken-seeded one. The F1 colored-full
plants were test crossed to the doubly recessive type
(colorless, shrunken). The F2 progeny are as follows:
Colored, full 4,032 Are the genes linked?
Colored, shrunken 149 What is the map
Colorless full 152 distance?
Colorless shrunken 4,032 C’some configuration of
F1 heterozygote?
Total 8,368
Which is the correct use of chi-square test in determining
linkage?

a. 0.05 > p, reject hypothesis of Independent Assortment

b. 0.05 > p, support hypothesis of Independent Assortment

c. 0.05 > p, reject hypothesis of Linkage

d. p > 0.05, support hypothesis of Linkage

In tomatoes, tall (D) is dominant over dwarf (d), and smooth fruit
(P) is dominant over pubescent fruit (p) (covered with fine hairs).
A farmer has two tall and smooth plants, Plant A and Plant B.
He crosses these plants with the same dwarf and pubescent
plant, and obtains the following numbers of progeny:

Progeny of Progeny of Plant

Plant A B
•What are the genotypes of plant A
Dd Pp 122 2 and plant B?
•Are the loci linked? What is the mu?
Dd pp 6 82
•Explain why different proportions of
dd Pp 4 82 progeny are produced when plant A
and plant B are crossed with the
same dwarf pubescent plant.
dd pp 124 4
■ What are the genotypes of plant A and plant B? Plant A: DP/dp
Plant B: Dp/dP

■ Are the loci linked? Yes. What is the mu?

– Data from Plant A: 3.9 mu
– Data from Plant B: 3.5 mu
– Combined data: 3.75% (16 recomb. Out of 426 total progeny)
■ Explain why different proportions of progeny are produced when
plant A and plant B are crossed with the same dwarf pubescent
plant.
– Plant A is in cis for its alleles, while Plant B is in trans.
Is the heterozygous parent in cis or in trans?
Is the heterozygous parent in cis or in trans?
##A cross between individuals with genotypes a+ a b+b X aa bb
produces the following progeny:
a+ a b+b 21
a+ a bb 83
aa b+b 77
aa bb 19

a.) Does the evidence indicate that the a and b loci are linked?
b.) What is the map distance between a and b?
c.) Are the alleles in the heterozygous parent in coupling configuration
or repulsion? How do you know?
a.) Does the evidence indicate that the a and b loci are linked? yes
b.) What is the map distance between a and b? 20 mu
c.) Are the alleles in the heterozygous parent in coupling
configuration or repulsion? In repulsion (in trans)
How do you know? The class of progeny with the highest frequency
represents the non-recombinant chromosome configuration of the
heterozygous parent. These progeny are a+a bb (83) and aa b+b
(77)
Crossing over Linkage
1. It leads to separation of linked 1. It keeps the genes together

2. It involves exchange of some 2. It involves individual chromosomes

segments between non-sister
chromatids of homologous
chromosomes
3. The frequency of crossing over can 3. The number of linkage groups can
never exceed 50% never be more than haploid
chromosome number
4.It increases variability by forming new 4. It reduces variability
genes
5. It provides equal frequency of the 5. It produces higher frequency of
parental and recombinant types in the parental types than recombinant type in
test cross progeny the test cross progeny
 Significance of Linkage in genetic improvement of
species
1. Linkage limits the variability among the individuals
2. Linkage between two or more loci controlling different
desirable character is advantages for plant and animal
breeders i.e. Linked genes controlling desirable traits will
help to improve traits simultaneous of both the character
3. Linkage is undesirable when desirable and undesirable
genes are linked together
4. The estimates of genetic variance for quantitative characters
are greatly influenced by the presence of linkage
Significance of crossing over in genetic
improvement of species

1. It increase variability
2. It helps to break linkages
3. It makes possible to construct chromosome maps